Index (biojava 4.2.1 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

A - Static variable in class org.biojava.nbio.aaproperties.Constraints
AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil: Valid Amino acids
aa2CTerminalPka - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2ExtinctionCoefficient - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2Hydrophathicity - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2MolecularWeight - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2NTerminalPka - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2PKa - Static variable in class org.biojava.nbio.aaproperties.Constraints
AAindexFactory - Class in org.biojava.nbio.core.alignment.matrices: Factory class to get Providers for substitution matrices the are provided by the AAINDEX database.
AAindexFactory() - Constructor for class org.biojava.nbio.core.alignment.matrices.AAindexFactory
AAIndexFileParser - Class in org.biojava.nbio.core.alignment.matrices
AAIndexFileParser() - Constructor for class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser
AAIndexProvider - Interface in org.biojava.nbio.core.alignment.matrices
aaScore(char, char) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
AboutDialog - Class in org.biojava.nbio.structure.align.gui
AboutDialog() - Constructor for class org.biojava.nbio.structure.align.gui.AboutDialog
abs(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
abs(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
absolutePercentialRNAsuiteness - Variable in class org.biojava.nbio.structure.validation.Entry
absolutePercentileClashscore - Variable in class org.biojava.nbio.structure.validation.Entry
absolutePercentileDCCRfree - Variable in class org.biojava.nbio.structure.validation.Entry
absolutePercentilePercentRamaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
absolutePercentilePercentRotaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
absolutePercentilePercentRSRZOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
AbstractAlignmentJmol - Class in org.biojava.nbio.structure.align.gui.jmol: An Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol.
AbstractAlignmentJmol() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
AbstractAnnotation - Class in org.biojava.nbio.ontology.utils: A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
AbstractAnnotation() - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation: Protected no-args constructor intended for sub-classes.
AbstractAnnotation(Annotation) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation: Copy-constructor.
AbstractAnnotation(Map) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation: Create a new Annotation by copying the key-value pairs from a map.
AbstractBean - Class in org.biojava.nbio.structure.io.mmcif.model: a generic class that implements the toString method for a bean
AbstractBean() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AbstractBean
AbstractCompound - Class in org.biojava.nbio.core.sequence.template: The details of a Compound
AbstractCompound() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound
AbstractCompound(String) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound
AbstractCompoundSet<C extends Compound> - Class in org.biojava.nbio.core.sequence.template
AbstractCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
AbstractCompoundTranslator<F extends Compound,T extends Compound> - Class in org.biojava.nbio.core.sequence.template
AbstractCompoundTranslator(SequenceCreatorInterface<T>, CompoundSet<F>, CompoundSet<T>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
AbstractEdit(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
AbstractEdit(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
AbstractFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features: A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that feature
AbstractFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.AbstractFeature: A feature has a type and a source
AbstractLocation - Class in org.biojava.nbio.core.sequence.location.template: Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand
AbstractLocation() - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation
AbstractLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation: Default constructor
AbstractLocation(Point, Point, Strand, boolean, boolean, AccessionID, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation: Default constructor
AbstractMatrixAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements common code for an Aligner which builds a score matrix during computation.
AbstractMatrixAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Before running an alignment, data must be sent in via calls to AbstractMatrixAligner.setGapPenalty(GapPenalty) and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Prepares for an alignment.
AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Prepares for an alignment.
AbstractNucleotideCompoundSet<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.template
AbstractNucleotideCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements common code for an Aligner for a pair of Sequences.
AbstractPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Prepares for a pairwise global sequence alignment.
AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Prepares for a pairwise sequence alignment.
AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements common code for an Aligner for a pair of Profiles.
AbstractProfileProfileAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Before running a profile-profile alignment, data must be sent in via calls to AbstractProfileProfileAligner.setQuery(Profile), AbstractProfileProfileAligner.setTarget(Profile), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AbstractProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment.
AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Profile<S, C>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment run concurrently.
AbstractScorer - Class in org.biojava.nbio.alignment.template: Implements common code for algorithms which compute a score.
AbstractScorer() - Constructor for class org.biojava.nbio.alignment.template.AbstractScorer
AbstractScoresCache - Class in org.biojava.nbio.structure.align.multiple: Abstact implementation of the ScoresCache with the shared code used in all objects with a variables cache.
AbstractScoresCache() - Constructor for class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
AbstractScoresCache(AbstractScoresCache) - Constructor for class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
AbstractSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence.template: The base class for DNA, RNA and Protein sequences.
AbstractSequence() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence
AbstractSequence(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence: Create a Sequence from a simple string where the values should be found in compoundSet
AbstractSequence(SequenceReader<C>, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence: A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location of the sequence data.
AbstractSequence.AnnotationType - Enum in org.biojava.nbio.core.sequence.template
AbstractStructureAlignment - Class in org.biojava.nbio.structure.align
AbstractStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.AbstractStructureAlignment
AbstractTerm - Class in org.biojava.nbio.ontology: Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
AbstractTerm() - Constructor for class org.biojava.nbio.ontology.AbstractTerm
AbstractUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce: Base class for a new structure alignment CLI.
AbstractUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
AccesionedLocation - Interface in org.biojava.nbio.core.sequence.location.template: A location which is bound to an AccessionID.
ACCESSION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
Accessioned - Interface in org.biojava.nbio.core.sequence.template: Indicates an entity is accessioned
AccessionID - Class in org.biojava.nbio.core.sequence: Used in Sequences as the unique indentifier.
AccessionID() - Constructor for class org.biojava.nbio.core.sequence.AccessionID
AccessionID(String) - Constructor for class org.biojava.nbio.core.sequence.AccessionID
AccessionID(String, DataSource) - Constructor for class org.biojava.nbio.core.sequence.AccessionID
AccessionID(String, DataSource, Integer, String) - Constructor for class org.biojava.nbio.core.sequence.AccessionID
acentricOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
ACETYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.ChooseDirAction
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.DBResultTable
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener: Invoked when the user presses the stop button.
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel: The user selected one of the Combo boxes...
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.JPrintPanel
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyAlignmentLoadListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyDistMaxListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyExportListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyOpenPdbFileListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MySaveFileListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.ShowPDBIDListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.gui.RasmolCommandListener: Deprecated.
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryListener
AD - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
adapter - Static variable in class org.biojava.nbio.structure.gui.BiojavaJmol
adapter - Static variable in class org.biojava.nbio.structure.gui.JmolViewerImpl
add(FeatureI) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Add specified feature to the end of the list.
add(Collection<FeatureI>) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Add all features in the specified list or collection to this list.
add(int, int, int, int) - Method in class org.biojava.nbio.structure.align.helper.JointFragments
add(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: add two atoms ( a + b).
add(AtomContact) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
add(GroupContact) - Method in class org.biojava.nbio.structure.contact.GroupContactSet
add(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
add(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
addActiveSite(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addAlgorithm(StructureAlignment) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory: Adds a new StructureAlignment algorithm to the list.
addAlignedSequence(S) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment: A sequence that has been aligned to other sequences will have inserts.
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
addAlignmentProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
addAlignmentProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.FarmJob
addAligPosListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
addAligPosListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
addAll(Collection<AtomContact>) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
addAltLoc(Group) - Method in interface org.biojava.nbio.structure.Group: Add a group that is an alternate location for this group.
addAltLoc(Group) - Method in class org.biojava.nbio.structure.HetatomImpl
addAnchor(int, int) - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Adds an additional anchor to the set of anchored compounds
addAnchors(AlignerHelper.Cut[], int[], boolean, int[]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
addASPFamPredicted(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addASSwissProt(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addAtom(Atom) - Method in interface org.biojava.nbio.structure.Group: Add an atom to this group.
addAtom(Atom) - Method in class org.biojava.nbio.structure.HetatomImpl: Add an atom to this group.
addAtomAsaC(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
addAtomAsaU(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
addAtomContact(AtomContact) - Method in class org.biojava.nbio.structure.contact.GroupContact
addAtomLinkage(StructureAtomLinkage) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound: Add a linkage.
addAtomLinkage(StructureAtomLinkage) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
addAtomLinkages(Collection<StructureAtomLinkage>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound: Add a collections of linkages.
addAtomLinkages(Collection<StructureAtomLinkage>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
addAtoms(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.contact.Grid: Adds the i and j atoms and fills the grid.
addAtoms(Atom[], BoundingBox, Atom[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid: Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
addAtoms(Atom[]) - Method in class org.biojava.nbio.structure.contact.Grid: Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts.
addAtoms(Atom[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid: Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts.
addAxis(Matrix4d, List<List<Integer>>, List<Integer>, Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes: Adds a new axis of symmetry.
addBond(Bond) - Method in interface org.biojava.nbio.structure.Atom: Add a bond
addBond(Bond) - Method in class org.biojava.nbio.structure.AtomImpl
addBridge(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState: Adds a Bridge to the residue.
addCDS(AccessionID, int, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence: Add a Coding Sequence region with phase to the transcript sequence
addCell(String, String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Add data to a cell
addChain(Chain) - Method in class org.biojava.nbio.structure.Compound: Add new Chain to this Compound
addChain(Chain) - Method in interface org.biojava.nbio.structure.Structure: Add a new chain.
addChain(Chain, int) - Method in interface org.biojava.nbio.structure.Structure: Add a new chain, if several models are available.
addChain(Chain) - Method in class org.biojava.nbio.structure.StructureImpl: Add a new chain.
addChain(Chain, int) - Method in class org.biojava.nbio.structure.StructureImpl: Add a new chain, if several models are available.
addCharges(Structure) - Static method in class org.biojava.nbio.structure.io.ChargeAdder: Function to add the charges to a given structure.
addChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary: add a new component to the dictionary
addChildElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper
addColumn(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
addColumns(ArrayList<String>, String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Add columns to worksheet and set default value
addCompound(C, C, Iterable<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
addCompound(C, C, C...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
addCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
addCompound(Compound) - Method in interface org.biojava.nbio.structure.Structure: Add a Compound to this Structure
addCompound(Compound) - Method in class org.biojava.nbio.structure.StructureImpl: Add a Compound to this Structure
addCompounds(F, T...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
addCompoundsToList(List<T>, List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
addCompoundToLists(List<List<T>>, T) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
addContinuousVariable(String, Double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
addDBReference(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addEquivalent(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
addExon(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence: Add an ExonSequence mainly used to mark as a feature
addExtension(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.
addExtension(String) - Method in interface org.biojava.nbio.structure.io.StructureIOFile: Associates a file extension with this particular StructureIOFile, indicating that files of that type can be parsed.
addFeature(int, int, FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Method to help set the proper details for a feature as it relates to a sequence where the feature needs to have a location on the sequence
addFeature(FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Add a feature to this sequence.
addGene(AccessionID, int, int, Strand) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence: Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0.
addGeneIDGFF2GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper: Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequences
addGeneMarkGTFGeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
addGFBuildMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addGFFalseDiscoveryRate(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addGFNewHampshire(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addGFTreeID(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addGlimmerGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
addGmodGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper: Load GFF3 file using mRNA as the gene feature as not all GFF3 files are complete
addGroup(Group) - Method in interface org.biojava.nbio.structure.Chain: add a group to the list of ATOM record group of this chain.
addGroup(Group) - Method in class org.biojava.nbio.structure.ChainImpl: add a group to the list of ATOM record group of this chain.
addGSAccessionNumber(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addGSdbReference(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addGSDescription(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addGSLook(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addGSOrganismClassification(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addGSOrganismSpecies(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addHelix(Helix) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
addIindex(int) - Method in class org.biojava.nbio.structure.contact.GridCell
addIndex(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Add an attribute that will be used as index for queries
addIndexes(List<String>) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Add a list of attributes that will be used as indexes for queries
addInteraction(String, String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper: To test for interactions use two variables and create a third variable where the two are multiplied together.
addIntron(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addIntron(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence: Add an Intron Currently used to mark an IntronSequence as a feature
addIntronsUsingExons() - Method in class org.biojava.nbio.core.sequence.GeneSequence: Once everything has been added to the gene sequence where you might have added exon sequences only then you can infer the intron sequences and add them.
addJindex(int) - Method in class org.biojava.nbio.structure.contact.GridCell
addKeyword(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder: Add a keyword associate with the PTM.
addKeywords(Collection<String>) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
addLigand(RCSBLigand) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigands
addLigandBinding(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addMatrixListener(MatrixListener) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
addMatrixListener(MatrixListener) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
addMember(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
addMirror(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
addMMcifConsumer(MMcifConsumer) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser: Add a MMcifConsumer that listens to even being triggered by the parser and processes the data into a backend provided by the Consumer.
addMMcifConsumer(MMcifConsumer) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
addModel(List<Chain>) - Method in interface org.biojava.nbio.structure.Structure: Add a new model.
addModel(List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl: Add a new model.
addMultipleAlignment(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Add a new MultipleAlignment to the end of the ensemble and set its parent ensemble to this.
addMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
addNote(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Add notes about this sequence that will get exported for GFF3
addNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
addOboFileEventListener(OboFileEventListener) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
addOneSystemProperty(String) - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
addPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
addPoint(Point3d, T) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
addPoint(Point3d, double) - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
addPolymer(RCSBPolymer) - Method in class org.biojava.nbio.structure.rcsb.RCSBDescription
addPosteriorProbability(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
addProperty(String, String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo: Add a property and type to associate with this DBReferenceInfo
addQualifier(String, Qualifier) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
addQualifier(String, Qualifier) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
addQualifier(String, Qualifier) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface: Add a qualifier
addQuantity(Number) - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature
addResidue(SiftsResidue) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
addRotation(Rotation) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
addRow(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
addRows(ArrayList<String>, String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Add rows to the worksheet and fill in default value
addSecondaryStructure(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addSegment(SiftsSegment) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
addSeqResGroup(Group) - Method in class org.biojava.nbio.structure.ChainImpl
addSequence(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure: Deprecated.
Use StockholmStructure.appendToSequence(String,String) instead
addSSBond(Bond) - Method in interface org.biojava.nbio.structure.Structure: Add a single disulfide Bond to this structure
addSSBond(Bond) - Method in class org.biojava.nbio.structure.StructureImpl: Adds a single disulfide Bond to this structure
addStartCodonSequence(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
addStopCodonSequence(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
addStrataInfoHashMap(LinkedHashMap<String, StrataInfo>, String) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
addStrings(String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
addSurfaceAccessibility(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addSynonym(Object) - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
addSynonym(Object) - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
addSynonym(Object) - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
addSynonym(Object) - Method in interface org.biojava.nbio.ontology.Term: Add a synonym for this term.
addSynonym(Object) - Method in class org.biojava.nbio.ontology.Term.Impl
addSynonym(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl
addToCache(String, File) - Static method in class org.biojava.nbio.core.util.FlatFileCache
addToGFComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addToRefAuthor(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
addToRefTitle(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
addTranscript(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence: Add a transcription sequence to a gene which describes a ProteinSequence
addTransformation(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
addTransMembrane(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addUniqueSequenceList(UniqueSequenceList) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
addUnknownDataTypeVariable(String, String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
AFP - Class in org.biojava.nbio.structure.align.model: A class to represent a FATCAT AFP
AFP() - Constructor for class org.biojava.nbio.structure.align.model.AFP
afp2Res(AFPChain, int, int[], int) - Static method in class org.biojava.nbio.structure.align.AFPTwister: Set the list of equivalent residues in the two proteins given a list of AFPs WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain!
AFPAlignmentDisplay - Class in org.biojava.nbio.structure.align.util
AFPAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
AFPCalculator - Class in org.biojava.nbio.structure.align.fatcat.calc: a class that performs calculations on AFPCHains
AFPCalculator() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
AFPChain - Class in org.biojava.nbio.structure.align.model: A bean to contain the core of a structure alignment.
AFPChain(String) - Constructor for class org.biojava.nbio.structure.align.model.AFPChain: Construction of an AFPChain needs the algorithm name, since downstream analysis methods (scores, display, etc) behave differently if the alignment is flexible (created with FatCat).
AFPChain() - Constructor for class org.biojava.nbio.structure.align.model.AFPChain: Deprecated.
AFPChain(AFPChain) - Constructor for class org.biojava.nbio.structure.align.model.AFPChain: Copy constructor
AFPChainCoordManager - Class in org.biojava.nbio.structure.align.gui.aligpanel
AFPChainCoordManager() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
AFPChainer - Class in org.biojava.nbio.structure.align.fatcat.calc: a class to chain AFPs to an alignment
AFPChainer() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
AFPChainFlipper - Class in org.biojava.nbio.structure.align.xml
AFPChainFlipper() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainFlipper
AFPChainScorer - Class in org.biojava.nbio.structure.align.util
AFPChainScorer() - Constructor for class org.biojava.nbio.structure.align.util.AFPChainScorer
AfpChainWriter - Class in org.biojava.nbio.structure.align.model: A class to convert the data in an AfpChain object to various String outputs.
AfpChainWriter() - Constructor for class org.biojava.nbio.structure.align.model.AfpChainWriter
AFPChainXMLConverter - Class in org.biojava.nbio.structure.align.xml
AFPChainXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
AFPChainXMLParser - Class in org.biojava.nbio.structure.align.xml
AFPChainXMLParser() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
AFPFromFasta - Class in demo: Demo displaying a structural alignment from a FASTA file using FastaAFPChainConverter.
AFPFromFasta() - Constructor for class demo.AFPFromFasta
AFPOptimizer - Class in org.biojava.nbio.structure.align.fatcat.calc
AFPOptimizer() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
afpPairConn(int, int, FatCatParameters, AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer: //Key function: calculate the connectivity of AFP pairs //no compatibility criteria is executed //note: afp1 is previous to afp2 in terms of the position //this module must be optimized
AFPPostProcessor - Class in org.biojava.nbio.structure.align.fatcat.calc: does post processing after alignment chaingin
AFPPostProcessor() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
AFPTwister - Class in org.biojava.nbio.structure.align
AFPTwister() - Constructor for class org.biojava.nbio.structure.align.AFPTwister
AgScore - Class in org.biojava.nbio.survival.cox.stats
AgScore() - Constructor for class org.biojava.nbio.survival.cox.stats.AgScore
algorithmName - Static variable in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeCPMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeSideChainMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat
algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
algorithmName - Static variable in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
algorithmName - Static variable in class org.biojava.nbio.structure.symmetry.internal.CeSymm
ALIGFACTOR - Static variable in class org.biojava.nbio.structure.align.pairwise.Gotoh
AligMatEl - Class in org.biojava.nbio.structure.align.helper
AligMatEl() - Constructor for class org.biojava.nbio.structure.align.helper.AligMatEl
align() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Performs alignment
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.CeCPMain: Aligns ca1 and ca2 using a heuristic to check for CPs.
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.CeMain: Align ca2 onto ca1.
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeMain
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain: Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
align(Atom[], Atom[], boolean, FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
align(Atom[], Atom[], FatCatParameters, boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
align(List<Atom[]>, Object) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
align(List<Atom[]>) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
align(List<Atom[]>) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner: Run an alignment while specifying the atoms to be aligned.
align(List<Atom[]>, Object) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner: Run an alignment and also send a bean containing the parameters.
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
align(Atom[], Atom[]) - Method in interface org.biojava.nbio.structure.align.StructureAlignment: Run an alignment while specifying the atoms to be aligned.
align(Atom[], Atom[], Object) - Method in interface org.biojava.nbio.structure.align.StructureAlignment: run an alignment and also send a bean containing the parameters.
align(Structure, Structure) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Calculate the alignment between the two full structures with default parameters
align(Structure, Structure, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Calculate the alignment between the two full structures with user provided parameters
align(Structure, String, Structure, String) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Align two chains from the structures.
align(Structure, String, Structure, String, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Aligns two chains from the structures using user provided parameters.
align(Atom[], Atom[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: calculate the protein structure superimposition, between two sets of atoms.
align(Structure, List<Chain>) - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
align(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
align_NPE(Matrix, StrucAligParameters) - Static method in class org.biojava.nbio.structure.align.pairwise.AligNPE: Align without penalizing end-gaps.
Alignable - Interface in org.biojava.nbio.structure.align.pairwise
AlignedPosition - Class in org.biojava.nbio.structure.gui.util
AlignedPosition() - Constructor for class org.biojava.nbio.structure.gui.util.AlignedPosition
AlignedSequence<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a data structure for a Sequence within an alignment.
AlignedSequence.Step - Enum in org.biojava.nbio.core.alignment.template: Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
Aligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes an alignment Profile from a list of Sequences.
AlignerHelper - Class in org.biojava.nbio.alignment.routines: Static utility to construct alignment routines from a common library of methods.
AlignerHelper() - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper
AlignerHelper.Anchor - Class in org.biojava.nbio.alignment.routines: Compounds in query and target sequences that must align
AlignerHelper.Anchor.QueryIndexComparator - Class in org.biojava.nbio.alignment.routines
AlignerHelper.Cut - Class in org.biojava.nbio.alignment.routines: Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
AlignerHelper.Last - Enum in org.biojava.nbio.alignment.routines: Define a traceback pointer for the three edit operations: substitution (match/replacement of a query compound with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and insertion (addition of a target compound opening a gap in the query sequence).
AlignerHelper.Subproblem - Class in org.biojava.nbio.alignment.routines: Alignment subproblem.
alignFlexible(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
ALIGNMENT_PANEL - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
alignmentAsMap(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Creates a Map specifying the alignment as a mapping between residue indices of protein 1 and residue indices of protein 2.
AlignmentCalc - Class in org.biojava.nbio.structure.align.gui: A class that obtains two structures via DAS and aligns them This is done in a separate thread.
AlignmentCalc(AlignmentGui, Structure, Structure, String, String) - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentCalc: requests an alignment of pdb1 vs pdb 2.
AlignmentCalc - Class in org.biojava.nbio.structure.gui.util: A class that obtains two structures via DAS and aligns them This is done in a separate thread.
AlignmentCalc(AlignmentGui, Structure, Structure) - Constructor for class org.biojava.nbio.structure.gui.util.AlignmentCalc: requests an alignment of pdb1 vs pdb 2.
AlignmentCalcDB - Class in org.biojava.nbio.structure.align.gui
AlignmentCalcDB(AlignmentGui, Structure, String, UserConfiguration, String, Boolean) - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
AlignmentCalculationRunnable - Interface in org.biojava.nbio.structure.align.gui
alignmentEnded() - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
alignmentEnded() - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
alignmentEnded() - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
AlignmentGui - Class in org.biojava.nbio.structure.align.gui: A JFrame that allows to trigger a pairwise structure alignment, either from files in a directory, or after manual upload.
AlignmentGui() - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentGui
AlignmentGuiDemo - Class in demo: Get an instance of the two alignment GUIs.
AlignmentGuiDemo() - Constructor for class demo.AlignmentGuiDemo
AlignmentPositionListener - Interface in org.biojava.nbio.structure.gui.events
AlignmentProgressListener - Interface in org.biojava.nbio.structure.align.events
AlignmentProgressListener - Class in org.biojava.nbio.structure.align.pairwise: A class to listen to progress of the structure alignment calculations
AlignmentProgressListener() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
AlignmentResult - Class in org.biojava.nbio.structure.align.pairwise: A class to track the alignment results in a flat file
AlignmentResult() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlignmentResult
Alignments - Class in org.biojava.nbio.alignment: Static utility to easily run alignment routines.
Alignments.PairInProfileScorerType - Enum in org.biojava.nbio.alignment: List of implemented sequence pair in a profile scoring routines.
Alignments.PairwiseSequenceAlignerType - Enum in org.biojava.nbio.alignment: List of implemented pairwise sequence alignment routines.
Alignments.PairwiseSequenceScorerType - Enum in org.biojava.nbio.alignment: List of implemented pairwise sequence scoring routines.
Alignments.ProfileProfileAlignerType - Enum in org.biojava.nbio.alignment: List of implemented profile-profile alignment routines.
Alignments.RefinerType - Enum in org.biojava.nbio.alignment: List of implemented profile refinement routines.
alignmentStarted(String, String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
alignmentStarted(String, String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
alignmentStarted(String, String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
AlignmentTextPanel - Class in org.biojava.nbio.structure.align.gui
AlignmentTextPanel() - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentTextPanel
AlignmentTools - Class in org.biojava.nbio.structure.align.util: Methods for analyzing and manipulating AFPChains and for other pairwise alignment utilities.
AlignmentTools() - Constructor for class org.biojava.nbio.structure.align.util.AlignmentTools
AlignmentTools.IdentityMap<K> - Class in org.biojava.nbio.structure.align.util: A Map can be viewed as a function from K to V.
alignmentToSIF(Writer, AFPChain, Atom[], Atom[], String, String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Creates a simple interaction format (SIF) file for an alignment.
alignOptimal(Atom[], Atom[], Object, AFPChain[]) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain: Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
alignPair(String, String) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
alignPair(String, String, String) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
AligNPE - Class in org.biojava.nbio.structure.align.pairwise
AligNPE() - Constructor for class org.biojava.nbio.structure.align.pairwise.AligNPE
alignPermuted(Atom[], Atom[], Object, int) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain: Aligns ca1 with ca2 permuted by cp residues.
alignRigid(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
alignRigid(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
alignSuperfamily() - Method in class demo.DemoSCOP
AlignTools - Class in org.biojava.nbio.structure.align.helper
AlignTools() - Constructor for class org.biojava.nbio.structure.align.helper.AlignTools
AligPanel - Class in org.biojava.nbio.structure.align.gui.aligpanel: A JPanel that can display an AFPChain in a nice way and interact with Jmol.
AligPanel() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
AligPanelMouseMotionListener - Class in org.biojava.nbio.structure.align.gui.aligpanel
AligPanelMouseMotionListener(AligPanel) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
AligUIManager - Class in org.biojava.nbio.structure.align.webstart
AligUIManager() - Constructor for class org.biojava.nbio.structure.align.webstart.AligUIManager
ALL_POLYMER_TYPES - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType: Convenience Set of all polymer types.
AllChemCompProvider - Class in org.biojava.nbio.structure.io.mmcif: A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.
AllChemCompProvider() - Constructor for class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider
allComponents() - Static method in class org.biojava.nbio.protmod.Component
allComponents() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
allIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
allKeywords() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
allModifications() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
allPdbccIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
allPsimodIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
allResidIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
AlreadyExistsException - Exception in org.biojava.nbio.ontology: Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
AlreadyExistsException() - Constructor for exception org.biojava.nbio.ontology.AlreadyExistsException
AlreadyExistsException(String) - Constructor for exception org.biojava.nbio.ontology.AlreadyExistsException
ALT_ID - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
AltAligComparator - Class in org.biojava.nbio.structure.align.pairwise: a comparator to sort AlternativeAlignments based on their number of equivalent residues and RMSD.
AltAligComparator() - Constructor for class org.biojava.nbio.structure.align.pairwise.AltAligComparator
altcode - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
AlternativeAlignment - Class in org.biojava.nbio.structure.align.pairwise: Implements a class which handles one possible (alternative) solution.
AlternativeAlignment() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
AlternativeAlignmentFrame - Class in org.biojava.nbio.structure.gui.util: a frame showing the alternative alignments, which are the result of a structure superimposition
AlternativeAlignmentFrame(Structure, Structure) - Constructor for class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
AmbiguityDNACompoundSet - Class in org.biojava.nbio.core.sequence.compound
AmbiguityDNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet
AmbiguityDNARNAHybridCompoundSet - Class in org.biojava.nbio.core.sequence.compound: Ambiguity set for hybrid DNA/RNA sequences.
AmbiguityDNARNAHybridCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet
AmbiguityRNACompoundSet - Class in org.biojava.nbio.core.sequence.compound
AmbiguityRNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet
AMBIGUOUS_AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil: Same as AA pattern but with two additional letters - XU
AMBIGUOUS_NUCLEOTIDE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil: Ambiguous nucleotide
AMINO_ACID_MATCHER - Static variable in class org.biojava.nbio.structure.AtomPositionMap: Matches CA atoms of protein groups
AminoAcid - Interface in org.biojava.nbio.structure: A Group that represents an AminoAcid.
AminoAcidComposition - Class in org.biojava.nbio.aaproperties.xml
AminoAcidComposition() - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
AminoAcidComposition(String, String, String, List<Name2Count>, List<Name2Count>) - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
AminoAcidCompositionTable - Class in org.biojava.nbio.aaproperties.xml
AminoAcidCompositionTable() - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
AminoAcidCompositionTable(List<AminoAcidComposition>) - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
AminoAcidCompound - Class in org.biojava.nbio.core.sequence.compound: Used to describe an Amino Acid.
AminoAcidCompound(AminoAcidCompoundSet, String, String, String, Float) - Constructor for class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
AminoAcidCompoundSet - Class in org.biojava.nbio.core.sequence.compound: Set of proteinogenic amino acids.
AminoAcidCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
AminoAcidImpl - Class in org.biojava.nbio.structure: AminoAcid inherits most from Hetatom.
AminoAcidImpl() - Constructor for class org.biojava.nbio.structure.AminoAcidImpl: inherits most from Hetero and has just a few extensions.
aminoAcidsCompounds(CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
amount(Atom) - Static method in class org.biojava.nbio.structure.Calc: Gets the length of the vector (2-norm)
analyze(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm: Analyze the symmetries of the input Atom array using the DEFAULT parameters.
analyze(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm: Analyze the symmetries of the input Atom array using the provided parameters.
analyzeLevel(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm: Analyze a single level of symmetry.
Anchor(int, int) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.routines: This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.
AnchoredPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Prepares for a pairwise global sequence alignment.
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Prepares for a pairwise global sequence alignment.
anchors - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
angle(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: Gets the angle between two vectors
angleCheckOk(FragmentPair, FragmentPair, float) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
AngleOrderDetectorPlus - Class in org.biojava.nbio.structure.symmetry.internal: Guesses an order of rotational symmetry from the angle.
AngleOrderDetectorPlus(double) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
AngleOrderDetectorPlus(int) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
AngleOrderDetectorPlus(int, double) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
AngleOrderDetectorPlus(int, double, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus: Determine order by finding the order (up to the maxOrder) which has the closest rotation angle to the observed rotation.
AngleOutlier - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
AngleOutlier() - Constructor for class org.biojava.nbio.structure.validation.AngleOutlier
angleOutlier - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
Annotatable - Interface in org.biojava.nbio.ontology.utils: Indicates that an object has an associated annotation.
Annotation - Interface in org.biojava.nbio.ontology.utils: Arbitrary annotation associated with one or more objects.
ANY - Static variable in class org.biojava.nbio.ontology.OntoTools
ANYTHING_MATCHER - Static variable in class org.biojava.nbio.structure.AtomPositionMap: Matches all atoms
apairs_from_idxlst(JointFragments) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: Set apairs according to a list of (i,j) tuples.
apairs_from_seed(int, int, int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: Set apairs according to a seed position.
App - Class in org.biojava.nbio.genome: Hello world!
App() - Constructor for class org.biojava.nbio.genome.App
App - Class in org.biojava.nbio.ontology: Hello world!
App() - Constructor for class org.biojava.nbio.ontology.App
append(T, Fastq...) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter: Append the specified FASTQ formatted sequences to the specified appendable.
append(T, Iterable<Fastq>) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter: Append the specified FASTQ formatted sequences to the specified appendable.
appendQuality(String) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder: Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.
appendQuality(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener: Notify this listener of a quality line.
appendSequence(String) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder: Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.
appendSequence(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener: Notify this parse listener of an additional sequence line.
appendToSequence(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
appendWorkSheetColumns(WorkSheet) - Method in class org.biojava.nbio.survival.data.WorkSheet: Add columns from a second worksheet to be joined by common row.
appendWorkSheetRows(WorkSheet) - Method in class org.biojava.nbio.survival.data.WorkSheet: Add rows from a second worksheet to be joined by common column.
applyAlignment(Map<T, T>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Applies an alignment k times.
applyAlignment(Map<S, T>, Map<T, S>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Applies an alignment k times.
applyColumnFilter(String, ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet: Apply filter to a column to change values from say numberic to nominal based on some range
applyValues() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
approach_ap3(Atom[], Atom[], FragmentPair[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
areInSameAxis(int, int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Returns true if both given transform ids belong to the same crystallographic axis (a, b or c) For two non-rotation transformations (i.e.
arrayLeftDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element left division, C = A.\B
arrayLeftDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element left division in place, A = A.\B
ArrayListProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
ArrayListProxySequenceReader() - Constructor for class org.biojava.nbio.core.sequence.loader.ArrayListProxySequenceReader
ArrayListSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage: Stores a Sequence as a collection of compounds in an ArrayList
ArrayListSequenceReader() - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
ArrayListSequenceReader(List<C>, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
ArrayListSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
arrayRightDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element right division, C = A./B
arrayRightDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element right division in place, A = A./B
arrayTimes(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element multiplication, C = A.*B
arrayTimesEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element multiplication in place, A = A.*B
AsaCalculator - Class in org.biojava.nbio.structure.asa: Class to calculate Accessible Surface Areas based on the rolling ball algorithm by Shrake and Rupley.
AsaCalculator(Structure, double, int, int, boolean) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator: Constructs a new AsaCalculator.
AsaCalculator(Atom[], double, int, int) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator: Constructs a new AsaCalculator.
asMap() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
asMap() - Method in interface org.biojava.nbio.ontology.utils.Annotation: Return a map that contains the same key/values as this Annotation.
AssertionFailure - Error in org.biojava.nbio.ontology.utils: An unchecked exception representing an Assertion failure.
AssertionFailure(String) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
AssertionFailure(Throwable) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
AssertionFailure(String, Throwable) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
assertLocation() - Method in class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
assertLocation() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
assignment - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
AssignmentXMLSerializer - Class in org.biojava.nbio.structure.domain
AssignmentXMLSerializer() - Constructor for class org.biojava.nbio.structure.domain.AssignmentXMLSerializer
Astral - Class in org.biojava.nbio.structure.scop: Provides programmatic access to ASTRAL representative sets.
Astral(Astral.AstralSet) - Constructor for class org.biojava.nbio.structure.scop.Astral: Constructs a new Astral object.
Astral(String, URL) - Constructor for class org.biojava.nbio.structure.scop.Astral: Constructs a new Astral object.
Astral(String, Reader) - Constructor for class org.biojava.nbio.structure.scop.Astral: Constructs a new Astral object.
Astral.AstralSet - Enum in org.biojava.nbio.structure.scop: An ASTRAL sequence-identity cutoff with an identifier such as:
Atom - Interface in org.biojava.nbio.structure: A simple interface for an Atom.
atom - Variable in class org.biojava.nbio.structure.validation.Clash
atom - Variable in class org.biojava.nbio.structure.validation.SymmClash
atom0 - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
atom0 - Variable in class org.biojava.nbio.structure.validation.BondOutlier
atom1 - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
atom1 - Variable in class org.biojava.nbio.structure.validation.BondOutlier
atom2 - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
ATOM_CA_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.FileParsingParameters: The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
AtomCache - Class in org.biojava.nbio.structure.align.util: A utility class that provides easy access to Structure objects.
AtomCache() - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Default AtomCache constructor.
AtomCache(String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(String, String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(String, boolean) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
isSplit parameter is ignored (4.0.0)
AtomCache(String, String, boolean) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
isSplit parameter is ignored (4.0.0)
AtomCache(UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Creates a new AtomCache object based on the provided UserConfiguration.
AtomContact - Class in org.biojava.nbio.structure.contact: A pair of atoms that are in contact
AtomContact(Pair<Atom>, double) - Constructor for class org.biojava.nbio.structure.contact.AtomContact
AtomContactSet - Class in org.biojava.nbio.structure.contact: A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations
AtomContactSet(double) - Constructor for class org.biojava.nbio.structure.contact.AtomContactSet
AtomIdentifier - Class in org.biojava.nbio.structure.contact
AtomIdentifier(int, String) - Constructor for class org.biojava.nbio.structure.contact.AtomIdentifier
AtomImpl - Class in org.biojava.nbio.structure: Implementation of an Atom of a PDB file.
AtomImpl() - Constructor for class org.biojava.nbio.structure.AtomImpl
AtomInfo - Class in org.biojava.nbio.structure.align.gui.jmol: This class uniquely describes an atom
AtomInfo() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
AtomInfoParser - Class in org.biojava.nbio.structure.align.gui.jmol
AtomInfoParser() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser
AtomIterator - Class in org.biojava.nbio.structure: an iterator over all atoms of a structure / group.
AtomIterator(Structure) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object.
AtomIterator(Group) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object.
AtomPositionMap - Class in org.biojava.nbio.structure: A map from ResidueNumbers to ATOM record positions in a PDB file.
AtomPositionMap(Atom[]) - Constructor for class org.biojava.nbio.structure.AtomPositionMap: Creates a new AtomPositionMap containing peptide alpha-carbon atoms
AtomPositionMap(Atom[], AtomPositionMap.GroupMatcher) - Constructor for class org.biojava.nbio.structure.AtomPositionMap: Creates a new AtomPositionMap containing only atoms matched by matcher.
AtomPositionMap(Structure) - Constructor for class org.biojava.nbio.structure.AtomPositionMap: Creates a new AtomPositionMap containing representative atoms from a structure.
AtomPositionMap.GroupMatcher - Interface in org.biojava.nbio.structure: Used as a Predicate to indicate whether a particular Atom should be mapped
ATOMRECORD - Static variable in interface org.biojava.nbio.structure.AminoAcid: Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
atoms - Variable in class org.biojava.nbio.structure.HetatomImpl
atoms - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier
atoms - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier
AtomSite - Class in org.biojava.nbio.structure.io.mmcif.model
AtomSite() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AtomSite
atomsToPoints(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Convert an array of atoms into an array of vecmath points
attemptedValidationSteps - Variable in class org.biojava.nbio.structure.validation.Entry
attribute(String, String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
attribute(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
attribute(String, String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Add an attribute to an element.
attribute(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Add an un-qualified attribute to an element.
attributes() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get the string of key/value attributes.
attributeValues(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a collection of the unique values for the specified key.
AuditAuthor - Class in org.biojava.nbio.structure.io.mmcif.model
AuditAuthor() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
AugmentedResidueRange - Class in org.biojava.nbio.structure: Created by douglas on 1/23/15.
AugmentedResidueRange(String, ResidueNumber, ResidueNumber, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
AugmentedResidueRange(String, String, String, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
Author - Class in org.biojava.nbio.structure: Describes author attributes for author information in a PDB file.
Author() - Constructor for class org.biojava.nbio.structure.Author
AUTHORS_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
AutoSuggestProvider - Interface in org.biojava.nbio.structure.align.gui.autosuggest: A class that provides auto-completion suggestions for JAutoSuggest
available() - Method in class org.biojava.nbio.core.util.UncompressInputStream
available() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
avgoccu - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
AVGTM_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
AxisAligner - Class in org.biojava.nbio.structure.symmetry.core
AxisAligner() - Constructor for class org.biojava.nbio.structure.symmetry.core.AxisAligner
axisStroke - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

B

BACKGROUND_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
BASE_COUNT_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
BASE_COUNT_TAG_FULL - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
baseURL - Static variable in class org.biojava.nbio.structure.rcsb.RCSBUpdates
basicLoad(PDBFileReader, boolean, String) - Method in class demo.DemoChangeChemCompProvider
basicLoad(String) - Method in class demo.DemoDomainsplit
basicLoad() - Method in class demo.DemoLoadStructure
BasicSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence: Bare bones version of the Sequence object to be used sparingly.
BasicSequence(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.BasicSequence
BasicSequence(ProxySequenceReader<C>) - Constructor for class org.biojava.nbio.core.sequence.BasicSequence
BerkeleyScopInstallation - Class in org.biojava.nbio.structure.scop: SCOPe: The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop.berkeley.edu/).
BerkeleyScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.BerkeleyScopInstallation
bestTrace1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTrace1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTrace2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTrace2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTraces1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTraces1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTraces2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTraces2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTraceScore - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTraceScore - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTracesN - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTracesN - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTracesScores - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTracesScores - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
BetaBridge - Class in org.biojava.nbio.structure.secstruc: Container that represents a beta Bridge between two residues.
BetaBridge(int, int, BridgeType) - Constructor for class org.biojava.nbio.structure.secstruc.BetaBridge
BIO_ASSEMBLY - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
BIO_NAME_PATTERN - Static variable in class org.biojava.nbio.structure.BioAssemblyIdentifier
BioAssemblyIdentifier - Class in org.biojava.nbio.structure
BioAssemblyIdentifier(String) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
BioAssemblyIdentifier(String, int) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
BioAssemblyInfo - Class in org.biojava.nbio.structure.quaternary: Representation of a Biological Assembly annotation as provided by the PDB.
BioAssemblyInfo() - Constructor for class org.biojava.nbio.structure.quaternary.BioAssemblyInfo: Empty constructor
BioAssemblyTools - Class in org.biojava.nbio.structure.quaternary
BioAssemblyTools() - Constructor for class org.biojava.nbio.structure.quaternary.BioAssemblyTools
bioEnd() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Get end index, in biocoordinates.
BIOJAVA_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo: Secondary strucuture calculated and assigned by DSSP of BioJava
BioJavaAADemo - Class in demo: Created by andreas on 8/9/14.
BioJavaAADemo() - Constructor for class demo.BioJavaAADemo
BiojavaJmol - Class in org.biojava.nbio.structure.gui: A class that provides a simple GUI for Jmol
BiojavaJmol() - Constructor for class org.biojava.nbio.structure.gui.BiojavaJmol
BioJavaStructureAlignment - Class in org.biojava.nbio.structure.align: Wrapper for the BioJava Structure Alignment Implementation
BioJavaStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.BioJavaStructureAlignment
BIOL_ASSEMBLY_IDENTIFIER - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
BiologicalAssemblyBuilder - Class in org.biojava.nbio.structure.quaternary: Reconstructs the quaternary structure of a protein from an asymmetric unit
BiologicalAssemblyBuilder() - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
BiologicalAssemblyTransformation - Class in org.biojava.nbio.structure.quaternary: The transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file.
BiologicalAssemblyTransformation() - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Default Constructor
BiologicalAssemblyTransformation(BiologicalAssemblyTransformation) - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Copy Constructor
bioStart() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Get start index, in biocoordinates.
bioStrand() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Get character representation of strand.
BioUnitDataProvider - Interface in org.biojava.nbio.structure.quaternary.io: Provides access to the data that is needed in order to rebuild the correct biological assembly of a protein.
BioUnitDataProviderFactory - Class in org.biojava.nbio.structure.quaternary.io: Factory to create BioUnitDataProvider instances.
BitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
BitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
BitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
BitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
bitMask() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: This method should return the bit mask to be used to extract the bytes you are interested in working with.
bitMask() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
bitMask() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
BitSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage: An implementation of the popular bit encodings.
BitSequenceReader(BitSequenceReader.BitArrayWorker<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader: Instance which allows you to supply a different @{BitArrayWorker} object.
BitSequenceReader.BitArrayWorker<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage: The logic of working with a bit has been separated out into this class to help developers create the bit data structures without having to put the code into an intermediate format and to also use the format without the need to copy this code.
bitsPerCompound() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: Returns how many bits are used to represent a compound e.g.
BLACK_WHITE_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper
blankOutBreakFlag(AFPChain, Atom[], int, int, CECalculator, boolean[][], int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
blankOutCEOrig(Atom[], int, int, CECalculator, Matrix, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
blankOutPreviousAlignment(AFPChain, Atom[], int, int, CECalculator, Matrix, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
BlastAlignmentParameterEnum - Enum in org.biojava.nbio.ws.alignment.qblast: Alignment request parameters accepted by QBlast service.
Not all are mandatory.
BlastClustReader - Class in org.biojava.nbio.structure.symmetry.utils
BlastClustReader(int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
BlastHitBuilder - Class in org.biojava.nbio.core.search.io.blast: Designed by Paolo Pavan.
BlastHitBuilder() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
BlastHomologyHits - Class in org.biojava.nbio.genome.homology
BlastHomologyHits() - Constructor for class org.biojava.nbio.genome.homology.BlastHomologyHits
BlastHspBuilder - Class in org.biojava.nbio.core.search.io.blast: Designed by Paolo Pavan.
BlastHspBuilder() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
BlastJob - Class in org.biojava.nbio.ws.alignment.qblast: Information about QBlast search job
BlastJob() - Constructor for class org.biojava.nbio.ws.alignment.qblast.BlastJob
BlastMatrixEnum - Enum in org.biojava.nbio.ws.alignment.qblast: Enum representing matrices supported by QBlast
BlastOutputAlignmentFormatEnum - Enum in org.biojava.nbio.ws.alignment.qblast: Enum representing available output alignment types.
BlastOutputFormatEnum - Enum in org.biojava.nbio.ws.alignment.qblast: Enum representing available output formats.
BlastOutputParameterEnum - Enum in org.biojava.nbio.ws.alignment.qblast: Output parameters accepted by QBlast service.
BlastProgramEnum - Enum in org.biojava.nbio.ws.alignment.qblast: Enum representing available blast programs.
BlastResult - Class in org.biojava.nbio.core.search.io.blast: This class models a Blast/Blast plus result.
BlastResult(String, String, String, String, HashMap<String, String>, int, String, String, int, List<Hit>, Sequence) - Constructor for class org.biojava.nbio.core.search.io.blast.BlastResult
BlastResultBuilder - Class in org.biojava.nbio.core.search.io.blast: Designed by Paolo Pavan.
BlastResultBuilder() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
BlastTabularParser - Class in org.biojava.nbio.core.search.io.blast: Designed by Paolo Pavan.
BlastTabularParser() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastTabularParser
BlastXMLParser - Class in org.biojava.nbio.core.search.io.blast: Re-designed by Paolo Pavan on the footprint of: org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis You may want to find my contacts on Github and LinkedIn for code info or discuss major changes.
BlastXMLParser() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastXMLParser
BlastXMLQuery - Class in org.biojava.nbio.genome.query
BlastXMLQuery(String) - Constructor for class org.biojava.nbio.genome.query.BlastXMLQuery
Block - Interface in org.biojava.nbio.structure.align.multiple: A Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in a sequential order.
BlockImpl - Class in org.biojava.nbio.structure.align.multiple: General implementation of a Block that supports any type of sequential alignment with gaps.
BlockImpl(BlockSet) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl: Constructor.
BlockImpl(BlockImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl: Copy constructor.
blockInfo(AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer: get the afp list and residue list for each block
BlockSet - Interface in org.biojava.nbio.structure.align.multiple: A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment.
BlockSetImpl - Class in org.biojava.nbio.structure.align.multiple: A general implementation of a BlockSet to store a flexible part of a multiple alignment.
BlockSetImpl(MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl: Constructor.
BlockSetImpl(BlockSetImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl: Copy constructor.
Blosum62 - Static variable in class org.biojava.nbio.ronn.RonnConstraint
Bond - Interface in org.biojava.nbio.structure: A simple bond -- it stores information about two atoms as well as information about its bond order.
BOND_TYPES_TO_PARSE - Static variable in class org.biojava.nbio.structure.io.BondMaker: The types of bonds that are read from struct_conn (type specified in field conn_type_id)
BondImpl - Class in org.biojava.nbio.structure: A simple bond -- it stores information about two atoms as well as information about its bond order.
BondImpl(Atom, Atom, int) - Constructor for class org.biojava.nbio.structure.BondImpl: Constructs a new bond from a pair of atoms and the bond order of the bond between them.
BondImpl(Atom, Atom, int, boolean) - Constructor for class org.biojava.nbio.structure.BondImpl: Constructs a new bond from a pair of atoms and the bond order of the bond between them.
BondLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
BondLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
BondMaker - Class in org.biojava.nbio.structure.io: Adds polymer bonds for peptides and nucleotides based on distance cutoffs and intra-group (residue) bonds based on data from the Chemical Component Dictionary to the Structure object.
BondMaker(Structure, FileParsingParameters) - Constructor for class org.biojava.nbio.structure.io.BondMaker
BondOutlier - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
BondOutlier() - Constructor for class org.biojava.nbio.structure.validation.BondOutlier
bondOutlier - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
BONDS_INITIAL_CAPACITY - Static variable in class org.biojava.nbio.structure.AtomImpl: The inital capacity of the bonds list.
BondType - Enum in org.biojava.nbio.structure: Work in progress - NOT final!
bottom - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
BoundingBox - Class in org.biojava.nbio.structure.contact: A bounding box for short cutting some geometrical calculations.
BoundingBox(double, double, double, double, double, double) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
BoundingBox(BoundingBox) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
BoundingBox(Atom[]) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox: Constructs a BoundingBox by calculating maxs and mins of given array of atoms.
BoundingBox(BoundingBox[]) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox: Given a set of bounding boxes returns a bounding box that bounds all of them.
bounds() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: The union of all locations of all features in this list, mapped to the positive strand.
BravaisLattice - Enum in org.biojava.nbio.structure.xtal: An enum to represent the 7 Bravais lattices
BridgeType - Enum in org.biojava.nbio.structure.secstruc: A bridge is formed by two non-overlapping stretches of three residues each (i-1,i,i+1) and (j-1,j,j+1), where i
BROAD_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
BROAD_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym
BrowserOpener - Class in org.biojava.nbio.structure.align.webstart
BrowserOpener() - Constructor for class org.biojava.nbio.structure.align.webstart.BrowserOpener
BufferedReaderBytesRead - Class in org.biojava.nbio.core.sequence.io: Need to keep track of actual bytes read and take advantage of buffered reader performance.
BufferedReaderBytesRead(Reader, int) - Constructor for class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead: Creates a buffering character-input stream that uses an input buffer of the specified size.
BufferedReaderBytesRead(Reader) - Constructor for class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead: Creates a buffering character-input stream that uses a default-sized input buffer.
build() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder: The method to finish any calls to the builder with which returns a transcription engine.
build() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
build() - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder: Build and return a new FASTQ formatted sequence configured from the properties of this builder.
build - Static variable in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
Builder() - Constructor for class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
Builder(String, ModificationCategory, ModificationOccurrenceType, ModificationCondition) - Constructor for class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
Builder(ProteinModification) - Constructor for class org.biojava.nbio.protmod.ProteinModificationImpl.Builder: Create a Builder from an existing ProteinModification.
builder() - Static method in class org.biojava.nbio.sequencing.io.fastq.Fastq: Create and return a new FastqBuilder.
buildFeatureAtrributeIndex(String, FeatureList) - Static method in class org.biojava.nbio.genome.parsers.gff.FeatureHelper: Build a list of individual features to allow easy indexing and to avoid iterating through large genome gff3 files The index for the returned HashMap is the value of the attribute used to build the index
buildSymmetryGraph(List<AFPChain>, Atom[], boolean) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Converts a set of AFP alignments into a Graph of aligned residues, where each vertex is a residue and each edge means the connection between the two residues in one of the alignments.
buildSymmetryGraph(AFPChain) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Converts a self alignment into a directed jGraphT of aligned residues, where each vertex is a residue and each edge means the equivalence between the two residues in the self-alignment.
buildTranslators() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
bulkSolventB - Variable in class org.biojava.nbio.structure.validation.Entry
bulkSolventK - Variable in class org.biojava.nbio.structure.validation.Entry
BYTES_PER_INT - Static variable in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
bytesRead - Variable in class org.biojava.nbio.ontology.obo.OboFileParser

C

C - Static variable in class org.biojava.nbio.aaproperties.Constraints
c - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange: first allowed c-term
C1_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C1' in RNA
C2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C2' in RNA
C2RotationSolver - Class in org.biojava.nbio.structure.symmetry.core
C2RotationSolver(Subunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.C2RotationSolver
C3_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C3' in RNA
C4_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C4' in RNA
C_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name for the backbone carbonyl
CA_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C-alpha atom.
CA_MIN_DIST - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc: min distance of two CA atoms if H-bonds are allowed to form
cache - Variable in class org.biojava.nbio.structure.align.client.FarmJobRunnable
cache(K, V) - Method in class org.biojava.nbio.structure.domain.SerializableCache: This will not cache null values.
CACHE_PROPERTY - Static variable in class org.biojava.nbio.core.util.InputStreamProvider
CachedRemoteScopInstallation - Class in org.biojava.nbio.structure.scop: An extension of the RemoteScopInstallation that caches some of the data locally.
CachedRemoteScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
CachedRemoteScopInstallation(boolean) - Constructor for class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
CacheFactory - Class in org.biojava.nbio.structure.align.util: provides a SoftHashMap singleton.
cacheFileName - Variable in class org.biojava.nbio.structure.domain.SerializableCache
CAConverter - Class in org.biojava.nbio.structure.io: Converts full atom representations to Calpha only ones.
CAConverter() - Constructor for class org.biojava.nbio.structure.io.CAConverter
calAfpRmsd(int, int[], int, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer: //return the rmsd of the residues from the segments that form the given AFP list //this value can be a measurement (1) for the connectivity of the AFPs
Calc - Class in org.biojava.nbio.structure: Utility operations on Atoms, AminoAcids, etc.
Calc() - Constructor for class org.biojava.nbio.structure.Calc
calc_rmsd(Atom[], Atom[], int, boolean, boolean) - Method in class org.biojava.nbio.structure.align.ce.CECalculator: Deprecated.
Use CECalculator.calc_rmsd(Atom[],Atom[],int,boolean) instead
calc_rmsd(Atom[], Atom[], int, boolean) - Method in class org.biojava.nbio.structure.align.ce.CECalculator: superimpose and get rmsd
calc_rmsd(Atom[], Atom[], int, boolean, boolean) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced: superimpose and get rmsd
calcAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together.
calcAsas(int, int, int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together.
CalcBioAssemblySymmetry - Class in org.biojava.nbio.structure.symmetry.analysis
CalcBioAssemblySymmetry(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
calcCenterOfRotation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
calcIdSimilarity(char[], char[], int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
calcLength(List<ResidueRangeAndLength>) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength: Calculates the combined number of residues of the ResidueRanges in rrs.
calcPairwiseAlignments() - Method in class org.biojava.nbio.structure.symmetry.core.ClusterMerger: Aligns all pairs of input clusters, calculating their pairwise alignments
calcQuatSymmetry(Subunits, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
calcRotationAngleInDegrees(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: Calculates the angle from centerPt to targetPt in degrees.
calcScale(int) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay: a value of 100 means that the whole sequence should be displayed in the current visible window a factor of 1 means that one amino acid shoud be drawn as big as possible
calcScores(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: calculates scores for this alignment ( %id )
calcScores(Subunits, Matrix4d, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer: Returns minimum, mean, and maximum RMSD and TM-Score for two superimposed sets of subunits TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
calcSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain
calculate(Structure, boolean) - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc: Predicts the secondary structure of this Structure object, using a DSSP implementation.
calculateAsas() - Method in class org.biojava.nbio.structure.asa.AsaCalculator: Calculates the Accessible Surface Areas for the atoms given in constructor and with parameters given.
calculateBlockGap(int[][][]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Method that calculates the number of gaps in each subunit block of an optimal AFP alignment.
calculatedFragmentPairs(List<FragmentPair>) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
calculateIndirectAmbiguities() - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet: Loops through all known nucleotides and attempts to find which are equivalent to each other.
calculateInterfaces(Structure) - Static method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculates the interfaces for a structure using default parameters
calculateMinCP(int[], int, int, int) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain: Finds the alignment index of the residues minCPlength before and after the duplication.
calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector
calculateOrder(AFPChain, Atom[]) - Method in interface org.biojava.nbio.structure.symmetry.internal.OrderDetector
calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector
calculateScores(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates and puts the RMSD and the average TM-Score of the MultipleAlignment.
calculateSuperpositionByIdx(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
calculateWaldTestInfo(CoxInfo) - Static method in class org.biojava.nbio.survival.cox.CoxR
calculator - Variable in class org.biojava.nbio.structure.align.ce.CeMain
call() - Method in class org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner
call() - Method in class org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer
call() - Method in class org.biojava.nbio.alignment.template.CallableProfileProfileAligner
call() - Method in class org.biojava.nbio.ronn.ORonn
call() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
call() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer
CallablePairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements a concurrency wrapper for a PairwiseSequenceAligner.
CallablePairwiseSequenceAligner(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner: Creates a pairwise sequence alignment task for simplified parallel execution.
CallablePairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements a concurrency wrapper for a PairwiseSequenceScorer.
CallablePairwiseSequenceScorer(PairwiseSequenceScorer<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer: Creates a pairwise sequence scoring task for simplified parallel execution.
CallableProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements a concurrency wrapper for a ProfileProfileAligner.
CallableProfileProfileAligner(ProfileProfileAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallableProfileProfileAligner: Creates a profile-profile alignment task for simplified parallel execution.
CallableStructureAlignment - Class in org.biojava.nbio.structure.align
CallableStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment: Default constructor.
CallableStructureAlignment(Atom[], Atom[], String, ConfigStrucAligParams) - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment: Constructor for all-to-all alignment calculation.
calNS(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
calSigAll(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
canComplement(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation: Uses the Sequence's CompoundSet to decide if a compound can be assgined to ComplementCompound meaning it can complement
CartesianProduct<T> - Class in org.biojava.nbio.structure.quaternary: A cartesian product between two lists A and B is the set of all ordered pairs of the elements of both sets.
CartesianProduct(List<T>, List<T>) - Constructor for class org.biojava.nbio.structure.quaternary.CartesianProduct: Class constructor specifying the two lists of a cartesian product.
CaseFreeAminoAcidCompoundSet - Class in org.biojava.nbio.aaproperties.xml: Set of proteinogenic amino acids.
CaseFreeAminoAcidCompoundSet() - Constructor for class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
CaseInsensitiveCompound - Class in org.biojava.nbio.core.sequence.transcription: Attempts to wrap compounds so it is possible to view them in a case insensitive manner
CaseInsensitiveCompound(NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
CaseInsensitiveTriplet(NucleotideCompound, NucleotideCompound, NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
CasePreservingProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io: A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.
CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
categorizeData(ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper: Take a collection of categorical data and convert it to numeric to be used in cox calculations
CATH_DOWNLOAD - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
CathCategory - Enum in org.biojava.nbio.structure.cath: The categories found within CATH.
CathDatabase - Interface in org.biojava.nbio.structure.cath: General API for interacting with CATH.
CathDomain - Class in org.biojava.nbio.structure.cath: A class which represents a single CATH domain.
CathDomain() - Constructor for class org.biojava.nbio.structure.cath.CathDomain
CathFactory - Class in org.biojava.nbio.structure.cath: Controls global CathDatabases being used.
CathFragment - Class in org.biojava.nbio.structure.cath
CathFragment() - Constructor for class org.biojava.nbio.structure.cath.CathFragment
CathInstallation - Class in org.biojava.nbio.structure.cath
CathInstallation(String, boolean, boolean) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
CathInstallation(String) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
CathInstallation() - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
CathNode - Class in org.biojava.nbio.structure.cath: Represents a node in the CATH hierarchy.
CathNode() - Constructor for class org.biojava.nbio.structure.cath.CathNode
CathSegment - Class in org.biojava.nbio.structure.cath
CathSegment() - Constructor for class org.biojava.nbio.structure.cath.CathSegment
CB_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the side-chain C-beta atom
ccp4Version - Variable in class org.biojava.nbio.structure.validation.Entry
CDSComparator - Class in org.biojava.nbio.core.sequence
CDSComparator() - Constructor for class org.biojava.nbio.core.sequence.CDSComparator
CDSSequence - Class in org.biojava.nbio.core.sequence: Represents a exon or coding sequence in a gene.
CDSSequence(TranscriptSequence, int, int, int) - Constructor for class org.biojava.nbio.core.sequence.CDSSequence
CE_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
CECalculator - Class in org.biojava.nbio.structure.align.ce: This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CECalculator(CeParameters) - Constructor for class org.biojava.nbio.structure.align.ce.CECalculator
CeCalculatorEnhanced - Class in org.biojava.nbio.structure.align.ce: This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CeCalculatorEnhanced(CeParameters) - Constructor for class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
ceColumnNames - Static variable in class org.biojava.nbio.structure.align.gui.DBResultTable
CeCPMain - Class in org.biojava.nbio.structure.align.ce: A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.
CeCPMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain
CeCPMain.CPRange - Class in org.biojava.nbio.structure.align.ce: Tiny wrapper for the disallowed regions of an alignment.
CECPParameters - Class in org.biojava.nbio.structure.align.ce: Provides parameters to CeCPMain
CECPParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CECPParameters
CECPParameters.DuplicationHint - Enum in org.biojava.nbio.structure.align.ce
CeCPStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
CeCPUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
CeCPUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
CeCPUserArgumentProcessor.CeCPStartupParams - Class in org.biojava.nbio.structure.align.ce
ceil(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Return the smallest key in the table >= k.
Cell - Class in org.biojava.nbio.structure.io.mmcif.model
Cell() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Cell
CeMain - Class in org.biojava.nbio.structure.align.ce: The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.
CeMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeMain
censored - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
CensorStatus - Class in org.biojava.nbio.survival.kaplanmeier.figure
CensorStatus() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
CensorStatus(String, Double, String) - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
CensorStatusSelect - Interface in org.biojava.nbio.survival.kaplanmeier.figure
center(Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
centerAtoms(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Center the atoms at the Centroid.
centerAtoms(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc: Center the atoms at the Centroid, if the centroid is already know.
centerOfMass(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
centerOfMass() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
centricOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
centroid(Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
CeParameters - Class in org.biojava.nbio.structure.align.ce: Contains the parameters that can be sent to CE
CeParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CeParameters
CeParameters.ScoringStrategy - Enum in org.biojava.nbio.structure.align.ce
CeSideChainMain - Class in org.biojava.nbio.structure.align.ce
CeSideChainMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainMain
CeSideChainUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
CeSideChainUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
CeStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
CeSymm - Class in org.biojava.nbio.structure.symmetry.internal: Identify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment.
CeSymmIterative - Class in org.biojava.nbio.structure.symmetry.internal: Iterative version of CeSymm that aims at identifying all symmetry axis (internal or quaternary) of a particular structure.
CeSymmIterative(CESymmParameters) - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative: For the iterative algorithm to work properly the refinement and optimization options should be turned on, because the alignment has to be consistent at every recursive step.
CESymmParameters - Class in org.biojava.nbio.structure.symmetry.internal: Provides parameters to CeSymm.
CESymmParameters() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
CESymmParameters.OrderDetectorMethod - Enum in org.biojava.nbio.structure.symmetry.internal
CESymmParameters.RefineMethod - Enum in org.biojava.nbio.structure.symmetry.internal
CESymmParameters.SymmetryType - Enum in org.biojava.nbio.structure.symmetry.internal: The internal symmetry detection can be divided into two types: CLOSE: includes the circular and dihedral symmetries, and OPEN: includes the helical and protein repeats symmetries.
CeSymmResult - Class in org.biojava.nbio.structure.symmetry.internal: This Class stores all the relevant information of an internal symmetry result obtained with CeSymm.
CeSymmResult() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
CeUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce: process the arguments from command line
CeUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
CeUserArgumentProcessor.CeStartupParams - Class in org.biojava.nbio.structure.align.ce
Chain - Interface in org.biojava.nbio.structure: Defines the interface for a Chain.
chain - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
CHAIN_NR_SYMBOL - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
CHAIN_REGEX - Static variable in class org.biojava.nbio.structure.ResidueRange
CHAIN_SPLIT_SYMBOL - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
ChainClusterer - Class in org.biojava.nbio.structure.symmetry.core: Wraps a sequence clustering with structural information
ChainClusterer(List<SequenceAlignmentCluster>) - Constructor for class org.biojava.nbio.structure.symmetry.core.ChainClusterer
chainEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
chainId - Variable in class org.biojava.nbio.structure.align.client.StructureName
CHAINID_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier: URL parameter specifying a single chain to include; overridden by residues
ChainImpl - Class in org.biojava.nbio.structure: A Chain in a PDB file.
ChainImpl() - Constructor for class org.biojava.nbio.structure.ChainImpl: Constructs a ChainImpl object.
ChainSignature - Class in org.biojava.nbio.structure.symmetry.misc
ChainSignature(String, int, List<String>) - Constructor for class org.biojava.nbio.structure.symmetry.misc.ChainSignature
change(String) - Method in interface org.biojava.nbio.survival.data.ChangeValue
changeColumnHeader(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
changeColumnHeader(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
changeColumnsHeaders(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.survival.data.WorkSheet: Change the columns in the HashMap Key to the name of the value
changeRowHeader(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
changeRowHeader(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
ChangeValue - Interface in org.biojava.nbio.survival.data
charAt(int) - Method in class org.biojava.nbio.survival.data.CompactCharSequence
ChargeAdder - Class in org.biojava.nbio.structure.io: A class to add appropriate charge information to a structure.
ChargeAdder() - Constructor for class org.biojava.nbio.structure.io.ChargeAdder
checkDoFirstInstall() - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider: Checks if the chemical components already have been installed into the PDB directory.
checkFileExists(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
checkPoint() - Method in class org.biojava.nbio.ronn.Timer
checkScaleMatrix(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Given a scale matrix parsed from a PDB entry (SCALE1,2,3 records), compares it to our calculated Mtranspose matrix to see if they coincide and returns true if they do.
checkScaleMatrixConsistency(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Given a scale matrix parsed from the PDB entry (SCALE1,2,3 records), checks that the matrix is a consistent scale matrix by comparing the cell volume to the inverse of the scale matrix determinant (tolerance of 1/100).
checkSequence(String) - Static method in class org.biojava.nbio.aaproperties.Utils: Checks if the sequence contains invalid characters.
checkSequence(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils: Checks if the sequence contains invalid characters.
checksum(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: Performs a simple CRC64 checksum on any given sequence.
CHEM_COMP_CACHE_DIRECTORY - Static variable in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
chem_comp_type - Variable in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType: String value of the type
ChemComp - Class in org.biojava.nbio.structure.io.mmcif.model: A definition for a Chemical Component, as maintained by the wwPDB.
ChemComp() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemComp
ChemCompAtom - Class in org.biojava.nbio.structure.io.mmcif.model: stores these fields: _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_residue_numbering _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_polymer_type _chem_comp_atom.pdbx_ref_id _chem_comp_atom.pdbx_component_id _chem_comp_atom.pdbx_ordinal
ChemCompAtom() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
ChemCompBond - Class in org.biojava.nbio.structure.io.mmcif.model
ChemCompBond() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
ChemCompConsumer - Class in org.biojava.nbio.structure.io.mmcif
ChemCompConsumer() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
ChemCompDescriptor - Class in org.biojava.nbio.structure.io.mmcif.model: Container object for _pdbx_chem_comp_descriptor
ChemCompDescriptor() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
ChemCompDistribution - Class in demo
ChemCompDistribution() - Constructor for class demo.ChemCompDistribution
ChemCompGroupFactory - Class in org.biojava.nbio.structure.io.mmcif
ChemCompGroupFactory() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
ChemCompProvider - Interface in org.biojava.nbio.structure.io.mmcif: Interface that is implemented by all classes that can provide ChemComp definitions.
ChemCompTools - Class in org.biojava.nbio.structure.io.mmcif.chem: Some tools for working with chemical compounds.
ChemCompTools() - Constructor for class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
ChemicalComponentDictionary - Class in org.biojava.nbio.structure.io.mmcif: A representation of the Chemical Component Dictionary.
ChemicalComponentDictionary() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
children() - Method in class org.biojava.nbio.alignment.GuideTree.Node
ChiSq - Class in org.biojava.nbio.survival.cox.stats
ChiSq() - Constructor for class org.biojava.nbio.survival.cox.stats.ChiSq
chiSq(double, int) - Static method in class org.biojava.nbio.survival.cox.stats.ChiSq
chol() - Method in class org.biojava.nbio.structure.jama.Matrix: Cholesky Decomposition
Cholesky2 - Class in org.biojava.nbio.survival.cox.stats
Cholesky2() - Constructor for class org.biojava.nbio.survival.cox.stats.Cholesky2
CholeskyDecomposition - Class in org.biojava.nbio.structure.jama: Cholesky Decomposition.
CholeskyDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.CholeskyDecomposition: Cholesky algorithm for symmetric and positive definite matrix.
ChooseDirAction - Class in org.biojava.nbio.structure.align.gui: Ask the user to provide a directory containting PDB files.
ChooseDirAction(JTextField, UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.gui.ChooseDirAction
ChromosomeSequence - Class in org.biojava.nbio.core.sequence: A ChromosomeSequence is a DNASequence but keeps track of geneSequences
ChromosomeSequence() - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence: Empty constructor used by tools that need a proper Bean that allows the actual sequence data to be set after construction.
ChromosomeSequence(String) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence: String is king and assume DNA
ChromosomeSequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence: Fairly important constructor given the size of a ChromsomeSequence where the ProxySequenceReader could load from disk via RandomAccessFile so that the sequence doesn't need to be kept in memory.
ChromosomeSequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence: Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet
ChromosomeSequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence: Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet
Chsolve2 - Class in org.biojava.nbio.survival.cox.stats
Chsolve2() - Constructor for class org.biojava.nbio.survival.cox.stats.Chsolve2
cid - Variable in class org.biojava.nbio.structure.validation.Clash
CIRCULAR_DNA - Static variable in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
circularLocation(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
circularLocation(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools: Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
claFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
Clash - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
Clash() - Constructor for class org.biojava.nbio.structure.validation.Clash
clash - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
clashmag - Variable in class org.biojava.nbio.structure.validation.Clash
clashmag - Variable in class org.biojava.nbio.structure.validation.SymmClash
clashscore - Variable in class org.biojava.nbio.structure.validation.Entry
classEqual(Object, Object) - Static method in class org.biojava.nbio.core.util.Equals: This method should be called before beginning any equals methods.
ClasspathResource - Class in org.biojava.nbio.core.sequence.io.util: This object represents a classpath resource on the local system.
ClasspathResource(String) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource: Basic constructor only allowing you to specify where to find the file.
ClasspathResource(String, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource: Advanced constructor which allows you to optionally pre-cache the data
ClasspathResource(String, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource: Advanced constructor which lets you set the preCache variable and to force the type of file we are decompressing.
cleanSequence(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils: Returns a new sequence with all invalid characters being replaced by '-'.
cleanSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil: Removes all whitespace chars in the sequence string
cleanup() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc
cleanup() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
cleanup() - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
cleanUp() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
cleanup() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
cleanUp() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
cleanup() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
cleanup(List<Domain>) - Static method in class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
cleanup() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc
cleanup() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
cleanUp() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
clear() - Method in class org.biojava.nbio.core.util.FlatFileCache
clear() - Method in class org.biojava.nbio.core.util.SoftHashMap
clear() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider: reset all suggestions
clear() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
clear() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
clear() - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache: Clear the cached scores.
clear() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Clear scores and other properties which depend on the specific alignment.
clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
clear() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Clear scores and other properties which depend on the specific alignment.
clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Clear scores and other properties which depend on the specific alignment.
clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Clear scores and other properties which depend on the specific alignment.
clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
clear() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Clears all domains, requiring the file to be reparsed for subsequent accesses
clear() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
clear() - Method in interface org.biojava.nbio.structure.gui.Selection
clear() - Method in class org.biojava.nbio.structure.gui.SelectionImpl
clear() - Method in interface org.biojava.nbio.structure.gui.StructureViewer: Clear the current display
clear() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper: Clears all finite endpoints
clear() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
clear() - Method in class org.biojava.nbio.survival.data.WorkSheet: See if we can free up memory
clearAlgorithms() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory: Removes all algorithms from the list
clearAtoms() - Method in interface org.biojava.nbio.structure.Group: Remove all atoms from this group.
clearAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl: remove all atoms
clearCache() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
clearCache() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Nullifies cached arrays/objects.
clearCache() - Static method in class org.biojava.nbio.structure.PDBStatus: The status of PDB IDs are cached to reduce server overload.
clearConsumers() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser: Remove all consumers from the parser.
clearConsumers() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
clearExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: clear the supported file extensions
clearListeners() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
clearListeners() - Method in class org.biojava.nbio.structure.align.FarmJob
clearListeners() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
clearListeners() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
clearListeners() - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
ClinicalMetaDataOutcome - Class in org.biojava.nbio.survival.kaplanmeier.metadata
ClinicalMetaDataOutcome() - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
CliTools - Class in org.biojava.nbio.structure.align.util: Utilities for autoconfiguring javabeans based on command line arguments.
clone() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Creates and returns a copy of this object.
clone(Object) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache: Subclasses should override clone and use the copy constructor.
clone() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Creates and returns an identical copy of this block.
clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
clone() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Creates and returns an identical copy of this blockset, including a deep copy of all constituent Blocks.
clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Creates and returns an identical copy of this alignment, including a deep copy of all constituent BlockSets.
clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Creates and returns an identical copy of this ensemble, including a deep clone of all constituent alignments.
clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
clone() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
clone() - Method in class org.biojava.nbio.structure.AminoAcidImpl: returns and identical copy of this Group object .
clone() - Method in class org.biojava.nbio.structure.asa.GroupAsa
clone() - Method in interface org.biojava.nbio.structure.Atom: Return an identical copy of this object .
clone() - Method in class org.biojava.nbio.structure.AtomImpl: returns and identical copy of this object .
clone() - Method in interface org.biojava.nbio.structure.Chain: returns an identical copy of this Chain.
clone() - Method in class org.biojava.nbio.structure.ChainImpl: Returns an identical copy of this Chain .
clone() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
clone() - Method in interface org.biojava.nbio.structure.Group: returns and identical copy of this Group object .
clone() - Method in class org.biojava.nbio.structure.GroupIterator: Creates and returns a copy of this object.
clone() - Method in class org.biojava.nbio.structure.HetatomImpl: returns and identical copy of this Group object .
clone() - Method in class org.biojava.nbio.structure.io.SSBondImpl
clone() - Method in class org.biojava.nbio.structure.jama.Matrix: Clone the Matrix object.
clone() - Method in class org.biojava.nbio.structure.NucleotideImpl
clone() - Method in class org.biojava.nbio.structure.scop.ScopDescription
clone() - Method in class org.biojava.nbio.structure.scop.ScopDomain
clone() - Method in class org.biojava.nbio.structure.secstruc.HBond
clone() - Method in interface org.biojava.nbio.structure.Structure: Return an identical copy of this Structure object
clone() - Method in class org.biojava.nbio.structure.StructureImpl: returns an identical copy of this structure .
clone() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
clone() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
clone() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
cloneAtomArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: Provides an equivalent copy of Atoms in a new array.
cloneCAArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: Deprecated.
Use the better-named StructureTools.cloneAtomArray(Atom[]) instead
cloneDM(BasicSymmetricalDistanceMatrix) - Static method in class org.biojava.nbio.phylo.ForesterWrapper: Helper function to clone a forester symmetrical DistanceMatrix.
cloneGroups(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: Clone a set of representative Atoms, but returns the parent groups
clonePoint() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
clonePoint() - Method in interface org.biojava.nbio.core.sequence.location.template.Point: Returns a copy of this point
clonePoint3dArray(Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
close() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
close() - Method in class org.biojava.nbio.core.sequence.io.FastaReader
close() - Method in class org.biojava.nbio.core.sequence.io.GenbankReader
close(Closeable) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Closes any Object which implements the interface Closeable and sending any error to the logger but not forcing any explicit catching of stream errors.
close() - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
close() - Method in interface org.biojava.nbio.core.util.XMLWriter: Close this XMLWriter, and it's underlying stream.
close() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser: Method closes current sequence and it's necessary to invoke it before setting new current sequence.
close() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
closeParser() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser: Method closes random access file descriptor.
closeTag(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
closeTag(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
closeTag(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Closes an element
closeTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Closes an un-qualified element.
cluster(AlternativeAlignment[]) - Static method in class org.biojava.nbio.structure.align.ClusterAltAligs
cluster(AlternativeAlignment[], int) - Static method in class org.biojava.nbio.structure.align.ClusterAltAligs
cluster(List<Domain>, PDPDistanceMatrix) - Static method in class org.biojava.nbio.structure.domain.pdp.ClusterDomains
ClusterAltAligs - Class in org.biojava.nbio.structure.align: A class that clusters alternative alignments according to their similarity.
ClusterAltAligs() - Constructor for class org.biojava.nbio.structure.align.ClusterAltAligs
ClusterDomains - Class in org.biojava.nbio.structure.domain.pdp
ClusterDomains() - Constructor for class org.biojava.nbio.structure.domain.pdp.ClusterDomains
ClusterMerger - Class in org.biojava.nbio.structure.symmetry.core: Merges clusters based on their sequence identity.
ClusterMerger(List<SequenceAlignmentCluster>, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ClusterMerger
ClusterProteinChains - Class in org.biojava.nbio.structure.symmetry.core: Clusters the chains of one or two structures by sequence.
ClusterProteinChains(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
ClusterProteinChains(Structure, Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
Codon(Table.CaseInsensitiveTriplet, AminoAcidCompound, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon
Codon(Table.CaseInsensitiveTriplet) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon
CodonCompound - Class in org.biojava.nbio.core.sequence.compound: Define a codon
CodonCompound(NucleotideCompound, NucleotideCompound, NucleotideCompound, boolean) - Constructor for class org.biojava.nbio.core.sequence.compound.CodonCompound
CollectionTools - Class in org.biojava.nbio.structure.align.util: Utilities for working with collections.
CollectionTools() - Constructor for class org.biojava.nbio.structure.align.util.CollectionTools
colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that colors subunits by their sequence cluster ids.
colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that colors subunits by their sequence cluster ids.
colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that colors the subunits of a structure by different colors
colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that colors the subunits of a structure by different colors
colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that colors subunits to highlight the symmetry within a structure
colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that colors subunits to highlight the symmetry within a structure Different subunits should have a consistent color scheme or different shade of the same colors
colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
ColorConverter - Class in org.biojava.nbio.structure.symmetry.jmolScript
ColorConverter() - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
coloring - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
ColorInterpolator - Interface in org.biojava.nbio.structure.gui.util.color
colorPalette - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
ColorUtils - Class in org.biojava.nbio.structure.gui.util.color
ColorUtils() - Constructor for class org.biojava.nbio.structure.gui.util.color.ColorUtils
colorWheel - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
column - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
CombinationGenerator - Class in org.biojava.nbio.structure.symmetry.utils
CombinationGenerator(int, int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
combine(BiologicalAssemblyTransformation, BiologicalAssemblyTransformation) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Returns the combination (product) of two biological assembly transformations.
combine(List<Integer>, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
combineWith(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup: Combine the ResidueGroup with the alignment block.
comFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
COMMAND_LINE_HELP - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
CommandPrompt - Class in org.biojava.nbio.aaproperties
CommandPrompt() - Constructor for class org.biojava.nbio.aaproperties.CommandPrompt
CommandPrompt.PropertyName - Enum in org.biojava.nbio.aaproperties
COMMENT - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
COMMENT_CHAR - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
COMMENT_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
CompactCharSequence - Class in org.biojava.nbio.survival.data: http://www.javamex.com/tutorials/memory/ascii_charsequence.shtml
CompactCharSequence(String) - Constructor for class org.biojava.nbio.survival.data.CompactCharSequence
COMPARATOR - Static variable in class org.biojava.nbio.ontology.Synonym
compare(AlignerHelper.Anchor, AlignerHelper.Anchor) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator
compare(CDSSequence, CDSSequence) - Method in class org.biojava.nbio.core.sequence.CDSComparator: Used to sort two CDSSequences where Negative Strand makes it tough
compare(ExonSequence, ExonSequence) - Method in class org.biojava.nbio.core.sequence.ExonComparator
compare(AbstractSequence<?>, AbstractSequence<?>) - Method in class org.biojava.nbio.core.sequence.SequenceComparator
compare(int[], int[]) - Method in class org.biojava.nbio.structure.align.helper.IdxComparator
compare(AlternativeAlignment, AlternativeAlignment) - Method in class org.biojava.nbio.structure.align.pairwise.AltAligComparator
compare(Segment, Segment) - Method in class org.biojava.nbio.structure.domain.pdp.SegmentComparator
compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator
compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.MeanModelComparator
compare(SurvivalInfo, SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator
compare(SurvivalInfo, SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator
compareTo(Point) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
compareTo(Point) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
compareTo(FastaSequence) - Method in class org.biojava.nbio.data.sequence.FastaSequence
compareTo(Cytoband) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
compareTo(GeneChromosomePosition) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
compareTo(GeneName) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
compareTo(Synonym) - Method in class org.biojava.nbio.ontology.Synonym
compareTo(ProteinModification) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
compareTo(ModifiedCompound) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
compareTo(StructureGroup) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
compareTo(PdbPair) - Method in class org.biojava.nbio.structure.align.client.PdbPair
compareTo(StructureName) - Method in class org.biojava.nbio.structure.align.client.StructureName: Orders identifiers lexicographically by PDB ID and then full Identifier
compareTo(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterface
compareTo(Domain) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
compareTo(Segment) - Method in class org.biojava.nbio.structure.domain.pdp.Segment
compareTo(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
compareTo(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber
compareTo(Site) - Method in class org.biojava.nbio.structure.Site
compareTo(ChainSignature) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
compareTo(SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
compareTo(SurvivalInfoIndex) - Method in class org.biojava.nbio.survival.cox.SurvivalInfoIndex
compareTo(CensorStatus) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
compareTo(HmmerDomain) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
compareTo(HmmerResult) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
Comparison - Class in org.biojava.nbio.phylo: This class provides static methods for the calculation of the percentage of identity between two aligned sequences.
Comparison() - Constructor for class org.biojava.nbio.phylo.Comparison
ComplementCompound - Interface in org.biojava.nbio.core.sequence.template
ComplementSequenceView<C extends ComplementCompound> - Class in org.biojava.nbio.core.sequence.views: For a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlying base e.g.
ComplementSequenceView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.views.ComplementSequenceView
complete() - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener: Notify this listener the FASTQ formatted sequence is complete.
complete() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
completeCircularPasses(int, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e.
completeCircularPasses(int, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools: Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e.
completeGroup() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup: Starts with an incomplete set of group generators in `permutations` and expands it to include all possible combinations.
Component - Class in org.biojava.nbio.protmod: contains information about a certain Component.
COMPONENTS_FILE_LOCATION - Static variable in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider
ComponentXMLConverter - Class in org.biojava.nbio.protmod.io
ComponentXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.ComponentXMLConverter
Compound - Interface in org.biojava.nbio.core.sequence.template
Compound - Class in org.biojava.nbio.structure: An object to contain the info from the PDB header for a Molecule.
Compound() - Constructor for class org.biojava.nbio.structure.Compound
Compound(Compound) - Constructor for class org.biojava.nbio.structure.Compound: Constructs a new Compound copying all data from the given one but not setting the Chains
CompoundFinder - Class in org.biojava.nbio.structure.io: Heuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure.
CompoundFinder(Structure) - Constructor for class org.biojava.nbio.structure.io.CompoundFinder
CompoundNotFoundException - Exception in org.biojava.nbio.core.exceptions
CompoundNotFoundException(String) - Constructor for exception org.biojava.nbio.core.exceptions.CompoundNotFoundException
compoundsEqual(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
compoundsEquivalent(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
compoundsEquivalent(C, C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
CompoundSet<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: Should return the maximum amount of compounds we can encode per int
compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
compoundToInt(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
CompoundTranslator<F extends Compound,T extends Compound> - Interface in org.biojava.nbio.core.sequence.template
computeMolecularWeight(ElementTable) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable: Computes and store the molecular weight of each amino acid by its symbol in aaSymbol2MolecularWeight.
ConcurrencyTools - Class in org.biojava.nbio.core.util: Static utility to easily share a thread pool for concurrent/parallel/lazy execution.
cond() - Method in class org.biojava.nbio.structure.jama.Matrix: Matrix condition (2 norm)
cond() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Two norm condition number
ConfigPDBInstallPanel - Class in org.biojava.nbio.structure.align.gui
ConfigStrucAligParams - Interface in org.biojava.nbio.structure.align.ce
ConfigurationException - Exception in org.biojava.nbio.structure.align.util
ConfigurationException(String) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException: Constructs a ConfigurationException object.
ConfigurationException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
ConfigurationException(Throwable) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException: Constructs a ConfigurationException object.
ConfigurationException() - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
configureBean(Object, String[]) - Static method in class org.biojava.nbio.structure.align.util.CliTools: Configure a JavaBean based on a set of command line arguments.
configureParameters() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
configureParameters() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
ConfigXMLHandler - Class in org.biojava.nbio.structure.align.webstart: XML content handler for serialisation of RegistryConfiguration class
ConfigXMLHandler() - Constructor for class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
consistentAccessions(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: Scans a list of locations and returns true if all the given locations are linked to the same sequence.
CONSORTIUM_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
constrain(double) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant: Constrain the specified quality score in double precision to the minimum and maximum quality scores in int precision.
Constraints - Class in org.biojava.nbio.aaproperties: This class is used to support the implementation of properties stated in IPeptideProperties.
Constraints() - Constructor for class org.biojava.nbio.aaproperties.Constraints
constructWithCopy(double[][]) - Static method in class org.biojava.nbio.structure.jama.Matrix: Construct a matrix from a copy of a 2-D array.
contacts(Point3d[], Point3d[], double) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
contains(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location contains the other.
contains(ResidueNumber) - Method in class org.biojava.nbio.structure.AugmentedResidueRange
contains(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Is the key in the table?
contains(ResidueNumber, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange
contains(Subunits) - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
containsChainId(String, String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
containsKey(Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap
containsKey(Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
containsKey(Object) - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
containsKey(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
containsProperty(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
containsProperty(Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation: Returns whether there the property is defined.
containsTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
containsTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology: Determines if this ontology currently contains a term named name
containsTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
containsTriple(Term, Term, Term) - Method in class org.biojava.nbio.ontology.IntegerOntology
containsTriple(Term, Term, Term) - Method in interface org.biojava.nbio.ontology.Ontology: See if a triple exists in this ontology
containsTriple(Term, Term, Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl
containsUniProtId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
containsValue(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
ContinuousColorMapper - Interface in org.biojava.nbio.structure.gui.util.color: Provides a mapping between real numbers and Colors.
ContinuousColorMapperTransform - Class in org.biojava.nbio.structure.gui.util.color: Maps colors by performing a transform of the input data and then passing the transformed value to a ContinuousColorMapper for rendering.
ContinuousColorMapperTransform(ContinuousColorMapper) - Constructor for class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform: Creates a transform.
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge: Class for the conversion of protein sequence into charge
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity: Class for the conversion of protein sequence into hydrophobicity
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume: Class for the conversion of protein sequence into normalized van der waals volume
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity: Class for the conversion of protein sequence into polarity
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability: Class for the conversion of protein sequence into polarizability
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure: Class for the conversion of protein sequence into secondary structure
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility: Class for the conversion of protein sequence into solvent accessibility
convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor: Returns the grouping of the amino acid character.
convert(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor: Returns the converted sequence.
convert(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.ForesterWrapper: Convert a BioJava MultipleSequenceAlignment to a forester Msa.
convert(Fastq, FastqVariant) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools: Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.
convert(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriter
convert(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.SangerFastqWriter
convert(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriter
Convert2Charge - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2Charge() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
Convert2Hydrophobicity - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2Hydrophobicity() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
Convert2NormalizedVanDerWaalsVolume - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2NormalizedVanDerWaalsVolume() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
Convert2Polarity - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2Polarity() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
Convert2Polarizability - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2Polarizability() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
Convert2SecondaryStructure - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2SecondaryStructure() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
Convert2SolventAccessibility - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convert2SolventAccessibility() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
convert_3code_1code(String) - Static method in class org.biojava.nbio.structure.StructureTools: Deprecated.
Use StructureTools.get1LetterCodeAmino(String) instead
convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator: copy data from this class into AFPChain container object.
convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced: copy data from this class into AFPChain container object.
convertAtomsToSeq(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
convertAtomToAtomSite(Atom, int, String, String) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: Converts an Atom object to an AtomSite object.
convertAtomToAtomSite(Atom, int, String, String, int) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: Converts an Atom object to an AtomSite object.
convertChainToAtomSites(Chain, int, String, String) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: Converts a Chain into a List of AtomSite objects
convertColor4f(Color) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
convertColor4f(Color[]) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
convertCrystalCellToCell(CrystalCell) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: Converts a CrystalCell object to a Cell object.
Convertor - Class in org.biojava.nbio.aaproperties.profeat.convertor
Convertor() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
convertPairsToXML(SortedSet<PdbPair>, String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
convertProteinSequencetoFasta(ProteinSequence) - Static method in class org.biojava.nbio.ronn.Jronn: Utility method to convert a BioJava ProteinSequence object to the FastaSequence object used internally in JRonn.
convertSpaceGroupToSymmetry(SpaceGroup) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: Converts a SpaceGroup object to a Symmetry object.
convertStreamToString(InputStream) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
convertStreamToString(InputStream) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
convertStructureToAtomSites(Structure) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: Converts a Structure into a List of AtomSite objects
convertTo(FastqVariant) - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq: Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.
convertXMLtoPairs(String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
CookBook - Class in demo
CookBook() - Constructor for class demo.CookBook
CookbookMSA - Class in demo
CookbookMSA() - Constructor for class demo.CookbookMSA
CoordManager - Class in org.biojava.nbio.structure.gui.util: a class that manages the conversion of sequence coordinate system to JPanel drawing coordinates
CoordManager() - Constructor for class org.biojava.nbio.structure.gui.util.CoordManager
copy(InputStream, OutputStream) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Moves the bytes from input to output using a 4KB byte array.
copy(File, File) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils: Copy the content of file src to dst TODO since java 1.7 this is provided in java.nio.file.Files
copy() - Method in class org.biojava.nbio.structure.jama.Matrix: Make a deep copy of a matrix
copyFile(File, File) - Static method in class org.biojava.nbio.phosphosite.Dataset
CoreSuperimposer - Class in org.biojava.nbio.structure.align.multiple.util: Superimposes the core aligned residues of every structure in a MultipleAlignment onto a reference structure.
CoreSuperimposer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer: Default Constructor.
CoreSuperimposer(int) - Constructor for class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer: Constructor using a specified structure as reference.
countAT(Sequence<NucleotideCompound>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: Returns the count of AT in the given sequence
countCompounds(C...) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader: Counts the number of times a compound appears in this sequence store
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Delegates to SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[])
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
countCompounds(C...) - Method in interface org.biojava.nbio.core.sequence.template.Sequence: Returns the number of times we found a compound in the Sequence
countCompounds(Sequence<C>, C...) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: For the given vargs of compounds this method counts the number of times those compounds appear in the given sequence
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
countGC(Sequence<NucleotideCompound>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: Returns the count of GC in the given sequence
countMatchesInSequence(String, String) - Static method in class org.biojava.nbio.data.sequence.FastaSequence
CountProgressListener - Class in org.biojava.nbio.structure.align.client
CountProgressListener() - Constructor for class org.biojava.nbio.structure.align.client.CountProgressListener
CoxCC - Class in org.biojava.nbio.survival.cox
CoxCC() - Constructor for class org.biojava.nbio.survival.cox.CoxCC
CoxCoefficient - Class in org.biojava.nbio.survival.cox
CoxCoefficient() - Constructor for class org.biojava.nbio.survival.cox.CoxCoefficient
CoxComparatorInterface - Interface in org.biojava.nbio.survival.cox.comparators
CoxHelper - Class in org.biojava.nbio.survival.cox: The CoxHelper class is provided to start with a tab delimited file in a similar process in R and return the results as a CoxInfo class.
CoxHelper() - Constructor for class org.biojava.nbio.survival.cox.CoxHelper
CoxInfo - Class in org.biojava.nbio.survival.cox: Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R
CoxInfo() - Constructor for class org.biojava.nbio.survival.cox.CoxInfo
CoxMart - Class in org.biojava.nbio.survival.cox
CoxMart() - Constructor for class org.biojava.nbio.survival.cox.CoxMart
CoxMethod - Enum in org.biojava.nbio.survival.cox
coxphfitSCleanup(CoxInfo, boolean, boolean, ArrayList<String>) - Method in class org.biojava.nbio.survival.cox.CoxR
CoxR - Class in org.biojava.nbio.survival.cox: This is a port of the R survival code used for doing Cox Regression.
CoxR() - Constructor for class org.biojava.nbio.survival.cox.CoxR
coxsafe(double) - Method in class org.biojava.nbio.survival.cox.CoxR
CoxScore - Class in org.biojava.nbio.survival.cox
CoxScore() - Constructor for class org.biojava.nbio.survival.cox.CoxScore
CoxVariables - Class in org.biojava.nbio.survival.cox
CoxVariables(String, String, String) - Constructor for class org.biojava.nbio.survival.cox.CoxVariables
CoxVariablesOverallModelFitComparator - Class in org.biojava.nbio.survival.cox.comparators
CoxVariablesOverallModelFitComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator: Variables are stored as a string representation of an ArrayList [META_GENE] or [trtg, META_GENE] add variables used in cox regression to an array and then do toString.
CoxVariablesVariableComparator - Class in org.biojava.nbio.survival.cox.comparators
CoxVariablesVariableComparator(String, String) - Constructor for class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
cpFastaToAfpChain(String, String, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
cpFastaToAfpChain(File, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
cpFastaToAfpChain(ProteinSequence, ProteinSequence, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
cpPoint - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters: The CP point, specified as a residue index
CPRange() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
CRC64Checksum - Class in org.biojava.nbio.core.util: Utility class that calculates a CRC64 checksum on a stream of bytes.
CRC64Checksum() - Constructor for class org.biojava.nbio.core.util.CRC64Checksum
createAFPChain(Atom[], Atom[], ResidueNumber[], ResidueNumber[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Fundamentally, an alignment is just a list of aligned residues in each protein.
createAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of AngleOutlier
createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP: Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.
createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
createBlastHit() - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
createBlastHsp() - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
createBlastResult() - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
createBondOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of BondOutlier
createClash() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of Clash
createDNASequence(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools: Create and return a new DNASequence from the specified FASTQ formatted sequence.
createDNASequenceWithErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools: Create and return a new DNASequence with error probabilities from the specified FASTQ formatted sequence.
createDNASequenceWithQualityScores(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools: Create and return a new DNASequence with quality scores from the specified FASTQ formatted sequence.
createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools: Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence.
createEntry() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of Entry
createErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools: Create and return a new QuantityFeature from the error probabilities of the specified FASTQ formatted sequence.
createGradients() - Static method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
createImage(String, String, Object, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
createImageIcon(String) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator: Returns an ImageIcon, or null if the path was invalid.
createIterator(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: Creates a simple sequence iterator which moves through a sequence going from 1 to the length of the Sequence.
createModelledSubgroup() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of ModelledSubgroup
createMogAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of MogAngleOutlier
createMogBondOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of MogBondOutlier
createObjects(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
createObjects(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
createObjects(double) - Method in interface org.biojava.nbio.core.search.io.ResultFactory: Launch the parsing and get back a list of Result objects representing the search result in the specified file.
createOntology(String, String) - Method in interface org.biojava.nbio.ontology.OntologyFactory: Creates a new Ontology
createOntologyTerm(Ontology) - Method in class org.biojava.nbio.ontology.Ontology.Impl
createOutput(String, String) - Method in class org.biojava.nbio.aaproperties.xml.SchemaGenerator
createProgram() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of Program
createPrograms() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of Programs
createQualityScores(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools: Create and return a new QualityFeature from the quality scores of the specified FASTQ formatted sequence.
createSequence(Sequence<F>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
createSequence(Sequence<F>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator
createSequence(Sequence<NucleotideCompound>, Frame) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
createSequence(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
createSequences(Sequence<F>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
createSequences(Sequence<F>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator
createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator: Overloaded local version which delegates to an optional translator when told to (specified during construction).
createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator: Performs the core conversion of RNA to Peptide.
createSubSequence(Sequence<C>, int, int) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: Creates a simple sub sequence view delimited by the given start and end.
createSymmClash() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of SymmClash
createTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
createTerm(String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
createTerm(String, String, Object[]) - Method in class org.biojava.nbio.ontology.IntegerOntology
createTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology: Create a new term in this ontology.
createTerm(String, String) - Method in interface org.biojava.nbio.ontology.Ontology: Create a new term in this ontology.
createTerm(String, String, Object[]) - Method in interface org.biojava.nbio.ontology.Ontology: Create a new term in this ontology.
createTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
createTerm(String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
createTerm(String, String, Object[]) - Method in class org.biojava.nbio.ontology.Ontology.Impl
createTriple(Term, Term, Term, String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
createTriple(Term, Term, Term, String, String) - Method in interface org.biojava.nbio.ontology.Ontology: Creates a new Triple.
createTriple(Term, Term, Term, String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
createVariable(String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
createVariable(String, String) - Method in interface org.biojava.nbio.ontology.Ontology: Create a new term in this ontology that is used as a variable.
createVariable(String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
createVirtualCBAtom(AminoAcid) - Static method in class org.biojava.nbio.structure.Calc: creates a virtual C-beta atom.
createWwPDBValidationInformation() - Method in class org.biojava.nbio.structure.validation.ObjectFactory: Create an instance of WwPDBValidationInformation
crossChains() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
crossChains() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
CrystalBuilder - Class in org.biojava.nbio.structure.xtal: A class containing methods to find interfaces in a given crystallographic Structure by reconstructing the crystal lattice through application of symmetry operators
CrystalBuilder(Structure) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder
CrystalCell - Class in org.biojava.nbio.structure.xtal: A crystal cell's parameters.
CrystalCell() - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell
CrystalCell(double, double, double, double, double, double) - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell
CrystalTransform - Class in org.biojava.nbio.structure.xtal: Representation of a transformation in a crystal: - a transformation id (each of the transformations in a space group, 0 to m) - a crystal translation The transformation matrix in crystal basis is stored, representing the basic transformation together with the crystal translation.
CrystalTransform(SpaceGroup) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform: Creates a new CrystalTransform representing the identity transform in cell (0,0,0)
CrystalTransform(SpaceGroup, int) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform: Represents the n-th transform
CrystalTransform(CrystalTransform) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform: Copy constructor
CS_HSV - Static variable in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace: The HSV color space
Cut(int, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
Cut - Class in org.biojava.nbio.structure.domain.pdp
Cut() - Constructor for class org.biojava.nbio.structure.domain.pdp.Cut
cut(Atom[], Domain, CutValues, int[][], PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.Cut
CUT_OFF_VALUE - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CUT_OFF_VALUE1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CUT_OFF_VALUE1M - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CUT_OFF_VALUE1S - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CUT_OFF_VALUE2 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CutDomain - Class in org.biojava.nbio.structure.domain.pdp
CutDomain(Atom[], PDPDistanceMatrix) - Constructor for class org.biojava.nbio.structure.domain.pdp.CutDomain
cutDomain(Domain, CutSites, PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.CutDomain
CutSites - Class in org.biojava.nbio.structure.domain.pdp
CutSites() - Constructor for class org.biojava.nbio.structure.domain.pdp.CutSites
cutsPerSection - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
CutValues - Class in org.biojava.nbio.structure.domain.pdp
CutValues() - Constructor for class org.biojava.nbio.structure.domain.pdp.CutValues
cyan - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
Cytoband - Class in org.biojava.nbio.genome.parsers.cytoband
Cytoband() - Constructor for class org.biojava.nbio.genome.parsers.cytoband.Cytoband
CytobandParser - Class in org.biojava.nbio.genome.parsers.cytoband: Parses the cytoband (karyotype) file from UCSC.
CytobandParser() - Constructor for class org.biojava.nbio.genome.parsers.cytoband.CytobandParser

D

D - Static variable in class org.biojava.nbio.aaproperties.Constraints
d2 - Static variable in class org.biojava.nbio.structure.io.FileConvert
d3 - Static variable in class org.biojava.nbio.structure.io.FileConvert
darker(Color, double) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils: Make a color darker.
dataAnisotropy - Variable in class org.biojava.nbio.structure.validation.Entry
DatabasePDBremark - Class in org.biojava.nbio.structure.io.mmcif.model
DatabasePDBremark() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
DatabasePDBrev - Class in org.biojava.nbio.structure.io.mmcif.model
DatabasePDBrev() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
DatabasePdbrevRecord - Class in org.biojava.nbio.structure.io.mmcif.model
DatabasePdbrevRecord() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
DatabaseReference(String, String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
DatabaseReference(String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
DatabaseReferenceInterface - Interface in org.biojava.nbio.core.sequence.features: If a SequenceProxyReader implements this interface then that external source has a list of cross reference id(s)
dataCompleteness - Variable in class org.biojava.nbio.structure.validation.Entry
Dataset - Class in org.biojava.nbio.phosphosite: Phosphosite is available under the PhosphoSitePlus® is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from http://www.phosphosite.org/staticDownloads.do Please acknowledge PhosphoSitePlus®, www.phosphosite.org" at appropriate locations.
Dataset() - Constructor for class org.biojava.nbio.phosphosite.Dataset
DataSource - Enum in org.biojava.nbio.core.sequence: GenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT UNIPROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier
dateFormat - Variable in class org.biojava.nbio.ontology.obo.OboFileParser
DBL - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
DBRef - Class in org.biojava.nbio.structure: A class to represent database cross references.
DBRef() - Constructor for class org.biojava.nbio.structure.DBRef
DBReferenceInfo - Class in org.biojava.nbio.core.sequence.features: If you have a uniprot ID then it is possible to get a collection of other id(s) that the protein is known by.
DBReferenceInfo(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.DBReferenceInfo: The source database and id
DBResultTable - Class in org.biojava.nbio.structure.align.gui
DBResultTable() - Constructor for class org.biojava.nbio.structure.align.gui.DBResultTable
DBSearchGUI - Class in org.biojava.nbio.structure.align.gui
DBSearchGUI() - Constructor for class org.biojava.nbio.structure.align.gui.DBSearchGUI
dbxp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
dccr - Variable in class org.biojava.nbio.structure.validation.Entry
dccRefinementProgram - Variable in class org.biojava.nbio.structure.validation.Entry
dccRfree - Variable in class org.biojava.nbio.structure.validation.Entry
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
debug - Static variable in class org.biojava.nbio.structure.align.util.AlignmentTools
declareNamespace(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
declareNamespace(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Hints that a namespace is going to be used in a sub-tree.
decorateRna(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder: Performs an optimisation where RNASequences are not translated into their own objects but are views onto the base DNA sequence.
deepCleanSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil: Removes all special characters and digits as well as whitespace chars from the sequence
DEF - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
DEF_NUM_CELLS - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder
DEFAULT - Static variable in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
DEFAULT - Static variable in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
DEFAULT_ALGORITHM_NAME - Static variable in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
DEFAULT_ASA_SPHERE_POINTS - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList: Default number of points to use when calculating ASAs
DEFAULT_BATCH_SIZE - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
DEFAULT_BUFFER_SIZE - Variable in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
DEFAULT_CHAIN_ID - Static variable in class org.biojava.nbio.structure.ChainImpl: The default chain identifier used to be an empty space
DEFAULT_CHAR_SIZE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: size per character
DEFAULT_CHAR_SIZE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Size per character
DEFAULT_CLUSTER_CUTOFF - Static variable in class org.biojava.nbio.structure.align.ClusterAltAligs
DEFAULT_CONNECTION_TIMEOUT - Static variable in class org.biojava.nbio.structure.align.util.HTTPConnectionTools
DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList: Any 2 interfaces with contact overlap score larger than this value will be considered to be clustered
DEFAULT_DISORDER - Static variable in class org.biojava.nbio.ronn.RonnConstraint
DEFAULT_FRAGLEN - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
DEFAULT_GAP_EXTENSION - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
DEFAULT_GAP_OPEN - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
DEFAULT_GENENAMES_URL - Static variable in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
DEFAULT_HEIGHT - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
DEFAULT_INTERFACE_DISTANCE_CUTOFF - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder: Default maximum distance between two chains to be considered an interface.
DEFAULT_JOB_TIME - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
DEFAULT_LIMIT - Static variable in class org.biojava.nbio.core.util.SoftHashMap
DEFAULT_LINE_LENGTH - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: number of chars per line
DEFAULT_LINE_LENGTH - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Number of chars per line
DEFAULT_LINE_SEPARATION - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: separation of line 1 and 2 in alignment
DEFAULT_LINE_SEPARATION - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Separation between sequences in the alignment
DEFAULT_LOCATION - Static variable in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
DEFAULT_MAPPING_URL - Static variable in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
DEFAULT_METHOD_NAME - Static variable in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
DEFAULT_MIN_COFACTOR_SIZE - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList: Default minimum size of cofactor molecule (non-chain HET atoms) that will be used
DEFAULT_MIN_CP_LENGTH - Static variable in class org.biojava.nbio.structure.align.ce.CECPParameters
DEFAULT_MINIMUM_INTERFACE_AREA - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList: Default minimum area for a contact between two chains to be considered a valid interface.
DEFAULT_N_SPHERE_POINTS - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
DEFAULT_NR_ALIGNMENTS - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
DEFAULT_NR_THREADS - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
DEFAULT_NTHREADS - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
DEFAULT_ORDER - Static variable in class org.biojava.nbio.ronn.RonnConstraint
DEFAULT_oRmsdThr - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
DEFAULT_PDB_API_URL - Static variable in class org.biojava.nbio.structure.domain.PDBDomainProvider
DEFAULT_PDB_FILE_SERVER - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory: The default server name, prefixed by the protocol string (http:// or ftp://).
DEFAULT_PDB_HOST - Static variable in class org.biojava.nbio.structure.domain.PDBDomainProvider
DEFAULT_PDB_PATH - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
DEFAULT_PDB_SERVER - Static variable in class org.biojava.nbio.structure.PDBStatus
DEFAULT_PROBE_SIZE - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
DEFAULT_PROVIDER_CLASS - Static variable in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
DEFAULT_PROVIDER_CLASSNAME - Static variable in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
DEFAULT_RANGE_PROBABILITY_THRESHOLD - Static variable in class org.biojava.nbio.ronn.RonnConstraint
DEFAULT_RESOLUTION - Static variable in class org.biojava.nbio.structure.PDBHeader
DEFAULT_RFREE - Static variable in class org.biojava.nbio.structure.PDBHeader
DEFAULT_RIGHT_SPACER - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: Space on the right side between sequence and legend.
DEFAULT_RIGHT_SPACER - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Space on the right side between sequence and legend.
DEFAULT_SCORING_STRATEGY - Static variable in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
DEFAULT_SCRIPT - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
DEFAULT_SERVER - Static variable in class org.biojava.nbio.structure.domain.RemotePDPProvider
DEFAULT_SERVER - Static variable in class org.biojava.nbio.structure.scop.RemoteScopInstallation
DEFAULT_SERVER_URL - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
DEFAULT_SERVERNAME - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
DEFAULT_SERVERNAME - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
DEFAULT_SUBSTITUTION_MATRIX - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
DEFAULT_SYMMETRY_THRESHOLD - Static variable in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
DEFAULT_VARIANT - Static variable in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder: Default FASTQ sequence format variant, FastqVariant.FASTQ_SANGER.
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathFactory
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.ecod.EcodFactory
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
DEFAULT_WIDTH - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
DEFAULT_X_RIGHT_BORDER - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
DEFAULT_X_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: left boundary
DEFAULT_X_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Left boundary
DEFAULT_X_START - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
DEFAULT_Y_BOTTOM - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
DEFAULT_Y_HEIGHT - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
DEFAULT_Y_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: top boundary
DEFAULT_Y_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Top boundary
DEFAULT_Y_START - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
DEFAULT_Y_STEP - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: size of space between rows
DEFAULT_Y_STEP - Variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Size of space between rows.
DEFAULT_Y_STEP - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
DefaultAAIndexProvider - Class in org.biojava.nbio.core.alignment.matrices: The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directory
DefaultAAIndexProvider() - Constructor for class org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider
DefaultAutoSuggestProvider - Class in org.biojava.nbio.structure.align.gui.autosuggest
DefaultAutoSuggestProvider() - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
DefaultMatrixMapper - Class in org.biojava.nbio.structure.gui.util.color: Color Mapper which mimics the default coloring of JMatrixPanel pixels.
DefaultMatrixMapper(double, float) - Constructor for class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
DefaultOps - Class in org.biojava.nbio.ontology: Default implementation of OntologyOps.
DefaultOps() - Constructor for class org.biojava.nbio.ontology.DefaultOps
defaultProperties - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo
DEFINITION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
Delete(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Delete
Delete(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Delete
delete(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Delete the key (and paired value) from table.
deleteStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Attempts to delete all versions of a structure from the local directory.
deleteTerm(Term) - Method in class org.biojava.nbio.ontology.IntegerOntology
deleteTerm(Term) - Method in interface org.biojava.nbio.ontology.Ontology: Remove a term from an ontology, together with all triples which refer to it.
deleteTerm(Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl
DELTA - Static variable in class org.biojava.nbio.structure.xtal.SpaceGroup
deltaComp(double, double, double) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
demo - package demo
DemoAlignmentFromFasta - Class in demo: Demo of how to use the FastaStructureParser class to read protein structures from a FASTA file.
DemoAlignmentFromFasta() - Constructor for class demo.DemoAlignmentFromFasta
DemoAlignProteins - Class in demo
DemoAlignProteins() - Constructor for class demo.DemoAlignProteins
DemoAsa - Class in demo
DemoAsa() - Constructor for class demo.DemoAsa
DemoAtomCache - Class in demo: Example of how to load PDB files using the AtomCache class.
DemoAtomCache() - Constructor for class demo.DemoAtomCache
DemoBerkeleyScop - Class in demo: A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP
DemoBerkeleyScop() - Constructor for class demo.DemoBerkeleyScop
DemoCATH - Class in demo: An example for how to access CATH data.
DemoCATH() - Constructor for class demo.DemoCATH
DemoCE - Class in demo: Example of how to run a structure alignment using the CE algorithm.
DemoCE() - Constructor for class demo.DemoCE
DemoCeSymm - Class in demo: Quick demo of how to call CE-Symm programmatically.
DemoCeSymm() - Constructor for class demo.DemoCeSymm
DemoChangeChemCompProvider - Class in demo: This demo shows how to use an alternative ChemCompProvider.
DemoChangeChemCompProvider() - Constructor for class demo.DemoChangeChemCompProvider
DemoCommandLineStartup - Class in demo
DemoCommandLineStartup() - Constructor for class demo.DemoCommandLineStartup
DemoContacts - Class in demo
DemoContacts() - Constructor for class demo.DemoContacts
DemoCrystalInterfaces - Class in demo
DemoCrystalInterfaces() - Constructor for class demo.DemoCrystalInterfaces
DemoDistanceTree - Class in demo: This demo contains the CookBook example to create a phylogenetic tree from a multiple sequence alignment (MSA).
DemoDistanceTree() - Constructor for class demo.DemoDistanceTree
DemoDomainsplit - Class in demo
DemoDomainsplit() - Constructor for class demo.DemoDomainsplit
DemoFATCAT - Class in demo
DemoFATCAT() - Constructor for class demo.DemoFATCAT
DemoLoadSecStruc - Class in demo: Demonstration of how to load a Structure with the SS information, either from the PDB file annotation (Author's assignment) or from the DSSP file in the PDB servers (DSSP assignment).
DemoLoadSecStruc() - Constructor for class demo.DemoLoadSecStruc
DemoLoadStructure - Class in demo: Example for how to load protein structures (from PDB files).
DemoLoadStructure() - Constructor for class demo.DemoLoadStructure
DemoLoadSubstMax - Class in demo
DemoLoadSubstMax() - Constructor for class demo.DemoLoadSubstMax
DemoMMCIFReader - Class in demo: An example of how to read MMcif files
DemoMMCIFReader() - Constructor for class demo.DemoMMCIFReader
DemoMultipleMC - Class in demo: Demo for running the MultipleMC Algorithm on a protein family.
DemoMultipleMC() - Constructor for class demo.DemoMultipleMC
DemoNWALignment - Class in demo
DemoNWALignment() - Constructor for class demo.DemoNWALignment
DemoOrientBioAssembly - Class in demo: Created by ap3 on 02/04/2015.
DemoOrientBioAssembly() - Constructor for class demo.DemoOrientBioAssembly
DemoRotationAxis - Class in demo: A demo for how to use RotationAxis to display the rotation for an alignment.
DemoRotationAxis() - Constructor for class demo.DemoRotationAxis
DemoSCOP - Class in demo: A class demonstrating the use of the SCOP parsing tools
DemoSCOP() - Constructor for class demo.DemoSCOP
DemoSecStrucCalc - Class in demo: Demonstration on how to use the Secondary Structure Prediction (DSSP) implementation in BioJava and obtain different SS representations and outputs.
DemoSecStrucCalc() - Constructor for class demo.DemoSecStrucCalc
DemoShowBiolAssembly - Class in demo
DemoShowBiolAssembly() - Constructor for class demo.DemoShowBiolAssembly
DemoShowCATHDomain - Class in demo
DemoShowCATHDomain() - Constructor for class demo.DemoShowCATHDomain
DemoShowLargeAssembly - Class in demo
DemoShowLargeAssembly() - Constructor for class demo.DemoShowLargeAssembly
DemoShowValidationResults - Class in demo
DemoShowValidationResults() - Constructor for class demo.DemoShowValidationResults
DemoSixFrameTranslation - Class in demo: Created by andreas on 8/10/15.
DemoSixFrameTranslation() - Constructor for class demo.DemoSixFrameTranslation
DemoStructureFromFasta - Class in demo: Demo of how to use the FastaStructureParser class to read protein structures from a FASTA file.
DemoStructureFromFasta() - Constructor for class demo.DemoStructureFromFasta
DemoSW3DAligner - Class in demo
DemoSW3DAligner() - Constructor for class demo.DemoSW3DAligner
description - Variable in class org.biojava.nbio.ontology.AbstractTerm
description() - Method in enum org.biojava.nbio.protmod.ModificationCategory
description(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener: Notify this parse listener of a description line.
deserialize(File) - Static method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
desFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
destroy() - Static method in class org.biojava.nbio.core.util.FlatFileCache
destroy() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Set all the member variables to null.
destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel: Clean up this instance for garbage collection, to avoid memory leaks...
destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
det() - Method in class org.biojava.nbio.structure.jama.LUDecomposition: Determinant
det() - Method in class org.biojava.nbio.structure.jama.Matrix: Matrix determinant
detectCicular(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: Loops through the given list of locations and returns true if it looks like they represent a circular location.
detectEnd(List<Location>, boolean) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: This will attempt to find what the last point is and returns that position.
detectStart(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: Assumes that the first element is the start & clones it
detectStrand(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: Loops through the given list of locations and returns the consensus Strand class.
diAA2Instability - Static variable in class org.biojava.nbio.aaproperties.Constraints
diag(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
diag(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
dialogAsk(String, String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
DIGIT - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil: A digit
disableCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
discreteQuantizer - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
DiscreteQuantizerInterface - Interface in org.biojava.nbio.survival.kaplanmeier.metadata
DISEASE_ASSOC - Static variable in class org.biojava.nbio.phosphosite.Dataset
DISJOINT_FROM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
display(AFPChain, Group[], Atom[], Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP: Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
display(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay: Display a MultipleAlignment with a JmolPanel.
display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay: Display an AFPChain alignment
display(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Displays a single structure in a cartoon representation with each symmetric repeat colored differently.
DisplayAFP - Class in org.biojava.nbio.structure.align.gui: A utility class for visualistion of structure alignments
DisplayAFP() - Constructor for class org.biojava.nbio.structure.align.gui.DisplayAFP
displayFull(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Displays a multiple alignment of the whole structure transformations colored by blocks, corresponding to the symmetric protodomains.
displayRepeats(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Displays a multiple alignment of the symmetry repeats.
dissimilarityScore(MultipleSequenceAlignment<C, D>, SubstitutionMatrix<D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The dissimilarity score is the additive inverse of the similarity score (sum of scores) between two aligned sequences using a substitution model (Substitution Matrix).
dist - Variable in class org.biojava.nbio.structure.validation.Clash
dist - Variable in class org.biojava.nbio.structure.validation.SymmClash
DIST_MATRICES - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
distance(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return distance between this location and the other location.
DISTANCE_INCREMENT - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
DistanceBox<T> - Class in org.biojava.nbio.structure.symmetry.geometry
DistanceBox(double) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.DistanceBox: Creates a new instance of DistanceBox
distanceIncrement - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
DistanceMatrixCalculator - Class in org.biojava.nbio.phylo: The DistanceMatrixCalculator methods generate a DistanceMatrix from a MultipleSequenceAlignment or other indirect distance infomation (RMSD).
distanceTree(BasicSymmetricalDistanceMatrix, TreeConstructorType) - Static method in class org.biojava.nbio.phylo.TreeConstructor
DistanceTreeEvaluator - Class in org.biojava.nbio.phylo: Check the accuracy of a Distance Tree by least squares error (LSE) of the Tree branch lengths and the original Distance Matrix.
DNA_ONLY - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType: Convenience Set of polymer types classified as DNA.
dnaCompounds(CompoundSet<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
DNACompoundSet - Class in org.biojava.nbio.core.sequence.compound
DNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.DNACompoundSet
dnaRnaTranslator(DNAToRNATranslator) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
DNASequence - Class in org.biojava.nbio.core.sequence: This is class should model the attributes associated with a DNA sequence
DNASequence() - Constructor for class org.biojava.nbio.core.sequence.DNASequence: Shouldn't be used but makes it bean happy
DNASequence(String) - Constructor for class org.biojava.nbio.core.sequence.DNASequence: String is king and create a sequence from DNA with default DNA compound set
DNASequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence: Create a sequence where the actual storage of the sequence data is somewhere else
DNASequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence: Create a sequence from a string with user defined compound set
DNASequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence: Create a sequence from a ProxySequencereader and user defined compound set
DNASequence.DNAType - Enum in org.biojava.nbio.core.sequence: The type of DNA sequence
DNASequenceCreator - Class in org.biojava.nbio.core.sequence.io: A helper class that allows different ways to read a string and create a DNA sequence.
DNASequenceCreator(CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.DNASequenceCreator
DNAToRNATranslator - Class in org.biojava.nbio.core.sequence.transcription: Performs the first stage of transcription by going from DNA to RNA.
DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound>, CompoundSet<NucleotideCompound>, CompoundSet<NucleotideCompound>, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
doChainAfp(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer: // Key function: chain (assembly) the AFPs // a AFP (k) is defined as (i, j, k), with i and j are staring points // AFP extension (eg.
documentEnd() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener: end of parsing a new OBO file
documentEnd() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
documentEnd() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
documentEnd() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer: called at end of document
documentEnd() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
documentStart() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener: starting to parse a new OBO file
documentStart() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
documentStart() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
documentStart() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer: called at start of document
documentStart() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer: Start the parsing
doesSequenceContainInvalidChar(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils: Checks if given sequence contains invalid characters.
doInBackground() - Method in class org.biojava.nbio.structure.align.gui.StructureLoaderThread
doIter0(int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
doIter0(int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
Domain - Class in org.biojava.nbio.structure.domain.pdp
Domain() - Constructor for class org.biojava.nbio.structure.domain.pdp.Domain
domainDescriptionFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
domainListFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
DomainProvider - Interface in org.biojava.nbio.structure.domain: Decomposes a structure from the PDB into representative domains
DomainProviderFactory - Class in org.biojava.nbio.structure.domain: A simple factory object that returns the system wide default DomainProvider
DOMAINS_PATH - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
domallFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
doPOST(URL, String) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: do a POST to a URL and return the response stream for further processing elsewhere.
doPOST(URL, String, int) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: do a POST to a URL and return the response stream for further processing elsewhere.
doPOST(URL, String) - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: do a POST to a URL and return the response stream for further processing elsewhere.
doPrintConnections() - Method in class org.biojava.nbio.structure.io.FileConvert: Returns if the Connections should be added default is true;
dot(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseVector: Calculates the dot product of this vector a with b
dot(double[], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
DOT_PLOT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
DotPlotListener(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener
DotPlotPanel - Class in org.biojava.nbio.structure.align.gui: Displays the dot plot trace for an alignment.
DotPlotPanel(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.DotPlotPanel
download() - Method in class org.biojava.nbio.phosphosite.Dataset
DownloadChemCompProvider - Class in org.biojava.nbio.structure.io.mmcif: This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.
DownloadChemCompProvider() - Constructor for class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
DownloadChemCompProvider(String) - Constructor for class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
downloadClaFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
downloadComFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
downloadDesFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
downloadDomainDescriptionFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
downloadDomainListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
downloadDomallFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
downloadFile() - Static method in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider: Downloads the components.cif.gz file from the wwPDB site.
downloadFile(URL, File) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils: Download the content provided at URL url and store the result to a local file, using a temp file to cache the content in case something goes wrong in download
downloadFileFromRemote(URL, File) - Method in class org.biojava.nbio.structure.cath.CathInstallation
downloadFileFromRemote(URL, File) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
downloadHieFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
downloadingStructures(String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
downloadingStructures(String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
downloadingStructures(String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
downloadNodeListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
downloadPDB(String) - Method in class org.biojava.nbio.structure.io.PDBFileReader: Deprecated.
downloadStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Downloads an MMCIF file from the PDB to the local path
downstream(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return the adjacent location of specified length directly downstream of this location.
drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that draws symmetry or inertia axes for a structure.
drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that draws symmetry or inertia axes for a structure.
drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
drawBoxes(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel: draw high scoring fragments that are used for the initial alignment seed selection
drawDistances(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel: For each element in matrix, draw it as a colored square or pixel.
drawIdx(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
drawPairs(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel: draw alternative alignments
drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that draws an invisible polyhedron around a structure.
drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that draws an invisible polyhedron around a structure.
drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
drawScale(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel: draw the Scale
drawSequence(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel: draw the Amino acid sequence
DSSP_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo: Secondary strucuture parsed from a DSSP output file
DSSPParser - Class in org.biojava.nbio.structure.secstruc: Class to parse a DSSP file (output of the DSSP program), that contains the secondary structure assignment of a structure.
DSSPParser() - Constructor for class org.biojava.nbio.structure.secstruc.DSSPParser
dump() - Method in class org.biojava.nbio.survival.cox.CoxInfo
dump(ArrayList<SurvivalInfo>, PrintStream, String) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper: For each analysis this allows outputing of the data used in the calculations to a printstream/file.
duplicateCA2(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: Utility method for working with circular permutations.
duplicationHint - Variable in class org.biojava.nbio.structure.align.ce.CECPParameters
duplicationHint - Variable in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

E

E - Static variable in class org.biojava.nbio.aaproperties.Constraints
ECOD_RE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
ECOD_URL - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
EcodDatabase - Interface in org.biojava.nbio.structure.ecod: General API for interacting with ECOD.
EcodDomain - Class in org.biojava.nbio.structure.ecod: An EcodDomain contains all the information of the ECOD database: id, classification groups (from higher to lower in the tree: X,H,T,F), PDB code, chain, residue ranges and status (manual or automatic classification).
EcodDomain() - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain: Default constructor with all null properties
EcodDomain(Long, String, Boolean, Integer, Integer, Integer, Integer, String, String, String, String, String, String, String, String, Long, Set<String>) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
EcodDomain(Long, String, Boolean, Integer, Integer, Integer, Integer, String, String, String, String, String, String, String, String, String, Long, Set<String>) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
EcodDomain(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
EcodDomain(EcodDomain) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
EcodFactory - Class in org.biojava.nbio.structure.ecod: Controls global EcodDatabases being used.
EcodInstallation - Class in org.biojava.nbio.structure.ecod: Provides access to the Evolutionary Classification of Protein Domains (ECOD).
EcodInstallation(String, String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation: Use EcodFactory to create instances.
EcodInstallation.EcodParser - Class in org.biojava.nbio.structure.ecod
EcodParser(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
EcodParser(File) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
EcodParser(Reader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
EcodParser(BufferedReader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
Edit<C extends Compound> - Interface in org.biojava.nbio.core.sequence.edits: Interface for carrying out edit operations on a Sequence.
edit(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
edit(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.edits.Edit
Edit.AbstractEdit<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits: Abstract class which defines all edit operations as a call to discover what 5' and 3' ends of an editing Sequence should be joined together with a target Sequence.
Edit.Delete<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits: Implementation which allows for the deletion of bases from a Sequence
Edit.Insert<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits: Edit implementation which allows us to insert a base at any position in a Sequence.
Edit.Substitute<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits: Allows for the substitution of bases into an existing Sequence.
edsr - Variable in class org.biojava.nbio.structure.validation.Entry
edsResolution - Variable in class org.biojava.nbio.structure.validation.Entry
edsResolutionLow - Variable in class org.biojava.nbio.structure.validation.Entry
ef - Variable in class org.biojava.nbio.survival.cox.CoxInfo
eig() - Method in class org.biojava.nbio.structure.jama.Matrix: Eigenvalue Decomposition
EigenvalueDecomposition - Class in org.biojava.nbio.structure.jama: Eigenvalues and eigenvectors of a real matrix.
EigenvalueDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.EigenvalueDecomposition: Check for symmetry, then construct the eigenvalue decomposition Structure to access D and V.
Element - Class in org.biojava.nbio.aaproperties.xml: One way to model the elements
Element() - Constructor for class org.biojava.nbio.aaproperties.xml.Element
Element(String, String, int, List<Isotope>, double) - Constructor for class org.biojava.nbio.aaproperties.xml.Element
Element - Enum in org.biojava.nbio.structure: Element is an enumeration of the elements of the periodic table.
ElementTable - Class in org.biojava.nbio.aaproperties.xml
ElementTable() - Constructor for class org.biojava.nbio.aaproperties.xml.ElementTable
ElementTable(List<Element>) - Constructor for class org.biojava.nbio.aaproperties.xml.ElementTable
ElementType - Enum in org.biojava.nbio.structure: ElementType is an enumeration of the types of elements found in the periodic table.
EMPTY - Static variable in interface org.biojava.nbio.core.sequence.location.template.Location: Basic location which is set to the minimum and maximum bounds of Integer.
EMPTY_ANNOTATION - Static variable in interface org.biojava.nbio.ontology.utils.Annotation: A really useful empty and immutable annotation object.
enableCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
encodeFileURL(String) - Method in class org.biojava.nbio.survival.cox.CoxVariables
end() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Get the ending index.
END_SEQUENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
endIndex - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair
ENDOFFILE - Static variable in class org.biojava.nbio.core.exceptions.Messages
ENDS - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
endsAfter(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location ends after other location ends.
endsBefore(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location ends before other location ends.
ENDSEND - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
ensureClaInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
ensureComInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
ensureDesInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
ensureDomainDescriptionInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
ensureDomainListInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
ensureDomainsFileInstalled() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Blocks until ECOD domains file has been downloaded and parsed.
ensureDomallInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
ensureHieInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
ensureNodeListInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
ent - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
Entity - Class in org.biojava.nbio.structure.io.mmcif.model: A simple class to represent Entity records in mmCif files
Entity() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Entity
entity_poly_type - Variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType
EntityPolySeq - Class in org.biojava.nbio.structure.io.mmcif.model: Container for _entity_poly_seq records
EntityPolySeq() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
EntitySrcGen - Class in org.biojava.nbio.structure.io.mmcif.model: Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated.
EntitySrcGen() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
EntitySrcNat - Class in org.biojava.nbio.structure.io.mmcif.model: Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue.
EntitySrcNat() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
EntitySrcSyn - Class in org.biojava.nbio.structure.io.mmcif.model: PDBX_ENTITY_SRC_SYN records the details about each chemically synthesized molecule (entity) in the asymmetric unit.
EntitySrcSyn() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
Entry - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
Entry() - Constructor for class org.biojava.nbio.structure.validation.Entry
entry - Variable in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
entrySet() - Method in class org.biojava.nbio.core.util.SoftHashMap
entrySet() - Method in class org.biojava.nbio.ontology.utils.SmallMap
entrySet() - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
entrySet() - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap: Always returns the empty set
entrySet() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
EQR_COLOR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
equal(int, int) - Static method in class org.biojava.nbio.core.util.Equals
equal(long, long) - Static method in class org.biojava.nbio.core.util.Equals
equal(boolean, boolean) - Static method in class org.biojava.nbio.core.util.Equals
equal(Object, Object) - Static method in class org.biojava.nbio.core.util.Equals: Does not compare class types.
equals(Object) - Method in class org.biojava.nbio.core.search.io.Hit: Implements conceptual comparisons of search results.
equals(Object) - Method in class org.biojava.nbio.core.search.io.Hsp: Experimental.
equals(Object) - Method in class org.biojava.nbio.core.search.io.Result: Experimental.
equals(Object) - Method in class org.biojava.nbio.core.sequence.AccessionID
equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
equals(Object) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
equals(Object) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
equals(Object) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
Equals - Class in org.biojava.nbio.core.util: A set of helper methods which return true if the two parameters are equal to each other.
Equals() - Constructor for class org.biojava.nbio.core.util.Equals
equals(Object) - Method in class org.biojava.nbio.data.sequence.FastaSequence
equals(GeneName) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
equals(Object) - Method in class org.biojava.nbio.genome.parsers.gff.Location
equals(Object) - Method in class org.biojava.nbio.ontology.Term.Impl
equals(Object) - Method in interface org.biojava.nbio.ontology.Triple: Check to see if an object is an equivalent Triple.
equals(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl: Two triples are equal if all their fields are identical.
equals(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
equals(Object) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
equals(Object) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureAtom
equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
equals(Object) - Method in class org.biojava.nbio.ronn.Jronn.Range
equals(Object) - Method in class org.biojava.nbio.ronn.ModelLoader.Model
equals(Object) - Method in class org.biojava.nbio.structure.align.client.PdbPair
equals(Object) - Method in class org.biojava.nbio.structure.align.client.StructureName
equals(Object) - Method in class org.biojava.nbio.structure.align.model.AFPChain: A week equality metric.
equals(Object) - Method in class org.biojava.nbio.structure.Author
equals(Object) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
equals(Object) - Method in class org.biojava.nbio.structure.contact.Pair
equals(Object) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
equals(Object) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
equals(Object) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
equals(Object) - Method in class org.biojava.nbio.structure.io.SSBondImpl
equals(PDBHeader) - Method in class org.biojava.nbio.structure.PDBHeader: Compare two PDBHeader objects
equals(Object) - Method in class org.biojava.nbio.structure.ResidueNumber
equals(Object) - Method in class org.biojava.nbio.structure.ResidueRange
equals(Object) - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
equals(Object) - Method in class org.biojava.nbio.structure.scop.ScopDescription: Compares the fields sunID, category, classificationId, and name for equality
equals(Object) - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
equals(Object) - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
equals(Object) - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
equals(Object) - Method in class org.biojava.nbio.structure.Site
equals(Object) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
equals(Object) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
equalsIgnoreCase(Compound) - Method in interface org.biojava.nbio.core.sequence.template.Compound
equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
equalsToIgnoreEndline(String, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper: compares two strings for equality, line by line, ignoring any difference of end line delimiters contained within the 2 Strings.
equalsToXml(String, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
EQUIVALENCE - Static variable in class org.biojava.nbio.ontology.OntoTools
EQUIVALENT - Static variable in class org.biojava.nbio.structure.gui.util.AlignedPosition: flag if this position is equivalent
EQUIVALENT_VERSIONS - Static variable in class org.biojava.nbio.structure.scop.BerkeleyScopInstallation: A map from SCOP version names which the Berkeley server offers as a download to an array of equivalent deprecated SCOP version names.
equivalentAxes(Matrix4d, Matrix4d, double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Determines if two symmetry axis are equivalent inside the error threshold.
errorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools: Return the error probabilities from the specified FASTQ formatted sequence.
errorProbabilities(Fastq, double[]) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools: Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.
errorProbability(char) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant: Convert the specified quality in ASCII format to an error probability.
errorProbability(int) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant: Calculate the error probability given the specified quality score.
escape(String, boolean) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
escapeChars - Static variable in class org.biojava.nbio.ontology.obo.OboFileParser
eval(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
evalString(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Execute a command String in the current Jmol panel.
evalString(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
evalString(String) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
evaluate(Phylogeny, DistanceMatrix) - Static method in class org.biojava.nbio.phylo.DistanceTreeEvaluator: Evaluate the goodness of fit of a given tree to the original distance matrix.
EXACT_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
EXACT_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym
execute(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative: This method uses iteratively CeSymm to calculate all symmetries in the input array of atoms and organize them in a multiple alignment of the repeats.
executeCmd(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
ExonComparator - Class in org.biojava.nbio.core.sequence: Sort Exon where it is a little confusing if exons shoud always be ordered left to right where a negative stranded gene should go the other direction.
ExonComparator() - Constructor for class org.biojava.nbio.core.sequence.ExonComparator
ExonSequence - Class in org.biojava.nbio.core.sequence: A gene contains a collection of Exon sequences
ExonSequence(GeneSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.ExonSequence: Need a parent gene sequence and the bioBegin and bioEnd.
expandUserHome(String) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils: Expands ~ in paths to the user's home directory.
ExperimentalTechnique - Enum in org.biojava.nbio.structure: An enum to represent the experimental technique of a PDB structure
EXPERT - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
ExpressionFigure - Class in org.biojava.nbio.survival.kaplanmeier.figure
ExpressionFigure() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
Exptl - Class in org.biojava.nbio.structure.io.mmcif.model
Exptl() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Exptl
extendFragments(Atom[], Atom[], JointFragments[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
extendFragments(Atom[], Atom[], JointFragments, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
extendHelix(int) - Method in class org.biojava.nbio.structure.symmetry.core.HelixExtender
extractAFPChains(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

F

F - Static variable in class org.biojava.nbio.aaproperties.Constraints
f(Double) - Method in class org.biojava.nbio.survival.cox.StrataInfo
f1Dot2(float) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
F_UNCLASSIFIED - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser: String for unclassified F-groups
FarmJob - Class in org.biojava.nbio.structure.align: A job as it can be run on the farm.
FarmJob() - Constructor for class org.biojava.nbio.structure.align.FarmJob
FarmJobParameters - Class in org.biojava.nbio.structure.align.client
FarmJobParameters() - Constructor for class org.biojava.nbio.structure.align.client.FarmJobParameters
FarmJobRunnable - Class in org.biojava.nbio.structure.align.client: Contains the single thread for a job that can run multiple alignments.
FarmJobRunnable(FarmJobParameters) - Constructor for class org.biojava.nbio.structure.align.client.FarmJobRunnable
FASTA_FORMAT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
FastaAFPChainConverter - Class in org.biojava.nbio.structure.io: A collection of static utilities to convert between AFPChains and FastaSequences.
FastaAFPChainConverter() - Constructor for class org.biojava.nbio.structure.io.FastaAFPChainConverter
fastaFileToAfpChain(File, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Reads the file fastaFile, expecting exactly two sequences which give a pairwise alignment.
FastaGeneWriter - Class in org.biojava.nbio.core.sequence.io: A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.
FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.FastaGeneWriter
FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean, int) - Constructor for class org.biojava.nbio.core.sequence.io.FastaGeneWriter
FastaHeaderFormatInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
FastaReader<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io: Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta files
FastaReader(InputStream, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaReader: If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.
FastaReader(File, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaReader: If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
FastaReaderHelper - Class in org.biojava.nbio.core.sequence.io
FastaReaderHelper() - Constructor for class org.biojava.nbio.core.sequence.io.FastaReaderHelper
FastaSequence - Class in org.biojava.nbio.data.sequence: A FASTA formatted sequence.
FastaSequence(String, String) - Constructor for class org.biojava.nbio.data.sequence.FastaSequence: Upon construction the any whitespace characters are removed from the sequence
FastaSequenceParser - Class in org.biojava.nbio.core.sequence.io: Used to parse a stream of a fasta file to get the sequence
FastaSequenceParser() - Constructor for class org.biojava.nbio.core.sequence.io.FastaSequenceParser
fastaStringToAfpChain(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
FastaStructureParser - Class in org.biojava.nbio.structure.io: Reads a protein sequence from a fasta file and attempts to match it to a 3D structure.
FastaStructureParser(InputStream, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
FastaStructureParser(File, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
FastaStructureParser(FastaReader<ProteinSequence, AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
fastaToAfpChain(Map<String, ProteinSequence>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment.
fastaToAfpChain(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: TODO Write comment
fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>, AminoAcidCompound>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Provided only for convenience.
FastaWriter<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io: The FastaWriter writes a collection of sequences to an outputStream.
FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriter: Use default line length of 60
FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriter: Set custom lineLength
FastaWriterHelper - Class in org.biojava.nbio.core.sequence.io: The class that should be used to write out fasta file of a sequence collection
FastaWriterHelper() - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriterHelper
Fastq - Class in org.biojava.nbio.sequencing.io.fastq: FASTQ formatted sequence.
fastq(Fastq) - Method in interface org.biojava.nbio.sequencing.io.fastq.StreamListener: Notify this listener of a FASTQ formatted sequence.
FastqBuilder - Class in org.biojava.nbio.sequencing.io.fastq: Fluent builder API for creating FASTQ formatted sequences.
FastqBuilder() - Constructor for class org.biojava.nbio.sequencing.io.fastq.FastqBuilder: Create a new FASTQ formatted sequence builder.
FastqReader - Interface in org.biojava.nbio.sequencing.io.fastq: Reader for FASTQ formatted sequences.
FastqTools - Class in org.biojava.nbio.sequencing.io.fastq: Utility methods for FASTQ formatted sequences.
FastqVariant - Enum in org.biojava.nbio.sequencing.io.fastq: FASTQ sequence format variant.
FastqWriter - Interface in org.biojava.nbio.sequencing.io.fastq: Writer for FASTQ formatted sequences.
FatCat - Class in org.biojava.nbio.structure.align.fatcat
FatCat() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCat
FATCAT_BLOCK - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
FATCAT_TEXT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
FatCatAligner - Class in org.biojava.nbio.structure.align.fatcat.calc: A class that does calculations on an AFPChain
FatCatAligner() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
FatCatFlexible - Class in org.biojava.nbio.structure.align.fatcat
FatCatFlexible() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
FatCatParameters - Class in org.biojava.nbio.structure.align.fatcat.calc
FatCatParameters() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
FatCatRigid - Class in org.biojava.nbio.structure.align.fatcat
FatCatRigid() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatRigid
FatCatStartupParams() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
FatCatUserArgumentProcessor - Class in org.biojava.nbio.structure.align.fatcat
FatCatUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
FatCatUserArgumentProcessor.FatCatStartupParams - Class in org.biojava.nbio.structure.align.fatcat
fatColumnNames - Static variable in class org.biojava.nbio.structure.align.gui.DBResultTable
FCAlignHelper - Class in org.biojava.nbio.structure.align.fatcat.calc
FCAlignHelper(double[][], int, int, double, double) - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper: do an alignment given the provided matrix sij0
fDot2(double) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Feature - Class in org.biojava.nbio.genome.parsers.gff: A Feature corresponds to a single row in a GFF file.
Feature(Feature) - Constructor for class org.biojava.nbio.genome.parsers.gff.Feature: Make a copy of the specified feature.
Feature(String, String, String, Location, Double, int, String) - Constructor for class org.biojava.nbio.genome.parsers.gff.Feature: Construct a new Feature from raw data (usually a GFF row).
FEATURE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
FeatureDbReferenceInfo<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features: It is DBReferenceInfo which implements FeatureInterface.
FeatureDbReferenceInfo(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
featureGlobalEnd - Variable in class org.biojava.nbio.core.sequence.location.InsdcParser: these variables are used to compute the global start and end of complex features
featureGlobalStart - Variable in class org.biojava.nbio.core.sequence.location.InsdcParser: these variables are used to compute the global start and end of complex features
FeatureHelper - Class in org.biojava.nbio.genome.parsers.gff
FeatureHelper() - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureHelper
FeatureI - Interface in org.biojava.nbio.genome.parsers.gff: A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.
FeatureInterface<S extends AbstractSequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.features: Interface class to handle describing arbitrary features.
FeatureList - Class in org.biojava.nbio.genome.parsers.gff: A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.
FeatureList() - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureList: Construct an empty list.
FeatureList(Collection<FeatureI>) - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureList: Construct a new list containing the same features as the specified list.
FeatureRetriever - Interface in org.biojava.nbio.core.sequence.features: If a SequenceProxyReader implements this interface then that external source has a list features
FeaturesKeyWordInterface - Interface in org.biojava.nbio.core.sequence.features: Models the keywords that are annotated for a protein sequence at Uniprot.
fetch(String, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser: Fetch and parse the DSSP file of the specified pdb code from the PDB web server and return the secondary structure annotation as a List of SecStrucState objects.
FIELD_LINE - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
figureLineInfoLowerPercentX - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
figureLineInfoLowerPercentY - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
FileConvert - Class in org.biojava.nbio.structure.io: Methods to convert a structure object into different file formats.
FileConvert(Structure) - Constructor for class org.biojava.nbio.structure.io.FileConvert: Constructs a FileConvert object.
FileDownloadUtils - Class in org.biojava.nbio.structure.io.util
FileDownloadUtils() - Constructor for class org.biojava.nbio.structure.io.util.FileDownloadUtils
FileParsingParameters - Class in org.biojava.nbio.structure.io: A class that configures parameters that can be sent to the PDB file parsers FileParsingParameters.setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms FileParsingParameters.setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.
FileParsingParameters() - Constructor for class org.biojava.nbio.structure.io.FileParsingParameters
FileProxyDNASequenceCreator - Class in org.biojava.nbio.core.sequence.io: This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
FileProxyDNASequenceCreator(File, CompoundSet<NucleotideCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator: Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
FileProxyProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io: This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
FileProxyProteinSequenceCreator(File, CompoundSet<AminoAcidCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator: Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
fileSeparator - Static variable in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
FILESPLIT - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
FILESPLIT - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
filterByCathCode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return list of CATH descriptions whose CATH codes (e.g.
filterByCathCode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
filterByClassificationId(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Get all scop descriptions that start with a classification ID, e.g.
filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
filterByDescription(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return list of CATH descriptions whose descriptions (name field) starts with the query.
filterByDescription(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
filterByDescription(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Get all scop descriptions that start with a certain name.
filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
filterByDomainName(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: search through SCOP and filter based on domain name
filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
filterByHierarchy(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase: Get a list of domains within a particular level of the hierarchy
filterByHierarchy(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Get a list of domains within a particular level of the hierarchy
filterByNodeName(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return list of CATH domains whose node name (e.g.
filterByNodeName(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain: Takes as input an AFPChain where ca2 has been artificially duplicated.
filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[], CECPParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
filterLigands(List<Group>) - Static method in class org.biojava.nbio.structure.StructureTools: Removes all polymeric and solvent groups from a list of groups
findAtomLinkages(Group, Group, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil: Find linkages between two groups within tolerance of bond length, from potential atoms.
findAtomLinkages(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil: Find linkages between two groups within tolerance of bond length, from potential atoms.
findChain(String) - Method in interface org.biojava.nbio.structure.Structure: Request a particular chain from a structure.
findChain(String, int) - Method in interface org.biojava.nbio.structure.Structure: Request a particular chain from a particular model
findChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl: Request a particular chain from a particular model
findChain(String) - Method in class org.biojava.nbio.structure.StructureImpl: Request a particular chain from a structure.
findCompounds() - Method in class org.biojava.nbio.structure.io.CompoundFinder: Utility method that employs some heuristics to find the Compounds for this Structure in case the information is missing in PDB/mmCIF file
findGroup(String, String) - Method in interface org.biojava.nbio.structure.Structure: Request a particular group from a structure.
findGroup(String, String, int) - Method in interface org.biojava.nbio.structure.Structure: Request a particular group from a structure.
findGroup(String, String, int) - Method in class org.biojava.nbio.structure.StructureImpl: Request a particular group from a structure.
findGroup(String, String) - Method in class org.biojava.nbio.structure.StructureImpl: Request a particular group from a structure.
findLinkage(Group, Group, String, String, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil: Find a linkage between two groups within tolerance of bond length.
findNearestAtomLinkage(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil: Find a linkage between two groups within tolerance of bond length, from potential atoms.
findUnescaped(String, char) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
findUnescaped(String, char, int, int) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
findUnescaped(String, char, int, int, boolean) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
finish(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
first_cut - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
flagLoading(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
flagLoadingFinished(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
FlatFileCache - Class in org.biojava.nbio.core.util: Provides a cache for storing multiple small files in memory.
flipAlignment(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser: Takes an XML representation of the alignment and flips the positions of name1 and name2
flipChain(AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainFlipper: Flip the position of name1 and name2 (as well as all underlying data) in an AFPChain.
flippableSidechain - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
floor(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Return the largest key in the table <= k.
flush() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
flushCache() - Method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
flushCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
flushCache() - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxCoefficient
fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxInfo
fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxVariables
fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
fmtpl(String, int) - Method in class org.biojava.nbio.survival.cox.CoxInfo: Pad left a string with spaces
fmtpr(String, int) - Method in class org.biojava.nbio.survival.cox.CoxInfo
foFcCorrelation - Variable in class org.biojava.nbio.structure.validation.Entry
ForesterWrapper - Class in org.biojava.nbio.phylo: This class contains wrapper methods for communication between BioJava and forester (e.g, Data Structure conversion).
FORMAT_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier: URL parameter specifying the file format (PDB or CIF)
formBondsFromStructConn(List<StructConn>) - Method in class org.biojava.nbio.structure.io.BondMaker
formDisulfideBonds(List<SSBondImpl>) - Method in class org.biojava.nbio.structure.io.BondMaker: Creates disulfide bond objects and references in the corresponding Atoms objects, given a list of SSBondImpls parsed from a PDB/mmCIF file.
formLinkRecordBond(PDBTemporaryStorageUtils.LinkRecord) - Method in class org.biojava.nbio.structure.io.BondMaker: Creates bond objects from a LinkRecord as parsed from a PDB file
FourBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
FourBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
FourBitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
FourBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
FourBitSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage: Four bit encoding of the bit formats.
FourBitSequenceReader(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
FourBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
FourBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
FourBitSequenceReader.FourBitArrayWorker<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage: A four bit per compound implementation of the bit array worker code.
fractionalDissimilarity(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The fractional dissimilarity (D) is defined as the percentage of sites that differ between two aligned sequences.
fractionalDissimilarityScore(MultipleSequenceAlignment<C, D>, SubstitutionMatrix<D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The fractional dissimilarity score (Ds) is a relative measure of the dissimilarity between two aligned sequences.
FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
FractionalIdentityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityInProfileScorer: Creates a fractional identity scorer for an aligned pair of sequences in the given alignment profile.
FractionalIdentityScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements an algorithm which computes a score for a sequence alignment pair.
FractionalIdentityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityScorer: Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
FractionalIdentityScorer(SequencePair<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityScorer: Creates a fractional identity scorer for an aligned pair of sequences.
FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
FractionalSimilarityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer: Creates a fractional similarity scorer for an aligned pair of sequences in the given alignment profile.
FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements an algorithm which computes a score for a sequence alignment pair.
FractionalSimilarityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityScorer: Creates a fractional similarity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
FractionalSimilarityScorer(SequencePair<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityScorer: Creates a fractional similarity scorer for an aligned pair of sequences.
frag_pairwise_compat(FragmentPair[], int, float, int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner: Calculate the pairwise compatibility of fpairs.
FragmentJoiner - Class in org.biojava.nbio.structure.align.pairwise: Joins the initial Fragments together to larger Fragments
FragmentJoiner() - Constructor for class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
FragmentPair - Class in org.biojava.nbio.structure.align.pairwise: a pair of fragments of two protein structures
FragmentPair(int, int, int) - Constructor for class org.biojava.nbio.structure.align.pairwise.FragmentPair
Frame - Enum in org.biojava.nbio.core.sequence.transcription: Indicates a way of translating a sequence.
frame() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get frame (aka phase).
frame - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
from - Variable in class org.biojava.nbio.ronn.Jronn.Range: Range starting position counts from 1 (the first position on the sequence is 1)
fromAFP(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Converts a refined symmetry AFPChain alignment into the standard representation of symmetry in a MultipleAlignment, that contains the entire Atom array of the strcuture and the symmetric repeats are orgaized in different rows in a single Block.
fromBio(int, int, char) - Static method in class org.biojava.nbio.genome.parsers.gff.Location: Create location from "biocoordinates", as in GFF file.
fromBioExt(int, int, char, int) - Static method in class org.biojava.nbio.genome.parsers.gff.Location: Create a location from MAF file coordinates, which represent negative strand locations as the distance from the end of the sequence.
fromCathCode(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory
fromCharacter(Character) - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType
fromCharacter(Character) - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType: Converts a Character representing a Secondary Structure type into the corresponding enum object.
fromCIEXYZ(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
fromConciseAlignmentString(String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
fromMultiXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
fromRGB(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
fromStartupParams(StartupParameters) - Static method in class org.biojava.nbio.structure.align.util.UserConfiguration
fromString(String) - Static method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
fromString(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory
fromString(String) - Static method in enum org.biojava.nbio.structure.PDBStatus.Status
fromString(String) - Static method in class org.biojava.nbio.structure.ResidueNumber: Convert a string representation of a residue number to a residue number object.
fromString(String) - Static method in enum org.biojava.nbio.structure.scop.ScopCategory
fromXML(String) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter
fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter
fromXML(String) - Static method in class org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter
fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.StructureAtomXMLConverter
fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.StructureGroupXMLConverter
fromXML(String, String, String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser: new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed
fromXML(String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
fromXML(String) - Method in class org.biojava.nbio.structure.align.xml.HasResultXMLConverter
fromXML(String) - Method in class org.biojava.nbio.structure.align.xml.PositionInQueueXMLConverter
fromXML(String) - Static method in class org.biojava.nbio.structure.align.xml.RepresentativeXMLConverter
fromXML(String) - Static method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer
fromXML(String) - Static method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
fromXML(String) - Static method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
fromXML(String) - Static method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
fromXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ListStringWrapper
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ScopDescriptions
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ScopDomains
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ScopNodes
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper
fromXML(String) - Static method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
fromXML(String) - Static method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
functionXY(String, int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
functionXYZ(String, int, int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
FuzzyPoint - Class in org.biojava.nbio.core.sequence.location: Implementation for resolving fuzzy locations.
FuzzyPoint(int, int) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint
FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint
FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint

G

G - Static variable in class org.biojava.nbio.aaproperties.Constraints
GAP_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
GAP_COVERAGE_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.CompoundFinder: Gap coverage value (num gaps over length of sequence) for each chain of the match: 2 chains with more gap coverage than this value will not be considered part of the same entity
GapArray - Class in org.biojava.nbio.structure.align.helper
GapArray() - Constructor for class org.biojava.nbio.structure.align.helper.GapArray
gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
gapPenalty - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
GapPenalty - Interface in org.biojava.nbio.alignment.template: Defines a data structure for the gap penalties used during a sequence alignment routine.
GapPenalty.Type - Enum in org.biojava.nbio.alignment.template: Defines the possible types of gap penalties.
GCStats - Class in org.biojava.nbio.genome.parsers.gff
GCStats() - Constructor for class org.biojava.nbio.genome.parsers.gff.GCStats
GENBANK_FORMAT - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser: The name of this format
GenbankHeaderFormatInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
GenbankProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
GenbankProxySequenceReader(String, String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
GenbankReader<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io: Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank files
GenbankReader(InputStream, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReader: If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.
GenbankReader(File, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReader: If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
GenbankReaderHelper - Class in org.biojava.nbio.core.sequence.io
GenbankReaderHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
GenbankSequenceParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
genbankSplitPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser: Decodes a split pattern.
GenbankWriter<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
GenbankWriter(OutputStream, Collection<S>, GenbankHeaderFormatInterface<S, C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriter: Use default line length of 60
GenbankWriter(OutputStream, Collection<S>, GenbankHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriter: Set custom lineLength
GenbankWriterHelper - Class in org.biojava.nbio.core.sequence.io: The class that should be used to write out genbank file of a sequence collection
GenbankWriterHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
GeneChromosomePosition - Class in org.biojava.nbio.genome.parsers.genename
GeneChromosomePosition() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
GeneChromosomePositionParser - Class in org.biojava.nbio.genome.parsers.genename: A parser that parses a file from the UCSC genome browser that contains mapping of gene name to chromosome positions
GeneChromosomePositionParser() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
GeneFeatureHelper - Class in org.biojava.nbio.genome
GeneFeatureHelper() - Constructor for class org.biojava.nbio.genome.GeneFeatureHelper
GeneIDGFF2Reader - Class in org.biojava.nbio.genome.parsers.gff: http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneIDGFF2Reader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
GeneIDXMLReader - Class in org.biojava.nbio.genome.parsers.geneid
GeneIDXMLReader(String) - Constructor for class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
GeneMarkGTFReader - Class in org.biojava.nbio.genome.parsers.gff: http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneMarkGTFReader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
GeneName - Class in org.biojava.nbio.genome.parsers.genename: A simple bean that contains gene name information as available from www.genenames.org
GeneName() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneName
GeneNamesParser - Class in org.biojava.nbio.genome.parsers.genename: Parses a file from the www.genenames.org website that contains a mapping of human gene names to other databases
GeneNamesParser() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: Returns what the value of a compound is in the backing bit storage i.e.
generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker: Returns a Map which encodes the contents of CompoundSet.
generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker: Returns a Map which encodes TCAG into positions 0,1,2,3.
generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: Should return the inverse information that BitSequenceReader.BitArrayWorker.generateCompoundsToIndex() returns i.e.
generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker: Returns a List which reverse encodes the Compound, Integer map
generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker: Returns a List which encodes TCAG into positions 0,1,2,3.
GenericFastaHeaderFormat<S extends AbstractSequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io: We store the original header if the sequence is parsed from a fasta file and will use that exact sequence if we write out the sequences to a fasta file.
GenericFastaHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat
GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io: The default fasta header parser where some headers are well defined based on the source database which allows us to set the source of the protein sequence and the identifier that can be used in future implementations to load features from external sources If the user has a custom header with local data then they can create their own implementation of a FastaHeaderParserInterface
GenericFastaHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser
GenericGenbankHeaderFormat<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
GenericGenbankHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
GenericGenbankHeaderFormat(String) - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
GenericGenbankHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
GenericInsdcHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat
GeneSequence - Class in org.biojava.nbio.core.sequence
GeneSequence(ChromosomeSequence, int, int, Strand) - Constructor for class org.biojava.nbio.core.sequence.GeneSequence: A class that keeps track of the details of a GeneSequence which is difficult to properly model.
get(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence: Returns the window specified at the given index in offsets i.e.
get(Object) - Method in class org.biojava.nbio.core.util.SoftHashMap
get(Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap
get(Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
get(Object) - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
get(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Gets the interface corresponding to given id.
get(K) - Method in class org.biojava.nbio.structure.domain.SerializableCache
get(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
get(int, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Get a single element.
get(int, int) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix: access a value at i,j
get(int) - Method in class org.biojava.nbio.structure.math.SparseVector: get a value
get(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Return the value paired with given key; null if key is not in table.
get(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
get(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
get1LetterCode(String) - Static method in class org.biojava.nbio.structure.StructureTools: Convert a three letter amino acid or nucleotide code into a single character code.
get1LetterCodeAmino(String) - Static method in class org.biojava.nbio.structure.StructureTools: Convert three character amino acid codes into single character e.g.
GET_ASSEMBLY - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
GET_ASSEMBLY_GENS - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
GET_STRUCT_OPER - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getA() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
getA() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getAAComposition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the composition of the 20 standard amino acid in the sequence.
getAAComposition(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAAComposition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getAACompositionChar(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAACompositionString(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAAIndexProvider() - Static method in class org.biojava.nbio.core.alignment.matrices.AAindexFactory
getAboutMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getAbsoluteMinimumSequenceLength() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getAbsolutePercentialRNAsuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
getAbsolutePercentileClashscore() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the absolutePercentileClashscore property.
getAbsolutePercentileDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry
getAbsolutePercentilePercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the absolutePercentilePercentRamaOutliers property.
getAbsolutePercentilePercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the absolutePercentilePercentRotaOutliers property.
getAbsolutePercentilePercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the absolutePercentilePercentRSRZOutliers property.
getAbsorbance(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the absorbance (optical density) of sequence.
getAbsorbance(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to returns the absorbance (optical density) of sequence.
getAbsorbance(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getAbsorpt_coefficient_mu() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getAbsorpt_correction_T_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getAbsorpt_correction_T_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getAbsorpt_correction_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getAbsorpt_process_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getAcc() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getAccept1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getAccept2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getAcceptedAtomNames() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: By default the parser will read in all atoms (unless using the CAonly switch).
getAccession() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getAccession() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getAccession() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getAccession() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
getAccession() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
getAccession() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
getAccession() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
getAccession() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
getAccession() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Unsupoorted
getAccession() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getAccession() - Method in interface org.biojava.nbio.core.sequence.template.Accessioned: Returns the AccessionID this location is currently bound with
getAccession() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getAccessionNr() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getAccessionNumber() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getAccessions() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: Pull uniprot accessions associated with this sequence
getAccessions() - Method in class org.biojava.nbio.structure.io.FastaStructureParser: Gets the protein accessions mapped from the Fasta file.
getAccessions() - Method in class org.biojava.nbio.structure.rcsb.RCSBMacromolecule
getAcentricOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the acentricOutliers property.
getAdapter() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
getAddress() - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
getAdjustedMinimumSequenceLength() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
getAfpAftIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpBefIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpChain() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
getAFPChain() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
getAfpChain() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
getAFPChainFromServer(String, String, String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
getAFPChainFromServer(String, String, String, String, Atom[], Atom[], int) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
getAfpChainLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpChainList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpChainTwiBin() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpChainTwiList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpChainTwiNum() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getAfpDisCut0() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getAfpIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAfpSet() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Get the set of AFPs for this alignment.
getAlgebraicFromMatrix(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
getAlgorithm() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
getAlgorithm() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
getAlgorithm() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getAlgorithm() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
getAlgorithm(String) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeCPMain
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeMain
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner: Get the name of this Algorithm.
getAlgorithmName() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.StructureAlignment: Get the name of the Algorithm
getAliases() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: Pull uniprot protein aliases associated with this sequence
getAligMap() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
getAligMat() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getAligMat(int, int) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getAligMat() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getAlign(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay: Extract the alignment output
getAlign(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay: Sets the following properties: The alignment strings alnseq1, alnseq2, and alnsymb alnbeg1 and 2 alnLength and gapLen
getAlign_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getAlign_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getAlign_se1() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getAlign_se1() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getAlign_se2() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getAlign_se2() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getAlignedAtoms1(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
getAlignedAtoms2(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
getAlignedCalphaAtoms() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getAlignedResIndex(Group, Chain) - Method in class org.biojava.nbio.structure.Compound: Given a Group g of Chain c (member of this Compound) return the corresponding position in the alignment of all member sequences (1-based numbering), i.e.
getAlignedSequence(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getAlignedSequence(S) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getAlignedSequence(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns AlignedSequence at given index.
getAlignedSequence(S) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Searches for the given Sequence within this alignment profile.
getAlignedSequence(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment: Uses bioIndex starting at 1 instead of 0
getAlignedSequence(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile: Returns Sequence at given index.
getAlignedSequences() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getAlignedSequences(int...) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getAlignedSequences(S...) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getAlignedSequences() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a List containing the individual AlignedSequences of this alignment.
getAlignedSequences(int...) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a List containing some of the individual AlignedSequences of this alignment.
getAlignedSequences(S...) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a List containing some of the individual AlignedSequences of this alignment.
getAlignedSequences() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment: Get the list of sequences
getAlignedSequences() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile: Returns a List containing the individual Sequences of this alignment.
getAlignedStructure(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
getAlignedStructure(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP: Get an artifical Structure containing both chains.
getAlignedStructure(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay: Get an artifical Structure containing a different model for every input structure, so that the alignment result can be viewed in Jmol.
getAlignedStructure(Structure, Structure) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: create an artifical Structure object that contains the two structures superimposed onto each other.
getAlignedUserCollection(String) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Takes a protein sequence string with capital and lowercase letters and sets its user collection to record which letters are uppercase (aligned) and which are lowercase (unaligned).
getAlignment() - Method in class org.biojava.nbio.core.search.io.Hsp
getAlignment() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
getAlignment1() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getAlignment2() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getAlignmentAtoms(Structure) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Returns the atoms that are being used for the alignment.
getAlignmentFractionThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getAlignmentFromFasta() - Static method in class demo.DemoAlignmentFromFasta
getAlignmentIndexAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getAlignmentIndexAt(int) - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the column index within an alignment corresponding to the given index in the original Sequence.
getAlignmentLengthFraction() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
getAlignmentMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getAlignmentNumber() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
getAlignmentOption(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: This method forwards to NCBIQBlastAlignmentProperties.getAlignmentOption(BlastAlignmentParameterEnum).
getAlignmentOption(BlastAlignmentParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Gets the value of specified parameter or null if it is not set.
getAlignmentOption(String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties: Method that returns the value associated with the key given in parameter.
getAlignmentOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Gets parameters, which are currently set
getAlignmentOptions() - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties: Method to get all keys to the information stored in this object.
getAlignmentOutputFormat() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
getAlignmentPairsFromServer() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable: talk to centralized server and fetch all alignments to run.
getAlignmentPanelMenu(JFrame, ActionListener, AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator: Create the menu for the Alignment Panel representation of Structural Alignments.
getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Extracts the actual Blast report for given request id according to options provided in outputProperties argument.
getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService: Getting the actual alignment results from this instantiated service for a given ID with specific formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object.
getAlignments() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getAlignments() - Method in class org.biojava.nbio.structure.align.StructurePairAligner: return the alternative alignments that can be found for the two structures
getAlignmentString() - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
getAlignmentTextMenu(JFrame, ActionListener, AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator: Create the menu for the Text representations of Structural Alignments.
getAlignPairs() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters: The file that contains a list of PDB pairs to be aligned
getAlignPos(int[][]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper: record the aligned pairs in alignList[][0], alignList[][1]; return the number of aligned pairs
getAlignRes() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Returns the double List containing the aligned residues for each structure.
getAlignRes() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getAlignResCounts() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Returns the number of non null positions (residues) of each structure in the alignment Block.
getAlignResCounts() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getAlignResCounts() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Returns the number of non null positions (residues) of each structure in the alignment Block Set.
getAlignResCounts() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
getAlignResCounts() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the number of non null positions (residues) of each structure in the alignment.
getAlignResCounts() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getAlignScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlignScoreUpdate() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAligSeq(Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: returns the AligSeq (0 or 1) for a point returns -1 if not over an alig seq.
getAligSeq(Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Returns the index of the structure, for a given point in the Panel.
getAliLenth() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getAll() - Static method in class org.biojava.nbio.structure.rcsb.GetRepresentatives: Returns the current list of all PDB IDs.
getAllAlgorithmNames() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
getAllAlgorithms() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
getAllAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Convert all atoms of the structure (first model) into an Atom array
getAllAtomArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Returns and array of all atoms of the chain (first model), including Hydrogens (if present) and all HETATOMs.
getAllColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet: Get the list of column names including those that may be hidden
getAllCompounds() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
getAllCompounds() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
getAllCompounds() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
getAllCompounds() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
getAllCompounds() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
getAllCytobands(URL) - Method in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
getAllCytobands(InputStream) - Method in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
getAllDomains() - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase: Get all ECOD domains
getAllDomains() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Get all ECOD domains
getAllFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame: Delegates to Frame.values()
getAllNonHAtomArray(Structure, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Returns and array of all non-Hydrogen atoms in the given Structure, optionally including HET atoms or not.
getAllNonHAtomArray(Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Returns and array of all non-Hydrogen atoms in the given Chain, optionally including HET atoms or not Waters are not included.
getAllowsChildren() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getAllOxidationStates() - Method in enum org.biojava.nbio.structure.Element: Returns a list of all oxidation states the element is found in.
getAllPairsAlignments(List<S>, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method which computes a sequence alignment for all Sequence pairs in the given List.
getAllPairsScorers(List<S>, Alignments.PairwiseSequenceScorerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method which sets up a sequence pair scorer for all Sequence pairs in the given List.
getAllPairsScores(List<S>, Alignments.PairwiseSequenceScorerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method which computes a sequence pair score for all Sequence pairs in the given List.
getAllPairsScores() - Method in class org.biojava.nbio.alignment.GuideTree: Returns a sequence pair score for all Sequence pairs in the given List.
getAllPDBIDs() - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider: Returns a list of all PDB IDs that are available in this installation
getAllRows() - Method in class org.biojava.nbio.survival.data.WorkSheet: Get all rows including those that may be hidden
getAllSpaceGroups() - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser
getAllViruses() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: Get the PDB IDs of all virus structures in the current PDB
getAlnbeg1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlnbeg2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlnLength() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlnseq1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlnseq2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlnSequences() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
getAlnsymb() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getAlpha() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
getAlpha() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getAlt_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getAltAligNumber() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: returns the sequential number of this alternative alignment
getAltcode() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the altcode property.
getAlternativeAligs() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
getAlternativeAligs() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
getAltLoc() - Method in interface org.biojava.nbio.structure.Atom: Get alternate Location.
getAltLoc() - Method in class org.biojava.nbio.structure.AtomImpl: Get alternate Location.
getAltLoc1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getAltLoc2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getAltLocGroup(Character) - Method in interface org.biojava.nbio.structure.Group: Gets the alternate location group to this group that has the alt-loc character code passed.
getAltLocGroup(Character) - Method in class org.biojava.nbio.structure.HetatomImpl
getAltLocs() - Method in interface org.biojava.nbio.structure.Group: Get the list of alternate locations.
getAltLocs() - Method in class org.biojava.nbio.structure.HetatomImpl
getAltShortSymbol() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets the alternative international short name (as sometimes used in PDB), e.g.
getAmbiguity(NucleotideCompound...) - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet: Calculates the best symbol for a collection of compounds.
getAminoacid() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
getAminoAcid() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
getAminoAcid(String) - Static method in class org.biojava.nbio.structure.StandardAminoAcid: get a standard amino acid.
getAminoAcidCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
getAminoAcidCompoundSet() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
getAminoAcidCompoundSet() - Static method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
getAminoAcidCompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
getAminoAcids(Chain) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil: Get all amino acids in a chain.
getAminoAcidSubstitutionMatrix(String) - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns a substitution matrix for amino acids given by the name name.
getAminoOneLetter(String) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
getAminoThreeLetter(Character) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
getAminoType() - Method in interface org.biojava.nbio.structure.AminoAcid: Returns the name of the AA, in single letter code.
getAminoType() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Returns the name of the AA, in single letter code.
getAnchors() - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Returns the list of anchors.
getAngle() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: The rotation angle
getAngle(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis: Calculate the rotation angle for a structure
getAngle(Matrix) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis: Calculate the rotation angle for a given matrix
getAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Helix: Returns the pitch angle of the helix
getAngle(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Returns the magnitude of the angle between the first and second blocks of afpChain, measured in degrees.
getAngle_alpha() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getAngle_alpha_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getAngle_beta() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getAngle_beta_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getAngle_gamma() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getAngle_gamma_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getAngleDiff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the angleOutlier property.
getAngleThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getAniso_B() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getAnnotation() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
getAnnotation() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
getAnnotation() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
getAnnotation() - Method in class org.biojava.nbio.ontology.Term.Impl
getAnnotation() - Method in class org.biojava.nbio.ontology.Triple.Impl
getAnnotation() - Method in interface org.biojava.nbio.ontology.utils.Annotatable: Should return the associated annotation object.
getAnnotationType() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getApliphaticIndex(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the apliphatic index of sequence.
getApliphaticIndex(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the apliphatic index of sequence.
getApliphaticIndex(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getApprovedName() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getApprovedSymbol() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getArchitectureId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getArchitectureName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getArray() - Method in class org.biojava.nbio.structure.jama.Matrix: Access the internal two-dimensional array.
getArrayCopy() - Method in class org.biojava.nbio.structure.jama.Matrix: Copy the internal two-dimensional array.
getAsaC() - Method in class org.biojava.nbio.structure.asa.GroupAsa: Returns the ASA of the residue in the complexed state
getAsaU() - Method in class org.biojava.nbio.structure.asa.GroupAsa: Returns the ASA of the residue in the uncomplexed state
getAsList() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getAsList() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getAsList() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getAsList() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
getAsList() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
getAsList() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader: Returns this Sequence store as a List
getAsList() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
getAsList() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Delegates to SequenceMixin.toList(org.biojava.nbio.core.sequence.template.Sequence)
getAsList() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getAsList() - Method in interface org.biojava.nbio.core.sequence.template.Sequence: Returns the Sequence as a List of compounds
getAsList() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getAssembly_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
getAssemblyId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getAssignment() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
getAssignments() - Method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer
getAsym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getAsym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getAsym_id_list() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
getAsymmetryParameter(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getAsymUnit(String) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider: load the asym unit, but set the info how to re-create the bio unit in the PdbHeader object
getAsymUnit(String) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
getAsymUnit() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider: get the asym unit for this PDB ID
getAsymUnit(String) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
getAsymUnit(String) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
getAtcc() - Method in class org.biojava.nbio.structure.Compound
getAtom(String) - Method in interface org.biojava.nbio.structure.Group: Get an atom given its PDB name.
getAtom(int) - Method in interface org.biojava.nbio.structure.Group: Get at atom by position.
getAtom(String) - Method in class org.biojava.nbio.structure.HetatomImpl: Get an atom given its PDB name.
getAtom(int) - Method in class org.biojava.nbio.structure.HetatomImpl: Get at atom by position.
getAtom() - Method in class org.biojava.nbio.structure.validation.Clash: Gets the value of the atom property.
getAtom() - Method in class org.biojava.nbio.structure.validation.SymmClash: Gets the value of the atom property.
getAtom0() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the atom0 property.
getAtom0() - Method in class org.biojava.nbio.structure.validation.BondOutlier: Gets the value of the atom0 property.
getAtom1() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
getAtom1() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the atom1 property.
getAtom1() - Method in class org.biojava.nbio.structure.validation.BondOutlier: Gets the value of the atom1 property.
getAtom2() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
getAtom2() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the atom2 property.
getAtom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getAtom_id_1() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getAtom_id_2() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getAtomA() - Method in interface org.biojava.nbio.structure.Bond: Gets atom 'A' of this bond.
getAtomA() - Method in class org.biojava.nbio.structure.BondImpl: Gets atom 'A' of this bond.
getAtomArray(Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
getAtomArray(Atom[], List<Group>) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP: Returns the first atom for each group
getAtomArray(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools: Returns an array of the requested Atoms from the Structure object.
getAtomArray(Chain, String[]) - Static method in class org.biojava.nbio.structure.StructureTools: Returns an array of the requested Atoms from the Chain object.
getAtomArrayAllModels(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools: Returns an array of the requested Atoms from the Structure object.
getAtomArrays() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
getAtomArrays() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the array of Atoms for each structure from its parent Ensemble.
getAtomArrays() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Get an array of representative atoms for each structure (CA atoms for proteins).
getAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getAtomAsaCs() - Method in class org.biojava.nbio.structure.asa.GroupAsa
getAtomAsaUs() - Method in class org.biojava.nbio.structure.asa.GroupAsa
getAtomB() - Method in interface org.biojava.nbio.structure.Bond: Gets atom 'B' of this bond.
getAtomB() - Method in class org.biojava.nbio.structure.BondImpl: Gets atom 'B' of this bond.
getAtomCAArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Returns an Atom array of the C-alpha atoms.
getAtomCAArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Return an Atom array of the C-alpha atoms.
getAtomCache() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getAtomCache() - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider
getAtomCache() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
getAtomCache() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getAtomCache() - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
getAtomCache() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
getAtomCaThreshold() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
getAtomContacts() - Method in class org.biojava.nbio.structure.contact.GroupContact
getAtomCoordinateBounds(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
getAtomDistance(Atom, Atom) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
getAtomForAligPos(AFPChain, int, int, Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP: return the atom at alignment position aligPos.
getAtomForSequencePosition(MultipleAlignment, List<Integer>, int, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Returns the Atom of the specified structure that is aligned in the sequence alignment position specified.
getAtomGroup(int) - Method in interface org.biojava.nbio.structure.Chain: Return the Group at given position, from within Groups with observed density in the chain, i.e.
getAtomGroup(int) - Method in class org.biojava.nbio.structure.ChainImpl: Return the Group at given position, from within Groups with observed density in the chain, i.e.
getAtomGroups() - Method in interface org.biojava.nbio.structure.Chain: Return all Groups with observed density in the chain, i.e.
getAtomGroups(GroupType) - Method in interface org.biojava.nbio.structure.Chain: Return a List of all (observed) Groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
getAtomGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl: Return a List of all (observed) Groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
getAtomGroups() - Method in class org.biojava.nbio.structure.ChainImpl: Return all Groups with observed density in the chain, i.e.
getAtomicMass() - Method in enum org.biojava.nbio.structure.Element: Returns the atomic mass for this Element.
getAtomicNumber() - Method in enum org.biojava.nbio.structure.Element: Returns the atomic number of this Element.
getAtomLength() - Method in interface org.biojava.nbio.structure.Chain: Returns the number of Groups with observed density in the chain, i.e.
getAtomLength() - Method in class org.biojava.nbio.structure.ChainImpl: Returns the number of Groups with observed density in the chain, i.e.
getAtomLigands() - Method in interface org.biojava.nbio.structure.Chain: Gets all groups that are not polymer groups and that are not solvent groups.
getAtomLigands() - Method in class org.biojava.nbio.structure.ChainImpl: Gets all groups that are not polymer groups and that are not solvent groups.
getAtomLinkages() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
getAtomLinkages() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
getAtomName() - Method in class org.biojava.nbio.protmod.structure.StructureAtom
getAtomName() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
getAtomNames(Group) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
getAtoms(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the CA atoms for the provided name.
getAtoms(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache
getAtoms() - Method in interface org.biojava.nbio.structure.Group: Get list of atoms.
getAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl: Get list of atoms.
getAtoms() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getAtoms() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getAtoms() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the atoms property.
getAtoms() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the atoms property.
getAtomsCAInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools: Returns the set of intra-chain contacts for the given chain for C-alpha atoms (including non-standard aminoacids appearing as HETATM groups), i.e.
getAtomSequence() - Method in interface org.biojava.nbio.structure.Chain: Returns the sequence of amino acids as it has been provided in the ATOM records.
getAtomSequence() - Method in class org.biojava.nbio.structure.ChainImpl: Returns the sequence of amino acids as it has been provided in the ATOM records.
getAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
getAtomsInContact(Chain, String[], double) - Static method in class org.biojava.nbio.structure.StructureTools: Returns the set of intra-chain contacts for the given chain for given atom names, i.e.
getAtomsInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools: Returns the set of intra-chain contacts for the given chain for all non-H atoms of non-hetatoms, i.e.
getAtomsInContact(Chain, Chain, String[], double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Returns the set of inter-chain contacts between the two given chains for the given atom names.
getAtomsInContact(Chain, Chain, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Returns the set of inter-chain contacts between the two given chains for all non-H atoms.
getAtomSiteHeader() - Static method in class org.biojava.nbio.structure.io.FileConvert
getAttemptedValidationSteps() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the attemptedValidationSteps property.
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor: Return the attribute of the grouping
getAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get value of specified attribute key.
getAttribute(String) - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Get the attribute value for this key.
getAttributeOld(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
getAttributes() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
getAttributes() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
getAuBoundingBox(int) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox: Get the AU BoundingBox for the given cell index (cellIdx=0 would be original AU) The AU BoundingBox is the BoundingBox that bounds all chains belonging to the AU
getAuth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getAuth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getAuth_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getAuth_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getAuth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getAuth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getAuth_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getAuth_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getAuth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getAuth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getAuth_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getAuth_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getAuthorList() - Method in class org.biojava.nbio.structure.JournalArticle: Get the list of Authors of the JournalArticle
getAuthors() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getAuthors() - Method in class org.biojava.nbio.structure.PDBHeader: Return the names of the authors as listed in the AUTHORS section of a PDB file.
getAutoFetch() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration: Deprecated.
Use UserConfiguration.getFetchBehavior()
getAutoSuggestProvider() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
getAverageResidueDistances(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.
getAverageResidueDistances(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.
getAverageScore() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster: Returns the average similarity score between all pairs of members in the cluster
getAverageTraceRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Deprecated.
use QuatSymmetryResults.getScores() instead.
getAverageTraceTmScoreMin() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Deprecated.
use QuatSymmetryResults.getScores() instead.
getAvgHydropathy(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the average hydropathy value of sequence.
getAvgHydropathy(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the average hydropathy value of sequence.
getAvgHydropathy(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getAvgoccu() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the avgoccu property.
getAvgTMScore(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the average TMScore of all the possible pairwise structure comparisons of the given alignment.
getAvgTMScore(List<Atom[]>, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the average TMScore all the possible pairwise structure comparisons of the given a set of superimposed Atoms and the original structure lengths.
getAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getAxisAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Helix: Returns the AxisAngle of the helix transformation
getAxisAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getAxisAngle(int, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
getAxisAngle(int, AxisAngle4f) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
getAxisAngle(int, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
getAxisAngle4d() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Returns the rotation axis and angle in a single javax.vecmath.AxisAngle4d object
getAxisFoldType(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Given a transformId returns the type of axis of rotation: 1 (no rotation), 2, 3, 4 or 6 -fold and for improper rotations: -1, -2, -3, -4 and -6
getAxisTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getAxisTypes() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getB() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
getB() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getB_iso_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getB_iso_mean() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getB_iso_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getB_iso_or_equiv() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getB_iso_or_equiv_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getBackboneAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Return an Atom array of the main chain atoms: CA, C, N, O Any group that contains those atoms will be included, be it a standard aminoacid or not
getBackingSequence() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence: Access the sequence which backs this window
getBadRmsd() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getBase() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
getBaseIdentifier() - Method in class org.biojava.nbio.structure.align.client.StructureName: StructureName wraps another StructureIdentifier.
getBegin() - Method in class org.biojava.nbio.genome.parsers.gff.Location
getBeta() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
getBeta() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getBinaryOperators() - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver: Returns a list of operators for this assembly.
getBioAssemblies() - Method in class org.biojava.nbio.structure.PDBHeader: Return the map of biological assemblies.
getBioBegin() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getBioEnd() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getBioEnd() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getBioEnd() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView: 1-indexed, inclusive.
getBiol_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getBiolAssembly(String, int) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
getBiologicalAssembly(String, int, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Loads the biological assembly for a given PDB ID and bioAssemblyId.
getBiologicalAssembly(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Loads the default biological unit (e.g.
getBiologicalAssembly(String, int) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Loads the default biological unit (e.g.
getBiologicalAssembly(String) - Static method in class org.biojava.nbio.structure.StructureIO: Returns the first biologicalAssembly that is available for a protein structure.
getBiologicalAssembly(String, int) - Static method in class org.biojava.nbio.structure.StructureIO: By default the getStructure method loads asym units.
getBiologicalAssembly(String, int, AtomCache) - Static method in class org.biojava.nbio.structure.StructureIO
getBiologicalAssembly(String, int, AtomCache, BioUnitDataProvider) - Static method in class org.biojava.nbio.structure.StructureIO
getBiologicalMoleculeBounds(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
getBiologicalMoleculeCentroid(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools: Returns the centroid of the biological molecule.
getBiologicalMoleculeMaximumExtend(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools: Returns the maximum extend of the biological molecule in the x, y, or z direction.
getBiologicalUnit(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
Renamed to AtomCache.getBiologicalAssembly(String) in 4.2
getBiologicalUnit() - Method in class org.biojava.nbio.structure.Compound
getBioSequences() - Method in class org.biojava.nbio.alignment.io.StockholmStructure: used to retrieve sequences from the structure
getBioSequences(boolean, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure: This function tolerates mixed case letters, and allows for forcing the output biosequence type (PFAM/RFAM).
getBioSequences(boolean) - Method in class org.biojava.nbio.alignment.io.StockholmStructure: Because some database files have incorrectly small letters (e.g.
getBioStart() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getBioStart() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView: 1-indexed, inclusive.
getBioUnitDataProvider() - Static method in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
getBioUnitDataProviderClass() - Static method in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory: Get the class of providers to be instantiated.
getBioUnitTransformationList(PdbxStructAssembly, List<PdbxStructAssemblyGen>, List<PdbxStructOperList>) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder: Returns a list of transformation matrices for the generation of a macromolecular assembly for the specified assembly Id.
getBioUnitTransformationList(String, int) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider: get the data for a particular assembly, counting starts at 1...
getBioUnitTransformationList(String, int) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
getBioUnitTransformationList(String, int) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
getBioUnitTransformationList(String, int) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
getBJSequence() - Method in interface org.biojava.nbio.structure.Chain: Converts the SEQRES groups of a Chain to a Biojava Sequence object.
getBJSequence() - Method in class org.biojava.nbio.structure.ChainImpl: Converts the SEQRES groups of a Chain to a Biojava Sequence object.
getBlastAdvancedOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
getBlastDatabase() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
getBlastExpect() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
getBlastFromPosition() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
getBlastGapCosts() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Returns the actual string for the GAPCOSTS parameter which is used to build the URL
getBlastGapCreation() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Returns the value for the GAP_CREATION parameter (first half of GAPCOSTS parameter)
getBlastGapExtension() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Returns the value for the gap extension parameter (second half of GAPCOSTS parameter)
getBlastMatrix() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Returns the value of the specified substitution matrix
getBlastProgram() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
getBlastToPosition() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
getBlastWordSize() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Returns the value of the WORD_SIZE parameter used for this blast run
getBlock(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the Block with the specified index of the MultipleAlignment.
getBlock(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getBlock2Afp() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockForSequencePosition(MultipleAlignment, List<Integer>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Returns the block number of a specified position in the sequence alignment, given the mapping from structure to function.
getBlockGap() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockNrForAlignPos(AFPChain, int) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP: Deprecated.
use AFPAlignmentDisplay.getBlockNrForAlignPos instead...
getBlockNrForAlignPos(AFPChain, int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay: get the block number for an aligned position
getBlockNum() - Method in class org.biojava.nbio.structure.align.model.AFPChain: The number of blocks in the alignment
getBlockNumClu() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockNumIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockNumSpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockResList() - Method in class org.biojava.nbio.structure.align.model.AFPChain: tracks the residues of the initial blocks (before optimization)
getBlockResSize() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockRotationMatrix() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlocks() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Returns the List of alignment Blocks of the BlockSet.
getBlocks() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
getBlocks() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Convenience method to get a List of all Blocks from all BlockSets.
getBlocks() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getBlockScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockSequenceAlignment(MultipleAlignment, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
getBlockSequenceAlignment(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
getBlockSet() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Returns the parent BlockSet of the Block.
getBlockSet() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getBlockSet(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the BlockSet with the specified index of the MultipleAlignment.
getBlockSet(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getBlockSets() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the BlockSet List of the multiple structure alignment.
getBlockSets() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getBlockShiftVector() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlockSize() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getBlosum100() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 100 matrix by Henikoff & Henikoff
getBlosum30() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 30 matrix by Henikoff & Henikoff
getBlosum35() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 35 matrix by Henikoff & Henikoff
getBlosum40() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 40 matrix by Henikoff & Henikoff
getBlosum45() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 45 matrix by Henikoff & Henikoff
getBlosum50() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 50 matrix by Henikoff & Henikoff
getBlosum55() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 55 matrix by Henikoff & Henikoff
getBlosum60() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 60 matrix by Henikoff & Henikoff
getBlosum62() - Static method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getBlosum62() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 62 matrix by Henikoff & Henikoff
getBlosum65() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 65 matrix by Henikoff & Henikoff
getBlosum70() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 70 matrix by Henikoff & Henikoff
getBlosum75() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 75 matrix by Henikoff & Henikoff
getBlosum80() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 80 matrix by Henikoff & Henikoff
getBlosum85() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 85 matrix by Henikoff & Henikoff
getBlosum90() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 90 matrix by Henikoff & Henikoff
getBondOrder() - Method in interface org.biojava.nbio.structure.Bond: Gets the bond order of this bond.
getBondOrder() - Method in class org.biojava.nbio.structure.BondImpl: Gets the bond order of this bond.
getBondOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the bondOutlier property.
getBonds() - Method in interface org.biojava.nbio.structure.Atom: Get all Bonds this atom is part of.
getBonds() - Method in class org.biojava.nbio.structure.AtomImpl: Get all Bonds this atom is part of.
getBonds() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getBottom() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getBravLattice() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getBridge1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getBridge2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getBsa() - Method in class org.biojava.nbio.structure.asa.GroupAsa: Returns the BSA value for this group, i.e.
getBsaToAsaRatio() - Method in class org.biojava.nbio.structure.asa.GroupAsa: Returns the bsa/asa(uncomplexed) ratio, i.e.
getBtype() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getBufferedReader() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource: Returns the reader representation of this classpath resource
getBuildMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getBulkSolventB() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the bulkSolventB property.
getBulkSolventK() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the bulkSolventK property.
getByCategory(ModificationCategory) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
getByCategory(CathCategory) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return list of CATH descriptions for node representatives at a CATH category (e.g.
getByCategory(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getByCategory(ScopCategory) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Get all records of a particular classification.
getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getByChainId(String, String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
getByComponent(Component, Component...) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry: Get ProteinModifications that involves one or more components.
getById(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
getByKeyword(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
getByLabel(String) - Static method in enum org.biojava.nbio.protmod.ModificationCategory
getByLabel(String) - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType
getByLargestContacts() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
getByLargestContactsNotLowestAngle() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
getByLowestAngle() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
getByName(String) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique: Returns the ExpTechnique given an experimental technique name as used in the PDB, e.g.
getByName(String) - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice
getByOccurrenceType(ModificationOccurrenceType) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
getByPdbccId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
getByPsimodId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
getByResidId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
getBytesRead() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead: Keep track of bytesread via ReadLine to account for CR-LF in the stream.
getByUniProtId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
getC() - Method in interface org.biojava.nbio.structure.AminoAcid: Get C atom.
getC() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Get C atom.
getC() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
getC() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getC2Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getC3Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getC4Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getCA() - Method in interface org.biojava.nbio.structure.AminoAcid: Get CA atom.
getCA() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Get CA atom.
getCa1() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
getCa1() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
getCa1() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
getCa1Length() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getCa2() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
getCa2() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
getCa2Length() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getCache() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
getCache() - Static method in class org.biojava.nbio.structure.align.util.CacheFactory
getCacheFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getCacheFilePath() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getCacheFilePath() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
getCacheLocation() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getCacheLocation() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Get the location of the cache directory (usually set to the PDB_CACHE_DIR property).
getCacheLocation() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getCachePath() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the path that contains the caching file for utility data, such as domain definitions.
getCalculationTime() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getCalculationTime() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the running time of the structure alignment calculation, in milliseconds.
getCalculationTime() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getCalculationTime() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getCalphaAtoms() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getCalphaCoordinates() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getCalphaCount() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getCalphaTraces() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getCalphaTraces() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
getCAOnly(List<Chain>) - Static method in class org.biojava.nbio.structure.io.CAConverter: Deprecated.
Use the more generic CAConverter.getRepresentativeAtomsOnly(List) instead
getCAOnly(Chain) - Static method in class org.biojava.nbio.structure.io.CAConverter: Deprecated.
Use the more generic CAConverter.getRepresentativeAtomsOnly(Chain) instead
getCartn_x() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getCartn_x_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getCartn_y() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getCartn_y_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getCartn_z() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getCartn_z_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getCategories() - Method in class demo.DemoSCOP: Get various categories
getCategory() - Method in class org.biojava.nbio.ontology.Synonym
getCategory() - Method in interface org.biojava.nbio.protmod.ProteinModification
getCategory() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getCategory() - Method in class org.biojava.nbio.structure.cath.CathNode
getCategory() - Method in class org.biojava.nbio.structure.scop.ScopDescription
getCATH() - Method in class org.biojava.nbio.structure.cath.CathDomain
getCathDatabase() - Static method in class org.biojava.nbio.structure.cath.CathFactory: Returns the default (singleton) CathDatabase.
getCathDatabase(String) - Static method in class org.biojava.nbio.structure.cath.CathFactory: Returns a CATH database of the specified version.
getCathDownloadUrl() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getCathNode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return the CathNode for a node ID.
getCathNode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getCathVersion() - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return the CATH release version.
getCathVersion() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getCB() - Method in interface org.biojava.nbio.structure.AminoAcid: Get CB atom.
getCB() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Get CB atom.
getCCP4Version() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the ccp4Version property.
getCdsEnd() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getCDSSequences() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence: Get the CDS sequences that have been added to the TranscriptSequences
getCdsStart() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getCECalculator() - Method in class org.biojava.nbio.structure.align.ce.CeMain
getCell() - Method in class org.biojava.nbio.structure.Compound
getCell(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Get cell value
getCell_setting() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
getCellColor() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
getCellColor() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
getCellDouble(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
getCellIndices(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Get the index of a unit cell to which the query point belongs.
getCellLine() - Method in class org.biojava.nbio.structure.Compound
getCellTranslation(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getCellTranslations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getCellularLocation() - Method in class org.biojava.nbio.structure.Compound
getCenter(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools: get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
getCenter1() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getCenter2() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getCenters() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getCenterVector(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Returns the Vector that needs to be applied to shift a set of atoms to the Centroid.
getCenterVector(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc: Returns the Vector that needs to be applied to shift a set of atoms to the Centroid, if the centroid is already known
getCentricOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the centricOutliers property.
getCentroid(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Returns the center of mass of the set of atoms.
getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getChain() - Method in interface org.biojava.nbio.structure.Group: Returns the parent Chain of the Group.
getChain() - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
getChain() - Method in class org.biojava.nbio.structure.HetatomImpl: Returns the parent Chain of the Group.
getChain(int) - Method in interface org.biojava.nbio.structure.Structure: Retrieve a chain by its position within the Structure .
getChain(int, int) - Method in interface org.biojava.nbio.structure.Structure: Retrieve a chain by its position within the Structure and model number.
getChain(int) - Method in class org.biojava.nbio.structure.StructureImpl: Retrieve a chain by its position within the Structure .
getChain(int, int) - Method in class org.biojava.nbio.structure.StructureImpl: Retrieve a chain by its position within the Structure and model number.
getChain() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the chain property.
getChain1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getChain1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
getChain2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getChainBoundingBox(int, int) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox: Get the chain BoundingBox for the given cell index (cellIdx=0 would be original AU) and chain index
getChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure: Request a chain by its PDB code by default takes only the first model
getChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure: Request a chain by its PDB code by default takes only the first model
getChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl: Request a chain by its PDB code by default takes only the first model
getChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl: Request a chain by its PDB code by default takes only the first model
getChainId() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
getChainId() - Method in class org.biojava.nbio.structure.align.client.StructureName: Gets the chain ID, for structures where it is unique and well-defined.
getChainId() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
getChainID() - Method in interface org.biojava.nbio.structure.Chain: Gets the name of this chain (Chain id in PDB file ).
getChainID() - Method in class org.biojava.nbio.structure.ChainImpl: Gets the name of this chain (Chain id in PDB file ).
getChainId() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
getChainId() - Method in class org.biojava.nbio.structure.DBRef: The chain ID of the corresponding chain.
getChainId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getChainId() - Method in interface org.biojava.nbio.structure.Group: Utility method for returning the chainId of the Group or null if no Chain has been set.
getChainId() - Method in class org.biojava.nbio.structure.HetatomImpl: Utility method for returning the chainId of the Group or null if no Chain has been set.
getChainId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getChainId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getChainId() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Returns the chain identifier this transformation should be applied to.
getChainId() - Method in class org.biojava.nbio.structure.ResidueNumber
getChainId() - Method in class org.biojava.nbio.structure.ResidueRange
getChainId() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getChainId1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getChainID1() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getChainID1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getChainId2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getChainID2() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getChainID2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getChainIds() - Method in class org.biojava.nbio.structure.Compound: Return the list of member chain IDs that are described by this Compound, only unique chain IDs are contained in the list.
getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getChainIds() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
getChainIdsInEntry(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
getChainLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getChainRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getChains() - Method in class org.biojava.nbio.structure.cath.CathDomain: Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
getChains() - Method in class org.biojava.nbio.structure.Compound: Get the list of chains that are part of this Compound.
getChains() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getChains() - Method in class org.biojava.nbio.structure.scop.ScopDomain: Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
getChains() - Method in interface org.biojava.nbio.structure.Structure: Retrieve all chains - if it is a NMR structure will return the chains of the first model.
getChains(int) - Method in interface org.biojava.nbio.structure.Structure: Retrieve all chains of a model.
getChains(int) - Method in class org.biojava.nbio.structure.StructureImpl: retrieve all chains of a model.
getChains() - Method in class org.biojava.nbio.structure.StructureImpl: Retrieve all chains - if it is a NMR structure will return the chains of the first model.
getCharge() - Method in interface org.biojava.nbio.structure.Atom: Get the charge of this atom
getCharge() - Method in class org.biojava.nbio.structure.AtomImpl
getCharge() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getChemComp() - Method in interface org.biojava.nbio.structure.Group: Get the chemical component that closer describes this group.
getChemComp() - Method in class org.biojava.nbio.structure.HetatomImpl
getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider: Returns a new instance of a chemical component definition.
getChemComp(String) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
getChemComp(String) - Method in interface org.biojava.nbio.structure.io.mmcif.ChemCompProvider: Returns a new instance of a chemical component definition.
getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider: Loads the definitions for this ChemComp from a local file and instantiates a new object.
getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider
getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider
getChemCompProvider() - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
getChild1() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getChild1() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the first child node of this node.
getChild2() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getChild2() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the second child node of this node.
getChildAt(int) - Method in class org.biojava.nbio.alignment.GuideTree.Node
getChildCount() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getChildren() - Method in class org.biojava.nbio.structure.scop.ScopNode
getChildrenFeatures() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature: Get the children features
getChildrenFeatures() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
getChildrenFeatures() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface: Get the features contained by this feature
getChiSquare() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getChrLoc() - Method in class org.biojava.nbio.phosphosite.Site
getChromosome() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
getChromosome() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getChromosome() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getChromosomeMappings() - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
getChromosomeMappings(InputStream) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
getChromosomeNumber() - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
getChromosomeSequenceFromDNASequence(LinkedHashMap<String, DNASequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
getCid() - Method in class org.biojava.nbio.structure.validation.Clash: Gets the value of the cid property.
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron: Returns the radius of a circumscribed sphere, that goes through all vertices
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron: Returns the radius of a circumscribed sphere, that goes through all vertices
getCirumscribedRadius() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism: Returns the radius of a circumscribed sphere, that goes through all vertices
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism: Returns the radius of a circumscribed sphere (length of diagonal of rectangular prism/2, that goes through at least four vertices
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron: Returns the radius of a circumscribed sphere, that goes through all vertices
getClaFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getClan() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getClash() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the clash property.
getClashmag() - Method in class org.biojava.nbio.structure.validation.Clash: Gets the value of the clashmag property.
getClashmag() - Method in class org.biojava.nbio.structure.validation.SymmClash: Gets the value of the clashmag property.
getClashscore() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the clashscore property.
getClassId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getClassId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getClassification() - Method in class org.biojava.nbio.structure.PDBHeader
getClassificationId(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathDomain
getClassificationId() - Method in class org.biojava.nbio.structure.scop.ScopDescription
getClassificationId(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopDescription: Return a portion of the classificationID corresponding to the specified category (class, fold, superfamily, family).
getClassificationId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getClaURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
getCloseMenuItem(JFrame) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getCluster() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: get the number of the cluster this alignment belongs to
getCluster() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getCluster() - Method in class org.biojava.nbio.structure.contact.StructureInterface
getCluster1() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
getCluster2() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
getClusters(double) - Method in class org.biojava.nbio.core.util.SingleLinkageClusterer: Get the clusters by cutting the dendrogram at given cutoff
getClusters() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculate the interface clusters for this StructureInterfaceList using a contact overlap score to measure the similarity of interfaces.
getClusters(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculate the interface clusters for this StructureInterfaceList using a contact overlap score to measure the similarity of interfaces.
getClusterValue() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getCode() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
getCodingSequence() - Method in class org.biojava.nbio.core.sequence.CDSSequence: A CDS sequence if negative stranded needs to be reverse complement to represent the actual coding sequence.
getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable: Returns the compound set of codons
getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava.nbio.core.sequence.transcription.Table
getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable: Returns a list of codons where the source and target compounds are the same as those given by the parameters.
getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava.nbio.core.sequence.transcription.Table
getCoeff() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getCoefficient(String) - Method in class org.biojava.nbio.survival.cox.CoxInfo
getCoefficientsList() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getCoefficientText(boolean, String, String, String, String) - Method in class org.biojava.nbio.survival.cox.CoxInfo
getCohortName() - Method in class org.biojava.nbio.survival.cox.CoxVariables
getCol() - Method in class org.biojava.nbio.structure.align.helper.IndexPair
getColor() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
getColor() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
getColor(double) - Method in interface org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper
getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform: Return the color corresponding to submapper.getColor(transform(value)).
getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
getColor(int) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
getColorPalette() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Return the color pattelete of the AlignmentJmol instance.
getCols() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getCols() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getCols() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getColumn(AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getColumn(C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getColumn(C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
getColumnDimension() - Method in class org.biojava.nbio.structure.jama.Matrix: Get column dimension.
getColumnIndex(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
getColumnLookup() - Method in class org.biojava.nbio.survival.data.WorkSheet
getColumnPackedCopy() - Method in class org.biojava.nbio.structure.jama.Matrix: Make a one-dimensional column packed copy of the internal array.
getColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet: Get the list of column names.
getComFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getComment() - Static method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getComment() - Method in class org.biojava.nbio.structure.cath.CathDomain
getComments(int) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getComments(int) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getComments(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Get comments about a SCOP domain by its sunid
getComments(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getCommentsFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getCommentsXML(List<String>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getCommon_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getCommonValence() - Method in enum org.biojava.nbio.structure.Element: Returns the common valence for this Element.
getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
getComparator(int) - Method in class org.biojava.nbio.structure.align.gui.MyTableRowSorter
getComplement() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
getComplement() - Method in class org.biojava.nbio.core.sequence.DNASequence: Returns a Sequence which will complement every base
getComplement() - Method in class org.biojava.nbio.core.sequence.RNASequence: Get the complement view of the RNA sequence
getComplement() - Method in interface org.biojava.nbio.core.sequence.template.ComplementCompound
getComplexSignature() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
getComplexStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
getComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
getComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
getComponents() - Method in interface org.biojava.nbio.protmod.ModificationCondition
getComponents() - Method in class org.biojava.nbio.protmod.ModificationConditionImpl: }
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties: Returns the composition of the specific grouping for the given attribute.
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getComposition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties: An adaptor method which returns the composition of the specific grouping for the given attribute.
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getComposition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getComposition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getComposition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getComposition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getComposition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getComposition(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: Does a linear scan over the given Sequence and records the number of times each base appears.
getCompositionId() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
getCompositionId(String) - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
getCompound() - Method in interface org.biojava.nbio.structure.Chain: Returns the Compound for this chain.
getCompound() - Method in class org.biojava.nbio.structure.ChainImpl: Returns the Compound for this chain.
getCompoundAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getCompoundAt(int, int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundAt(S, int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundAt(int, int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the Compound at row of given sequence and column of alignment index.
getCompoundAt(S, int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the Compound at row of given sequence and column of alignment index.
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: Returns the compound at the specified biological index
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader: Returns the compound at the specified biological index
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Always returns the compound given at construction
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getCompoundAt(int) - Method in interface org.biojava.nbio.core.sequence.template.Sequence: Returns the Compound at the given biological index
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.views.ReversedSequenceView
getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
getCompoundById(int) - Method in interface org.biojava.nbio.structure.Structure: Request a particular compound by its molId (entity_id in mmCIF dictionary)
getCompoundById(int) - Method in class org.biojava.nbio.structure.StructureImpl: Request a particular compound by its molId (entity_id in mmCIF dictionary)
getCompoundCountsAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundCountsAt(int, List<C>) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundCountsAt(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the number of each Compound in the given column for all compounds in CompoundSet.
getCompoundCountsAt(int, List<C>) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the number of each Compound in the given column only for compounds in the given list.
getCompoundForString(String) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
getCompoundForString(String) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
getCompoundForString(String) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
getCompoundForString(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
getCompoundForString(String) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet: Return null if not recognised.
getCompoundInQueryAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getCompoundInQueryAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the Compound in query sequence at given column index in alignment.
getCompoundInTargetAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getCompoundInTargetAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the Compound in target sequence at given column index in alignment.
getCompounds(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence: For a given position into the windowed view this will return those compounds we can see in the window.
getCompounds() - Method in interface org.biojava.nbio.structure.Structure: Get all the Compounds for this Structure.
getCompounds() - Method in class org.biojava.nbio.structure.StructureImpl: Get all the Compounds for this Structure.
getCompoundsAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundsAt(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the Compound elements of the original Sequences at the given column.
getCompoundsAt(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment: Get a list of compounds at a sequence position
getCompoundsAt(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile: Returns the Compound elements of the original Sequences at the given column.
getCompoundSet() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getCompoundSet() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getCompoundSet() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getCompoundSet() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getCompoundSet() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getCompoundSet() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getCompoundSet() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundSet() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns CompoundSet of all AlignedSequences
getCompoundSet() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns the CompoundSet on which the matrix is defined.
getCompoundSet() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
getCompoundSet() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getCompoundSet() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getCompoundSet() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
getCompoundSet() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment: Get the Compounds defined in the first sequence
getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: Returns the compound set backing this store
getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader: Returns the compound set backing this store
getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Returns the compound set given at construction
getCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getCompoundSet() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile: Returns CompoundSet of all Sequences
getCompoundSet() - Method in interface org.biojava.nbio.core.sequence.template.Sequence: Gets the compound set used to back this Sequence
getCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getCompoundsOfQuery() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getCompoundsOfQuery() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getCompoundsOfQuery() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getCompoundsOfTarget() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getCompoundsOfTarget() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getCompoundsOfTarget() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getCompoundsToIndexLookup() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: Returns a map which converts from compound to an integer representation
getCompoundType() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getCompoundWeightsAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundWeightsAt(int, List<C>) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundWeightsAt(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the fraction of each Compound in the given column for all compounds in CompoundSet.
getCompoundWeightsAt(int, List<C>) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the fraction of each Compound in the given column only for compounds in the given list.
getComputationTime() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getComputationTime() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getComputationTime() - Method in interface org.biojava.nbio.alignment.template.Aligner: Returns the computation time needed for an alignment computed in nanoseconds.
getComURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
getCondition() - Method in interface org.biojava.nbio.protmod.ProteinModification
getCondition() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getConfig() - Method in class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
getConn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getConn_type_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getConnectedFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getConnectedTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getConnections() - Method in interface org.biojava.nbio.structure.Structure: Deprecated.
use Atom.getBonds() instead
getConnections() - Method in class org.biojava.nbio.structure.StructureImpl: Return the connections value.
getConsAnnotation() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
getConsituents() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound: Deprecated.
replaced with NucleotideCompound.getConstituents() due to typographical error
getConstituents() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
getContact(Atom, Atom) - Method in class org.biojava.nbio.structure.contact.AtomContactSet: Returns the corresponding AtomContact or null if no contact exists between the 2 given atoms
getContact(Group, Group) - Method in class org.biojava.nbio.structure.contact.GroupContactSet: Returns the corresponding GroupContact or null if no contact exists between the 2 given groups
getContactOverlapScore(StructureInterface, boolean) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Calculates the contact overlap score between this StructureInterface and the given one.
getContacts() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getContacts() - Method in class org.biojava.nbio.structure.contact.Grid: Returns all contacts, i.e.
getContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface
getContacts() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getContactsToOtherCell(GridCell, Atom[], Atom[], double) - Method in class org.biojava.nbio.structure.contact.GridCell: Calculates all distances of atoms between this cell and the given cell returning those that are within the given cutoff as a list of AtomContacts
getContactsWithinCell(Atom[], Atom[], double) - Method in class org.biojava.nbio.structure.contact.GridCell: Calculates all distances of atoms within this cell returning those that are within the given cutoff as a list of AtomContacts
getContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContactSet: Returns the list of contacts from this set that are within the given distance.
getContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.GroupContact: Returns the list of atom contacts in this GroupContact that are within the given distance.
getContig() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
getContinuousVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getConvergenceSteps() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getCoordManager() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
getCoordManager() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
getCoordpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getCoords() - Method in interface org.biojava.nbio.structure.Atom: Get the coordinates.
getCoords() - Method in class org.biojava.nbio.structure.AtomImpl: Get the coordinates.
getCopy() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
getCopyWorkSheet(WorkSheet) - Static method in class org.biojava.nbio.survival.data.WorkSheet: Create a copy of a worksheet.
getCopyWorkSheetSelectedRows(WorkSheet, ArrayList<String>) - Static method in class org.biojava.nbio.survival.data.WorkSheet: Create a copy of a worksheet.
getCoreElectronCount() - Method in enum org.biojava.nbio.structure.Element: Returns the number of core electrons for this Element.
getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Returns the number of aligned positions (columns) without gaps in the Block.
getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all Block core lengths.
getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all BlockSet core lengths.
getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getCoreOntology() - Static method in class org.biojava.nbio.ontology.OntoTools: Get the Ontology that defines our core "central dogma".
getCorePositions(Block) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate a List of alignment indicies that correspond to the core of a Block, which means that all structures have a residue in that positon.
getCoreResidues(double, double) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns the residues belonging to the interface core, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is above the given bsaToAsaCutoff
getCorrelation_coeff_Fo_to_Fc() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getCorrelation_coeff_Fo_to_Fc_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getCount() - Method in class org.biojava.nbio.aaproperties.xml.Name2Count
getCovalentRadius() - Method in enum org.biojava.nbio.structure.Element: Returns the covalent radius of this Element.
getCoverage1() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Get the coverage of protein 1 with the alignment
getCoverage2() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Get the coverage of protein 2 with the alignment
getCoverages() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the coverage of the alignment for each structure in the alignment as a fraction between 0.0 and 1.0.
getCoverages() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getCovered() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getCoxInfo(String) - Method in class org.biojava.nbio.survival.cox.CoxVariables
getCoxInfoHashMap() - Method in class org.biojava.nbio.survival.cox.CoxVariables
getCPPoint() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
getCreate_co() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getCreator() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
getCrystalCell() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo: Return the crystal cell
getCrystalIds() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns a pair of identifiers for each of the 2 member molecules that identify them uniquely in the crystal: <molecule id (asym unit id)>+<operator id>+<crystal translation>
getCrystallographicInfo() - Method in class org.biojava.nbio.structure.PDBHeader
getCrystallographicInfo() - Method in interface org.biojava.nbio.structure.Structure: Get crystallographic information for this structure
getCrystallographicInfo() - Method in class org.biojava.nbio.structure.StructureImpl: Gets crystallographic information for this structure
getCrystals_number() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getCrystalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
getCurrent(String) - Static method in class org.biojava.nbio.structure.PDBStatus: Gets the current version of a PDB ID.
getCurrentChain() - Method in class org.biojava.nbio.structure.AtomIterator: Get the chain that contains the current atom.
getCurrentChain() - Method in class org.biojava.nbio.structure.GroupIterator: Get the current Chain.
getCurrentModel() - Method in class org.biojava.nbio.structure.AtomIterator: Get the model number of the model containing the current atom.
getCurrentModel() - Method in class org.biojava.nbio.structure.GroupIterator: Get the model number of the current model.
getCurrentPDBIds() - Static method in class org.biojava.nbio.structure.PDBStatus: Returns a list of current PDB IDs
getCurrentPDBIds() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: get the list of current PDB IDs
getCurrentSequencePosition() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
getCustomChain1() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getCustomFile1() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getCut_sites() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
getCutoff() - Method in class org.biojava.nbio.structure.contact.Grid
getCuts(int, AlignerHelper.Subproblem, int[], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
getCutsPerSection() - Method in class org.biojava.nbio.alignment.routines.GuanUberbacher: Returns the number of cuts added to each section during each pass.
getD() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition: Return the block diagonal eigenvalue matrix
getData() - Method in class org.biojava.nbio.structure.scop.server.ListStringWrapper
getData() - Method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper
getData() - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
getDataAnisotropy() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the dataAnisotropy property.
getDatabase() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
getDatabase() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
getDatabase() - Method in class org.biojava.nbio.structure.DBRef: The database of the db-ref.
getDatabaseReferences() - Method in interface org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface
getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: The Uniprot mappings to other database identifiers for this sequence
getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getDataColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
getDataCompleteness() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the dataCompleteness property.
getDataRows() - Method in class org.biojava.nbio.survival.data.WorkSheet: Get the list of row names
getDataSource() - Method in class org.biojava.nbio.core.sequence.AccessionID
getDataSource() - Method in class org.biojava.nbio.core.sequence.location.InsdcParser
getDataSource() - Method in class org.biojava.nbio.core.sequence.TaxonomyID
getDataVariables() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getDate() - Method in class org.biojava.nbio.structure.cath.CathDomain
getDate() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
getDate_original() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
getDb_align_beg() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getDb_align_end() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getDb_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getDb_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getDb_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getDbAccession() - Method in class org.biojava.nbio.structure.DBRef: Sequence database accession code.
getDbComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getDbFile() - Method in class org.biojava.nbio.core.search.io.Result
getDbIdCode() - Method in class org.biojava.nbio.structure.DBRef: Sequence database identification code.
getDbReferences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getDBRefs() - Method in interface org.biojava.nbio.structure.Structure: Get the list of database references
getDBRefs() - Method in class org.biojava.nbio.structure.StructureImpl: Get the list of database references
getDBResultMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getDBSearch() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
getDBSearchParameters() - Static method in class org.biojava.nbio.structure.align.StrucAligParameters
getDbSearchResult(AFPChain) - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
getDbSeqBegin() - Method in class org.biojava.nbio.structure.DBRef: Initial sequence number of the database seqment.
getDbSeqEnd() - Method in class org.biojava.nbio.structure.DBRef: Ending sequence position of the database segment.
getDbxrefList(String, int, int) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
getDCCR() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the dccr property.
getDCCRefinementProgram() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the dccRefinementProgram property.
getDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the dccRfree property.
getDcl() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getDefault() - Static method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine: Default instance to use when Transcribing from DNA -> RNA -> Protein.
getDefaultConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
getDefaultFactory() - Static method in class org.biojava.nbio.ontology.OntoTools
getDefaultFrame() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script to set the default orientation for a structure
getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script to set the default orientation for a structure
getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getDefaultParameters() - Static method in class org.biojava.nbio.structure.align.StrucAligParameters
getDefaultText() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
getDefinition() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getDegreeFreedom() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getDelta() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getDendrogram() - Method in class org.biojava.nbio.core.util.SingleLinkageClusterer: Get the full dendrogram (size n-1) result of the hierarchical clustering
getDensityCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getDepDate() - Method in class org.biojava.nbio.structure.PDBHeader
getDesc() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getDescription() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getDescription() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getDescription() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns the description of this matrix.
getDescription() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
getDescription() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
getDescription() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
getDescription() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface: Get the description that can be used to describe the feature
getDescription() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
getDescription() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getDescription() - Method in interface org.biojava.nbio.core.sequence.template.Compound
getDescription() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
getDescription() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
getDescription() - Method in class org.biojava.nbio.ontology.IntegerOntology
getDescription() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
getDescription() - Method in interface org.biojava.nbio.ontology.Ontology: Return a human-readable description of this ontology, or the empty string if none is available
getDescription() - Method in class org.biojava.nbio.ontology.Ontology.Impl
getDescription() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
getDescription() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
getDescription() - Method in interface org.biojava.nbio.ontology.Term: Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in class org.biojava.nbio.ontology.Term.Impl
getDescription() - Method in class org.biojava.nbio.ontology.Triple.Impl
getDescription() - Method in interface org.biojava.nbio.protmod.ProteinModification
getDescription() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getDescription() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound: return a description of this compound
getDescription() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
getDescription() - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq: Return the description of this FASTQ formatted sequence.
getDescription() - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder: Return the description for this FASTQ formatted sequence builder.
getDescription() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant: Return the description of this FASTQ sequence format variant.
getDescription() - Method in class org.biojava.nbio.structure.cath.CathNode
getDescription() - Method in class org.biojava.nbio.structure.PDBHeader
getDescription() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getDescription() - Method in class org.biojava.nbio.structure.scop.ScopDescription
getDescription() - Method in class org.biojava.nbio.structure.Site: gets the REMARK 800 description of the site
getDescription() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
getDescription() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
getDescription2() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Get a textual description for the protein 2 of the alignment.
getDescriptionByCathId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return CATH description for CATH domain ID.
getDescriptionByCathId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDescriptionByNodeId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return CATH description for node representative by node ID.
getDescriptionByNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDescriptionNumber() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
getDescriptor() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
getDescriptors() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getDesFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getDesURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
getDetails() - Method in class org.biojava.nbio.structure.Compound
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getDetails() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getDetails() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getDf() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
getDiagonalAtK(Atom[], int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools
getDiagonalDistance() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getDiagonalDistance2() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getDictionary() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
getDimension() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getDimension() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getDimension() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getDimensions() - Method in class org.biojava.nbio.structure.contact.BoundingBox: Returns the dimensions of this bounding box.
getDir(String, boolean) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Gets the directory in which the file for a given MMCIF file would live, creating it if necessary.
getDirection() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getDiscreteColumnValues(String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Get back a list of unique values in the column
getDiscreteRowValues(String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Get back a list of unique values in the row
getDiscreteValues() - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
getDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters: Get the distance cutoff used during AFP chain connectivity checks
getDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
getDisFilter() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getDisorder(FastaSequence) - Static method in class org.biojava.nbio.ronn.Jronn: Calculates the disordered regions of the sequence.
getDisorder(List<FastaSequence>) - Static method in class org.biojava.nbio.ronn.Jronn: Calculates the disordered regions of the sequence for many sequences in the input.
getDisorder(String) - Static method in class org.biojava.nbio.ronn.Jronn: Calculates the disordered regions of the protein sequence.
getDisorderScores(FastaSequence) - Static method in class org.biojava.nbio.ronn.Jronn: Calculates the probability value for each residue in the protein sequence, telling the probability that the residue belongs to disordered region.
getDisorderScores(ProteinSequence) - Static method in class org.biojava.nbio.ronn.Jronn: Calculates the probability value for each residue in the protein sequence, telling the probability that the residue belongs to disordered region.
getDisorderScores(List<FastaSequence>) - Static method in class org.biojava.nbio.ronn.Jronn: Calculates the probability of disorder scores for each residue in the sequence for many sequences in the input.
getDisSmooth() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getDist() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
getDist() - Method in class org.biojava.nbio.structure.validation.Clash: Gets the value of the dist property.
getDist() - Method in class org.biojava.nbio.structure.validation.SymmClash: Gets the value of the dist property.
getDist1() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getDist1() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getDist2() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getDist2() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getDisTable1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getDisTable2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getDistance() - Method in class org.biojava.nbio.alignment.template.AbstractScorer
getDistance(double) - Method in class org.biojava.nbio.alignment.template.AbstractScorer
getDistance() - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns score as a distance between 0.0 and 1.0.
getDistance(double) - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns score as a distance between 0.0 and scale.
getDistance() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
getDistance(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: calculate distance between two atoms.
getDistance() - Method in class org.biojava.nbio.structure.contact.AtomContact
getDistanceCutoff() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getDistanceCutoff() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getDistanceFast(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: Will calculate the square of distances between two atoms.
getDistanceIncrement() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getDistanceMatrices() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Returns a List of internal Distance Matrices, one for each structure in the alignment.
getDistanceMatrices() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
getDistanceMatrices() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
getDistanceMatrix() - Method in class org.biojava.nbio.alignment.GuideTree: Returns the distance matrix used to construct this guide tree.
getDistanceMatrix() - Method in interface org.biojava.nbio.alignment.template.HierarchicalClusterer: Returns the distance matrix used in clustering.
getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools: Matrix of all distances between two sets of Atoms.
getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.model.AFPChain: A matrix with ca1length rows and ca2length columns.
getDistanceMatrix() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the List containing the interatomic distance Matrix of each structure.
getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: The distance matrix this alignment is based on
GetDistanceMatrix - Class in org.biojava.nbio.structure.domain.pdp
GetDistanceMatrix() - Constructor for class org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix
getDistanceMatrix(Atom[]) - Method in class org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix: A set of Calpha atoms that are representing the protein
getDistanceToParent() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getDistanceToParent() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the difference in height of this node and it's parent node.
getDistMat() - Method in class org.biojava.nbio.structure.align.StructurePairAligner: return the difference of distance matrix between the two structures
getDistribution(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: Analogous to SequenceMixin.getComposition(Sequence) but returns the distribution of that Compound over the given sequence.
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties: Computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
Example: "1111122222"
For the above example,
position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getDistributionPosition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties: An adaptor method which computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
Example: "1111122222"
For the above example,
position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getDistributionPosition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getDkMatrix(Atom[], Atom[], int, double[], double[], int, int) - Method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
getDkMatrix(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
getDNACodingSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence: Get the stitched together CDS sequences then maps to the cDNA
getDNACodingSequences() - Method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
getDnaCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
getDNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet
getDNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.DNACompoundSet
getDNAOneLetter(String) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
getDNARNAHybridCompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet
getDnaRnaTranslator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
getDnaToRna() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
getDNATwoLetter(Character) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
getDNAType() - Method in class org.biojava.nbio.core.sequence.DNASequence
getDoi() - Method in class org.biojava.nbio.structure.JournalArticle: Get the value of DOI field.
getDomain(String, AtomCache) - Method in interface org.biojava.nbio.structure.domain.PDPProvider: Get the structure for a particular PDP domain
getDomain(String, AtomCache) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider: Get the structure for a particular PDP domain
getDomainByCathId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return CATH domain for CATH domain ID.
getDomainByCathId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getDomainByScopID(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getDomainCounter() - Method in class org.biojava.nbio.structure.cath.CathDomain
getDomainDescriptionFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDomainId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getDomainId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getDomainId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getDomainListFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDomainName() - Method in class org.biojava.nbio.structure.cath.CathDomain
getDomainNames(String) - Method in interface org.biojava.nbio.structure.domain.DomainProvider: Get a list of constituent domain identifiers
getDomainNames(String) - Method in class org.biojava.nbio.structure.domain.PDBDomainProvider: Gets a list of domain representatives for a given PDB ID.
getDomainNames(String) - Method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
getDomainProvider() - Static method in class org.biojava.nbio.structure.domain.DomainProviderFactory
getDomainRangesFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getDomainRangesXML(SortedSet<String>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getDomains() - Method in class org.biojava.nbio.structure.domain.pdp.CutDomain
getDomains() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
getDomains() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getDomainsById(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase: Get a particular ECOD domain by the domain ID (e.g.
getDomainsById(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Get a particular ECOD domain by the domain ID (e.g.
getDomainsByNodeId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return all CATH domains for a particular CATH node.
getDomainsByNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDomainsForPdb(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return all CATH domains for a PDB ID.
getDomainsForPdb(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDomainsForPdb(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase: Get a list of all ECOD domains for a particular PDB ID
getDomainsForPdb(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: public EcodInstallation(String cacheLocation) { this( cacheLocation, DEFAULT_VERSION ); } /** Get a list of all ECOD domains for a particular PDB ID
getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getDomainsForPDB(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Get a list of ScopDomains that have been assigned to a PDB ID
getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getDomainsFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getDomainsXML(SortedSet<Domain>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getDomallFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getDonor1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getDonor2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getDoublePivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition: Return pivot permutation vector as a one-dimensional double array
getDuplicationHint() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
getDuplicationHint() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
getDVar() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getEcNums() - Method in class org.biojava.nbio.structure.Compound
getEcodDatabase() - Static method in class org.biojava.nbio.structure.ecod.EcodFactory: Returns the (singleton) database for the current default version
getEcodDatabase(String) - Static method in class org.biojava.nbio.structure.ecod.EcodFactory
getEditorList() - Method in class org.biojava.nbio.structure.JournalArticle: Get the list of editors of the JournalArticle
getEDSR() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the edsr property.
getEDSResolution() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the edsResolution property.
getEDSResolutionLow() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the edsResolutionLow property.
getElement() - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
getElement(String) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
getElement() - Method in interface org.biojava.nbio.structure.Atom: Get element of the atom, e.g.
getElement() - Method in class org.biojava.nbio.structure.AtomImpl: Get element of the atom, e.g.
getElement1() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
getElement2() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
getElementaryAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes: Return all elementary axes of symmetry of the structure, that is, the axes stored in the List as unique and from which all the symmetry axes are constructed.
getElementFromHillIndex(int) - Static method in enum org.biojava.nbio.structure.Element: Returns the Element that corresponds to the specified Hill Order.
getElementList() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
getElementType() - Method in enum org.biojava.nbio.structure.Element: Returns the Element Type for this Element.
getElipsisRadii() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getEmail() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Get the email for QBlast.
getEmbTrees() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getEmptyChemComp() - Static method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp: Creates a new instance of the dummy empty ChemComp.
getEmptySequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit: Returns an empty sequence with the given compound set of the editing sequence
getEnd() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getEnd() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the Point within an alignment of the last element of the original Sequence.
getEnd() - Method in interface org.biojava.nbio.core.alignment.template.ProfileView: Returns the column index of the viewed Profile corresponding to the final element in this view
getEnd() - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
getEnd(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute: Must use this rather than the no-args getEnd as this can return -1 and the length of a sub is dependent on the length of the Sequence; we cannot assume 1:1 mapping between characters in a String and the number of compounds we will have to insert.
getEnd() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
getEnd() - Method in interface org.biojava.nbio.core.sequence.location.template.Location: End of the location
getEnd() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
getEnd() - Method in class org.biojava.nbio.genome.parsers.gff.Location
getEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
getEnd() - Method in class org.biojava.nbio.structure.ResidueRange
getEndLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
getEndLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
getEnergy() - Method in class org.biojava.nbio.structure.secstruc.HBond
getEngineered() - Method in class org.biojava.nbio.structure.Compound
getEnrichment(ProteinSequence, AminoAcidCompound) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the composition of specified amino acid in the sequence.
getEnrichment(String, PeptideProperties.SingleLetterAACode) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the composition of specified amino acid in the sequence.
getEnrichment(String, char) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the composition of specified amino acid in the sequence.
getEnrichment(String, String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the composition of specified amino acid in the sequence.
getEnrichment(ProteinSequence, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getEnsemble() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the parent Ensemble of the MultipleAlignment.
getEnsemble() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getEnsemblGeneId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getEnt() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the ent property.
getEntities() - Method in class org.biojava.nbio.structure.io.sifts.SiftsXMLParser
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getEntityId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
getEntry() - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation: Gets the value of the entry property.
getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
getEnumValuesAsString(Class<T>) - Static method in class org.biojava.nbio.structure.align.util.CliTools: Constructs a comma-separated list of values for an enum.
getEnzClass() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getEqr() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: returns the number of euqivalent residues in this alignment
getEQRAlignmentPos(AFPChain) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
getEquivalent() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
getEquivalentCompounds(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
getEquivalentCompounds(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
getEvalCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getEvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getEvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getEvalueThreshold() - Method in class org.biojava.nbio.core.search.io.SearchIO
getEvCode() - Method in class org.biojava.nbio.structure.Site: gets the REMARK 800 EVIDENCE CODE for the site.
getExampleUnitCell() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
getExitMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getExonCount() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getExonEnds() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getExonSequences() - Method in class org.biojava.nbio.core.sequence.GeneSequence: Get the exons as an ArrayList
getExonStarts() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getExpectedExecutionTime() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
getExperimentalTechniques() - Method in class org.biojava.nbio.structure.PDBHeader: Return the Set of ExperimentalTechniques, usually the set is of size 1 except for hybrid experimental techniques when the Set will contain 2 or more values
getExportPDBMenuItem(AbstractAlignmentJmol) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getExpression_system_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getExpressionSystem() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemAtccNumber() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemCell() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemCellLine() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemCellularLocation() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemGene() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemOrgan() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemOrganelle() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemOtherDetails() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemPlasmid() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemStrain() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemTaxId() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemTissue() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemVariant() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemVector() - Method in class org.biojava.nbio.structure.Compound
getExpressionSystemVectorType() - Method in class org.biojava.nbio.structure.Compound
getExtensionPenalty() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty: Returns the negative of the extension penalty passed to the constructor.
getExtensionPenalty() - Method in interface org.biojava.nbio.alignment.template.GapPenalty: Returns penalty given when an already open gap elongates by a single element
getExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
getExtensions() - Method in interface org.biojava.nbio.structure.io.StructureIOFile: Returns a list of extensions supported by this class
getExtensions() - Method in enum org.biojava.nbio.structure.StructureIO.StructureFiletype
getExtinctionCoefficient(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the extinction coefficient of sequence.
getExtinctionCoefficient(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the extinction coefficient of sequence.
getExtinctionCoefficient(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getFailedLines() - Method in class org.biojava.nbio.structure.scop.Astral: Gets a map describing lines read in the file that weren't understood.
getFalseDiscoveryRate() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getFamilyId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getFarmJob() - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
getFatCatAligner() - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
getFeatureRetriever() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getFeatures() - Method in interface org.biojava.nbio.core.sequence.features.FeatureRetriever
getFeatures(String) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getFeatures() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getFeatures() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
getFeatures(String, int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Return features at a sequence position by type
getFeatures(int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Return features at a sequence position
getFeatures() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getFeaturesByType(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getFeaturesKeyWord() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getFetchBehavior() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Get the behavior for fetching files from the server
getFetchBehavior() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
getFetchBehavior() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Get the behavior for fetching files from the server
getFGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getFGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getFile() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
getFile1() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getFile2() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getFileAnnotation() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
getFileExtension(File) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils
getFileExtensions() - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
getFileExtensions() - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
getFileExtensions() - Method in interface org.biojava.nbio.core.search.io.ResultFactory: returns a list of file extensions associated to this ResultFactory
getFileFormat() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
getFileFormatSelect() - Static method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
getFilename(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Converts a PDB ID into a filename with the proper extension
getFilename(String) - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
getFilename(String) - Method in class org.biojava.nbio.structure.io.PDBFileReader
getFileName() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
getFileName() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
getFileParsingParameters() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.PDBFileParser
getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
getFileParsingParameters() - Method in interface org.biojava.nbio.structure.io.StructureProvider: Get the parameters that should be used for file parsing
getFileParsingParams() - Method in class org.biojava.nbio.structure.align.util.AtomCache
getFilePath1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
getFilePrefix(File) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils
getFinalIndex(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block: Calculates and returns the last position of the specified structure in the alignment that is not null.
getFinalIndex(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getFinalResidue(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block: Calculates and returns the last residue of the specified structure in the alignment that is not null.
getFinalResidue(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getFirst(String) - Method in class org.biojava.nbio.structure.AtomPositionMap
getFirst() - Method in class org.biojava.nbio.structure.AtomPositionMap
getFirst() - Method in class org.biojava.nbio.structure.contact.Pair
getFirstAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
getFirstGroupAsa(ResidueNumber) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Gets the GroupAsa for the corresponding residue number of first chain
getFirstGroupAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Gets a map of ResidueNumbers to GroupAsas for all groups of first chain.
getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit: Should return the 5-prime end of the given Sequence according to the edit.
getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Insert
getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute
getFlippableSidechain() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the flippableSidechain property.
getFocusAfpList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getFocusAfpn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getFocusRes1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getFocusRes2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getFocusResn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getFoFcCorrelation() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the foFcCorrelation property.
getFold() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getFold() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getFoldId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getFolds() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer: Get valid symmetry order for this stoichiometry.
getFolds() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getFoldType() - Method in enum org.biojava.nbio.structure.xtal.TransformType
getFormat() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getFormat() - Method in class org.biojava.nbio.structure.cath.CathDomain
getFormatedSequence(int) - Method in class org.biojava.nbio.data.sequence.FastaSequence: Format sequence per width letter in one string.
getFormattedFasta() - Method in class org.biojava.nbio.data.sequence.FastaSequence
getFormula() - Method in interface org.biojava.nbio.protmod.ProteinModification
getFormula() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getFormula() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getFormula() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getFormula_weight() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getFormula_weight() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getForwardFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame: Returns all frames in the forward orientation
getFragCompat() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getFragLen() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getFragLen() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
getFragLen() - Method in class org.biojava.nbio.structure.align.model.AFP
getFragLenSq() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getFragment(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools: get a continue subset of Atoms based by the starting position and the length
getFragment() - Method in class org.biojava.nbio.structure.Compound
getFragmentFromIdxList(Atom[], int[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools: get a subset of Atoms based by their positions
getFragmentId() - Method in class org.biojava.nbio.structure.cath.CathFragment
getFragmentLength() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getFragmentMiniDistance() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getFragmentNoClone(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools: get a continue subset of Atoms based by the starting position and the length does not clone the original atoms.
getFragmentPairs() - Method in class org.biojava.nbio.structure.align.StructurePairAligner: get the results of step 1 - the FragmentPairs used for seeding the alignment
getFragmentPairs() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
getFragmentPairs() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
getFragmentsByPdbId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
getFragmentsByPdbId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getFragScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getFrame() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
getFrame() - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
getFrom() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
getFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getFromCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
getFromFtp() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
getFromHeteroAtomId(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromHeteroAtomId(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromHeteroAtomIds(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromHeteroAtomIds(List<String>) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromHeteroAtomIds(String...) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromPdbId(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromPdbId(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromPdbIds(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromPdbIds(List<String>) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromPdbIds(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFromPdbIds(String...) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
getFullAtomSequence(List<Group>, Map<Integer, Integer>, boolean) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner: Returns the full sequence of the Atom records of a parent with X instead of HETATMSs.
getFullMatrix() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Returns a matrix that describes both rotation and translation.
getGagPolyproteins() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: get all PDB IDs of gag-polyproteins
getGamma() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
getGamma() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getGapCreate() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getGapExtCol() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getGapExtCol() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getGapExtend() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getGapExtend() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
getGapExtend() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
getGapExtension() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getGapExtension() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
getGapExtension() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getGapExtension() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getGapExtRow() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getGapExtRow() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getGapLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getGapOpen() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getGapOpen() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
getGapOpen() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getGapOpen() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
getGapOpen() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
getGapOpen() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getGapOpenCol() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getGapOpenCol() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getGapOpenRow() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getGapOpenRow() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getGapPenalty() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Returns the gap penalties.
getGaps() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: return the number of gaps in this alignment
getGatheringThreshs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation: Not always 2.
It may undergo further change.
getGC() - Method in class org.biojava.nbio.core.sequence.RNASequence
getGCCount() - Method in class org.biojava.nbio.core.sequence.DNASequence: Get the GC count in the DNA Sequence
getGCGChecksum(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Calculates GCG checksum for entire list of sequences
getGCGChecksum(S) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Calculates GCG checksum for a given sequence
getGCGHeader(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Assembles a GCG file header
getGCGType(CompoundSet<C>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Determines GCG type
getGCStats(Collection<DNASequence>) - Static method in class org.biojava.nbio.genome.parsers.gff.GCStats
getGCStatsString(Collection<String>) - Static method in class org.biojava.nbio.genome.parsers.gff.GCStats
getGenbankDirectoryCache() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader: Local directory cache of Genbank that can be downloaded
getGene(String) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence: Get the gene based on accession.
getGene() - Method in class org.biojava.nbio.structure.Compound
getGene_src_common_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_dev_stage() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_genus() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_species() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_strain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_tissue() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGene_src_tissue_fraction() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getGenebankId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getGeneName() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: Get the gene name associated with this sequence.
getGeneName() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getGeneNames() - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
getGeneNames(InputStream) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser: Get a list of GeneNames from an input stream.
getGenes() - Method in class org.biojava.nbio.survival.cox.CoxVariables
getGeneSequences() - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence: Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key.
getGeneSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
getGeneSet() - Method in class org.biojava.nbio.survival.cox.CoxVariables
getGeneSymb() - Method in class org.biojava.nbio.phosphosite.Site
getGenus() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner: Returns a transformation matrix transform polyhedra for Cn structures.
getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner: Returns a transformation matrix transform polyhedra for Cn structures.
getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner: Returns the geometric center of polyhedron.
getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner: Returns the geometric center of polyhedron.
getGlobalSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Returns list of global quaternary structure symmetry results
getGonnet250() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns PAM 250 matrix by Gonnet, Cohen & Benner
getGradientMapper(int, double, double) - Static method in class org.biojava.nbio.structure.gui.util.color.GradientMapper: Constructs a gradientMapper to draw one of the pre-defined gradients For example, GradientMapper.getGradientMapper(GradientMapper.RAINBOW_GRADIENT, 0, 10)
getGroup() - Method in class org.biojava.nbio.phosphosite.Site
getGroup() - Method in class org.biojava.nbio.protmod.structure.StructureAtom
getGroup() - Method in class org.biojava.nbio.structure.asa.GroupAsa
getGroup() - Method in interface org.biojava.nbio.structure.Atom: Return the parent Group of the Atom.
getGroup() - Method in class org.biojava.nbio.structure.AtomImpl: Return the parent Group of the Atom.
getGroup() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
getGroup_PDB() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getGroupAsas() - Method in class org.biojava.nbio.structure.asa.AsaCalculator: Calculates ASA for all atoms and return them as a GroupAsa array (one element per residue in structure) containing ASAs per residue and per atom.
getGroupByPDB(ResidueNumber) - Method in interface org.biojava.nbio.structure.Chain: Get a group by its PDB residue numbering.
getGroupByPDB(ResidueNumber) - Method in class org.biojava.nbio.structure.ChainImpl: Get a group by its PDB residue numbering.
getGroupByPDBResidueNumber(Structure, ResidueNumber) - Static method in class org.biojava.nbio.structure.StructureTools: Get a group represented by a ResidueNumber.
getGroupCategories(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getGroupCategories(String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
getGroupContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface
getGroupDistancesWithinShell(Structure, Atom, Set<ResidueNumber>, double, boolean, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Finds Groups in structure that contain at least one Atom that is within radius Angstroms of centroid.
getGroupFromChemCompDictionary(String) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor: Returns the groupings of the attribute
getGroups() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
getGroups(boolean) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
getGroups() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
getGroups(boolean) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
getGroups() - Method in class org.biojava.nbio.structure.Site
getGroups(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Returns the List of Groups of the corresponding representative Atom array.
getGroups() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure: Get the name of the groups that are being plotted in the figure
getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in interface org.biojava.nbio.structure.Chain: Get all groups that are located between two PDB residue numbers.
getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in interface org.biojava.nbio.structure.Chain: Get all groups that are located between two PDB residue numbers.
getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in class org.biojava.nbio.structure.ChainImpl: Deprecated.
getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.ChainImpl: Get all groups that are located between two PDB residue numbers.
getGroupsWithinShell(Structure, Atom, Set<ResidueNumber>, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
getGroupsWithinShell(Structure, Group, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Returns a Set of Groups in a structure within the distance specified of a given group.
getGroupTable() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
getH() - Method in class org.biojava.nbio.structure.jama.QRDecomposition: Return the Householder vectors
getHazardRatio() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getHazardRatioHiCI() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getHazardRatioLoCI() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getHeader() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getHeader(S) - Method in class org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat
getHeader(S) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
getHeader(S) - Method in interface org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface
getHeader(S) - Method in interface org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface
getHeader() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
getHeaderParser() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
getHeaderVars() - Method in class org.biojava.nbio.structure.Compound
getHeight() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
getHeight() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism: Returns the radius of a sphere, that is tangent to each of the octahedron's edges
getHelix(int) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
getHelixLayers() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getHelixLayers() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
getHelixRmsdThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getHelixRmsdToRiseRatio() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getHelpMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getHetero() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
getHetero() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getHetGroups() - Method in interface org.biojava.nbio.structure.Structure
getHetGroups() - Method in class org.biojava.nbio.structure.StructureImpl: Caution: we should probably remove this to avoid confusion.
getHgncId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getHGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getHGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getHieFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getHieURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
getHigherOrderRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
getHillOrder() - Method in enum org.biojava.nbio.structure.Element: Returns the Hill Order of this Element.
getHitAccession() - Method in class org.biojava.nbio.core.search.io.Hit
getHitCounter() - Method in class org.biojava.nbio.core.search.io.Result
getHitDef() - Method in class org.biojava.nbio.core.search.io.Hit
getHitId() - Method in class org.biojava.nbio.core.search.io.Hit
getHitLen() - Method in class org.biojava.nbio.core.search.io.Hit
getHitNum() - Method in class org.biojava.nbio.core.search.io.Hit
getHitSequence() - Method in class org.biojava.nbio.core.search.io.Hit: returns the reference to the original and whole sequence hit in the database.
getHitsQueryDef(double) - Method in class org.biojava.nbio.genome.query.BlastXMLQuery
getHmmAcc() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getHmmDesc() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getHmmFrom() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getHmmName() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getHmmTo() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getHomologyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getHost_org_common_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getHost_org_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getHost_org_genus() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getHost_org_species() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getHost_org_strain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getHRText() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getHSDMTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate a phylogenetic tree of the MultipleAlignment using dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for distantly related proteins, structure-derived) and the Neighbor Joining algorithm from forester.
getHspAlignLen() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspBitScore() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspEvalue() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspGaps() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspHitFrame() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspHitFrom() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspHitTo() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspHseq() - Method in class org.biojava.nbio.core.search.io.Hsp: HSP aligned hit sequence string
getHspIdentity() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspIdentityString() - Method in class org.biojava.nbio.core.search.io.Hsp: Identity string representing correspondence between aligned residues
getHspNum() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspPositive() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspQseq() - Method in class org.biojava.nbio.core.search.io.Hsp: HSP aligned query sequence string
getHspQueryFrame() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspQueryFrom() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspQueryTo() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspScore() - Method in class org.biojava.nbio.core.search.io.Hsp
getHSVColorSpace() - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
getIclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
getIcode() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the icode property.
getiCode1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getiCode2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getIcon(ActionListener, String) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getID() - Method in class org.biojava.nbio.core.sequence.AccessionID
getId() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
getId() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
getID() - Method in class org.biojava.nbio.core.sequence.TaxonomyID
getId() - Method in class org.biojava.nbio.data.sequence.FastaSequence: Gets the value of id
getId() - Method in interface org.biojava.nbio.protmod.ProteinModification
getId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getId() - Method in class org.biojava.nbio.structure.align.model.AFP
getId() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getId() - Method in interface org.biojava.nbio.structure.Chain: Get the ID used by Hibernate.
getId() - Method in class org.biojava.nbio.structure.ChainImpl: Get the ID used by Hibernate.
getId() - Method in class org.biojava.nbio.structure.Compound: get the ID used by Hibernate
getId() - Method in class org.biojava.nbio.structure.contact.StructureInterface
getId() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
getId() - Method in class org.biojava.nbio.structure.DBRef: Get the ID used by Hibernate.
getId() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
getId() - Method in class org.biojava.nbio.structure.HetatomImpl: the Hibernate database ID
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getId() - Method in class org.biojava.nbio.structure.PDBHeader: Get the ID used by Hibernate.
getId() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo: The identifier for this Biological Assembly, from 1 to n
getId() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Returns the identifier for this biological assembly transformation.
getId() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getId() - Method in class org.biojava.nbio.structure.rcsb.RCSBTaxonomy
getId() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
getId() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement: Returns the ID of this element.
getId() - Method in interface org.biojava.nbio.structure.Structure: Get the ID used by Hibernate
getId() - Method in class org.biojava.nbio.structure.StructureImpl: get the ID used by Hibernate
getId() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
getId() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets the standard numeric identifier for the space group.
getId() - Method in enum org.biojava.nbio.structure.xtal.TransformType
getId() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getId() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob: Request id (RID) as received from QBlast server
getIdbnsBegin() - Method in class org.biojava.nbio.structure.DBRef: Insertion code of initial residue of the segment, if PDB is the reference.
getIdbnsEnd() - Method in class org.biojava.nbio.structure.DBRef: Insertion code of the ending residue of the segment, if PDB is the reference.
getIdCode() - Method in class org.biojava.nbio.structure.DBRef: get the idCode for this entry
getIdCode() - Method in class org.biojava.nbio.structure.PDBHeader: The PDB code for this protein structure.
getIdenticalSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getIdentification() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getIdentifiedModifiedCompound() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
getIdentifier() - Method in class org.biojava.nbio.core.sequence.AccessionID: In case if AccessionID.getID() in not unique keeps the alternative id, eg.
getIdentifier() - Method in class org.biojava.nbio.structure.align.client.StructureName: Get the original form of the identifier
getIdentifier() - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier
getIdentifier() - Method in class org.biojava.nbio.structure.cath.CathDomain
getIdentifier() - Method in class org.biojava.nbio.structure.domain.PDPDomain
getIdentifier() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getIdentifier() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
getIdentifier() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
getIdentifier() - Method in class org.biojava.nbio.structure.PassthroughIdentifier
getIdentifier() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getIdentifier() - Method in interface org.biojava.nbio.structure.Structure: Get a string representing this structure's contents.
getIdentifier() - Method in interface org.biojava.nbio.structure.StructureIdentifier: Get the String form of this identifier.
getIdentifier() - Method in class org.biojava.nbio.structure.StructureImpl: Get a string representing this structure's contents.
getIdentifier() - Method in class org.biojava.nbio.structure.SubstructureIdentifier: Get the String form of this identifier.
getIdentifier() - Method in class org.biojava.nbio.structure.URLIdentifier
getIdentity() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
getIdentity() - Method in class org.biojava.nbio.structure.align.model.AFPChain: The percent of residues that are sequence-identical in the alignment.
getIDFormat(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Creates format String for accession IDs
getIdx1() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: the positions of the structure equivalent positions in atom set 1
getIdx1() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay: get the identical position in the alignment
getIdx2() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: the positions of the structure equivalent atoms in atom set 2
getIdx2() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay: get the identical position in the alignment
getIdxlist() - Method in class org.biojava.nbio.structure.align.helper.JointFragments
getImagEigenvalues() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition: Return the imaginary parts of the eigenvalues
getImat() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getInChI() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getInChIKey() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getIndex(TreeNode) - Method in class org.biojava.nbio.alignment.GuideTree.Node
getIndex() - Method in class org.biojava.nbio.structure.align.helper.GapArray
getIndex() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getIndex() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement: Returns the index of the SSE for its type.
getIndex() - Method in class org.biojava.nbio.survival.data.HeaderInfo
getIndexColumnName() - Method in class org.biojava.nbio.survival.data.WorkSheet
getIndexInQueryAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getIndexInQueryAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the query index corresponding to a given alignment column.
getIndexInQueryForTargetAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getIndexInQueryForTargetAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the query index corresponding to a given target index.
getIndexInTargetAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getIndexInTargetAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the target index corresponding to a given alignment column.
getIndexInTargetForQueryAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getIndexInTargetForQueryAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the target index corresponding to a given query index.
getIndexOf(C) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getIndexOf(C) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getIndexOf(C) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Searches for the given Compound within this alignment profile.
getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader: Returns the first occurrence of the given compound in this store; performs a linear search
getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Returns 1 if the given compound is equal to the one given during construction; otherwise will return -1.
getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getIndexOf(C) - Method in interface org.biojava.nbio.core.sequence.template.Sequence: Scans through the Sequence looking for the first occurrence of the given compound
getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
getIndexOf(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
getIndexOfComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
getIndexOfComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
getIndexToCompoundsLookup() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: Returns a list of compounds the index position of which is used to translate from the byte representation into a compound.
getIndicesAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getIndicesAt(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the indices in the original Sequences corresponding to the given column.
getInertiaTensor() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getInitialK() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getInitials() - Method in class org.biojava.nbio.structure.Author
getInputStream() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource: Returns the InputStream instance of this classpath resource
getInputStream(String) - Static method in class org.biojava.nbio.core.util.FlatFileCache
getInputStream(String) - Method in class org.biojava.nbio.core.util.InputStreamProvider: Get an InputStream for given file path.
getInputStream(URL) - Method in class org.biojava.nbio.core.util.InputStreamProvider
getInputStream(File) - Method in class org.biojava.nbio.core.util.InputStreamProvider: Get an InputStream for the file.
getInputStream(URL, int) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: connect to DAS server and return result as an InputStream.
getInputStream(URL) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: connect to DAS server and return result as an InputStream.
getInputStream(URL, boolean, int) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: open a URL and return an InputStream to it if acceptGzipEncoding == true, use GZIPEncoding to compress communication
getInputStream(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Load or download the specified structure and return it as an InputStream for direct parsing.
getInputStreamToAAindexFile() - Method in class org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider
getInsCode() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
getInsCode() - Method in class org.biojava.nbio.structure.ResidueNumber
getInsCode() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getInsCode() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getInsCode1() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getInsCode2() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron: Returns the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces
getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron: Returns the radius of an inscribed sphere, that is tangent to each of the octahedron's faces
getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism: Returns the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces
getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron: Returns the radius of an inscribed sphere, that is tangent to each of the tetrahedrons's faces
getInsertBegin() - Method in class org.biojava.nbio.structure.DBRef: Initial insertion code of the PDB sequence segment.
getInsertEnd() - Method in class org.biojava.nbio.structure.DBRef: Ending insertion code of the PDB sequence segment.
getInstabilityIndex(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the instability index of sequence.
getInstabilityIndex(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the instability index of sequence.
getInstabilityIndex(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getInstalledDomainDescription() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getInstalledDomainList() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getInstalledDomall() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getInstalledNodeList() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getInstance() - Static method in class org.biojava.nbio.core.sequence.io.IUPACParser
getInstance() - Static method in class org.biojava.nbio.core.util.FlatFileCache
getInstance() - Static method in class org.biojava.nbio.structure.align.gui.AlignmentGui
getInstance() - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
getInstance(int) - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
getInstance() - Static method in class org.biojava.nbio.structure.gui.util.ScopInstallationInstance
getInstance(QuatSymmetryResults) - Static method in class org.biojava.nbio.structure.symmetry.core.AxisAligner: Returns an instance of AxisAligner for differnt type of QuatSymmetryResults (factory method)
getInstance() - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
getInstance(AxisAligner, String) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns an instance of a JmolSymmetryScriptGenerator, based on the symmetry of a structure (factory method)
getInstanceNoVisibilityChange() - Static method in class org.biojava.nbio.structure.align.gui.AlignmentGui
getInstanceNoVisibilityChange() - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
getInstanceNoVisibilityChange() - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
getInstantaneousOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that sets a specific orientation instantaneously
getInt_Tables_number() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
getIntegerOntology() - Static method in class org.biojava.nbio.ontology.OntoTools: Get the Ontology that defines integers.
getInteractingRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
getInterfacingResidues(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns the residues belonging to the interface, i.e.
getIntermediate(Color, Color, int, int) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
getInternalChainID() - Method in interface org.biojava.nbio.structure.Chain: If available, returns the internal chain ID that is used in mmCIF files (asym_id), otherwise null
getInternalChainID() - Method in class org.biojava.nbio.structure.ChainImpl
getInterpolator() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
getIntersection(DistanceBox<T>) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
getIntronSequences() - Method in class org.biojava.nbio.core.sequence.GeneSequence: Get the introns as an ArrayList
getInverse() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getInverse() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getInverse() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getInverse() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
getInverse() - Method in class org.biojava.nbio.core.sequence.RNASequence: Get the inverse view of the sequence.
getInverse() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
getInverse() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
getInverse() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
getInverse() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
getInverse() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getInverse() - Method in interface org.biojava.nbio.core.sequence.template.Sequence: Does the right thing to get the inverse of the current Sequence.
getInverse() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getIoTime() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getIoTime() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the io time for this object, in milliseconds.
getIoTime() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getIoTime() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getIoverSigma() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the ioverSigma property.
getIsoelectricPoint(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the isoelectric point of sequence.
getIsoelectricPoint(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
getIsoelectricPoint(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the isoelectric point of sequence.
getIsoelectricPoint(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
getIsoelectricPoint(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getIsoelectricPoint(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getIsotope(String) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
getIsotopeList() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
getIsotopes() - Method in class org.biojava.nbio.aaproperties.xml.Element
getIterationNumber() - Method in class org.biojava.nbio.core.search.io.Result
getJclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
getJmolColor(Color4f) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
getJmolColorScript(Map<Color4f, List<String>>) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
getJmolLigandScript() - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
getJmolPanel() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Return the jmolPanel instance of the AlignmentJmol.
getJmolPoint(Tuple3d) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
getJmolScript(Atom[]) - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Returns a Jmol script which will display the axis of rotation.
getJmolScript(Atom[], int) - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Returns a Jmol script which will display the axis of rotation.
getJmolScript4Block(AFPChain, Atom[], Atom[], int) - Static method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
getJmolString(MultipleAlignment, List<Atom[]>, ColorBrewer, boolean) - Static method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol: Generate a Jmol command String that colors the aligned residues of every structure.
getJmolString(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
getJoinRMSCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getJournalArticle() - Method in class org.biojava.nbio.structure.PDBHeader: Get the associated publication as defined by the JRNL records in a PDB file.
getJournalArticle() - Method in interface org.biojava.nbio.structure.Structure: Get the associated publication as defined by the JRNL records in a PDB file.
getJournalArticle() - Method in class org.biojava.nbio.structure.StructureImpl: get the associated publication as defined by the JRNL records in a PDB file.
getJournalName() - Method in class org.biojava.nbio.structure.JournalArticle
getJSpecViewProperty(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
getKappa() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getKey() - Method in class org.biojava.nbio.ontology.utils.KeyedWeakReference
getKeywords() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getKeyWords() - Method in interface org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface
getKeyWords() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getKeyWords() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
getKeyWords() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: Pull UniProt key words which is a mixed bag of words associated with this sequence
getKeywords() - Method in interface org.biojava.nbio.protmod.ProteinModification
getKeywords() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getKimuraTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate a phylogenetic tree of the MultipleAlignment using Kimura distances and the Neighbor Joining algorithm from forester.
getKMFigureInfo() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getL() - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition: Return triangular factor.
getL() - Method in class org.biojava.nbio.structure.jama.LUDecomposition: Return lower triangular factor
getLabel_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getLabel_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getLabel_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getLabel_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getLabel_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getLabel_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getLabel_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getLabel_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getLabel_entity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getLabel_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getLabel_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getLabelOfAtomOnComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
getLabelOfAtomOnComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
getLargestSubunit() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getLast(String) - Method in class org.biojava.nbio.structure.AtomPositionMap
getLast() - Method in class org.biojava.nbio.structure.AtomPositionMap
getLastIndexOf(C) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getLastIndexOf(C) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getLastIndexOf(C) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Searches for the given Compound within this alignment profile.
getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader: Returns the last occurrence of the given compound in this store; performs a linear search
getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Returns the length of the Sequence if the given compound was equal to the one given during construction.
getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getLastIndexOf(C) - Method in interface org.biojava.nbio.core.sequence.template.Sequence: Scans through the Sequence looking for the last occurrence of the given compound
getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
getLastIndexOf(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
getLayerLines() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getLcmp() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getLcmp() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getLeft() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getLegend(String) - Static method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: provide the coordinates for where to draw the legend for line X and if it is chain 1 or 2
getLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Provide the coordinates for where to draw the legend for line X given the structure index.
getLength() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getLength() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getLength() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the number of columns in the alignment profile.
getLength() - Method in class org.biojava.nbio.core.sequence.CDSSequence
getLength() - Method in class org.biojava.nbio.core.sequence.ExonSequence
getLength() - Method in class org.biojava.nbio.core.sequence.GeneSequence
getLength() - Method in class org.biojava.nbio.core.sequence.IntronSequence
getLength() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getLength() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getLength() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: The sequence length
getLength() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
getLength() - Method in interface org.biojava.nbio.core.sequence.location.template.Location: Returns the length of the outer bounds of this location
getLength() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment: Get the length of the MSA where it is assumed that all sequence position
getLength() - Method in class org.biojava.nbio.core.sequence.StartCodonSequence
getLength() - Method in class org.biojava.nbio.core.sequence.StopCodonSequence
getLength() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
getLength() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
getLength() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader: Returns the length of the sequence
getLength() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
getLength() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Returns the length given during construction
getLength() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getLength() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile: Returns the number of columns in the alignment profile.
getLength() - Method in interface org.biojava.nbio.core.sequence.template.Sequence: Returns the length of the Sequence
getLength() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getLength() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
getLength() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence: Returns the size of the windowed sequence which is the length by the window size.
getLength() - Method in class org.biojava.nbio.data.sequence.FastaSequence
getLength() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getLength(int, int, String) - Method in class org.biojava.nbio.structure.AtomPositionMap: Calculates the number of residues of the specified chain in a given range, inclusive.
getLength(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap: Calculates the number of atoms between two ResidueNumbers, inclusive.
getLength() - Method in interface org.biojava.nbio.structure.Bond: Gets the distance between the two atoms of this bond.
getLength() - Method in class org.biojava.nbio.structure.BondImpl: Gets the distance between the two atoms of this bond.
getLength() - Method in class org.biojava.nbio.structure.cath.CathDomain
getLength() - Method in class org.biojava.nbio.structure.cath.CathFragment
getLength() - Method in class org.biojava.nbio.structure.cath.CathSegment
getLength() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getLength() - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
getLength() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement: Return the length (number of residues) in the SSE.
getLength() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism: Returns the radius of a circumscribed sphere, that goes through all vertices
getLength1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getLength2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getLength_a() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getLength_a_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getLength_b() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getLength_b_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getLength_c() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getLength_c_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getLengthDirectional(int, int, String) - Method in class org.biojava.nbio.structure.AtomPositionMap: Calculates the number of residues of the specified chain in a given range.
getLengthDirectional(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap: Calculates the number of atoms between two ResidueNumbers, inclusive.
getLfrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getLigands() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getLigands() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigands
getLigRSRnbrMean() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the ligRSRnbrMean property.
getLigRSRnbrStdev() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the ligRSRnbrStdev property.
getLigRSRnumnbrs() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the ligRSRnumnbrs property.
getLigRSRZ() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the ligRSRZ property.
getLikeSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getLinearPredictor() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getLineLength() - Method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter
getLineLength() - Method in class org.biojava.nbio.core.sequence.io.FastaWriter
getLineLength() - Method in class org.biojava.nbio.core.sequence.io.GenbankWriter
getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getLineLoops() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
getLinkages() - Method in interface org.biojava.nbio.protmod.ModificationCondition
getLinkages() - Method in class org.biojava.nbio.protmod.ModificationConditionImpl: }
getList() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource: Returns this resource as a list of Strings
getList(BufferedReader) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Returns the contents of a buffered reader as a list of strings
getList(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Delegates to IOUtils.getList(BufferedReader) by wrapping the InputStream in a valid reader.
getList(File) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Delegates to IOUtils.getList(InputStream) by wrapping the File in a valid stream.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer
getLoadMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getLocalDir() - Method in class org.biojava.nbio.phosphosite.Dataset
getLocalFile(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Searches for previously downloaded files
getLocalFileName(String) - Static method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider: Returns the file name that contains the definition for this ChemComp
getLocalFiles() - Method in class org.biojava.nbio.phosphosite.Dataset
getLocalSymmetries() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Returns a list of lists of local quaternary structure symmetry results
getLocalTimeLimit() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getLocation() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getLocationInAlignment() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getLocationInAlignment() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the Location of the original Sequence within an alignment.
getLocations() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature: A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
getLocations() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
getLocations() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface: The location(s) of this feature where the location should contain a reference to parent and sequence etc.
getLocus() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
getLogScale(double) - Method in class org.biojava.nbio.survival.data.WorkSheet: Get the log scale of this worksheet where a zero value will be set to .1 as Log(0) is undefined
getLogScale(double, double) - Method in class org.biojava.nbio.survival.data.WorkSheet: Get the log scale of this worksheet
getLongName() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
getLongName() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
getLongName() - Method in interface org.biojava.nbio.core.sequence.template.Compound
getLongName() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
getLongName() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
getLower() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getLowerBound() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getLs_d_res_high() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_d_res_low() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_matrix_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_number_parameters() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_number_reflns_all() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_number_reflns_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_number_reflns_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_number_reflns_R_work() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_number_restraints() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_percent_reflns_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_percent_reflns_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_R_factor_all() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_R_factor_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_R_factor_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_R_factor_R_free_error() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_R_factor_R_free_error_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_R_factor_R_work() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_redundancy_reflns_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_wR_factor_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLs_wR_factor_R_work() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getLto() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getM() - Method in class org.biojava.nbio.structure.align.model.AFP
getMacromolecularSize() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
getManual() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getMappingSequence() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
getMapProperty() - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
getMapSeqToStruct() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
getMass() - Method in class org.biojava.nbio.aaproperties.xml.Element
getMass() - Method in class org.biojava.nbio.aaproperties.xml.Isotope
getMatches(File, double) - Static method in class org.biojava.nbio.genome.homology.BlastHomologyHits
getMatchingAtomRes(Chain, List<Chain>) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
getMatMatrix() - Method in class org.biojava.nbio.structure.align.ce.CECalculator: Caution: this matrix is overwriten with very different data at several points in the alignment algorithm.
getMatMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced: Caution: this matrix is overwriten with very different data at several points in the alignment algorithm.
getMatrices() - Method in class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser
getMatrix(String) - Method in interface org.biojava.nbio.core.alignment.matrices.AAIndexProvider
getMatrix(String) - Method in class org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider
getMatrix() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getMatrix() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getMatrix() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns entire matrix.
getMatrix() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
getMatrix() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
getMatrix() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix(int, int, int, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Get a submatrix.
getMatrix(int[], int[]) - Method in class org.biojava.nbio.structure.jama.Matrix: Get a submatrix.
getMatrix(int, int, int[]) - Method in class org.biojava.nbio.structure.jama.Matrix: Get a submatrix.
getMatrix(int[], int, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Get a submatrix.
getMatrix11() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix12() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix13() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix21() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix22() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix23() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix31() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix32() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrix33() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getMatrixAsString() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getMatrixAsString() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getMatrixAsString() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns this matrix as a formatted String with Compound labels along the axes.
getMatrixFromAAINDEX(String) - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns any matrix from the AAINDEX database file
getMatrixFromAlgebraic(String) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getMatrixPanel() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
getMatTransform() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
getMax() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getMax() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
getMax(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: Scans through a list of locations to find the Location with the highest end
getMax(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools: Scans through a list of locations to find the Location with the highest end
getMaxAtoms() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: The maximum numbers of atoms to load in a protein structure (prevents memory overflows)
getMaxDimension() - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Gets the maximum dimension of the unit cell.
getMaxExtension() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns the maximum extension (length) of structure
getMaxExtension() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup: Returns the maximum extension (length) of structure
getMaxGap() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getMaxGapFrag() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getMaxGapSize() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: the Max gap size parameter G .
getMaxGapSize() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams: CE specific parameter: set the Max gap size parameter G (during AFP extension).
getMaximumCovalentValence() - Method in enum org.biojava.nbio.structure.Element: Returns the maximum valence for this Element.
getMaximumExtend(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools: Returns the maximum extend of the structure in the x, y, or z direction.
getMaximumLocalCombinations() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMaximumLocalResults() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMaximumLocalSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMaximumSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
getMaximumValence() - Method in enum org.biojava.nbio.structure.Element: Returns the maximum valence for this Element.
getMaxIter() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getMaxNrIterationsForOptimization() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: Get the maximum nr of times the (slow) optimiziation of alignment should iterate.
getMaxNrSuggestions() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider: Get the maximun nr of suggestions
getMaxNrSuggestions() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
getMaxNrSuggestions() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
getMaxOptRMSD() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)
getMaxOptRMSD() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams: (jCE specific): maximum RMSD that shall be calculated for the alignment.
getMaxPenalty() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getMaxrefine() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getMaxRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getMaxScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
getMaxScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
getMaxScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getMaxScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
getMaxScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getMaxScore() - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns maximum possible score.
getMaxSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getMaxSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getMaxSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
getMaxSingleCompoundStringLength() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet: Returns the maximum size of a compound String this set holds
getMaxSymmOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getMaxTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getMaxTra() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters: get the maximum number of Twists that are allowed...
getMaxTra() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
getMaxTra() - Method in class org.biojava.nbio.structure.align.model.AFPChain: get the maximum nr of Twists that are allowed...
getMaxValue() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getMaxValue() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getMaxValue() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns the maximum value in this matrix.
getMCScore(MultipleAlignment, double, double, double) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the MC score, specific for the MultipleAlignment algorithm.
getMean() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the mean property.
getMean() - Method in class org.biojava.nbio.structure.validation.BondOutlier: Gets the value of the mean property.
getMean() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the mean property.
getMean() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the mean property.
getMean() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getMeanExtension() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup: Returns the mean extension (length) of structure
getMembers() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
getMembership() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getMergedClusters(double) - Method in class org.biojava.nbio.structure.symmetry.core.ClusterMerger: Combine clusters based on the given sequence identity
getMessage() - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
getMetaDataColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
getMetaDataColumnsHashMap() - Method in class org.biojava.nbio.survival.data.WorkSheet
getMetaDataFilter() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getMetaDataRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
getMetaDataRowsHashMap() - Method in class org.biojava.nbio.survival.data.WorkSheet
getMethod() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
getMethod() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getMethod() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Returns name of method used for symmetry perception.
getMethod_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
getMethod_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron: Returns the radius of a sphere, that is tangent to each of the icosahedron's edges
getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron: Returns the radius of a sphere, that is tangent to each of the octahedron's edges
getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron: Returns the radius of a sphere, that is tangent to each of the tetrahedron's edges
getMin() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getMin() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
getMin(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: Scans through a list of locations to find the Location with the lowest start
getMin(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools: Scans through a list of locations to find the Location with the lowest start
getMinAlignedStructures() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getMinBlockLen() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getMinCoreLength() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getMinCPLength() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
getMinCPLength() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
getMindiff() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the mindiff property.
getMindiff() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the mindiff property.
getMinDistance() - Method in class org.biojava.nbio.structure.contact.GroupContact
getMinimumHelixAngle() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMinimumHelixRise() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMinimumSequenceLength() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMinimumSequenceLengthFraction() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getMinimumSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
getMinimumValence() - Method in enum org.biojava.nbio.structure.Element: Returns the minimum valence for this Element.
getMinLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getMinMax(double[]) - Method in class org.biojava.nbio.structure.contact.BoundingBox: Returns an array of size 2 with min and max values of given double array
getMinRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getMinScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
getMinScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
getMinScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getMinScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
getMinScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getMinScore() - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns minimum possible score.
getMinSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getMinSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getMinSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getMinTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getMinValue() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getMinValue() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getMinValue() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns the minimum value in this matrix.
getMirrors() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getMisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getMisLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getMismatchCount() - Method in class org.biojava.nbio.core.search.io.Hsp
getMisScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getMMcifConsumer() - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
getMod_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
getModDate() - Method in class org.biojava.nbio.structure.PDBHeader
getModel(int) - Method in class org.biojava.nbio.ronn.ModelLoader
getModel(int) - Method in interface org.biojava.nbio.structure.Structure: Retrieve all Chains belonging to a model .
getModel(int) - Method in class org.biojava.nbio.structure.StructureImpl: retrieve all Chains belonging to a model .
getModel() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the model property.
getModel_Cartn_x() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getModel_Cartn_y() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getModel_Cartn_z() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getModelledSubgroup() - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation: Gets the value of the modelledSubgroup property.
getModelNumber() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
getModelNumber() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getModelVariables() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
getModelVariables() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
getModification() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
getModification() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
getModType() - Method in class org.biojava.nbio.phosphosite.Site
getMogAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the mogAngleOutlier property.
getMogBondOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the mogBondOutlier property.
getMogulIgnore() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the mogulIgnore property.
getMolecularWeight(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the molecular weight of sequence.
getMolecularWeight(ProteinSequence, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the molecular weight of sequence.
getMolecularWeight(ProteinSequence, File, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the molecular weight of sequence.
getMolecularWeight(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the molecular weight of sequence.
getMolecularWeight(String, File, File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the molecular weight of sequence.
getMolecularWeight(String, File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the molecular weight of sequence.
getMolecularWeight(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getMolecularWeight(ProteinSequence, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getMolecularWeight(ProteinSequence, File, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getMolecularWeight(Character) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
getMolecularWeight() - Method in interface org.biojava.nbio.core.sequence.template.Compound
getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the molecular weight of sequence.
getMolecularWeightBasedOnXML(String, AminoAcidCompositionTable) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method that returns the molecular weight of sequence.
getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getMolecule() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getMoleculeIds() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Return the pair of identifiers identifying each of the 2 molecules of this interface in the asymmetry unit (usually the chain identifier if this interface is between 2 chains)
getMolecules() - Method in class org.biojava.nbio.structure.contact.StructureInterface
getMolId() - Method in class org.biojava.nbio.structure.Compound: Return the molecule identifier, called entity_id in mmCIF dictionary.
getMolName() - Method in class org.biojava.nbio.structure.Compound
getMomentsOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getMon_nstd_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getMon_nstd_parent_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getMTranspose() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
getMultiBlockJmolString(MultipleAlignment, List<Atom[]>, ColorBrewer, boolean) - Static method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol: Colors every Block of the structures with a different color, following the palette.
getMultipleAlignment() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
getMultipleAlignment() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
getMultipleAlignment() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Returns the parent MultipleAlignment of the BlockSet.
getMultipleAlignment() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
getMultipleAlignment(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the MultipleAlignments at the specified index in the ensemble.
getMultipleAlignment(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getMultipleAlignment() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getMultipleAlignmentMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getMultipleAlignments() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the List of MultipleAlignments in the ensemble.
getMultipleAlignments() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getMultipleSequenceAlignment(List<S>, Object...) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method which computes a multiple sequence alignment for the given List of Sequences.
getMultipleStructureAligner() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
getMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getMutation() - Method in class org.biojava.nbio.structure.Compound
getN() - Method in interface org.biojava.nbio.structure.AminoAcid: Get N atom.
getN() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Get N atom.
getNaive_imat() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getNaiveVariance() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getName() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
getName() - Method in class org.biojava.nbio.aaproperties.xml.Element
getName() - Method in class org.biojava.nbio.aaproperties.xml.Isotope
getName() - Method in class org.biojava.nbio.aaproperties.xml.Name2Count
getName() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getName() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the name of this node.
getName() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getName() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getName() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns the name (short description) of this matrix.
getName() - Method in class org.biojava.nbio.core.sequence.features.Qualifier
getName() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
getName() - Method in class org.biojava.nbio.ontology.IntegerOntology
getName() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
getName() - Method in interface org.biojava.nbio.ontology.Ontology: Return the name of this ontology
getName() - Method in class org.biojava.nbio.ontology.Ontology.Impl
getName() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
getName() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
getName() - Method in class org.biojava.nbio.ontology.Synonym
getName() - Method in interface org.biojava.nbio.ontology.Term: Return the name of this term.
getName() - Method in class org.biojava.nbio.ontology.Term.Impl
getName() - Method in class org.biojava.nbio.ontology.Triple.Impl
getName() - Method in class org.biojava.nbio.structure.align.client.StructureName: Deprecated.
use StructureName.getIdentifier()
getName() - Method in interface org.biojava.nbio.structure.Atom: Get atom name, e.g.
getName() - Method in class org.biojava.nbio.structure.AtomImpl: Get atom name, e.g.
getName() - Method in class org.biojava.nbio.structure.cath.CathDomain
getName() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique
getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
getName() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getName() - Method in class org.biojava.nbio.structure.rcsb.RCSBMacromolecule
getName() - Method in class org.biojava.nbio.structure.rcsb.RCSBTaxonomy
getName() - Method in class org.biojava.nbio.structure.scop.ScopDescription
getName() - Method in interface org.biojava.nbio.structure.Structure: Get biological name of Structure.
getName() - Method in class org.biojava.nbio.structure.StructureImpl: Get biological name of Structure.
getName() - Method in class org.biojava.nbio.structure.validation.Program: Gets the value of the name property.
getName() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
getName() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getName() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getName1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getName1() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
getName1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getName1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getName2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getName2() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
getName2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getName2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getNames() - Method in class org.biojava.nbio.structure.gui.util.SelectMultiplePanel
getNames() - Method in class org.biojava.nbio.structure.scop.Astral
getnAtom() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getnAtom() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getNatomsEDS() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the natomsEDS property.
getNaturalPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getNavMap() - Method in class org.biojava.nbio.structure.AtomPositionMap
getNcbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
getNcens() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getNclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
getNcsOperators() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo: Get the NCS operators.
getNcuts() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
getNdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getNdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getNdead() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getNdom() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getNearestAtRisk(double) - Method in class org.biojava.nbio.survival.cox.StrataInfo: Selection of number of risk will depend on the precision and rounding of time in the survival table.
getNearestTime(double) - Method in class org.biojava.nbio.survival.cox.StrataInfo: Need to find the actual time for the nearest time represented as a percentage Would be used to then look up the number at risk at that particular time
getNeighbors(Point3d) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
getNeighborsWithCache(Point3d) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
getNestedValue(NestedValue, String, int) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
getNetCharge(ProteinSequence, boolean, double) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Returns the net charge of sequence at pH 7.
getNetCharge(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
getNetCharge(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
getNetCharge(String, boolean, double) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the net charge of sequence at pH 7.
getNetCharge(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
getNetCharge(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
getNetCharge(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getNetCharge(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getNetCharge(ProteinSequence, boolean, double) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
getNeutronsNum() - Method in class org.biojava.nbio.aaproperties.xml.Isotope
getNevent() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getNewDocument() - Static method in class org.biojava.nbio.core.util.XMLHelper
getNewickString(Phylogeny, boolean) - Static method in class org.biojava.nbio.phylo.ForesterWrapper: Convert a Phylogenetic tree to its Newick representation, so that it can be exported to an external application.
getNext() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
getNext() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
getNMRStructures() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: get list of all current NMR structures
getNodeId() - Method in class org.biojava.nbio.structure.cath.CathNode
getNodeListFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
getNoiseCutoffs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation: Not always 2.
It may undergo further change.
getNonenantpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getNormAlignScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getNotesList() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getNotObserved() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getNrAlignments() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getNrAtoms(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Count how many Atoms are contained within a Structure object.
getNrBioAssemblies() - Method in class org.biojava.nbio.structure.PDBHeader: Get the number of biological assemblies available in the PDB header
getNrBiolAssemblies(String) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider: Returns the number of available biological assemblies.
getNrBiolAssemblies(String) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
getNrBiolAssemblies() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getNrBiolAssemblies(String) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
getNrBiolAssemblies() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: Returns the number of available biological assemblies.
getNrBiolAssemblies(String) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
getNrBiolAssemblies() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getNrBiologicalAssemblies(String) - Static method in class org.biojava.nbio.structure.StructureIO
getNrCPU() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getNreported() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getNrEQR() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Get the number of structurally equivalent residues
getNrGroups(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Count how many groups are contained within a structure object.
getNrisk() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getNrThreads() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getNseg() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
getnStart() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getNStart() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation: Returns the number of starts if this rotation represents a helical rotation
getNuc4_2() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Nuc 4.2 matrix by Lowe Only the first nucleotide sequence to align can contain ambiguous nucleotides
getNuc4_4() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Nuc 4.4 matrix by Lowe Both of the nucleotide sequences to align can contain ambiguous nucleotides
getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getNucleotides() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
getNullValue() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
getNum() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
getNum() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
getNumAtomContacts() - Method in class org.biojava.nbio.structure.contact.GroupContact
getNumberCoefficients() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getNumberDiscreteValues() - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
getNumberOfInvalidChar(String, Set<Character>, boolean) - Static method in class org.biojava.nbio.aaproperties.Utils: Return the number of invalid characters in sequence.
getNumberVariables() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getNumericalBondOrder() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond: Converts this ChemCompBond's value_order attribute into an int using the conversion:
getNumericRepresentation() - Method in enum org.biojava.nbio.core.sequence.Strand
getNumFreeReflections() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the numFreeReflections property.
getNumGaps() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getNumGaps() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns number of gaps in the sequence.
getNumHReduce() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the numHReduce property.
getNumHReduce() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the numHReduce property.
getNumIdenticals() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getNumIdenticals() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the number of indices for which both the query and target sequences have an identical Compound.
getNumIindices() - Method in class org.biojava.nbio.structure.contact.GridCell
getNumJindices() - Method in class org.biojava.nbio.structure.contact.GridCell
getNumLeft() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
getNumLeft() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
getNumMillerIndices() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the numMillerIndices property.
getNumobs() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the numobs property.
getNumobs() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the numobs property.
getNumOperators() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets the number of symmetry operators corresponding to this SpaceGroup (counting the identity operator)
getNumRes() - Method in class org.biojava.nbio.structure.Compound
getNumSequences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getNumSimilars() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getNumSimilars() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the number of indices for which both the query and target sequences have a similar Compound.
getO() - Method in interface org.biojava.nbio.structure.AminoAcid: Get O atom.
getO() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Get O atom.
getO3Prime() - Method in class org.biojava.nbio.structure.NucleotideImpl: Returns the O3' atom if present, otherwise null
getO5Prime() - Method in class org.biojava.nbio.structure.NucleotideImpl: Returns the O5' atom if present, otherwise null
getObject() - Method in interface org.biojava.nbio.ontology.Triple: Return the object term of this triple.
getObject() - Method in class org.biojava.nbio.ontology.Triple.Impl
getOboFileEventListener() - Method in class org.biojava.nbio.ontology.obo.OboFileParser
getObs() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the obs property.
getObs() - Method in class org.biojava.nbio.structure.validation.BondOutlier: Gets the value of the obs property.
getObsoleteBehavior() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns how this instance deals with obsolete entries.
getObsoleteBehavior() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
getObsoleteBehavior() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Returns how this instance deals with obsolete entries.
getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Location of obsolete files within the directory, as an array of paths.
getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader
getObsval() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the obsval property.
getObsval() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the obsval property.
getOccupancy() - Method in interface org.biojava.nbio.structure.Atom: Get occupancy.
getOccupancy() - Method in class org.biojava.nbio.structure.AtomImpl
getOccupancy() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getOccupancy_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getOccupancy_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOccupancy_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOccurrenceType() - Method in interface org.biojava.nbio.protmod.ProteinModification
getOccurrenceType() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getOffset() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getOligomeric_count() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
getOligomeric_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
getOmega() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getOmimId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getOne() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
getOne() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
getOne() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
getOne_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getOneLetterCode(ChemComp, ChemicalComponentDictionary) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
getOneLetterCode(ChemComp) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
getOnelineFasta() - Method in class org.biojava.nbio.data.sequence.FastaSequence
getOntology() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
getOntology() - Method in interface org.biojava.nbio.ontology.OntologyTerm: Get the remote ontology referenced by this term
getOntology() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
getOntology() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
getOntology() - Method in interface org.biojava.nbio.ontology.Term: Return the ontology in which this term exists.
getOntology() - Method in class org.biojava.nbio.ontology.Term.Impl
getOntology() - Method in class org.biojava.nbio.ontology.Triple.Impl
getOpenPDBMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getOpenPenalty() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty: Returns the negative of the opening penalty passed to the constructor.
getOpenPenalty() - Method in interface org.biojava.nbio.alignment.template.GapPenalty: Returns penalty given when a deletion or insertion gap first opens
getOper_expression() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
getOperator() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
getOps() - Method in class org.biojava.nbio.ontology.IntegerOntology
getOps() - Method in interface org.biojava.nbio.ontology.Ontology: Return the associated OntologyOps.
getOps() - Method in class org.biojava.nbio.ontology.Ontology.Impl
getOptAln() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Tracks the Atom positions in the optimal alignment.
getOptAlnAsList(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Retrieves the optimum alignment from an AFPChain and returns it as a java collection.
getOptimization() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getOptimizationSteps() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getOptLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain: The length of each block
getOptLength() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getOptRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getOrbits() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getOrbits() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getOrbits() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getOrder() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
getOrder(List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
getOrder() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
getOrder() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getOrderDetectorMethod() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getOrderedPairs() - Method in class org.biojava.nbio.structure.quaternary.CartesianProduct: Generates the list of ordered pair between two sets.
getOrgan() - Method in class org.biojava.nbio.structure.Compound
getOrganelle() - Method in class org.biojava.nbio.structure.Compound
getOrganism() - Method in class org.biojava.nbio.phosphosite.Site
getOrganism_common_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
getOrganism_scientific() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
getOrganismCommon() - Method in class org.biojava.nbio.structure.Compound
getOrganismName() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: Get the organism name assigned to this sequence
getOrganismScientific() - Method in class org.biojava.nbio.structure.Compound
getOrganismTaxId() - Method in class org.biojava.nbio.structure.Compound
getOrientation() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that sets a specific orientation
getOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
getOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns the number of orientations available for this structure
getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns the name of a specific orientation
getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn: Returns the name of a specific orientation
getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn: Returns the name of a specific orientation
getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns the name of a specific orientation
getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getOrientationWithZoom(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that sets a specific orientation and zoom to draw either axes or polyhedron
getOrientationWithZoom(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that sets a specific orientation and zoom to draw either axes or polyhedron
getOrientationWithZoom(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getOrigGroup() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getOrigGroup() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getOriginalCenters() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getOriginalHeader() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getOriginalMetaData(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getOriginalModificationId() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl: Deprecated.
use getModification().getId()
getOriginalSequence() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getOriginalSequence() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the original Sequence before alignment.
getOriginalSequences() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getOriginalSequences() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a List containing the original Sequences used for alignment.
getORmsdThr() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: Get the Original RMSD threshold from which the alignment optimization is started
getOrthologousSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getOther(Atom) - Method in interface org.biojava.nbio.structure.Bond: A utility method to get the other atom in a bond, given one of its atoms.
getOther(Atom) - Method in class org.biojava.nbio.structure.BondImpl: A utility method to get the other atom in a bond, given one of its atoms.
getOtherTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Deprecated.
getOutFile() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
getOutFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getOutFile() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getOutFileLocation() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
getOutputFormat() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
getOutputOption(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: This method forwards to NCBIQBlastOutputProperties.getOutputOption(BlastOutputParameterEnum).
getOutputOption(BlastOutputParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: Gets the value of specified parameter or null if it is not set
getOutputOption(String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties: Method that returns the value associated with the key given in parameter.
getOutputOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: Gets output parameters, which are currently set
getOutputOptions() - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties: Method to get all keys to the information stored in this object.
getOverall_FOM_free_R_set() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOverall_FOM_work_R_set() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOverall_SU_B() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOverall_SU_ML() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOverall_SU_R_Cruickshank_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOverall_SU_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getOverallModelFitPvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getOverlapCount() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getOverlapCount() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the maximum number of elements contributed to a column of an alignment by this Sequence.
getOverlapLength(HmmerResult) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult: Get the overlap between two HmmerResult objects
getOwab() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the owab property.
getOxidationState() - Method in enum org.biojava.nbio.structure.Element: Returns a typical oxidation state for this Element.
getP() - Method in class org.biojava.nbio.structure.NucleotideImpl: Returns the P atom if present, otherwise null
getP1() - Method in class org.biojava.nbio.structure.align.model.AFP
getP2() - Method in class org.biojava.nbio.structure.align.model.AFP
getPair() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getPair() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getPair() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceAligner: Returns sequence alignment pair.
getPair() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileAligner: Returns alignment profile pair.
getPair() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
getPair() - Method in class org.biojava.nbio.structure.contact.AtomContact
getPair() - Method in class org.biojava.nbio.structure.contact.GroupContact
getPairInProfileScorer() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getPairInProfileScorer() - Method in interface org.biojava.nbio.alignment.template.RescoreRefiner: Returns class type of pairwise scoring subroutine.
getPairs() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
getPairwiseAligner(S, S, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method which constructs a pairwise sequence aligner.
getPairwiseAlignment(S, S, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method which computes a sequence alignment for the given Sequence pair.
getPairwiseAlignment(SequenceAlignmentCluster) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getPairwiseAlignmentMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getPairwiseStructureAligner() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
getPAM250() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns PAM 250 matrix by Dayhoff
getPanelPos(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: get the position of the sequence position on the Panel
getPanelPos(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Get the X position on the Panel of a particular sequence position.
getPanelPos(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
getPara(int, int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
getParameters() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
getParameters() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
getParameters() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeMain
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
getParameters() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
getParameters() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
getParameters() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner: Return the parameters of this algorithm instance.
getParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
getParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
getParameters() - Method in interface org.biojava.nbio.structure.align.StructureAlignment: Return the paramers for this algorithm.
getParameters() - Method in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
getParameters() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
getParams() - Method in class org.biojava.nbio.structure.align.FarmJob
getParams() - Method in class org.biojava.nbio.structure.align.StructurePairAligner: get the parameters.
getParams() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getParent() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getParent() - Method in interface org.biojava.nbio.structure.Chain: Deprecated.
use getStructure(Structure) instead.
getParent() - Method in class org.biojava.nbio.structure.ChainImpl: Deprecated.
use getStructure instead.
getParent() - Method in class org.biojava.nbio.structure.DBRef: Get the structure object that this DBRef relates to.
getParent(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary: Get the parent of a component.
getParentChains() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Finds the parent chains by looking up the references of first atom of each side of this interface
getParentChromosomeSequence() - Method in class org.biojava.nbio.core.sequence.GeneSequence: The parent ChromosomeSequence which contains the actual DNA sequence data
getParentCompounds() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Finds the parent compounds by looking up the references of first atom of each side of this interface
getParentFeature() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature: Get the parent Feature
getParentFeature() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
getParentFeature() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface: Get the parent feature
getParentId() - Method in class org.biojava.nbio.structure.cath.CathNode
getParentSequence() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getParentSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode
getPartner() - Method in class org.biojava.nbio.structure.secstruc.HBond
getPartner1() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
getPartner2() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
getPath() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getPath() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
getPath() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getPath() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Get the path that is used to cache PDB files.
getPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Returns the path value.
getPathSize() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getPathSize() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getPaulingElectronegativity() - Method in enum org.biojava.nbio.structure.Element: Returns the Pauling electronegativity for this Element.
getPdb1() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getPdb1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getPdb2() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getPdb2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
getPdb_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getPdb_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getPdb_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getPdb_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getPdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getPdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getPdb_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getPdb_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getPdbAln() - Method in class org.biojava.nbio.structure.align.model.AFPChain: used temporarily during XML serialization to track the PDB positions of the alignmnet
getPdbccId() - Method in interface org.biojava.nbio.protmod.ProteinModification
getPdbccId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getPdbccIds() - Method in class org.biojava.nbio.protmod.Component
getPdbccName() - Method in interface org.biojava.nbio.protmod.ProteinModification
getPdbccName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getPdbChainIdClusters() - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
getPdbChainIdClusters(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
getPDBCharacter(boolean, char, char, boolean, char) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Creates formatted String for a single character of PDB output
getPDBCode() - Method in interface org.biojava.nbio.structure.Structure: Get PDB code of structure.
getPDBCode() - Method in class org.biojava.nbio.structure.StructureImpl: Get PDB code of structure.
getPDBCode1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getPDBCode2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getPDBConservation(boolean, char, char, boolean) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Creates formatted String for displaying conservation in PDB output
getPDBDirField() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
getPdbEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getPdbFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getPdbFilePath() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getPdbFilePath() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
getPdbGroup() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getPdbGroup() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getPDBHeader() - Method in interface org.biojava.nbio.structure.Structure: Return the header information for this PDB file
getPDBHeader() - Method in class org.biojava.nbio.structure.StructureImpl: Return the header information for this PDB file
getPdbId() - Method in class org.biojava.nbio.structure.align.client.StructureName: Get the PDB ID for this name, if any.
getPdbId() - Method in class org.biojava.nbio.structure.cath.CathDomain: Deprecated.
This method is poorly named; use CathDomain.getThePdbId() or CathDomain.getPdbIdAndChain() instead
getPdbId() - Method in class org.biojava.nbio.structure.domain.PDPDomain
getPdbId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getPdbId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getPdbId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getPdbId() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getPdbId() - Method in class org.biojava.nbio.structure.rcsb.RCSBDescription
getPdbId() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigands
getPdbId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getPdbId() - Method in interface org.biojava.nbio.structure.Structure: Deprecated.
From BioJava 4.2, use Structure.getPDBCode() or getStructureIdentifier().toCanonical().getPdbId()
getPdbId() - Method in class org.biojava.nbio.structure.StructureImpl: Deprecated.
getPdbId() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
getPdbIdAndChain() - Method in class org.biojava.nbio.structure.cath.CathDomain: Returns a string of the form PDBID.CHAIN.
getPdbInfo(Atom) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools: get jmol style info: jmol style: [MET]508:A.CA/1 #3918 insertion code: [ASP]1^A:A.CA/1 #2
getPdbInfo(Atom, boolean) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools
getPDBLegend() - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Creates formatted String for displaying conservation legend in PDB output
getPDBName() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
getPDBName() - Method in interface org.biojava.nbio.structure.Group: Get the PDB 3-letter name for this group.
getPDBName() - Method in class org.biojava.nbio.structure.HetatomImpl: Returns the PDBName.
getPDBNameOfPotentialAtomsOnComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
getPDBNameOfPotentialAtomsOnComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
getPdbPairs(String, int, String) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
getPDBResidueNumber() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
getPdbResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getPDBresnum(int, AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP: Return a list of pdb Strings corresponding to the aligned positions of the molecule.
getPDBresnum(int, MultipleAlignment, Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay: Utility method used in the MultipleAlignmentJmol Frame, when the aligned residues of a structure in the alignment have to be selected for formatting them (coloring and style).
getPdbResNum() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getPdbResNum() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getPdbResNum() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getPDBresnum1() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
getPDBresnum2() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
getPDBRevisionNumber() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the pdbRevisionNumber property.
getPDBserial() - Method in interface org.biojava.nbio.structure.Atom: Get PDB atom number.
getPDBserial() - Method in class org.biojava.nbio.structure.AtomImpl: Get PDB atom number.
getPdbSerial() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
getPdbStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getPDBUploadPanel() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
getPdbx_align() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_align_begin() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getPdbx_alt_source_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_alt_source_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_ambiguous_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_aromatic_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_aromatic_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getPdbx_atcc() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_auth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getPdbx_auth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getPdbx_auth_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getPdbx_auth_seq_align_beg() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_auth_seq_align_end() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_auth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getPdbx_auth_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_beg_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_beg_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_blank_PDB_chainid_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
getPdbx_CASP_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
getPdbx_cell() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_cell_line() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_cellular_location() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_component_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_component_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_component_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_data_cutoff_high_absF() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_data_cutoff_high_rms_absF() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_data_cutoff_low_absF() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_db_accession() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getPdbx_db_accession() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_db_align_beg_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_db_align_end_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_description() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getPdbx_description() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_descriptor() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
getPdbx_diffrn_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_dist_value() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ec() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getPdbx_end_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_end_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_evidence_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getPdbx_formal_charge() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getPdbx_formal_charge() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_fragment() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getPdbx_fragment() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_full_space_group_name_H_M() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
getPdbx_gene_src_atcc() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_cell() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_cell_line() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_cellular_location() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_fragment() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_gene() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_ncbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_organ() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_organelle() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_plasmid() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_plasmid_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_scientific_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_gene_src_variant() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_atcc() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_cell() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_cell_line() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_cellular_location() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_culture_collection() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_gene() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_ncbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_organ() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_organelle() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_scientific_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_strain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_tissue() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_tissue_fraction() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_variant() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_vector() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_host_org_vector_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_ideal_coordinates_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_ideal_coordinates_missing_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_initial_date() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_isotropic_thermal_model() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_keywords() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
getPdbx_leaving_atom_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_leaving_atom_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_leaving_atom_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ls_cross_valid_method() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_ls_sigma_F() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_ls_sigma_I() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_method_to_determine_struct() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_model_Cartn_x_ideal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_model_Cartn_y_ideal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_model_Cartn_z_ideal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_model_coordinates_db_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_model_coordinates_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_model_coordinates_missing_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_model_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
getPdbx_model_type_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
getPdbx_modified() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
getPdbx_modified_date() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_mutation() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getPdbx_ncbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_num_res() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getPdbx_num_residues() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
getPdbx_number_of_molecules() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_organ() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_organelle() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_organism_scientific() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_overall_ESU_R() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_overall_ESU_R_Free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_overall_phase_error() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_overall_SU_R_Blow_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_overall_SU_R_free_Blow_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_overall_SU_R_free_Cruickshank_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_PDB_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_PDB_id_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_pdb_id_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getPdbx_pdb_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_PDB_model_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getPdbx_pdb_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_plasmid_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_plasmid_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_polymer_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_processing_site() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_ptnr1_label_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr1_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr1_standard_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr2_label_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr2_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr3_label_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr3_label_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr3_label_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr3_label_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr3_label_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_ptnr3_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_R_Free_selection_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_ref_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_refine_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_release_status() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_replaced_by() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_replaces() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_residue_numbering() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_secretion() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_seq_align_beg_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_seq_align_end_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_seq_db_accession_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_seq_db_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_seq_db_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getPdbx_seq_one_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
getPdbx_seq_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_solvent_ion_probe_radii() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_solvent_shrinkage_radii() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_solvent_vdw_probe_radii() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_src_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPdbx_src_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbx_starting_model() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_stereo_config() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getPdbx_stereo_config() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getPdbx_stereochem_target_val_spec_case() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_stereochemistry_target_values() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getPdbx_subcomponent_list() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_synonyms() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_TLS_residual_ADP_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getPdbx_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPdbx_unique_axis() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getPdbx_value_order() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPdbx_variant() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getPdbxStructAssemblies() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
getPdbxStructAssemblies() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getPdbxStructAssemblies() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: Data access method for list describing all assemblies
getPdbxStructAssemblies() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getPdbxStructAssembly(int) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getPdbxStructAssembly(int) - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: get the data for a particular pdbxStructAssembly.
getPdbxStructAssembly(int) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getPdbxStructAssemblyGen(int) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getPdbxStructAssemblyGen(int) - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: get the data for a particular pdbxStructAssemblyGen.
getPdbxStructAssemblyGen(int) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getPdbxStructAssemblyGens() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
getPdbxStructAssemblyGens() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getPdbxStructAssemblyGens() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: Data access method for list describing all assemblies
getPdbxStructAssemblyGens() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getPdbxStructOperList() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
getPdbxStructOperList() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: Get all the possible operators
getPdbxStructOperList() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getPdbxStructOperLists() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
getPDPDomain(String) - Method in interface org.biojava.nbio.structure.domain.PDPProvider: Get a StructureIdentifier representing the specified PDP domain.
getPDPDomain(String) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider: Get a StructureIdentifier representing the specified PDP domain.
getPDPDomainNamesForPDB(String) - Method in interface org.biojava.nbio.structure.domain.PDPProvider: Get a list of all PDP domains for a given PDB entry
getPDPDomainNamesForPDB(String) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider: Get a list of all PDP domains for a given PDB entry
getPdpprovider() - Method in class org.biojava.nbio.structure.align.util.AtomCache
getPercentage() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
getPercentageIdentity() - Method in class org.biojava.nbio.core.search.io.Hsp
getPercentFreeReflections() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the percentFreeReflections property.
getPercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the percentRamaOutliers property.
getPercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the percentRotaOutliers property.
getPercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the percentRSRZOutliers property.
getPercId() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
getPeriod() - Method in enum org.biojava.nbio.structure.Element: Returns the period in the periodic table of this Element.
getPermutation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getPermutation(int) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
getPermutation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getPermutationSize() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getPfamAccession() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getPhase() - Method in class org.biojava.nbio.core.sequence.CDSSequence
getPhi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc: Calculate the phi angle.
getPhi() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getPhi() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the phi property.
getPivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition: Return pivot permutation vector
getPlasmid_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPlasmid_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getPmid() - Method in class org.biojava.nbio.structure.JournalArticle: Get the value of PMID field.
getPointGroup() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
getPolygonVertices(int, double, Point3d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.Prism: Returns the vertices of an n-fold polygon of given radius and center
getPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getPolymers() - Method in class org.biojava.nbio.structure.rcsb.RCSBDescription
getPolymerType() - Method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType: Gets the associated PolymerType, which are less specific
getPolymerType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getPos(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
getPos1() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getPos1() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
getPos2() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getPos2() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
getPosition() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
getPosition() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
getPosition() - Method in interface org.biojava.nbio.core.sequence.location.template.Point: Returns the position held by this object
getPosition(ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap: Gets the 0-based index of residueNumber to the matched atoms
getPositionInQueue(String, String, String, String) - Method in class org.biojava.nbio.structure.align.client.JFatCatClient
getPositionInQueue(String, String, String, String, int) - Method in class org.biojava.nbio.structure.align.client.JFatCatClient
getPredicate() - Method in interface org.biojava.nbio.ontology.Triple: Return a Term which defines the type of relationship between the subject and object terms.
getPredicate() - Method in class org.biojava.nbio.ontology.Triple.Impl
getPredominantGroupType(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Get the predominant GroupType for a given Chain, following these rules: if the ratio of number of residues of a certain GroupType to total non-water residues is above the threshold 0.95, then that GroupType is returned if there is no GroupType that is above the threshold then the GroupType with most members is chosen, logging it
getPreferredHeight() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: Y coordinate size
getPreferredHeight() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Y coordinate size
getPreferredSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
getPreferredWidth() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: X coordinate size
getPreferredWidth() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: X coordinate size
getPreviousIDs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getPreviousNames() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getPreviousSymbols() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getPrimitiveMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getPrincipalAxes() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getPrincipalAxisIndex() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
getPrincipalMomentsOfInertia() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getPrintMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getProbability() - Method in class org.biojava.nbio.structure.align.model.AFPChain: The probability (FATCAT) or Z-score (CE) of the alignment.
getProfile() - Method in class org.biojava.nbio.alignment.FractionalIdentityInProfileScorer
getProfile() - Method in class org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer
getProfile() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getProfile() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getProfile() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getProfile() - Method in interface org.biojava.nbio.alignment.template.Aligner: Returns the alignment Profile produced by this alignment algorithm.
getProfile() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the profile stored at this node.
getProfile() - Method in interface org.biojava.nbio.alignment.template.PairInProfileScorer: Returns the Profile from which the aligned pair originated.
getProfileFuture() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getProfileFuture() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the profile future stored at this node, but does not force the calculation, yet.
getProfileProfileAligner() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getProfileProfileAligner() - Method in interface org.biojava.nbio.alignment.template.PartitionRefiner: Returns class type of profile-profile alignment subroutine.
getProfileProfileAligner() - Method in interface org.biojava.nbio.alignment.template.RescoreRefiner: Returns class type of profile-profile alignment subroutine.
getProgram() - Method in class org.biojava.nbio.core.search.io.Result
getProgram() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
getProgram() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
getProgram() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
getProgram() - Method in class org.biojava.nbio.structure.validation.Programs: Gets the value of the program property.
getProgram_version() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
getProgram_version() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
getProgram_version() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
getPrograms() - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation: Gets the value of the programs property.
getProgramSpecificParameter(String) - Method in class org.biojava.nbio.core.search.io.Result
getProgramSpecificParametersList() - Method in class org.biojava.nbio.core.search.io.Result
getProgressiveAlignment(GuideTree<S, C>, Alignments.ProfileProfileAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method to run the profile-profile alignments of a progressive multiple sequence alignment concurrently.
getProjectedDistance(Atom) - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Get the distance from a point to the axis of rotation
getProjectedPoint(Atom) - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Projects a given point onto the axis of rotation
getProperties() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo: Get the properties
getProperties() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation: Implement this to return the Map delegate.
getProperties() - Method in class org.biojava.nbio.ontology.utils.SmallAnnotation
getProperties() - Method in interface org.biojava.nbio.structure.Group: return properties.
getProperties() - Method in class org.biojava.nbio.structure.HetatomImpl: return properties.
getProperties() - Method in class org.biojava.nbio.structure.validation.Program: Gets the value of the properties property.
getProperty(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
getProperty(Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation: Retrieve the value of a property by key.
getProperty(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
getProperty(String) - Method in interface org.biojava.nbio.structure.Group: get a single property .
getProperty(String) - Method in class org.biojava.nbio.structure.HetatomImpl: get a single property .
getProtein() - Method in class org.biojava.nbio.phosphosite.Site
getProteinCDSSequences() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence: Return a list of protein sequences based on each CDS sequence where the phase shift between two CDS sequences is assigned to the CDS sequence that starts the triplet.
getProteinChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
getProteinChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
getProteinGraph() - Method in class org.biojava.nbio.structure.symmetry.core.SubunitGraph
getProteinSequence() - Method in class org.biojava.nbio.core.sequence.RNASequence: Get the ProteinSequence from the RNA sequence
getProteinSequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.RNASequence: Get the ProteinSequene from the RNA sequence with user defined transcription engine
getProteinSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence: Get the protein sequence
getProteinSequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence: Get the protein sequence with user defined TranscriptEngine
getProteinSequenceCreator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
getProteinSequenceForStructure(Structure, Map<Integer, Group>) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher: Generates a ProteinSequence corresponding to the sequence of struct, and maintains a mapping from the sequence back to the original groups.
getProteinSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
getProteinSequences() - Method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
getProxySequenceReader() - Method in interface org.biojava.nbio.core.sequence.location.template.AccesionedLocation: Return the proxy reader used to get sequence for this location.
getProxySequenceReader() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getPseudoStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getPsi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc: Calculate the psi angle.
getPsi() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getPsi() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the psi property.
getPsimodId() - Method in interface org.biojava.nbio.protmod.ProteinModification
getPsimodId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getPsimodName() - Method in interface org.biojava.nbio.protmod.ProteinModification
getPsimodName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getPtnr1_auth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_auth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_auth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_label_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_label_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_label_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_label_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr1_symmetry() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_auth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_auth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_auth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_label_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_label_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_label_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_label_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPtnr2_symmetry() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
getPublicationDate() - Method in class org.biojava.nbio.structure.JournalArticle
getPublisher() - Method in class org.biojava.nbio.structure.JournalArticle
getPvalue() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getPvalue() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
getPvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getPx() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getQ() - Method in class org.biojava.nbio.structure.jama.QRDecomposition: Generate and return the (economy-sized) orthogonal factor
getQualifiers() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
getQualifiers() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
getQualifiers() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface: Get the qualifiers for this feature
getQualities() - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
getQualities(int, int) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
getQuality() - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq: Return the quality scores for this FASTQ formatted sequence.
getQualityAt(int) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
getQuantities() - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature
getQuat4d(int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
getQuat4d(int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
getQuaternaryStructure(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Method that converts the symmetric units of a structure into different chains, so that internal symmetry can be translated into quaternary.
getQuaternarySymmetry(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Given a symmetry result, it calculates the overall global symmetry, factoring out the alignment and detection steps of QuatSymmetryDetector algorithm.
getQuery() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
getQuery() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
getQuery() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
getQuery() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getQuery() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getQuery() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceScorer: Returns the first sequence of the pair.
getQuery() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileScorer: Returns the first profile of the pair.
getQuery() - Method in class org.biojava.nbio.core.alignment.SimpleProfilePair
getQuery() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getQuery() - Method in interface org.biojava.nbio.core.alignment.template.ProfilePair: Returns the first Profile of the pair.
getQuery() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the first AlignedSequence of the pair.
getQueryDef() - Method in class org.biojava.nbio.core.search.io.Result
getQueryEndIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
getQueryID() - Method in class org.biojava.nbio.core.search.io.Result
getQueryIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
getQueryIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
getQueryLength() - Method in class org.biojava.nbio.core.search.io.Result
getQuerySequence() - Method in class org.biojava.nbio.core.search.io.Result: returns the reference to the original and whole sequence used to query the database.
getQueryStartIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
getR() - Method in class org.biojava.nbio.structure.jama.QRDecomposition: Return the upper triangular factor
getRadius(Atom) - Static method in class org.biojava.nbio.structure.asa.AsaCalculator: Gets the van der Waals radius of the given atom following the values defined by Chothia (1976) J.Mol.Biol.105,1-14 NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates" slightly the heavy atoms to account for Hydrogens.
getRadius() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner: Returns the radius for drawing polyhedra
getRadius() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getRadius() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner: Returns the radius for drawing the minor rotation axis in the xy-plane
getRadiusOfGyration() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getRama() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the rama property.
getRandomDataColumns(int) - Method in class org.biojava.nbio.survival.data.WorkSheet
getRandomDataColumns(int, ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
getRandomSeed() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getRandomSleepTime() - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
getRandomUsername() - Static method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
getRange() - Method in class org.biojava.nbio.structure.ecod.EcodDomain: Get the range of this domain, in PDB residue numbers (mmCif's _pdbx_poly_seq_scheme.pdb_seq_num and pdb_ins_code).
getRange() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement: Returns the residue range of this SSE.
getRanges() - Method in class org.biojava.nbio.structure.AtomPositionMap: Returns a list of ResidueRanges corresponding to this entire AtomPositionMap.
getRanges() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getRanges() - Method in interface org.biojava.nbio.structure.Structure: Deprecated.
From BioJava 4.2, use getStructureIdentifier().toCanonical().getRanges()
getRanges() - Method in class org.biojava.nbio.structure.StructureImpl: Deprecated.
getRealEigenvalues() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition: Return the real parts of the eigenvalues
getRealEnd() - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
getRealStart() - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
getReason() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult: Return a String describing the reasons for the CE-Symm final decision in this particular result.
getRecordAdditionalAttachments() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
getRecordType() - Method in interface org.biojava.nbio.structure.AminoAcid: Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
getRecordType() - Method in class org.biojava.nbio.structure.AminoAcidImpl: Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
getRecordUnidentifiableCompounds() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
getReducedCAStructure(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools: Deprecated.
Use the more generic BioAssemblyTools.getReducedStructure(Structure)
getReducedStructure(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools: reduce a structure to a single-atom representation (e.g.
getReducedStructure(Structure, String) - Static method in class org.biojava.nbio.structure.StructureTools: Deprecated.
Use StructureIdentifier.reduce(Structure) instead (v. 4.2.0)
getReducedStructure(Structure, int) - Static method in class org.biojava.nbio.structure.StructureTools: Deprecated.
Use StructureIdentifier.reduce(Structure) instead (v. 4.2.0)
getRef() - Method in class org.biojava.nbio.structure.JournalArticle: Get the value of REF field.
getRef_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getRefAuthor() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
getRefChainId() - Method in class org.biojava.nbio.structure.Compound: Return the ref chain id value.
getRefComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getReference() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
getReference() - Method in class org.biojava.nbio.core.search.io.Result
getReferences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getRefinedScoreThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getRefineMethod() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getRefLocation() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
getRefmacVersion() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the refmacVersion property.
getRefMedline() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
getRefn() - Method in class org.biojava.nbio.structure.JournalArticle: Get the value of REFN field.
getRefRMSD(MultipleAlignment, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: /** Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.
getRefRMSD(List<Atom[]>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.
getRefseqIds() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getRefTitle() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
getRefTMScore(MultipleAlignment, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.
getRefTMScore(List<Atom[]>, List<Integer>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.
getRegistryInfo() - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
getRelativeAsaC() - Method in class org.biojava.nbio.structure.asa.GroupAsa: Returns the relative (complexed) ASA, i.e.
getRelativeAsaU() - Method in class org.biojava.nbio.structure.asa.GroupAsa: Returns the relative (uncomplexed) ASA, i.e.
getRelativePercentileClashscore() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the relativePercentileClashscore property.
getRelativePercentileDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry
getRelativePercentilePercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the relativePercentilePercentRamaOutliers property.
getRelativePercentilePercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the relativePercentilePercentRotaOutliers property.
getRelativePercentilePercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the relativePercentilePercentRSRZOutliers property.
getRelativePercentileRNAsuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
getRelevantSubLocations() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation: Returns the normalised list of sub locations i.e.
getRelevantSubLocations() - Method in interface org.biojava.nbio.core.sequence.location.template.Location: An extension to Location.getSubLocations() which returns sub-locations of sub-locations; this will continue until it runs out of those locations.
getRelevantSubSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
getRelevantSubSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.location.template.Location: Will return a SequenceReader object which offers a view of all resolved locations i.e.
getRemoteBlastInfo() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: A simple method to check the availability of the QBlast service.
getRemoteTerm() - Method in interface org.biojava.nbio.ontology.RemoteTerm: Return the imported term
getRemoteTerm() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
getRemoteTerms() - Method in interface org.biojava.nbio.ontology.OntologyOps: Get the set of all remote terms.
getRepeatRelation(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes: Return the repeat superposition relation needed to obtain the axis of symmetry (which repeats and in which order have to be superimposed to obtain the axis).
getRepeatsID() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult: Return the symmetric repeats as structure identifiers, if the result is symmetric and it was refined, return null otherwise.
getRepeatTransform(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes: Return the transformation that needs to be applied to a determinate repeat so that all get superimposed to the same point.
getRepeatUnitCenters() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
getRepeatUnitIndices() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
getRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
getRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getReplaced(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary: if ChemComp is replacing another one, get the old version otherwise return the same ChemComp again.
getReplaced(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
getReplacement(String, boolean, boolean) - Static method in class org.biojava.nbio.structure.PDBStatus: Gets the PDB which superseded oldPdbId.
getReplacer(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary: if ChemComp is replaced by another one, get the newer version otherwise return the same ChemComp again.
getReplacer(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
getReplaces() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
getReplaces(String, boolean) - Static method in class org.biojava.nbio.structure.PDBStatus: Get the ID of the protein which was made obsolete by newPdbId.
getRepresentative() - Method in class org.biojava.nbio.structure.cath.CathNode
getRepresentative() - Method in class org.biojava.nbio.structure.Compound: Get the representative Chain for this Compound.
getRepresentative() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
getRepresentativeAtomArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Gets a representative atom for each group that is part of the chain backbone.
getRepresentativeAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Gets a representative atom for each group that is part of the chain backbone.
getRepresentativeAtoms(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the representative atoms for the provided name.
getRepresentativeAtoms(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache
getRepresentativeAtomsInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools: Returns the set of intra-chain contacts for the given chain for C-alpha or C3' atoms (including non-standard aminoacids appearing as HETATM groups), i.e.
getRepresentativeAtomsOnly(List<Chain>) - Static method in class org.biojava.nbio.structure.io.CAConverter: Convert a List of chain objects to another List of chains, containing Representative atoms only.
getRepresentativeAtomsOnly(Chain) - Static method in class org.biojava.nbio.structure.io.CAConverter: Convert a Chain to a new Chain containing C-alpha atoms only.
getRepresentativeChain(String, String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
getRepresentativeDomains() - Method in interface org.biojava.nbio.structure.domain.DomainProvider: Get the full list of representative domains for the PDB.
getRepresentativeDomains() - Method in class org.biojava.nbio.structure.domain.PDBDomainProvider: Gets a list of all domain representatives
getRepresentativeDomains() - Method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
getRepresentatives(String, int) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
GetRepresentatives - Class in org.biojava.nbio.structure.rcsb: TODO Move this to Representatives.
GetRepresentatives() - Constructor for class org.biojava.nbio.structure.rcsb.GetRepresentatives
getRepresentatives(int) - Static method in class org.biojava.nbio.structure.rcsb.GetRepresentatives: Returns a representative set of PDB protein chains at the specified sequence identity cutoff.
getRepresentatives(Astral.AstralSet) - Static method in class org.biojava.nbio.structure.scop.Astral: Get a list of representatives' names for the specified ASTRAL cutoff.
getRepresentatives(String) - Static method in class org.biojava.nbio.structure.scop.Astral: Get a list of representatives' names for the specified ASTRAL cutoff.
getRepresentatives(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
getResidId() - Method in interface org.biojava.nbio.protmod.ProteinModification
getResidId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getResidName() - Method in interface org.biojava.nbio.protmod.ProteinModification
getResidName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getResidual() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getResidualVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getResidue() - Method in class org.biojava.nbio.phosphosite.Site
getResidue(int) - Method in class org.biojava.nbio.structure.AugmentedResidueRange: Returns the ResidueNumber that is at position positionInRange in this ResidueRange.
getResidue(int, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange: Returns the ResidueNumber that is at position positionInRange in this ResidueRange.
getResidueName() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
getResidueNumber() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
getResidueNumber() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
getResidueNumber() - Method in interface org.biojava.nbio.structure.Group: returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.
getResidueNumber() - Method in class org.biojava.nbio.structure.HetatomImpl: returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.
getResidueRanges() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getResidueRanges() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getResidueRanges() - Method in interface org.biojava.nbio.structure.Structure: Deprecated.
From BioJava 4.2, use getStructureIdentifier().toCanonical().getResidueRanges()
getResidueRanges() - Method in class org.biojava.nbio.structure.StructureImpl: Deprecated.
getResidueRanges() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
getResidues() - Method in class org.biojava.nbio.structure.io.FastaStructureParser: For each residue in the fasta file, return the ResidueNumber in the corresponding structure.
getResidues() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
getResidueType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getResidueTypeFromString(String) - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType
getResidueTypes() - Method in enum org.biojava.nbio.structure.GroupType: Get a set of ResidueTypes loosely equivalent to this GroupType.
getResname() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the resname property.
getResName1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getResName2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getResNames() - Method in class org.biojava.nbio.structure.Compound
getResnum() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the resnum property.
getResnum1() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getResnum2() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getResolution() - Method in class org.biojava.nbio.structure.cath.CathDomain
getResolution() - Method in class org.biojava.nbio.structure.PDBHeader
getResolver() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
getResourceManager(String) - Static method in class org.biojava.nbio.structure.align.util.ResourceManager
getResScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getResSeq1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getResSeq2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getRestypesNotcheckedForBondAngleGeometry() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the restypesNotcheckedForBondAngleGeometry property.
getResultFile() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
getRev_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
getReverse() - Method in class org.biojava.nbio.core.sequence.DNASequence: Returns a Sequence which runs in the current reverse order
getReverse() - Method in enum org.biojava.nbio.core.sequence.Strand
getReverse() - Method in class org.biojava.nbio.structure.align.client.PdbPair
getReverseComplement() - Method in class org.biojava.nbio.core.sequence.DNASequence: Delegates to AbstractSequence.getInverse() for the reverse complement
getReverseComplement() - Method in class org.biojava.nbio.core.sequence.RNASequence: Get reverse complement view of the sequence
getReverseFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame: Returns all frames which are in the reverse orientation
getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getRevisionRecords() - Method in class org.biojava.nbio.structure.PDBHeader
getRfree() - Method in class org.biojava.nbio.structure.PDBHeader
getRibosomes() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
getRight() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getRimResidues(double, double) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns the residues belonging to the interface rim, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is below the given bsaToAsaCutoff
getRise() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getRms() - Method in class org.biojava.nbio.structure.align.helper.JointFragments
getRMS(Atom[], Atom[], JointFragments) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner: get the RMS of the JointFragments pair frag
getRms() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getRMS(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.SVDSuperimposer: Calculate the RMS (root mean square) deviation of two sets of atoms.
getRmsd() - Method in class org.biojava.nbio.structure.align.model.AFP
getRMSD(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the RMSD of all-to-all structure comparisons (distances) of the given MultipleAlignment.
getRMSD(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates the RMSD of all-to-all structure comparisons (distances), given a set of superimposed atoms.
getRmsd() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
getRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
getRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getRmsd() - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
getRmsdCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getRmsdCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters: The cutoff to be used during AFP detection
getRmsdCut() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
getRmsdIntra() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getRMSDMatrix(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate the RMSD matrix of a MultipleAlignment, that is, entry (i,j) of the matrix contains the RMSD between structures i and j.
getRmsdThr() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: RMSD Threshold
getRmsdThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getRmsdThrJoin() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: RMSD threshold for joining of AFPs
getRnaAminoAcidTranslator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
getRnaCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
getRNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet
getRNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.RNACompoundSet
getRNASequence() - Method in class org.biojava.nbio.core.sequence.DNASequence: Return the RNASequence equivalent of the DNASequence using default Transcription Engine.
getRNASequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.DNASequence: Allow a user to pass in a rules engine to do the DNA to RNA translation
getRNASequence(Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence: Allows the user to pass in the Frame shift.
getRNASequence(TranscriptionEngine, Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence
getRnaSequenceCreator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
getRnaSuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
getRnaToDna() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
getRndSeed() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getRobustStdError() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getRoot() - Method in class org.biojava.nbio.alignment.GuideTree: Returns the root GuideTree.Node which corresponds to the full multiple sequence alignment.
getRoot() - Method in interface org.biojava.nbio.alignment.template.HierarchicalClusterer: Returns the root node of the tree resulting from this clustering algorithm.
getRootURL() - Method in class org.biojava.nbio.structure.scop.ScopMirror: Get the URL for the root download directory, or null if none is set.
getRot() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getRota() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the rota property.
getRotatedAtoms(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay: New structures are downloaded if they were not cached in the alignment and they are entirely transformed here with the superposition information in the Multiple Alignment.
getRotation() - Method in class org.biojava.nbio.structure.SVDSuperimposer: Get the Rotation matrix that is required to superimpose the two atom sets.
getRotation(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
getRotationAxis() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Get a unit vector along the rotation axis
getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry: Deprecated.
getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Returns rotation group (point group) information representing rotational quaternary symmetry, see http://en.wikipedia.org/wiki/Rotation_group_SO(3)
getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getRotationMatrix() - Method in class org.biojava.nbio.structure.align.ce.CECalculator: Gets the rotation matrix from the last call to calc_rmsd.
getRotationMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced: Gets the rotation matrix from the last call to calc_rmsd.
getRotationMatrix() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1
getRotationMatrix() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Get the rotation matrix corresponding to this axis
getRotationMatrix(double) - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Get the rotation matrix corresponding to a rotation about this axis
getRotationMatrix(Matrix4d) - Static method in class org.biojava.nbio.structure.Calc: Convert Vecmath transformation into a JAMA rotation matrix.
getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
getRotationPos() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Get a position on the rotation axis.
getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getRotAxisAndAngle(Matrix3d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup: Given a rotation matrix calculates the rotation axis and angle for it.
getRotAxisAngle(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getRotAxisType(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup: Given a transformation matrix containing a rotation returns the type of rotation: 1 for identity, 2 for 2-fold rotation, 3 for 3-fold rotation, 4 for 4-fold rotation, 6 for 6-fold rotation, -1 for inversions, -2 for mirror planes, -3 for 3-fold improper rotation, -4 for 4-fold improper rotation and -6 for 6-fold improper rotation
getRotMax(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
getRow(AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getRow(C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getRow(C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
getRow() - Method in class org.biojava.nbio.structure.align.helper.IndexPair
getRowDimension() - Method in class org.biojava.nbio.structure.jama.Matrix: Get row dimension.
getRowHeader() - Method in class org.biojava.nbio.survival.data.WorkSheet
getRowIndex(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
getRowLookup() - Method in class org.biojava.nbio.survival.data.WorkSheet
getRowPackedCopy() - Method in class org.biojava.nbio.structure.jama.Matrix: Make a one-dimensional row packed copy of the internal array.
getRows() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getRows() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getRows() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getRows() - Method in class org.biojava.nbio.survival.data.WorkSheet: Get the list of row names.
getRscc() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the rscc property.
getRscore() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getRscoreLogrankTestpvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getRsr() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the rsr property.
getRsrz() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the rsrz property.
getS() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Return the diagonal matrix of singular values
getSaid() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the said property.
getSaturation() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel: Deprecated.
getSaturation() - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
getSaveAlignmentMenuItem(AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getSaveOutputDir() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getScale() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getScale() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
getScale() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
getScale() - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
getScaleableMatrixPanel(Matrix) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
getScalevalue() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel: Deprecated.
getScalevalue() - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
getScid() - Method in class org.biojava.nbio.structure.validation.SymmClash: Gets the value of the scid property.
getSCOP() - Method in class org.biojava.nbio.structure.gui.util.ScopInstallationInstance
getSCOP() - Static method in class org.biojava.nbio.structure.scop.ScopFactory: Get the current default instance for the default version
getSCOP(boolean) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
getSCOP(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory: requests a particular version of SCOP.
getSCOP(String, boolean) - Static method in class org.biojava.nbio.structure.scop.ScopFactory: Gets an instance of the specified scop version.
getScopDescription() - Method in class org.biojava.nbio.structure.scop.server.ScopDescriptions
getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getScopDescriptionBySunid(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Return the SCOP description for a node in the hierarchy by its "sunid" id.
getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getScopDescriptionFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopDescriptionsXML(List<ScopDescription>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopDescriptionXML(ScopDescription) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopDomain() - Method in class org.biojava.nbio.structure.scop.server.ScopDomains
getScopDomainFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getScopDomainsBySunid(Integer) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Get a SCOP domain by its sunid
getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getScopDomainsXML(List<ScopDomain>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopDomainXML(ScopDomain) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopDownloadURL() - Method in class org.biojava.nbio.structure.scop.ScopInstallation: Deprecated.
getScope() - Method in class org.biojava.nbio.ontology.Synonym
getScopId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getScopNode(int) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getScopNode(int) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getScopNode(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Access a particular ScopNode.
getScopNode(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getScopNode() - Method in class org.biojava.nbio.structure.scop.server.ScopNodes
getScopNodeFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopNodesXML(List<ScopNode>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopNodeXML(ScopNode) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
getScopSelectPanel() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
getScopVersion() - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getScopVersion() - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getScopVersion() - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: Returns the SCOP version
getScopVersion() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
getScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
getScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
getScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getScore() - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns score resulting from algorithm.
getScore() - Method in class org.biojava.nbio.structure.align.model.AFP
getScore(String) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
getScore(String) - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache: Get the value for a particular score.
getScore() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
getScore() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: the alignment score
getScore() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
getScore() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
getScore() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
getScore() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getScore() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
getScoreLogrankTest() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getScoreLogrankTestpvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getScoreMatrix() - Method in class org.biojava.nbio.alignment.GuideTree: Returns the similarity matrix used to construct this guide tree.
getScoreMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getScoreMatrix() - Method in interface org.biojava.nbio.alignment.template.MatrixAligner: Returns the entire score matrix built during alignment.
getScoreMatrixAsString() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getScoreMatrixAsString() - Method in interface org.biojava.nbio.alignment.template.MatrixAligner: Returns a depiction of the score matrix as a String.
getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getScores(File) - Method in class org.biojava.nbio.ronn.ORonnModel
getScores() - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
getScores() - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache: Get a collection of all scores that have been set.
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers: Returns QuatSymmetryScores averaged over all rotations (except the first rotation, which is the unit operation E)
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup: Returns QuatSymmetryScores averaged over all rotations (except the first rotation, which is the unit operation E)
getScoringStrategy() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getScoringStrategy() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
getScrewTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Get the component of translation parallel to the axis of rotation
getScriptGenerator() - Method in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
getSearchFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters: An input file to be used for the DB search
getSearchMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getSecond() - Method in class org.biojava.nbio.structure.contact.Pair
getSecondAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
getSecondGroupAsa(ResidueNumber) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Gets the GroupAsa for the corresponding residue number of second chain
getSecondGroupAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Gets a map of ResidueNumbers to GroupAsas for all groups of second chain.
getSecretion() - Method in class org.biojava.nbio.structure.Compound
getSecStrucElements(Structure) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools: Obtain the List of secondary structure elements (SecStrucElement) of a Structure.
getSecStrucElements(List<Group>) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools: Obtain the List of secondary structure elements (SecStrucElement) of a List of Groups (assumed to be sequential, this is, connected in the original Structure).
getSecStrucInfo(Structure) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools: Obtain the List of secondary structure information (SecStrucInfo) of a Structure.
getSeedFragmentLength() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getSeedRmsdCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getSegId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
getSegmentAtPos(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
getSegmentId() - Method in class org.biojava.nbio.structure.cath.CathSegment
getSegments() - Method in class org.biojava.nbio.structure.cath.CathDomain
getSegments() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
getSegments() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
getSelectedAlignmentPos() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
getSelectedAlignmentPos() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
getSelection() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
getSelection() - Method in interface org.biojava.nbio.structure.gui.Selection
getSelection() - Method in class org.biojava.nbio.structure.gui.SelectionImpl
getSelection() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
getSelectPDBPanel() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
getSelfAlignment() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getSeparatorSequence() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
getSeq() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the seq property.
getSeq_align_beg() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getSeq_align_end() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
getSeq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
getSeq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
getSeq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
getSeqBegin() - Method in class org.biojava.nbio.structure.DBRef: Initial sequence number of the PDB sequence segment.
getSeqEnd() - Method in class org.biojava.nbio.structure.DBRef: Ending sequence number of the PDB sequence segment.
getSeqIdRange() - Method in class org.biojava.nbio.structure.ecod.EcodDomain: Get the range of this domain, in 1-based residue indices (mmCif's _pdbx_poly_seq_scheme.seq_id) Note that EcodDomain.getRange() is used when constructing the domain.
getSeqMisMatches() - Method in interface org.biojava.nbio.structure.Chain: Get annotated sequence mismatches for this chain.
getSeqMisMatches() - Method in class org.biojava.nbio.structure.ChainImpl
getSeqNum() - Method in class org.biojava.nbio.structure.ResidueNumber
getSeqNum() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getSeqNum() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getSeqPos(int, Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: Convert from a X position in the JPanel to alignment position
getSeqPos(int, Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Convert from an X position in the JPanel to the position in the sequence alignment.
getSeqPos(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager: start counting at 0...
getSeqresEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getSeqResGroup(int) - Method in interface org.biojava.nbio.structure.Chain: Return the Group at given position, from within groups in the SEQRES records of the chain, i.e.
getSeqResGroup(int) - Method in class org.biojava.nbio.structure.ChainImpl: Return the Group at given position, from within groups in the SEQRES records of the chain, i.e.
getSeqResGroups(GroupType) - Method in interface org.biojava.nbio.structure.Chain: Returns a List of all SEQRES groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
getSeqResGroups() - Method in interface org.biojava.nbio.structure.Chain: Returns a list of all groups in SEQRES records of the chain, i.e.
getSeqResGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl: Returns a List of all SEQRES groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
getSeqResGroups() - Method in class org.biojava.nbio.structure.ChainImpl: Returns a list of all groups in SEQRES records of the chain, i.e.
getSeqResLength() - Method in interface org.biojava.nbio.structure.Chain: Returns the number of groups in the SEQRES records of the chain, i.e.
getSeqResLength() - Method in class org.biojava.nbio.structure.ChainImpl: Returns the number of groups in the SEQRES records of the chain, i.e.
getSeqResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getSeqResSequence() - Method in interface org.biojava.nbio.structure.Chain: Returns the PDB SEQRES sequence as a one-letter sequence string.
getSeqResSequence() - Method in class org.biojava.nbio.structure.ChainImpl: Returns the PDB SEQRES sequence as a one-letter sequence string.
getSeqResSequence() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getSeqresStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator: Assumes all compounds were uppercase
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.FastaSequenceParser
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator: Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator: Should be able to extend the same concept to a remote URL call or database connection.
getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator: Not sure of use case and currently not supported
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator: Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator: Should be able to extend the same concept to a remote URL call or database connection.
getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator: Not sure of use case and currently not supported
getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
getSequence(String, long) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
getSequence(ProxySequenceReader<C>, long) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
getSequence(List<C>) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
getSequence(BufferedReader, int) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceParserInterface
getSequence() - Method in class org.biojava.nbio.core.sequence.location.SequenceLocation
getSequence() - Method in class org.biojava.nbio.data.sequence.FastaSequence: Gets the value of sequence
getSequence() - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq: Return the sequence for this FASTQ formatted sequence.
getSequence() - Method in class org.biojava.nbio.structure.cath.CathDomain
getSequence() - Method in class org.biojava.nbio.structure.cath.CathSegment
getSequence5PrimeTo3Prime() - Method in class org.biojava.nbio.core.sequence.GeneSequence: Try to give method clarity where you want a DNASequence coding in the 5' to 3' direction Returns the DNASequence representative of the 5' and 3' reading based on strand
getSequenceAlignment(MultipleAlignment, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate the sequence alignment Strings for the whole alignment.
getSequenceAlignment(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate the sequence alignment Strings for the whole alignment.
getSequenceAlignmentClusters() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getSequenceAlignmentClusters(double) - Method in class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains: Get a non-redundent set of clusters for a given sequence cutoff
getSequenceAlignmentClusters() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
getSequenceAlignmentLength() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getSequenceAsString() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader: Returns the sequence as a String
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
getSequenceAsString(List<C>, CompoundSet<C>, Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Delegates to SequenceMixin.toList(org.biojava.nbio.core.sequence.template.Sequence)
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
getSequenceAsString() - Method in interface org.biojava.nbio.core.sequence.template.Sequence: Returns the String representation of the Sequence
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.ReversedSequenceView
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
getSequenceClusterCount() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getSequenceClusterIds() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getSequenceClusterIds() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getSequenceCollection() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
getSequenceCount() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getSequenceFromString(String) - Method in class org.biojava.nbio.core.util.SequenceTools
getSequenceHeader() - Method in class org.biojava.nbio.structure.cath.CathDomain
getSequenceHeader() - Method in class org.biojava.nbio.structure.cath.CathSegment
getSequenceHeaderParser() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
getSequenceIdentityThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
getSequenceIdentityThresholds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getSequenceIndexAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getSequenceIndexAt(int) - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the index in the original Sequence corresponding to the given index within an alignment.
getSequenceNames() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
getSequencePseudoSymmetryThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
getSequences() - Method in class org.biojava.nbio.alignment.GuideTree: Returns the Sequences which make up the leaves of this tree.
getSequences() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
getSequences() - Method in class org.biojava.nbio.structure.io.FastaStructureParser: Gets the protein sequences read from the Fasta file.
getSequences() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
getSequenceScore() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Provide place holder for a metric that indicate a score associated with the sequence
getSequenceString(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getSequenceUsage() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
getSeqWeight() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
getSerialversionuid() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getSerNum() - Method in class org.biojava.nbio.structure.io.SSBondImpl
getServer() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getServer() - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider
getServer() - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getServerName() - Static method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Return the String with the PDB server name, including the leading protocol String (http:// or ftp://).
getShift() - Method in class org.biojava.nbio.structure.align.ce.CECalculator: Gets the shift from the last call to calc_rmsd.
getShift() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced: Gets the shift from the last call to calc_rmsd.
getShift() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: returns the shift vector that has to be applied on structure to to shift on structure one
getShorName() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
getShortDescription() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
getShortDescription() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
getShortDescription() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface: Get the short description that can be used to describe the feature
getShortName() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
getShortName() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
getShortName() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
getShortName() - Method in interface org.biojava.nbio.core.sequence.template.Compound
getShortName() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
getShortName() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
getShortName() - Method in enum org.biojava.nbio.structure.xtal.TransformType
getShortSymbol() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets the international short name (as used in PDB), e.g.
getShowDBresult() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
getShowPDBMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getSiftsMapping(String) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
getSimCount() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getSimilarity() - Method in class org.biojava.nbio.alignment.template.AbstractScorer
getSimilarity(double) - Method in class org.biojava.nbio.alignment.template.AbstractScorer
getSimilarity() - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns score as a similarity between 0.0 and 1.0.
getSimilarity(double) - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns score as a similarity between 0.0 and scale.
getSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Returns the similarity score for the alignment.
getSimilarity1() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Deprecated.
use getCoverage1() instead
getSimilarity2() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Deprecated.
use getCoverage2() instead
getSingularValues() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Return the one-dimensional array of singular values
getSite_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getSiteID() - Method in class org.biojava.nbio.structure.Site
getSites() - Method in interface org.biojava.nbio.structure.Structure
getSites() - Method in class org.biojava.nbio.structure.StructureImpl
getSize() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getSize() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the number of rows in this profile.
getSize() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment: Get the number of sequences in the MSA
getSize() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile: Returns the number of rows in this profile.
getSize() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
getSmiles() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getSOILD() - Method in class org.biojava.nbio.structure.cath.CathDomain
getSolvent_model_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getSolvent_model_param_bsol() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getSolvent_model_param_ksol() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
getSortVariable() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
getSortVariable() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
getSource() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature: The feature source
getSource() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
getSource() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface: The source of the feature.
getSource() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Added support for the source of this sequence for GFF3 export If a sub sequence doesn't have source then check for parent source
getSource() - Method in class org.biojava.nbio.structure.align.client.StructureName
getSource() - Method in class org.biojava.nbio.structure.cath.CathDomain
getSourceSeed() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getSourceStructure() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getSpace_group_name_H_M() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
getSpace_group_name_Hall() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
getSpaceGroup() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo: Get the SpaceGroup
getSpaceGroup(int) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser: Gets the space group for the given standard identifier.
getSpaceGroup(String) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser: Get the space group for the given international short name, using the PDB format, e.g.
getSparse() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getSpecies() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getSpeciesId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getSphereCount() - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
getSphereCount() - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
getSplitDirPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Location of split files within the directory, as an array of paths.
getSplitDirPath() - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
getSplitDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader
getSplitpat1() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getSplitpat2() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getSqFrom() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getSqTo() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getSrc_method() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getSsBondListFromBondList(List<Bond>) - Static method in class org.biojava.nbio.structure.io.SSBondImpl
getSSBonds() - Method in interface org.biojava.nbio.structure.Structure: Get the list of disulfide Bonds as they have been defined in the PDB files
getSSBonds() - Method in class org.biojava.nbio.structure.StructureImpl: Get the list of disulfide Bonds as they have been defined in the PDB files
getSSEThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getStainTypeFromString(String) - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType
getStandardDeviation() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getStart() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getStart() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the Point within an alignment of the first element of the original Sequence.
getStart() - Method in interface org.biojava.nbio.core.alignment.template.ProfileView: Returns the column index of the viewed Profile corresponding to the first element in this view
getStart() - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
getStart() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
getStart() - Method in interface org.biojava.nbio.core.sequence.location.template.Location: Start of the location
getStart() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
getStart() - Method in class org.biojava.nbio.structure.cath.CathFragment
getStart() - Method in class org.biojava.nbio.structure.cath.CathSegment
getStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
getStart() - Method in class org.biojava.nbio.structure.ResidueRange
getStart_construct_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
getStartCodonSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
getStartIndex(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block: Calculates and returns the first position of the specified structure in the alignment that is not null.
getStartIndex(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getStartPage() - Method in class org.biojava.nbio.structure.JournalArticle
getStartResidue(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block: Calculates and returns the first residue of the specified structure in the alignment that is not null.
getStartResidue(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
getStartTimestamp() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor: StartupParameters is a bean to store all the possible command line parameters.
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
getStatus() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getStatus() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
getStatus(String) - Static method in class org.biojava.nbio.structure.PDBStatus: Get the status of the PDB in question.
getStatus(String[]) - Static method in class org.biojava.nbio.structure.PDBStatus: Get the status of the a collection of PDBs in question in a single query.
getStatus() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getStatus() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getStatusListener() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
getStderr() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getStdError() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getStdev() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the stdev property.
getStdev() - Method in class org.biojava.nbio.structure.validation.BondOutlier: Gets the value of the stdev property.
getStdev() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the stdev property.
getStdev() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the stdev property.
getStdlow() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getStepSize() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters: how many pairs should be requested for alignment from server?
getStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
getStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getStop() - Method in class org.biojava.nbio.structure.cath.CathFragment
getStop() - Method in class org.biojava.nbio.structure.cath.CathSegment
getStopCodonSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
getStrain() - Method in class org.biojava.nbio.structure.Compound
getStrain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getStrain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
getStrand() - Method in class org.biojava.nbio.core.sequence.CDSSequence
getStrand() - Method in class org.biojava.nbio.core.sequence.GeneSequence: A gene should have Strand
getStrand() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
getStrand() - Method in interface org.biojava.nbio.core.sequence.location.template.Location: Strand which the location is located on
getStrand() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
getStrata() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getStrataInfoHashMap() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
getString(String) - Method in class org.biojava.nbio.structure.align.util.ResourceManager
getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
getStringForCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
getStringForCompound(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
getStringRepresentation() - Method in enum org.biojava.nbio.core.sequence.Strand
getStructAssemblies() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
getStructAssemblyGens() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
getStructOpers() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
getStructuralTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Calculate a phylogenetic tree of the MultipleAlignment using RMSD distances and the Neighbor Joining algorithm from forester.
getStructure() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Return the current Structure in the AlignmentJmol instance.
getStructure(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Request a Structure based on a name.
getStructure(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Get the structure corresponding to the given StructureIdentifier.
getStructure() - Method in interface org.biojava.nbio.structure.Chain: Returns the parent Structure of this chain.
getStructure() - Method in class org.biojava.nbio.structure.ChainImpl: Returns the parent Structure of this chain.
getStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
getStructure(URL) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
getStructure(File) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Handles the actual parsing of the file into a Structure object.
getStructure() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer: This method will return the parsed protein structure, once the parsing has been finished
getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.PDBFileReader
getStructure(String) - Method in interface org.biojava.nbio.structure.io.StructureIOFile: Open filename and return a Structure object.
getStructure(File) - Method in interface org.biojava.nbio.structure.io.StructureIOFile: Read file from File and returns a Structure object.
getStructure(String) - Static method in class org.biojava.nbio.structure.StructureIO: Loads a structure based on a name.
getStructure(String) - Static method in class org.biojava.nbio.structure.StructureTools: Short version of StructureTools.getStructure(String, PDBFileParser, AtomCache) which creates new parsers when needed
getStructure(String, PDBFileParser, AtomCache) - Static method in class org.biojava.nbio.structure.StructureTools: Flexibly get a structure from an input String.
getStructure1() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBDirPanel
getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBServerPanel
getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
getStructure1() - Method in class org.biojava.nbio.structure.gui.util.ScopSelectPanel
getStructure1() - Method in interface org.biojava.nbio.structure.gui.util.StructurePairSelector
getStructure2() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBDirPanel
getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBServerPanel
getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
getStructure2() - Method in class org.biojava.nbio.structure.gui.util.ScopSelectPanel
getStructure2() - Method in interface org.biojava.nbio.structure.gui.util.StructurePairSelector
getStructureAlignment() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
getStructureAlignment() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
getStructureAtom(Atom, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
getStructureAtomLinkage(Atom, boolean, Atom, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
getStructureById(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
getStructureById(String) - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
getStructureById(String) - Method in interface org.biojava.nbio.structure.io.StructureProvider: get the structure for a PDB ID
getStructureForCathDomain(StructureName) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns a Structure corresponding to the CATH identifier supplied in structureName, using the the CathDatabase at CathFactory.getCathDatabase().
getStructureForCathDomain(StructureName, CathDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns a Structure corresponding to the CATH identifier supplied in structureName, using the specified CathDatabase.
getStructureForDomain(ScopDomain) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForDomain(ScopDomain, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForDomain(ScopDomain, ScopDatabase, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForDomain(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForDomain(String, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache: Loads a structure directly by PDB ID
getStructureFromFasta() - Static method in class demo.DemoStructureFromFasta
getStructureGroup(Group, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
getStructureId() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
getStructureId() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getStructureIdentifier(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the StructureIdentifier associated with the structure index from its parent Ensemble.
getStructureIdentifier(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
getStructureIdentifier() - Method in interface org.biojava.nbio.structure.Structure: Get an identifier corresponding to this structure
getStructureIdentifier() - Method in class org.biojava.nbio.structure.StructureImpl
getStructureIdentifiers() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
getStructureIdentifiers() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getStructureIds() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getStructurePairAligner() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
getStructures() - Method in class org.biojava.nbio.structure.gui.util.SelectMultiplePanel
getStructures() - Method in class org.biojava.nbio.structure.io.FastaStructureParser: Gets the protein structures mapped from the Fasta file.
getSubject() - Method in interface org.biojava.nbio.ontology.Triple: Return the subject term of this triple
getSubject() - Method in class org.biojava.nbio.ontology.Triple.Impl
getSubLocations() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
getSubLocations() - Method in interface org.biojava.nbio.core.sequence.location.template.Location: Gives access to the sub locations for this location.
getSubproblems(List<AlignerHelper.Anchor>, int, int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem: Convert a list of anchors into a subproblem list.
getSubProfile(Location) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getSubProfile(Location) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a ProfileView windowed to contain only the given Location.
getSubRanges(Structure, String) - Static method in class org.biojava.nbio.structure.StructureTools: Deprecated.
Use StructureIdentifier instead (4.2.0)
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
getSubSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation: If circular this will return the sequence represented by the sub locations joined.
getSubSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.location.template.Location: Will return a SequenceReader object which represents the outer bounds of this Location
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
getSubSequence(int, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader: Returns a sub sequence view
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Creates a SequenceProxyView for the given coordinates
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getSubSequence(Integer, Integer) - Method in interface org.biojava.nbio.core.sequence.template.Sequence: Returns a portion of the sequence from the different positions.
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getSubstitutionMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Returns the substitution matrix.
getSubstitutionMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getSubstitutionScoreVector(int) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Returns score for the alignment of the query column to all target columns
getSubstitutionScoreVector(int, AlignerHelper.Subproblem) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Returns score for the alignment of the query column to all target columns
getSubstructureMatchingProteinSequence(ProteinSequence, Structure) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher: Get a substructure of wholeStructure containing only the Groups that are included in sequence.
getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getSubunitRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Returns protein subunit information that was used to determine symmetry information
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getSubunitTypeCount() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
getSuggestion(String) - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider: get a list of suggestions for a userInput
getSuggestion(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
getSuggestion(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
getSummaryPos() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
getSummaryPos() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
getSunID() - Method in class org.biojava.nbio.structure.scop.ScopDescription
getSunid() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode
getSuperfamilyId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
getSurfaceResidues(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns the residues belonging to the surface
getSurname() - Method in class org.biojava.nbio.structure.Author
getSurv() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getSurvivalFitInfo() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getSurvivalInfoList() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getSurvivalInfoList() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure: The data used to draw the graph
getSurvivalTimePercentile(String, double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure: To get the median percentile for a particular group pass the value of .50.
getSwissprotId() - Method in interface org.biojava.nbio.structure.Chain: Gets the Swissprot id of this chain.
getSwissprotId() - Method in class org.biojava.nbio.structure.ChainImpl: get the Swissprot id of this chains .
getSym1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getSym2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
getSymbol() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
getSymbolSet() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
getSymDeviation() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getSymmClash() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup: Gets the value of the symmClash property.
getSymmetry() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry: String representation of Symmetry, e.g.
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Returns the symmetry group.
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getSymmetryAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes: Deprecated.
because it does not work as expected for open symmetry
getSymmetryClass(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.C2RotationSolver
getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.HelixSolver
getSymmetryOperations() - Method in interface org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver
getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.RotationSolver
getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.SystematicSolver
getSymmetryOrder(Map<Integer, Integer>, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Helper for AlignmentTools.getSymmetryOrder(Map, Map, int, float) with a true identity function (X->X).
getSymmetryOrder(Map<Integer, Integer>, Map<Integer, Integer>, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Tries to detect symmetry in an alignment.
getSymmetryOrder(AFPChain, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Guesses the order of symmetry in an alignment
getSymmGroup() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getSymmLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getSymmLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getSymmOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult: Return the symmetry order determined by the order detector if the symmetry is significant.
getSymmTitle(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Create a symmetry title for a display frame (Jmol, alignment, etc).
getSymmType() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getSymop() - Method in class org.biojava.nbio.structure.validation.SymmClash: Gets the value of the symop property.
getSynonyms() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getSynonyms() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
getSynonyms() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
getSynonyms() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
getSynonyms() - Method in interface org.biojava.nbio.ontology.Term: Return the synonyms for this term.
getSynonyms() - Method in class org.biojava.nbio.ontology.Term.Impl
getSynonyms() - Method in class org.biojava.nbio.ontology.Triple.Impl
getSynonyms() - Method in class org.biojava.nbio.structure.Compound
getSynonyms() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getSynthetic() - Method in class org.biojava.nbio.structure.Compound
getSystematicName() - Method in interface org.biojava.nbio.protmod.ProteinModification
getSystematicName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
getT() - Method in class org.biojava.nbio.structure.align.model.AFP
getTable(String) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser: Returns a table by its name
getTable(Integer) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser: Returns a table by its identifier i.e.
getTable() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
getTables() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser: Returns a list of all available IUPAC tables
getTabPane() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
getTarget() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
getTarget() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
getTarget() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
getTarget() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getTarget() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getTarget() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceScorer: Returns the second sequence of the pair.
getTarget() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileScorer: Returns the second profile of the pair.
getTarget() - Method in class org.biojava.nbio.core.alignment.SimpleProfilePair
getTarget() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getTarget() - Method in interface org.biojava.nbio.core.alignment.template.ProfilePair: Returns the second Profile of the pair.
getTarget() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the second AlignedSequence of the pair.
getTargetEndIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
getTargetIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
getTargetIndex(int) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
getTargetOntology() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
getTargetSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit: Returns the Sequence which is our edit.
getTargetStartIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
getTaxonomy() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getTaxonomy() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getTempBuffer() - Method in class org.biojava.nbio.ontology.obo.OboFileParser
getTempFactor() - Method in interface org.biojava.nbio.structure.Atom: Get temp factor.
getTempFactor() - Method in class org.biojava.nbio.structure.AtomImpl
getTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
getTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology: Fetch the term with the specified name.
getTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
getTerms() - Method in class org.biojava.nbio.ontology.IntegerOntology
getTerms() - Method in interface org.biojava.nbio.ontology.Ontology: Return all the terms in this ontology
getTerms() - Method in class org.biojava.nbio.ontology.Ontology.Impl
getTest() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
getText(Group) - Method in class org.biojava.nbio.structure.io.GroupToSDF
getText() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
getText() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
getTGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getTGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getThePdbId() - Method in class org.biojava.nbio.structure.cath.CathDomain: Returns the PDB ID.
getThreadPool() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools: Returns current shared thread pool.
getThreads() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getThree() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
getThree() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
getThree() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
getThree_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit: Should return the 3-prime end of the given Sequence according to the edit.
getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Insert
getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute
getTime() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getTime() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getTime() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getTimeAxisIncrementPercentage() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure: Get the percentage increment for the time axis
getTimeout() - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
getTimeout() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
getTissue() - Method in class org.biojava.nbio.structure.Compound
getTissue() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getTissue_fraction() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
getTitle() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Return the title of the AlignmentJmol window.
getTitle() - Method in class org.biojava.nbio.structure.Compound
getTitle() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
getTitle() - Method in class org.biojava.nbio.structure.JournalArticle: Get the value of title
getTitle() - Method in class org.biojava.nbio.structure.PDBHeader
getTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getTmIntra() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
getTMScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Returns the tmScore of the alignment.
getTMScore(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPChainScorer
getTMScore(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.SVDSuperimposer: Calculate the TM-Score for the superposition.
getTMScoreAlternate(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.SVDSuperimposer: Calculate the TM-Score for the superposition.
getTo() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
getTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder
getToCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
getTool() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Get the tool identifier for QBlast.
getTop() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getTopologyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
getTorsionPenalty() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getTotal() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
getTotal() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
getTotalArea() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns the total area buried upon formation of this interface, defined as: 1/2[ (ASA1u-ASA1c) + (ASA2u-ASA2u) ] , with:
getTotalArea() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster: Return the average buried surface area for this interface cluster
getTotalLenIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getTotalLenOpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getTotalRmsdIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain: this is the init-RMSD, not the final RMSD after refinement.
getTotalRmsdOpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain: The RMSD of the final alignment.
getTraceRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getTraces() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getTraceTmScoreMin() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getTrans() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getTranscoefpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
getTranscript(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence: Get the transcript sequence by accession
getTranscriptionEnd() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getTranscriptionStart() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getTranscripts() - Method in class org.biojava.nbio.core.sequence.GeneSequence: Get the collection of transcription sequences assigned to this gene
getTransfAlgebraic(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets a transformation algebraic string given its index.
getTransfAlgebraic() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
getTransformation(Matrix, Matrix) - Static method in class org.biojava.nbio.structure.Calc: Convert JAMA rotation and translation to a Vecmath transformation matrix.
getTransformation(Matrix, Atom) - Static method in class org.biojava.nbio.structure.Calc: Convert JAMA rotation and translation to a Vecmath transformation matrix.
getTransformation() - Method in class org.biojava.nbio.structure.SVDSuperimposer
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns transformation matrix to orient structure
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getTransformation(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets a transformation by index expressed in crystal axes basis.
getTransformationMap() - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser: Returns a map of bioassembly transformations
getTransformationMatrix() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Return the transformation (both rotational and translational component) as a 4x4 transformation matrix.
getTransformationMatrix() - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
getTransformations() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Returns a transformation matrix for each structure giving the 3D superimposition information of the multiple structure alignment.
getTransformations() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
getTransformations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Gets all transformations except for the identity in crystal axes basis.
getTransformationsOrthonormal() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo: Gets all symmetry transformation operators corresponding to this structure's space group (including the identity, at index 0) expressed in the orthonormal basis.
getTransformedCoordinates() - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
getTransformId() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
getTransforms() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Return the 2 crystal transform operations performed on each of the molecules of this interface.
getTransforms() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo: Return the list of BiologicalAssemblyTransformations needed to generate the biological assembly.
getTransformType() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Returns the TransformType of this transformation: AU, crystal translation, fractional translation , 2 3 4 6-fold rotations, 2 3 4 6-fold screw rotations, -1 -3 -2 -4 -6 inversions/rotoinversions.
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties: Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getTransition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties: An adaptor method which returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getTransition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getTransition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getTransition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getTransition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getTransition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
getTranslatedBbs(Vector3d) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox: Returns a new BoundingBoxes object containing the same bounds as this BoundingBoxes object translated by the given translation
getTranslation(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
getTranslation() - Method in class org.biojava.nbio.structure.SVDSuperimposer: Get the shift vector.
getTranslationVector(Matrix4d) - Static method in class org.biojava.nbio.structure.Calc: Extract the translational vector of a Vecmath transformation.
getTranslScrewComponent() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
getTranslScrewComponent(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.CrystalTransform: Given a transformation matrix containing a rotation and translation returns the screw component of the rotation.
getTransmembraneProteins() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: get all Transmembrane proteins
getTransNCS() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the transNCS property.
getTree(CathDomain) - Method in interface org.biojava.nbio.structure.cath.CathDatabase: Return the CATH sub-tree for a particular domain.
getTree(CathDomain) - Method in class org.biojava.nbio.structure.cath.CathInstallation
getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
getTree(ScopDomain) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase: get the SCOP sub-tree for a particular domain.
getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
getTreshold(int) - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
getTriples(Term, Term, Term) - Method in class org.biojava.nbio.ontology.IntegerOntology
getTriples(Term, Term, Term) - Method in interface org.biojava.nbio.ontology.Ontology: Return all triples from this ontology which match the supplied pattern.
getTriples(Term, Term, Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl
getTriplet() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
getTrustedCutoffs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation: Not always 2.
It may undergo further change.
getTurn() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
getTwi() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getTwinFraction() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the twinFraction property.
getTwinL() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the twinL property.
getTwinL2() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the twinL2 property.
getTwistedGroups() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
getTwo() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
getTwo() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
getTwo() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
getTwoFoldsPerpendicular() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
getType() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
getType() - Method in interface org.biojava.nbio.alignment.template.GapPenalty: Returns GapPenalty.Type stored.
getType() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature: The feature type
getType() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
getType() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface: The type of the feature.
getType() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
getType() - Method in class org.biojava.nbio.structure.AminoAcidImpl
getType() - Method in interface org.biojava.nbio.structure.Group: Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE
getType() - Method in class org.biojava.nbio.structure.HetatomImpl: Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getType() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
getType() - Method in class org.biojava.nbio.structure.NucleotideImpl
getType() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getType() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getType() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
getType() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement: Returns the SecStrucType of this element.
getType() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
getType() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
getType_symbol() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
getType_symbol() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
getTypeField() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getU() - Method in class org.biojava.nbio.structure.jama.LUDecomposition: Return upper triangular factor
getU() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Return the left singular vectors
getUid() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getUnalignedGroups(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: List of groups from the structure not included in ca (e.g.
getUnaryOperators() - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver: Returns a list of operators for this assembly.
getUnderlyingCompound() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
getUnidentifiableAtomLinkages() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
getUnidentifiableModifiedResidues() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
getUniprot() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getUniprot() - Method in class org.biojava.nbio.phosphosite.Site
getUniProtAccessionId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getUniprotbaseURL() - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: The current UniProt URL to deal with caching issues.
getUniprotDirectoryCache() - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: Local directory cache of XML that can be downloaded
getUniprotEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getUniProtId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getUniProtId() - Method in interface org.biojava.nbio.structure.SeqMisMatch
getUniProtId() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
getUniProtPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getUniProtResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
getUniprotStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
getUniqueID() - Method in class org.biojava.nbio.survival.cox.CoxVariables: Need a unique id from String
getUniqueInterfaces() - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder: Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.
getUniqueInterfaces(double) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder: Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.
getUniqueSequenceList() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
getUnitv() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getUnitVectors() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getUnknownDataTypeVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getUnrefinedScoreThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getUnweightedStrataInfoHashMap() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
getUpdates() - Method in class org.biojava.nbio.structure.rcsb.RCSBUpdates
getUpper() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getUpperBound() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
getUpperedBase() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
getUrl() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Get the top-level ECOD server URL.
getUrl() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
getURL() - Method in class org.biojava.nbio.structure.URLIdentifier
getUsed() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
getUsedAtomNames() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
getUserCollection() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Provided for convince if the developer needs to associate data with a sequence
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getUserConfigHelp() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams: The help text for each of these parameters.
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
getUserConfigHelp() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getUserConfigParameterNames() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams: The labels to be displayed to the user for each parameter
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getUserConfigParameters() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams: get the list of parameters that the user can change through the user interface.
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
getUserConfigParameters() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
getUserConfigTypes() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams: Get the data types of the parameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getUsername() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
getUserObject() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
getUserObject() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
getUserObject() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
getUserOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
getV() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition: Return the eigenvector matrix
getV() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Return the right singular vectors
getValenceElectronCount() - Method in enum org.biojava.nbio.structure.Element: Returns the number of valence electrons for this Element.
getValidFolds(List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer: Find valid symmetry orders for a given stoichiometry.
getValue(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getValue(C, C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getValue(C, C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns value in matrix for conversion from first Compound to the second.
getValue() - Method in class org.biojava.nbio.core.sequence.features.Qualifier
getValue() - Method in class org.biojava.nbio.core.util.CRC64Checksum
getValue() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
getValue() - Method in class org.biojava.nbio.structure.align.helper.GapArray
getValue_order() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
getValues() - Method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
getVarhaz() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getVariableResiduals() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getVariance() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getVariant() - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq: Return the FASTQ sequence format variant for this FASTQ formatted sequence.
getVariant() - Method in class org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReader
getVariant() - Method in class org.biojava.nbio.sequencing.io.fastq.SangerFastqReader
getVariant() - Method in class org.biojava.nbio.sequencing.io.fastq.SolexaFastqReader
getVariant() - Method in class org.biojava.nbio.structure.Compound
getVDWRadius() - Method in enum org.biojava.nbio.structure.Element: Returns the van der Waals radius of this Element.
getVector() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
getVector3dScrewTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
getVersion() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getVersion() - Method in class org.biojava.nbio.core.search.io.Result
getVersion() - Method in class org.biojava.nbio.core.sequence.AccessionID: In case if the AccessionID.getID() is not unique keeps the id version.
getVersion() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
getVersion() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeCPMain
getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeMain
getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
getVersion() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
getVersion() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
getVersion() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
getVersion() - Method in class org.biojava.nbio.structure.align.model.AFPChain
getVersion() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
getVersion() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Returns the version of the algorithm used to generate the MultipleAlignment objects.
getVersion() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
getVersion() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner: Get the Version information for this Algorithm.
getVersion() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
getVersion() - Method in interface org.biojava.nbio.structure.align.StructureAlignment: Get the Version information for this Algorithm.
getVersion() - Method in class org.biojava.nbio.structure.cath.CathDomain
getVersion() - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase: Return the release version.
getVersion() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
getVersion() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Return the ECOD version, as parsed from the file.
getVersion() - Method in class org.biojava.nbio.structure.validation.Program: Gets the value of the version property.
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron: Returns the vertices of an n-fold polygon of given radius and center
getVertices() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism: Returns the vertices of an n-fold polygon of given radius and center
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism: Returns the vertices of an n-fold polygon of given radius and center
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron: Returns the vertices of an n-fold polygon of given radius and center
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getViewCount() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
getViewedProfile() - Method in interface org.biojava.nbio.core.alignment.template.ProfileView: Returns the entire Profile being viewed
getViewedSequence() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
getViewedSequence() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView
getViewer() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getViewMatrix(int) - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
getViewName(int) - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
getVolume() - Method in class org.biojava.nbio.structure.JournalArticle
getVolume() - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Returns the volume of this unit cell.
getWaldTestInfo() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getWebStartConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
getWeight() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
getWeight() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
getWeight() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getWeight() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getWeighted() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getWidth() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism: Returns the radius of an inscribed sphere, that is tangent to each of the octahedron's faces
getWikipediaLink() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getWilsonBaniso() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the wilsonBaniso property.
getWilsonBestimate() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the wilsonBestimate property.
getWindowSize() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence: Access the current window size
getWinSize() - Method in class org.biojava.nbio.structure.align.ce.CeParameters: The window size to look at
getWinSize() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
getX() - Method in interface org.biojava.nbio.structure.Atom: Get coordinate X.
getX() - Method in class org.biojava.nbio.structure.AtomImpl: Get coordinate X.
getxAxisTimeCoordinates() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getxAxisTimeValues() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getXGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getXGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
getXMLcreationDate() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the xmLcreationDate property.
getXtriageInputColumns() - Method in class org.biojava.nbio.structure.validation.Entry: Gets the value of the xtriageInputColumns property.
getXYZEuler(Matrix) - Static method in class org.biojava.nbio.structure.Calc: Convert a rotation Matrix to Euler angles.
getY() - Method in interface org.biojava.nbio.structure.Atom: Get coordinate Y.
getY() - Method in class org.biojava.nbio.structure.AtomImpl: Get coordinate Y.
getZ() - Method in interface org.biojava.nbio.structure.Atom: Get coordinate Z.
getZ() - Method in class org.biojava.nbio.structure.AtomImpl: Get coordinate Z.
getZ() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo: Deprecated.
As of 4.0, use SpaceGroup.getMultiplicity() and Structure.size()
getZ() - Method in class org.biojava.nbio.structure.validation.AngleOutlier: Gets the value of the z property.
getZ() - Method in class org.biojava.nbio.structure.validation.BondOutlier: Gets the value of the z property.
getZ() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getZ_PDB() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns the Jmol zoom to fit polyhedron and symmetry axes.
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorI
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorO
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorT
getZscore() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier: Gets the value of the zscore property.
getZscore() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier: Gets the value of the zscore property.
getZYZEuler(Matrix) - Static method in class org.biojava.nbio.structure.Calc: Gets euler angles for a matrix given in ZYZ convention.
GFF3FromUniprotBlastHits - Class in org.biojava.nbio.genome.homology
GFF3FromUniprotBlastHits() - Constructor for class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
GFF3Reader - Class in org.biojava.nbio.genome.parsers.gff: http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GFF3Reader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GFF3Reader
GFF3Writer - Class in org.biojava.nbio.genome.parsers.gff
GFF3Writer() - Constructor for class org.biojava.nbio.genome.parsers.gff.GFF3Writer
GLOBAL_ALIGN1 - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
GLOBAL_ALIGN2 - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
gold - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
GOParser - Class in org.biojava.nbio.ontology.io: Simple parser for the Gene Ontology (GO) flatfile format.
GOParser() - Constructor for class org.biojava.nbio.ontology.io.GOParser
Gotoh - Class in org.biojava.nbio.structure.align.pairwise: a class to perform Gotoh algorithm
Gotoh(Alignable) - Constructor for class org.biojava.nbio.structure.align.pairwise.Gotoh
GradientMapper - Class in org.biojava.nbio.structure.gui.util.color: Maps a set of real values onto a gradient.
GradientMapper() - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
GradientMapper(Color, Color) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
GradientMapper(Color, Color, ColorSpace) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
GradientPanel - Class in org.biojava.nbio.structure.gui.util.color
GradientPanel(ContinuousColorMapper, double, double) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientPanel
GradientRenderer() - Constructor for class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer
gradients - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
GraphComponentOrderDetector - Class in org.biojava.nbio.structure.symmetry.internal: The GraphOrderDetector transforms the self-alignment into a Graph and extracts its maximally connected Components.
GraphComponentOrderDetector() - Constructor for class org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector
GraphComponentRefiner - Class in org.biojava.nbio.structure.symmetry.internal: The GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components.
GraphComponentRefiner() - Constructor for class org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner
grayOutCEOrig(Atom[], int, int, CECalculator, Matrix, int, double[], double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Grays out the main diagonal of a duplicated distance matrix.
grayOutPreviousAlignment(AFPChain, Atom[], int, int, CECalculator, Matrix, int, double[], double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Grid - Class in org.biojava.nbio.structure.contact: A grid to be used for calculating atom contacts through geometric hashing algorithm.
Grid(double) - Constructor for class org.biojava.nbio.structure.contact.Grid: Creates a Grid, the cutoff is in Angstroms and can be specified to a precision of 0.01A
GridCell - Class in org.biojava.nbio.structure.contact: A grid cell to be used in contact calculation via geometric hashing algorithm.
GridCell() - Constructor for class org.biojava.nbio.structure.contact.GridCell
group() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get the first item (everything before first semicolon, if it has one) in the attribute field, which is assumed to be a group identifer.
group() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Get the group id of the feature.
Group - Interface in org.biojava.nbio.structure: This is the data structure for a single Group of atoms.
group - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
group1 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor: Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf
An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.
The seven different attributes are
Hydrophobicity (Polar, Neutral, Hydrophobicity)
Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)
Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)
Polarizability (Value 0 - 1.08, 0.128 - 0.186, 0.219 - 0.409)
Charge (Positive, Neutral, Negative)
Secondary structure (Helix, Strand, Coil)
Solvent accessibility (Buried, Exposed, Intermediate)
group1 - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
group1WorseOutcome - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
group2 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
group2 - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
group3 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
GroupAsa - Class in org.biojava.nbio.structure.asa: A class to store the results of ASA calculations, it can hold ASA values per atom present in Group
GroupAsa(Group) - Constructor for class org.biojava.nbio.structure.asa.GroupAsa
groupByRange(double[], String, String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper: Need to allow a range of values similar to cut in R and a continuous c
GroupContact - Class in org.biojava.nbio.structure.contact: A pair of residues that are in contact
GroupContact() - Constructor for class org.biojava.nbio.structure.contact.GroupContact
GroupContactSet - Class in org.biojava.nbio.structure.contact: A set of residue-residue contacts.
GroupContactSet() - Constructor for class org.biojava.nbio.structure.contact.GroupContactSet
GroupContactSet(AtomContactSet) - Constructor for class org.biojava.nbio.structure.contact.GroupContactSet: Constructs a GroupContactSet by collapsing the given AtomContactSet into residue-residue (group-group) contacts.
GroupIterator - Class in org.biojava.nbio.structure: An iterator over all groups of a structure.
GroupIterator(Structure) - Constructor for class org.biojava.nbio.structure.GroupIterator: Constructs a GroupIterator object.
GroupLocation(List) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupResults - Class in org.biojava.nbio.survival.kaplanmeier.figure
GroupResults() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
GroupToSDF - Class in org.biojava.nbio.structure.io
GroupToSDF() - Constructor for class org.biojava.nbio.structure.io.GroupToSDF
GroupType - Enum in org.biojava.nbio.structure: This contains basic categories for Group types.
groupValues() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a collection of all unique group ids in the list, as defined by the group() method of the features.
GTSlikeScore(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
GuanUberbacher<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.routines: Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
GuanUberbacher() - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher: Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
GuanUberbacher(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher: Prepares for a pairwise global sequence alignment.
GuanUberbacher(S, S, GapPenalty, SubstitutionMatrix<C>, int) - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher: Prepares for a pairwise global sequence alignment.
guessFiletype(String) - Static method in class org.biojava.nbio.structure.StructureIO: Attempts to guess the type of a structure file based on the extension
guessOrderFromAngle(double, int) - Method in class org.biojava.nbio.structure.align.util.RotationAxis: Returns the rotation order o that gives the lowest value of |2PI / o - theta, given that the value is strictly lower than threshold, for orders o=1,...,maxOrder.
guessPDBID(String) - Static method in class org.biojava.nbio.structure.URLIdentifier: Recognizes PDB IDs that occur at the beginning of name followed by some delimiter.
guessScopDomain(String, ScopDatabase) - Static method in class org.biojava.nbio.structure.align.client.StructureName: Guess a scop domain.
guessSequentialAlignment(Map<Integer, Integer>, boolean) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Takes a potentially non-sequential alignment and guesses a sequential version of it.
GUIAlignmentProgressListener - Class in org.biojava.nbio.structure.align.gui: a GUI that allows to watch progress as multiple alignments are being processed.
GUIAlignmentProgressListener() - Constructor for class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
GuideTree<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements a data structure for a guide tree used during progressive multiple sequence alignment.
GuideTree(List<S>, List<PairwiseSequenceScorer<S, C>>) - Constructor for class org.biojava.nbio.alignment.GuideTree: Creates a guide tree for use during progressive multiple sequence alignment.
GuideTree.Node - Class in org.biojava.nbio.alignment: Implements a data structure for the node in a guide tree used during progressive multiple sequence alignment.
GuideTreeNode<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
GUIFarmJobRunnable - Class in org.biojava.nbio.structure.align.gui
GUIFarmJobRunnable(FarmJobParameters) - Constructor for class org.biojava.nbio.structure.align.gui.GUIFarmJobRunnable
GuiWrapper - Class in org.biojava.nbio.structure.align.ce: A class to wrap some of the strucutre.gui classes using Reflection
GuiWrapper() - Constructor for class org.biojava.nbio.structure.align.ce.GuiWrapper
GZIP_MAGIC - Static variable in class org.biojava.nbio.core.util.InputStreamProvider: The magic number found at the start of a GZIP stream.

H

H - Static variable in class org.biojava.nbio.aaproperties.Constraints
handleEvent(ValidationEvent) - Method in class org.biojava.nbio.aaproperties.xml.MyValidationEventHandler
handlePopupMenu(int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
has3D() - Method in interface org.biojava.nbio.structure.Group: Return true or false, depending if this group has 3D coordinates or not.
has3D() - Method in class org.biojava.nbio.structure.HetatomImpl: returns true or false, depending if this group has 3D coordinates or not.
hasAltLoc() - Method in interface org.biojava.nbio.structure.Group: Test if this group has alternate locations.
hasAltLoc() - Method in class org.biojava.nbio.structure.HetatomImpl
hasAminoAtoms() - Method in interface org.biojava.nbio.structure.Group: Calculate if this group has all atoms required for an amino acid backbone.
hasAminoAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl: Calculate if this group has all atoms required for an amino acid backbone.
hasAtom(String) - Method in interface org.biojava.nbio.structure.Group: Tell whether a particular atom exists within this group.
hasAtom(String) - Method in class org.biojava.nbio.structure.HetatomImpl: Tell whether a particular atom exists within this group.
hasAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
hasAttribute(String, String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
hasAttribute(String) - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Check if the feature has a value defined for the specified key.
hasAttribute(String, String) - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Check if the feature attributes include the specified key/value pair.
hasAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Check if any feature in list has the specified attribute key.
hasAttribute(String, String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Check if any feature in list has the specified attribute key/value pair.
hasBiolAssembly(String) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider: Does the PDB ID have biological assembly information?
hasBiolAssembly(String) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
hasBiolAssembly() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
hasBiolAssembly(String) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
hasBiolAssembly() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider: Does the PDB ID have biological assembly information?
hasBiolAssembly(String) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
hasBiolAssembly() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
hasBiologicalAssembly(String) - Static method in class org.biojava.nbio.structure.StructureIO: Does the provider PDB ID have a biological assembly?
hasChain(String) - Method in interface org.biojava.nbio.structure.Structure: Check if a chain with the id chainId is contained in this structure.
hasChain(String) - Method in class org.biojava.nbio.structure.StructureImpl: Check if a chain with the id chainId is contained in this structure.
hasCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
hasCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
hasCompound(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
hasCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
hasCompound(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
hasContact(Atom, Atom) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
hasContact(AtomIdentifier, AtomIdentifier) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
hasContact(Group, Group) - Method in class org.biojava.nbio.structure.contact.GroupContactSet: Tell whether the given group pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers
hasContact(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.contact.GroupContactSet: Tell whether the given pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers
hasContact(ResidueIdentifier, ResidueIdentifier) - Method in class org.biojava.nbio.structure.contact.GroupContactSet: Tell whether the given pair is a contact in this GroupContactSet, in a chain-identifier independent way: contacts happening between different copies of the same Compound(Entity) will be considered equal as long as they have the same residue numbers.
hasContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContactSet: Returns true if at least 1 contact from this set is within the given distance.
hasGap(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
hasGap(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns true if any AlignedSequence has a gap at the given index.
hasGaps(int) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Check size of gaps between successive features in list.
hash(int, boolean) - Static method in class org.biojava.nbio.core.util.Hashcoder
hash(int, char) - Static method in class org.biojava.nbio.core.util.Hashcoder
hash(int, int) - Static method in class org.biojava.nbio.core.util.Hashcoder: Used for ints, bytes and shorts
hash(int, long) - Static method in class org.biojava.nbio.core.util.Hashcoder: long support done by shifting by 32 (using unsigned shift)
hash(int, float) - Static method in class org.biojava.nbio.core.util.Hashcoder: float support done via Float.floatToIntBits(float) which allows the encoding of a float as an int.
hash(int, double) - Static method in class org.biojava.nbio.core.util.Hashcoder: double support which is done using the same techinque as float hashing except we convert to a long not to an int.
hash(int, Object) - Static method in class org.biojava.nbio.core.util.Hashcoder: o is a possibly-null object field, and possibly an array.
hashCode() - Method in class org.biojava.nbio.core.search.io.Hit
hashCode() - Method in class org.biojava.nbio.core.search.io.Hsp
hashCode() - Method in class org.biojava.nbio.core.search.io.Result
hashCode() - Method in class org.biojava.nbio.core.sequence.AccessionID
hashCode() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
hashCode() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
hashCode() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
hashCode() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
hashCode() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
hashCode() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
hashCode() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
hashCode() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
hashCode() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
hashCode() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
hashCode() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
hashCode() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
hashCode() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
hashCode() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
hashCode() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
hashCode() - Method in class org.biojava.nbio.data.sequence.FastaSequence
hashCode() - Method in class org.biojava.nbio.genome.parsers.gff.Location
hashCode() - Method in class org.biojava.nbio.ontology.Term.Impl
hashCode() - Method in interface org.biojava.nbio.ontology.Triple: The hashcode for a Triple.
hashCode() - Method in class org.biojava.nbio.ontology.Triple.Impl
hashCode() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
hashCode() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
hashCode() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
hashCode() - Method in class org.biojava.nbio.protmod.structure.StructureAtom
hashCode() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
hashCode() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
hashCode() - Method in class org.biojava.nbio.ronn.Jronn.Range
hashCode() - Method in class org.biojava.nbio.ronn.ModelLoader.Model
hashCode() - Method in class org.biojava.nbio.structure.align.client.PdbPair
hashCode() - Method in class org.biojava.nbio.structure.align.client.StructureName
hashCode() - Method in class org.biojava.nbio.structure.align.model.AFPChain
hashCode() - Method in class org.biojava.nbio.structure.Author
hashCode() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
hashCode() - Method in class org.biojava.nbio.structure.contact.Pair
hashCode() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
hashCode() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
hashCode() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
hashCode() - Method in class org.biojava.nbio.structure.io.SSBondImpl
hashCode() - Method in class org.biojava.nbio.structure.ResidueNumber
hashCode() - Method in class org.biojava.nbio.structure.ResidueRange
hashCode() - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
hashCode() - Method in class org.biojava.nbio.structure.scop.ScopDescription
hashCode() - Method in class org.biojava.nbio.structure.Site
hashCode() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
hashCode() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
Hashcoder - Class in org.biojava.nbio.core.util: Contains helper methods for generating a HashCode without having to resort to the commons lang hashcode builders.
Hashcoder() - Constructor for class org.biojava.nbio.core.util.Hashcoder
hasJournalArticle() - Method in class org.biojava.nbio.structure.PDBHeader: Return whether or not the entry has an associated journal article or publication.
hasJournalArticle() - Method in interface org.biojava.nbio.structure.Structure: Return whether or not the entry has an associated journal article or publication.
hasJournalArticle() - Method in class org.biojava.nbio.structure.StructureImpl: Return whether or not the entry has an associated journal article or publication.
hasMore() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
hasNext() - Method in class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator
hasNext(int, int) - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Check if next window of specified size is available.
hasNext() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Check if next window of default size is available.
hasNext() - Method in class org.biojava.nbio.structure.AtomIterator: Is there a next atom ?
hasNext() - Method in class org.biojava.nbio.structure.GroupIterator: is there a group after the current one in the structure?
hasNext() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
hasParent() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
hasPrecalculatedResult(String, String, String, String) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
hasPrecalculatedResult(String, String, String, String, int) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
hasProteinSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Returns true if structure contains protein subunits.
HasResultXMLConverter - Class in org.biojava.nbio.structure.align.xml
HasResultXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.HasResultXMLConverter
HBond - Class in org.biojava.nbio.structure.secstruc: Container that represents a hidrogen bond.
HBond() - Constructor for class org.biojava.nbio.structure.secstruc.HBond
HBond(HBond) - Constructor for class org.biojava.nbio.structure.secstruc.HBond
HBONDHIGHENERGY - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc: higher limit for H-bond energy
HBONDLOWENERGY - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc: Minimal H-bond energy in cal/mol
HeaderInfo - Class in org.biojava.nbio.survival.data
HeaderInfo(Integer) - Constructor for class org.biojava.nbio.survival.data.HeaderInfo
headerLine - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
height - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
HelicalRepeatUnit - Class in org.biojava.nbio.structure.symmetry.core
HelicalRepeatUnit(Subunits) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
Helix - Class in org.biojava.nbio.structure.symmetry.core
Helix() - Constructor for class org.biojava.nbio.structure.symmetry.core.Helix
HelixAxisAligner - Class in org.biojava.nbio.structure.symmetry.core
HelixAxisAligner(QuatSymmetryResults) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
HelixExtender - Class in org.biojava.nbio.structure.symmetry.core
HelixExtender(Subunits, Helix) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixExtender
HelixLayers - Class in org.biojava.nbio.structure.symmetry.core
HelixLayers() - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixLayers
HelixSolver - Class in org.biojava.nbio.structure.symmetry.core
HelixSolver(Subunits, int, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixSolver
HelpDialog - Class in org.biojava.nbio.structure.align.gui
HelpDialog() - Constructor for class org.biojava.nbio.structure.align.gui.HelpDialog
HetatomImpl - Class in org.biojava.nbio.structure: Generic Implementation of a Group interface.
HetatomImpl() - Constructor for class org.biojava.nbio.structure.HetatomImpl: Construct a Hetatom instance.
HetatomImpl.PerformanceBehavior - Enum in org.biojava.nbio.structure: Behaviors for how to balance memory vs.
hexPropertyNames - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo
hideAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script to hide axes
hideAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script to hide axes
hideAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
hideColumn(String, boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
hideEmptyColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
hideEmptyRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
hideMetaDataColumns(boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
hideMetaDataRows(boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
hidePolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
hidePolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
hidePolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
hideRow(String, boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
hideSuggest() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest: Force the suggestions to be hidden (Useful for buttons, e.g.
hieFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
HierarchicalClusterer<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a clustering algorithm that converts a distance matrix into a tree.
Hit - Class in org.biojava.nbio.core.search.io: This class models a search Hit.
Hit(int, String, String, String, int, List<Hsp>, Sequence) - Constructor for class org.biojava.nbio.core.search.io.Hit
HMMER_SERVICE - Static variable in class org.biojava.nbio.ws.hmmer.RemoteHmmerScan
HmmerDemo - Class in demo: The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service
HmmerDemo() - Constructor for class demo.HmmerDemo
HmmerDomain - Class in org.biojava.nbio.ws.hmmer: Provides the details of a domain hit
HmmerDomain() - Constructor for class org.biojava.nbio.ws.hmmer.HmmerDomain
HmmerResult - Class in org.biojava.nbio.ws.hmmer: The results of a Hmmer search for a single sequence
HmmerResult() - Constructor for class org.biojava.nbio.ws.hmmer.HmmerResult
HmmerScan - Interface in org.biojava.nbio.ws.hmmer: Interface for performing Hmmscans on sequences.
HOMSTRAD - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
Hsp<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.core.search.io: This class models a search Hsp.
Hsp(int, double, int, double, int, int, int, int, int, int, int, int, int, int, String, String, String, Double, Integer) - Constructor for class org.biojava.nbio.core.search.io.Hsp
HSVColorSpace - Class in org.biojava.nbio.structure.gui.util.color
HSVColorSpace() - Constructor for class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
HTTPConnectionTools - Class in org.biojava.nbio.structure.align.util: a class that takes care about opening HttpURLConnections and sets the proper timeouts
HTTPConnectionTools() - Constructor for class org.biojava.nbio.structure.align.util.HTTPConnectionTools
hypot(double, double) - Static method in class org.biojava.nbio.structure.jama.Maths: sqrt(a^2 + b^2) without under/overflow.

I

I - Static variable in class org.biojava.nbio.aaproperties.Constraints
icode - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
IcosahedralSampler - Class in org.biojava.nbio.structure.symmetry.geometry
Icosahedron - Class in org.biojava.nbio.structure.symmetry.geometry
Icosahedron() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
ID_KEY - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
Identifier - Class in org.biojava.nbio.structure: Deprecated.
Use StructureName instead. Deprecated in v. 4.2.0
Identifier() - Constructor for class org.biojava.nbio.structure.Identifier: Deprecated.
identify(Structure) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier: Identify all registered modifications in a structure.
identify(Structure, Set<ProteinModification>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier: Identify a set of modifications in a structure.
identify(Chain) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier: Identify all registered modifications in a chain.
identify(List<Chain>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier: Identify all registered modifications in chains.
identify(Chain, Set<ProteinModification>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier: Identify a set of modifications in a a chains.
identify(List<Chain>, Set<ProteinModification>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier: Identify a set of modifications in a a list of chains.
identity(int, int) - Static method in class org.biojava.nbio.structure.jama.Matrix: Generate identity matrix
IDENTITY - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder
IDENTITY - Static variable in class org.biojava.nbio.structure.xtal.CrystalTransform
identity(int) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
IDENTITY_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.CompoundFinder: Identity value for 2 chains to be considered part of same entity
IdentityMap() - Constructor for class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
identityMatch(Atom[], String, int, int, String) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster: Match a sequence to this cluster at 100% identity.
IDX_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
IdxComparator - Class in org.biojava.nbio.structure.align.helper
IdxComparator() - Constructor for class org.biojava.nbio.structure.align.helper.IdxComparator
IlluminaFastqReader - Class in org.biojava.nbio.sequencing.io.fastq: Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.
IlluminaFastqReader() - Constructor for class org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReader
IlluminaFastqWriter - Class in org.biojava.nbio.sequencing.io.fastq: Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences.
IlluminaFastqWriter() - Constructor for class org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriter
Impl(String, String) - Constructor for class org.biojava.nbio.ontology.Ontology.Impl
Impl(Ontology, Ontology) - Constructor for class org.biojava.nbio.ontology.OntologyTerm.Impl
Impl(Ontology, Ontology, Object[]) - Constructor for class org.biojava.nbio.ontology.OntologyTerm.Impl
Impl(Ontology, Term, String) - Constructor for class org.biojava.nbio.ontology.RemoteTerm.Impl
Impl(Ontology, Term, String, Object[]) - Constructor for class org.biojava.nbio.ontology.RemoteTerm.Impl
Impl(Ontology, String) - Constructor for class org.biojava.nbio.ontology.Term.Impl
Impl(Ontology, String, String) - Constructor for class org.biojava.nbio.ontology.Term.Impl
Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.nbio.ontology.Term.Impl
Impl(Term, Term, Term) - Constructor for class org.biojava.nbio.ontology.Triple.Impl
Impl(Term, Term, Term, Object[]) - Constructor for class org.biojava.nbio.ontology.Triple.Impl
Impl(Term, Term, Term, String, String) - Constructor for class org.biojava.nbio.ontology.Triple.Impl
Impl(Term, Term, Term, String, String, Object[]) - Constructor for class org.biojava.nbio.ontology.Triple.Impl
Impl(Ontology, String, String) - Constructor for class org.biojava.nbio.ontology.Variable.Impl
Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.nbio.ontology.Variable.Impl
importTerm(Term, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
importTerm(Term, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
importTerm(Term, String) - Method in interface org.biojava.nbio.ontology.Ontology: Create a view of a term from another ontology.
index - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair
INDEX - Static variable in class org.biojava.nbio.ronn.RonnConstraint
index - Variable in class org.biojava.nbio.structure.align.helper.GapArray
indexOf(Sequence<C>, C) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: Performs a linear search of the given Sequence for the given compound.
indexOf(String, String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
IndexPair - Class in org.biojava.nbio.structure.align.helper
IndexPair() - Constructor for class org.biojava.nbio.structure.align.helper.IndexPair
IndexPair(short, short) - Constructor for class org.biojava.nbio.structure.align.helper.IndexPair
INFINITY - Static variable in class org.biojava.nbio.alignment.io.StockholmFileParser: indicates reading as much as possible, without limits
init() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry: Initialization the static variables and register common modifications.
init(InputStream) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry: Initialization the static variables and register common modifications.
init(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
initAlignmentGUIMenu(JFrame) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
initCoords() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Display the structures after the variable initialization in the constructor.
initCoords() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
initCoords() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
initExtinctionCoefficient() - Static method in class org.biojava.nbio.aaproperties.Constraints: Does the initialization of extinction coefficient based on http://au.expasy.org/tools/protparam-doc.html
initializeBreakFlag(boolean[][]) - Method in interface org.biojava.nbio.structure.align.ce.MatrixListener
initializeCellTranslations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
initJmolMenu(JFrame, AbstractAlignmentJmol, AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator: Provide a JMenuBar that can be added to a JFrame containing a JmolPanel.
initMenu() - Static method in class org.biojava.nbio.structure.gui.util.MenuCreator: provide a JMenuBar that can be added to a JFrame
initMet(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
initMolecularWeight() - Static method in class org.biojava.nbio.aaproperties.Constraints: Does the initialization of molecular weights based on http://au.expasy.org/tools/findmod/findmod_masses.html#AA
initPaths() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Should be called whenever any of the path variables change.
initSumOfDistances(int, int, int, int, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
initSumOfDistances(int, int, int, int, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
InputStreamProvider - Class in org.biojava.nbio.core.util: A class that provides an InputStream from a File.
InputStreamProvider() - Constructor for class org.biojava.nbio.core.util.InputStreamProvider
inputStreamToDocument(InputStream) - Static method in class org.biojava.nbio.core.util.XMLHelper
InsdcLocations - Class in org.biojava.nbio.core.sequence.location: A collection of locations which are used whenever we work with INSDC; some of which could be deprecated (from INSDC's point of view) yet appear in records.
InsdcLocations() - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations
InsdcLocations.BondLocation - Class in org.biojava.nbio.core.sequence.location: Used to represent bond locations equivalent to bond(7,8) or bond(7).
InsdcLocations.GroupLocation - Class in org.biojava.nbio.core.sequence.location: Deprecated in INSDC yet still appears; equivalent to the order() directive except no 5' to 3' ordering is defined.
InsdcLocations.OneOfLocation - Class in org.biojava.nbio.core.sequence.location: Deprecated in INSDC; refers to a set of locations of which one location could be valid e.g.
InsdcLocations.OrderLocation - Class in org.biojava.nbio.core.sequence.location: Used to describe a 5' to 3' ordering but no firm assurance it is correct
InsdcParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.location: Parser for working with INSDC style locations.
InsdcParser() - Constructor for class org.biojava.nbio.core.sequence.location.InsdcParser
InsdcParser(DataSource) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcParser
Insert(String, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert
Insert(Sequence<C>, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert
Insert(String, int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert
Insert(Sequence<C>, int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert
IntegerOntology - Class in org.biojava.nbio.ontology
IntegerOntology.IntTerm - Class in org.biojava.nbio.ontology
interpolate(Color, Color, float) - Method in interface org.biojava.nbio.structure.gui.util.color.ColorInterpolator: Interpolates to a color between a and b
interpolate(Color, Color, float) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator: Interpolates to a color between a and b
INTERPRO - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
interrupt() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc: stops what is currently happening and does not continue
interrupt() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB: stops what is currently happening and does not continue
interrupt() - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
interrupt() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
interrupt() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch: stops what is currently happening and does not continue
interrupt() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc: stops what is currently happening and does not continue
interrupt() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
intersection(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return the intersection, or null if no overlap.
INTERSECTION_OF - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
IntronSequence - Class in org.biojava.nbio.core.sequence
IntronSequence(GeneSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.IntronSequence: Place holder for Intron sequence features
IntTerm(int) - Constructor for class org.biojava.nbio.ontology.IntegerOntology.IntTerm
IntTerm(int, Object[]) - Constructor for class org.biojava.nbio.ontology.IntegerOntology.IntTerm
intValue() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet: Attempts to provide an int version of this codon which multiplies each position by
intValue() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
InvalidTermException - Exception in org.biojava.nbio.ontology: Thrown to indicate that an ontology term is not acceptable or appropriate in a given context
InvalidTermException() - Constructor for exception org.biojava.nbio.ontology.InvalidTermException
InvalidTermException(String) - Constructor for exception org.biojava.nbio.ontology.InvalidTermException
InvalidTermException(Throwable) - Constructor for exception org.biojava.nbio.ontology.InvalidTermException
InvalidTermException(String, Throwable) - Constructor for exception org.biojava.nbio.ontology.InvalidTermException
inverse(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: A method which attempts to do the right thing when is comes to a reverse/reverse complement
inverse() - Method in class org.biojava.nbio.structure.jama.Matrix: Matrix inverse or pseudoinverse
invert(Atom) - Static method in class org.biojava.nbio.structure.Calc
invertAlignment(AFPChain) - Method in class org.biojava.nbio.structure.align.ce.CeCPMain: Swaps the order of structures in an AFPChain
IOUtils - Class in org.biojava.nbio.core.sequence.io.util
IOUtils() - Constructor for class org.biojava.nbio.core.sequence.io.util.IOUtils
IOUtils.ReaderProcessor - Interface in org.biojava.nbio.core.sequence.io.util: Closure interface used when working with IOUtils#processReader(String).
ioverSigma - Variable in class org.biojava.nbio.structure.validation.Entry
IPeptideProperties - Interface in org.biojava.nbio.aaproperties: An interface to generate some basic physico-chemical properties of protein sequences.
The following properties could be generated:
Molecular weight
Absorbance
Extinction coefficient
Instability index
Apliphatic index
Average hydropathy value
Isoelectric point
Net charge at pH 7
Composition of specified amino acid
Composition of the 20 standard amino acid
IProfeatProperties - Interface in org.biojava.nbio.aaproperties.profeat
IProfeatProperties.ATTRIBUTE - Enum in org.biojava.nbio.aaproperties.profeat: Enumeration of the seven different attributes
IProfeatProperties.DISTRIBUTION - Enum in org.biojava.nbio.aaproperties.profeat: Enumeration of the distribution for the first, first 25%, first 50%, first 75% and 100% of the grouping
IProfeatProperties.GROUPING - Enum in org.biojava.nbio.aaproperties.profeat: Enumeration of the three different groupings for each attributes
IProfeatProperties.TRANSITION - Enum in org.biojava.nbio.aaproperties.profeat: Enumeration of the transition between groupA and groupB
IS_A - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
IS_A - Static variable in class org.biojava.nbio.ontology.OntoTools
IS_DOMAIN_ASSEMBLY - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser: Deprecated way of indicating there is an assembly.
IS_OBSOLETE - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
IS_REPRESENTATIVE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser: Indicates a manual representative
isAfter(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location is entirely after the other location (no overlap).
isAlignSeqRes() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.
isAmbiguosProtein(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil: Check whether the sequence confirms to amboguous protein sequence
isAmbiguous() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
isAminoAcid() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
isAutoFetch() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
isAutoFetch() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
Use AtomCache.getFetchBehavior()
isAutoFetch() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Deprecated.
Use LocalPDBDirectory.getFetchBehavior()
isBefore(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location is entirely before other location (no overlap).
isBend() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
isBetaStrand() - Method in enum org.biojava.nbio.structure.secstruc.SecStrucType: A Beta-Strand is an extended set of sequential Bridges that, together with other Beta-Strands, is part of a Beta-Sheet.
isBetweenCompounds() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
isBetweenCompounds() - Method in interface org.biojava.nbio.core.sequence.location.template.Location: Returns true if the position is meant to represent a point between two points such as 78^79.
isBioAssembly() - Method in class org.biojava.nbio.structure.align.client.StructureName
isBiologicalAssembly() - Method in interface org.biojava.nbio.structure.Structure: Get flag that indicates if this structure is a biological assembly
isBiologicalAssembly() - Method in class org.biojava.nbio.structure.StructureImpl: Gets flag that indicates if this structure is a biological assembly
isCacheEnabled() - Method in class org.biojava.nbio.structure.domain.SerializableCache
isCathID() - Method in class org.biojava.nbio.structure.align.client.StructureName
isCellReasonable() - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Checks whether the dimensions of this crystal cell are reasonable for protein crystallography: if all 3 dimensions are below 10.0 the cell is considered unrealistic and false returned
isChainPureNonPolymer(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Returns true if the given chain is composed of non-polymeric groups only
isChainWaterOnly(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Returns true if the given chain is composed of water molecules only
isChalcogen() - Method in enum org.biojava.nbio.structure.Element: Returns true if Element is a chalcogen (O, S, Se, Te, Po).
isCircular() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
isCircular() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
isCircular() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns true if this Sequence wraps around from the last alignment column back to the first.
isCircular() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns true if any AlignedSequence is circular.
isCircular() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
isCircular() - Method in interface org.biojava.nbio.core.sequence.location.template.Location: Indicates if this location is circular.
isCompatible(ResidueGroup) - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup: Determine if two Residuegroups (maximally connected components of the alignment Graph) are compatible, based in the following criterion:
isComplementable() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
isComplementable() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
isComplementable() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
isComplementable() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
isComplementable() - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet: NucleotideCompounds can always complement
isComplementable() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
isComplete() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
isComplex() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
isComplex() - Method in interface org.biojava.nbio.core.sequence.location.template.Location: Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.
isCompoundStringLengthEqual() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
isCompoundStringLengthEqual() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
isCompoundStringLengthEqual() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
isCompoundStringLengthEqual() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
isCompoundStringLengthEqual() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet: Returns true if all String representations of Compounds are of the same length.
isConnected(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc: Test if two amino acids are connected, i.e.
isCrossLink() - Method in enum org.biojava.nbio.protmod.ModificationCategory
isCrystallographic() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique
isCrystallographic(Set<ExperimentalTechnique>) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique: Given a Set of ExperimentalTechniques returns true if at least one is crystallographic
isCrystallographic() - Method in interface org.biojava.nbio.structure.Structure: Test if this structure is a crystallographic structure, i.e.
isCrystallographic() - Method in class org.biojava.nbio.structure.StructureImpl: Whether this Structure is a crystallographic structure or not.
isCTerminal() - Method in class org.biojava.nbio.protmod.Component
isDebug() - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Deprecated.
isDefined() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
isDoAngleCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
isDoDensityCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
isDoDistanceCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
isDomainSplit() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
isDomainSplit() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
isDoRMSCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
isDownloadAll() - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider: By default this provider will download only some of the ChemComp files.
isEcodDomain() - Method in class org.biojava.nbio.structure.align.client.StructureName
isEmpty() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
isEmpty() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp: Indicates whether this compound was created with
isEnantiomorphic() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
isEquivalent(CrystalTransform) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Returns true if the given CrystalTransform is equivalent to this one.
isErrorXML(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser: returns true if the alignment XML contains an error message
isEscapeStarter(char) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
isFetchCurrent() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
Use FileParsingParameters#getObsoleteBehavior() instead (4.0.0)
isFetchCurrent() - Method in class org.biojava.nbio.structure.io.PDBFileReader: Deprecated.
Use FileParsingParameters#getObsoleteBehavior()
isFetchFileEvenIfObsolete() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
Use FileParsingParameters#getObsoleteBehavior() instead (4.0.0)
isFetchFileEvenIfObsolete() - Method in class org.biojava.nbio.structure.io.PDBFileReader: Deprecated.
Use FileParsingParameters#getObsoleteBehavior()
isFile() - Method in class org.biojava.nbio.structure.align.client.StructureName: Indicates that the identifier was determined to correspond to a file.
isFlexible() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
isFractionalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Tells whether this transformation contains a fractional translational component (whatever its rotational component).
isFullRank() - Method in class org.biojava.nbio.structure.jama.QRDecomposition: Is the matrix full rank?
isGap(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
isGap(int) - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns true if this Sequence has a gap at a particular alignment column.
isGap(char) - Static method in class org.biojava.nbio.phylo.Comparison: Method that determines if a character means a gap in the alignment.
isGaps() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
isGuiModuleInstalled() - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
isHalogen() - Method in enum org.biojava.nbio.structure.Element: Returns true if Element is a halogen (F, Cl, Br, I, At).
isHeaderOnly() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: Parse only the PDB file header out of the files
isHeavyAtom() - Method in enum org.biojava.nbio.structure.Element: Returns true is the Element is an not Hydrogen (or an isotope of Hydrogen).
isHelixType() - Method in enum org.biojava.nbio.structure.secstruc.SecStrucType: Helix type can be 3-10 helix, pi-helix or alpha-helix.
isHeteroAtom() - Method in enum org.biojava.nbio.structure.Element: Returns true if Element is not Hydrogen and not Carbon.
isHexProperty(String) - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
isHide() - Method in class org.biojava.nbio.survival.data.HeaderInfo
isHigher(Point) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
isHigher(Point) - Method in interface org.biojava.nbio.core.sequence.location.template.Point: Returns true if the point is higher in value to the current point
isHomomeric() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns true if the 2 molecules of this interface are the same entity (i.e.
isHydrogen() - Method in enum org.biojava.nbio.structure.Element: Returns true if this Element is Hydrogen.
isIdentity() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Tells whether this transformation is the identity: no rotation and no translation
isIllumina() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant: Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_ILLUMINA.
isInfinite() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Returns true if the transformation applied to the second molecule of this interface has an infinite character (pure translation or screw rotation) and both molecules of the interface have the same asymmetric unit identifier (chain id): in such cases the interface would lead to infinite fiber-like (linear or helical) assemblies
isInfinite() - Method in enum org.biojava.nbio.structure.xtal.TransformType: Tells whether the transform type produces infinite assemblies if interface happens between identical chains
isInterrupted() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
isIsologous() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Tell whether the interface is isologous, i.e.
isJoinFast() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
isJoinPlo() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
isLeaf() - Method in class org.biojava.nbio.alignment.GuideTree.Node
isLocal() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Returns whether alignment finds a region of similarity rather than aligning every compound.
isLocal() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults: Return true
isLocalSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
isLower(Point) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
isLower(Point) - Method in interface org.biojava.nbio.core.sequence.location.template.Point: Returns true if the current point is at a lower position than the point given.
isMatch(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList: Return true is the sequence and residues numbers of the passed in array of atoms matches those of this unique sequence list
isMetaDataColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
isMetaDataRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
isMetal() - Method in enum org.biojava.nbio.structure.Element: Returns true if ElementType is a metal.
isMetal() - Method in enum org.biojava.nbio.structure.ElementType: Returns true if ElementType is a metal.
isMetalloid() - Method in enum org.biojava.nbio.structure.Element: Returns true if ElementType is a metalloid.
isMetalloid() - Method in enum org.biojava.nbio.structure.ElementType: Returns true if ElementType is a metalloid.
isNegative() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if location is on negative strand.
isNmr() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique
isNmr(Set<ExperimentalTechnique>) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique: Given a Set of ExperimentalTechniques returns true if at least one is NMR
isNmr() - Method in interface org.biojava.nbio.structure.Structure: Test if this structure is an NMR structure.
isNmr() - Method in class org.biojava.nbio.structure.StructureImpl: Whether this Structure is a NMR structure or not.
isNonAmbNucleotideSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil: Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!) - B char
isNonMetal() - Method in enum org.biojava.nbio.structure.Element: Returns true if ElementType is a non-metal.
isNonMetal() - Method in enum org.biojava.nbio.structure.ElementType: Returns true if ElementType is a non-metal.
isNonsingular() - Method in class org.biojava.nbio.structure.jama.LUDecomposition: Is the matrix nonsingular?
isNoOverlap() - Method in class org.biojava.nbio.structure.contact.Grid: Tells whether (after having added atoms to grid) the i and j grids are not overlapping.
isNTerminal() - Method in class org.biojava.nbio.protmod.Component
isNucleicAcid(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Tell whether given chain is DNA or RNA
isNucleotide(String) - Static method in class org.biojava.nbio.structure.StructureTools: Test if the three-letter code of an ATOM entry corresponds to a nucleotide or to an aminoacid.
isNucleotideSequence(String) - Static method in class org.biojava.nbio.core.util.SequenceTools
isNucleotideSequence(FastaSequence) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
isOnTheFly() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
Isotope - Class in org.biojava.nbio.aaproperties.xml
Isotope() - Constructor for class org.biojava.nbio.aaproperties.xml.Isotope
Isotope(String, int, double) - Constructor for class org.biojava.nbio.aaproperties.xml.Isotope
isOutputPDB() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters: When writing the results to a file, don;t write as XML but write aligned PDB file
isParseBioAssembly() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: Should the biological assembly info (REMARK 350) be parsed from the PDB file?
isParseCAOnly() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: The flag if only the C-alpha atoms of the structure should be parsed.
isParseSecStruc() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: Is secondary structure assignment being parsed from the file? default is null
isPartial() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
isPartialOn3prime() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
isPartialOn5prime() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
isPdbDirSplit() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters: Deprecated.
Always returns true (4.0.0)
isPdbId() - Method in class org.biojava.nbio.structure.align.client.StructureName
isPDPDomain() - Method in class org.biojava.nbio.structure.align.client.StructureName
isPFam() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
isPreferredResult() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
isPrint - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator
isPrint - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
isPrintCE() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters: Display the output string in CE style
isPrintFatCat() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
isPrintXML() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
isProtein(Chain) - Static method in class org.biojava.nbio.structure.StructureTools: Tell whether given chain is a protein chain
isProteinSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
isPseudoSymmetric() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
isPublished() - Method in class org.biojava.nbio.structure.JournalArticle
isPureCrystalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Tells whether this transformation is a pure crystal lattice translation, i.e.
isPureTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Tells whether this transformation is a pure translation: either a pure crystal (lattice) translation or a fractional (within unit cell) translation: space groups Ixxx, Cxxx, Fxxx have operators with fractional translations within the unit cell.
isQuote(char) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
isReachable() - Method in class org.biojava.nbio.structure.scop.ScopMirror
isReady() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
isReady() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
isReady() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
isReady(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Wrapper method for NCBIQBlastService.isReady(String, long), omitting unnecessary present property.
isReady(String, long) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Checks for completion of request.
isReady(String, long) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService: Simple method to check if the specified request has been completed by the service used.
isRefined() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
isRefined(MultipleAlignment) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Returns true a symmetry multiple alignment has been refined, false otherwise.
isReplaced(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
isReplaced(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
isReplacer(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
isReplacer(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
isRFam() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
isRotation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform: Tells whether this transformation is a rotation disregarding the translational component, i.e.
isRunBackground() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters: Flag if a job that only runs one parallell job should be run in its own thread or in the main thread.
isSameStrand(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location is on same strand as other location.
isSanger() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant: Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_SANGER.
isScopName() - Method in class org.biojava.nbio.structure.align.client.StructureName
isScrew() - Method in enum org.biojava.nbio.structure.xtal.TransformType: Tells whether the transform type is a screw or glide plane
isSequentialAlignment() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Get whether this alignment has the normal topology, ie the residues aligned in each block increase sequentially over the original protein.
isSequentialAlignment(AFPChain, boolean) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Checks that the alignment given by afpChain is sequential.
isShortAlign() - Method in class org.biojava.nbio.structure.align.model.AFPChain
isShow3d() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
isShowAFPRanges() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
isShowAFPRanges() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
isShowMenu() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
isSignificant() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult: Conditions checked are: score above the threshold, order higher than 1 and refinement succeeded.
isSignificant(MultipleAlignment, double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Returns true if the symmetry alignment is significant, false otherwise.
isSignificantResult() - Method in class org.biojava.nbio.structure.align.model.AFPChain
isSolexa() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant: Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_SOLEXA.
isSPD() - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition: Is the matrix symmetric and positive definite?
isStandard() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
isStandardChemComp(ChemComp) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
isStart() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
isStart(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable: Returns true if the given compound was a start codon in this codon table.
isStart() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
isStart(AminoAcidCompound) - Method in interface org.biojava.nbio.core.sequence.transcription.Table: Returns true if the given compound could have been a start amino acid; this does not assert if the codon that actually coded for the amino acid was a start codon.
isStartAnchored() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem: Indicates whether the start query and start target index compounds are anchored to each other
isStop() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
isStoringScoreMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Returns choice to cache the score matrix or to save memory by deleting score matrix after alignment.
isStrictSCOP() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Deprecated.
since 4.2
isSuggestVisible() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
isSymRelated() - Method in class org.biojava.nbio.structure.contact.StructureInterface: Tells whether the interface corresponds to one mediated by crystallographic symmetry, i.e.
isTryAllCPs() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
isUnaryExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools: Checks if the passed in expression is a unary operator expression Example: (1,2,3) or (1-60) are unary operator expressions (1-60)(61-88) is a binary operator expression, representing a cartesian product of the two parenthesised lists
isUncertain() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
isUncertain() - Method in interface org.biojava.nbio.core.sequence.location.template.Point: Returns a true if the exact point is unknown.
isUnknown() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
isUnknown() - Method in interface org.biojava.nbio.core.sequence.location.template.Point: Returns true if the current position is unknown but is beyond the position encoded for.
isUpdateRemediatedFiles() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
isUpdateRemediatedFiles() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: Deprecated.
Properties which impact downloading and caching behavior have been moved to the StructureIOFile implementations. See LocalPDBDirectory#getFetchBehavior(LocalPDBDirectory.FetchBehavior)
isURL() - Method in class org.biojava.nbio.structure.align.client.StructureName
isURLProperty(String) - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
isUseInternalChainId() - Method in class org.biojava.nbio.structure.io.FileParsingParameters: Should we use internal (asym_id) or public facing (author) chain ids
isUseMmCif() - Method in class org.biojava.nbio.structure.align.util.AtomCache
isValidColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
isValidRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
isValidSequence(Sequence<AminoAcidCompound>) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
isValidSequence(Sequence<AminoAcidCompound>) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
isValidSequence(Sequence<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
isValidSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
isValidSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
isVerbose() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters: Flag if the job should be run in verbose mode.
isVerbose() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
isVerbose() - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
isVerbose() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
isWaitForAlignments() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
isWater() - Method in interface org.biojava.nbio.structure.Group: Determines if this group is water.
isWater() - Method in class org.biojava.nbio.structure.HetatomImpl
isWeighted() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
iterator() - Method in class org.biojava.nbio.alignment.GuideTree: Returns a post-order Iterator that traverses the tree from leaves to root.
iterator() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
iterator() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
iterator() - Method in class org.biojava.nbio.core.search.io.Hit
iterator() - Method in class org.biojava.nbio.core.search.io.Result
iterator() - Method in class org.biojava.nbio.core.search.io.SearchIO
iterator() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
iterator() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
iterator() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
iterator() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation: Iterates through all known sub-locations for this location but does not descend
iterator() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
iterator() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader: Provides basic iterable access to this class
iterator() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader: Iterator implementation which attempts to move through the 2D structure attempting to skip onto the next sequence as & when it is asked to
iterator() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Returns an instance of SequenceMixin.SequenceIterator
iterator() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
iterator() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
iterator() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence: Returns an iterator which will return the windows in a sequence in sequential order.
iterator() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Create a location iterator over this location with a window size of 1 and an increment of +1 (successive symbols from start to end).
iterator(int, int) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Create a location iterator over this location, using specified window size and increment.
iterator() - Method in class org.biojava.nbio.structure.AugmentedResidueRange: Returns a new Iterator over every ResidueNumber in this ResidueRange.
iterator() - Method in class org.biojava.nbio.structure.contact.AtomContactSet
iterator() - Method in class org.biojava.nbio.structure.contact.GroupContactSet
iterator() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
iterator() - Method in interface org.biojava.nbio.structure.Group: get an Atom Iterator.
iterator() - Method in class org.biojava.nbio.structure.HetatomImpl: return an AtomIterator.
iterator() - Method in class org.biojava.nbio.structure.math.SymbolTable: Return an Iterator for the keys in the table.
iterator(AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange: Returns a new Iterator over every ResidueNumber in this ResidueRange.
iterator(AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRangeAndLength: Returns a new Iterator over every ResidueNumber in this ResidueRange.
IUPAC_LOCATION - Static variable in class org.biojava.nbio.core.sequence.io.IUPACParser
IUPACParser - Class in org.biojava.nbio.core.sequence.io: Available translations 1 - UNIVERSAL 2 - VERTEBRATE_MITOCHONDRIAL 3 - YEAST_MITOCHONDRIAL 4 - MOLD_MITOCHONDRIAL 5 - INVERTEBRATE_MITOCHONDRIAL 6 - CILIATE_NUCLEAR 9 - ECHINODERM_MITOCHONDRIAL 10 - EUPLOTID_NUCLEAR 11 - BACTERIAL 12 - ALTERNATIVE_YEAST_NUCLEAR 13 - ASCIDIAN_MITOCHONDRIAL 14 - FLATWORM_MITOCHONDRIAL 15 - BLEPHARISMA_MACRONUCLEAR 16 - 2CHLOROPHYCEAN_MITOCHONDRIAL 21 - TREMATODE_MITOCHONDRIAL 23 - SCENEDESMUS_MITOCHONDRIAL Taken from NCBI with slight modification and put into the classpath resource.
IUPACParser() - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser: Default version and uses the classpath based IUPAC table
IUPACParser(InputStream) - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser: Allows you to specify a different IUPAC table.
IUPACParser.IUPACTable - Class in org.biojava.nbio.core.sequence.io: Holds the concept of a codon table from the IUPAC format
IUPACTable(String, int, String, String, String, String, String) - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
IUPACTable(String, Integer, String, String) - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable: Constructor which uses the basic IUPAC codon table format.

J

JAutoSuggest - Class in org.biojava.nbio.structure.align.gui.autosuggest: A JTextField that can make suggestions for auto-complete.
JAutoSuggest() - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
JAutoSuggest(int) - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
JAutoSuggest(Frame) - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
JFatCatClient - Class in org.biojava.nbio.structure.align.client
JFatCatClient() - Constructor for class org.biojava.nbio.structure.align.client.JFatCatClient
JMatrixPanel - Class in org.biojava.nbio.structure.gui: a JPanel that can display a difference of distance matrix and paths that have been taken for the alignment
JMatrixPanel() - Constructor for class org.biojava.nbio.structure.gui.JMatrixPanel
JmolAlignedPositionListener - Class in org.biojava.nbio.structure.gui.events
JmolAlignedPositionListener(BiojavaJmol, StructurePairAligner) - Constructor for class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
jmolColorByChain() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel: assign a custom color to the Jmol chains command.
jMolFloat(double) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a lower precision floating point number for Jmol
jmolInClassPath() - Static method in class org.biojava.nbio.structure.gui.BiojavaJmol: returns true if Jmol can be found in the classpath, otherwise false.
jmolPanel - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
JmolPanel - Class in org.biojava.nbio.structure.align.gui.jmol
JmolPanel() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
JmolSymmetryScriptGenerator - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGenerator() - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
JmolSymmetryScriptGeneratorC1 - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorC1(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
JmolSymmetryScriptGeneratorCn - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorCn(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
JmolSymmetryScriptGeneratorDn - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorDn(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
JmolSymmetryScriptGeneratorH - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorH(HelixAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
JmolSymmetryScriptGeneratorI - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorI(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorI
JmolSymmetryScriptGeneratorO - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorO(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorO
JmolSymmetryScriptGeneratorPointGroup - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorPointGroup(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
JmolSymmetryScriptGeneratorT - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorT(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorT
JmolTools - Class in org.biojava.nbio.structure.align.gui.jmol
JmolTools() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.JmolTools
JmolViewerImpl - Class in org.biojava.nbio.structure.gui
JmolViewerImpl() - Constructor for class org.biojava.nbio.structure.gui.JmolViewerImpl
JNLPProxy - Class in org.biojava.nbio.structure.align.webstart
JobKillException - Exception in org.biojava.nbio.structure.align.client
JobKillException(String) - Constructor for exception org.biojava.nbio.structure.align.client.JobKillException
join(AbstractCollection<String>, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
JoiningSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage: This reader actually proxies onto multiple types of sequence in order to allow a number of sequence objects to act as if they are one sequence.
JoiningSequenceReader(Sequence<C>...) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader: Allows creation of the store from Vargs Sequence objects.
JoiningSequenceReader(List<Sequence<C>>) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader: Allows creation of the store from List>.
JoiningSequenceReader(CompoundSet<C>, Sequence<C>...) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
JoiningSequenceReader(CompoundSet<C>, List<Sequence<C>>) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
JointFragments - Class in org.biojava.nbio.structure.align.helper: A utility class that defines which set of atoms are considered to be on equivalent positions.
JointFragments() - Constructor for class org.biojava.nbio.structure.align.helper.JointFragments
jointFragments(JointFragments[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
jointSeqStrucDistance(double[][]) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The joint sequence-structure distance (d_SS) is a combination of the sequence-based and the structure-based distances.
JOURNAL_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
JournalArticle - Class in org.biojava.nbio.structure: PDB-specific
JournalArticle() - Constructor for class org.biojava.nbio.structure.JournalArticle
JPrintPanel - Class in org.biojava.nbio.structure.align.gui
JPrintPanel() - Constructor for class org.biojava.nbio.structure.align.gui.JPrintPanel
Jronn - Class in org.biojava.nbio.ronn: This class gives public API to RONN functions.
Jronn() - Constructor for class org.biojava.nbio.ronn.Jronn
Jronn.Range - Class in org.biojava.nbio.ronn: Holder for the ranges, contain pointers to starting and ending position on the sequence which comprises a disordered region.

K

K - Static variable in class org.biojava.nbio.aaproperties.Constraints
KaplanMeierFigure - Class in org.biojava.nbio.survival.kaplanmeier.figure
KaplanMeierFigure() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
key - Variable in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements
KeyedWeakReference - Class in org.biojava.nbio.ontology.utils: Subclass of WeakReference which includes and extra field (the key) which can be used to help cleanup once this reference has been enqueued.
KeyedWeakReference(Object, Object) - Constructor for class org.biojava.nbio.ontology.utils.KeyedWeakReference
KeyedWeakReference(Object, Object, ReferenceQueue) - Constructor for class org.biojava.nbio.ontology.utils.KeyedWeakReference
keyMask - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
keyReleased(KeyEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener: takes care of the cursor up/down keys.
keyReleased(KeyEvent) - Method in class org.biojava.nbio.structure.gui.RasmolCommandListener: Deprecated.

takes care of the cursor up/down keys.
keys() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
keys() - Method in interface org.biojava.nbio.ontology.utils.Annotation: Get a set of key objects.
keys() - Method in class org.biojava.nbio.structure.math.SymbolTable: Return an Iterable for the keys in the table.
keySet() - Method in class org.biojava.nbio.ontology.utils.SmallMap
keySet() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
keySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
KEYWORDS_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
kimuraDistance(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The Kimura evolutionary distance (d) is a correction of the fractional dissimilarity (D) specially needed for large evolutionary distances.
kmf - Variable in class org.biojava.nbio.survival.cox.CoxInfo
KMFigureInfo - Class in org.biojava.nbio.survival.kaplanmeier.figure
KMFigureInfo() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
kmStroke - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

L

L - Static variable in class org.biojava.nbio.aaproperties.Constraints
label() - Method in enum org.biojava.nbio.protmod.ModificationCategory
label() - Method in enum org.biojava.nbio.protmod.ModificationOccurrenceType
Ladder - Class in org.biojava.nbio.structure.secstruc: A Ladder is a set of one or more consecutive bridges of identical type.
Ladder() - Constructor for class org.biojava.nbio.structure.secstruc.Ladder
LAST_REMEDIATION_DATE - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory: Date of the latest PDB file remediation
lastIndexOf(Sequence<C>, C) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: Performs a reversed linear search of the given Sequence by wrapping it in a ReversedSequenceView and passing it into SequenceMixin.indexOf(Sequence, Compound).
LATEST_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathFactory
LATEST_VERSION - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
left - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
legendColor - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
legendUpperPercentX - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
legendUpperPercentY - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
LENGTH - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature: Sort features by length.
length() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Get length of range.
length() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Returns the total number of aligned positions (columns) in the Block.
length() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
length() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Returns the total number of aligned residues (columns) in the alignment: the sum of all Block lengths.
length() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
length() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Returns the total number of aligned residues (columns) in the multiple alignment: the sum of all BlockSet lengths.
length() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
length() - Method in class org.biojava.nbio.survival.data.CompactCharSequence
lighter(Color, double) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils: Make a color lighter.
LightweightProfile<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.template: Defines a minimal data structure for reading and writing a sequence alignment.
LightweightProfile.StringFormat - Enum in org.biojava.nbio.core.sequence.template: List of output formats.
ligRSRnbrMean - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
ligRSRnbrStdev - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
ligRSRnumnbrs - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
ligRSRZ - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
line - Variable in class org.biojava.nbio.ontology.obo.OboFileParser
LINE_HEIGHT - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
LINEAR_DNA - Static variable in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
LinearColorInterpolator - Class in org.biojava.nbio.structure.gui.util.color
LinearColorInterpolator() - Constructor for class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
LinearColorInterpolator(ColorSpace) - Constructor for class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
LinearColorInterpolator.InterpolationDirection - Enum in org.biojava.nbio.structure.gui.util.color
linenum - Variable in class org.biojava.nbio.ontology.obo.OboFileParser
lineSplit - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
lineSplit - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
linkChains2Compound(Structure) - Method in class org.biojava.nbio.structure.io.PDBFileParser: After the parsing of a PDB file the Chain and Compound objects need to be linked to each other.
LinkRecord(String, String, String, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
ListStringWrapper - Class in org.biojava.nbio.structure.scop.server
ListStringWrapper() - Constructor for class org.biojava.nbio.structure.scop.server.ListStringWrapper
LOAD - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
load() - Static method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping: Loads the SIFTS mapping.
load(boolean) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping: Loads the SIFTS mapping.
LOAD_ALIGNMENT_XML - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
LOAD_DB_RESULTS - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
loadFastaAddGeneFeaturesFromGeneIDGFF2(File, File) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper: Loads Fasta file and GFF2 feature file generated from the geneid prediction algorithm
loadFastaAddGeneFeaturesFromGeneMarkGTF(File, File) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
loadFastaAddGeneFeaturesFromGlimmerGFF3(File, File) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
loadFastaAddGeneFeaturesFromGmodGFF3(File, File, boolean) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper: Lots of variations in the ontology or descriptors that can be used in GFF3 which requires writing a custom parser to handle a GFF3 generated or used by a specific application.
loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(File, File, boolean) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
loadFragment(long, int) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
loadFromDirectAccess() - Method in class demo.DemoMMCIFReader: An example demonstrating how to directly use the mmCif file parsing classes.
loadIdentifier(String, AtomCache) - Static method in class org.biojava.nbio.structure.Identifier: Deprecated.
Create a new StructureName instead.
loadPDB(String) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
loadSimple() - Method in class demo.DemoMMCIFReader: A basic example how to load an mmCif file and get a Structure object
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.align.client.StructureName
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.cath.CathDomain
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.domain.PDPDomain
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.PassthroughIdentifier: Passthrough identifiers don't know how to load a structure
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.scop.ScopDomain
loadStructure(AtomCache) - Method in interface org.biojava.nbio.structure.StructureIdentifier: Loads a structure encompassing the structure identified.
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.SubstructureIdentifier: Loads the complete structure based on SubstructureIdentifier.getPdbId().
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.URLIdentifier: Load the structure from the URL
loadStructureFromCache() - Method in class demo.DemoLoadStructure
loadStructureFromCifByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
loadStructureFromPdbByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
loadStructureIO() - Method in class demo.DemoLoadStructure
loadXML(String) - Static method in class org.biojava.nbio.core.util.XMLHelper
LocalPDBDirectory - Class in org.biojava.nbio.structure.io: Superclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and MMCIFFileReader.
LocalPDBDirectory(String) - Constructor for class org.biojava.nbio.structure.io.LocalPDBDirectory: Subclasses should provide default and single-string constructors.
LocalPDBDirectory() - Constructor for class org.biojava.nbio.structure.io.LocalPDBDirectory
LocalPDBDirectory.FetchBehavior - Enum in org.biojava.nbio.structure.io: Controls when the class should fetch files from the ftp server
LocalPDBDirectory.ObsoleteBehavior - Enum in org.biojava.nbio.structure.io: Behaviors for when an obsolete structure is requested.
LocalProteinDomainParser - Class in org.biojava.nbio.structure.domain: Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures.
LocalScopDatabase - Interface in org.biojava.nbio.structure.scop: Classes which implement ScopDatabase in a way which allows them to serve queries without accessing the internet should implement this interface instead.
location(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: Used as a thin wrapper to the LocationHelper.location(java.util.List, java.lang.String) method to bring the given location list together as a join (the default type)
location(List<Location>, String) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: Builds a location from a List of locations; this can be circular or linear joins.
location(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.
Location - Interface in org.biojava.nbio.core.sequence.location.template: Sets of integers used to represent the location of features on sequence.
location(List<Location>, Integer, String) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools: Used for building a location from a series of sub-locations
location(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools: Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.
location() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get location of feature.
location() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Get the location of the feature.
Location - Class in org.biojava.nbio.genome.parsers.gff: A location on a sequence.
Location(int, int) - Constructor for class org.biojava.nbio.genome.parsers.gff.Location: Construct new location from coordinates.
Location(Location) - Constructor for class org.biojava.nbio.genome.parsers.gff.Location: Clone other location.
Location.Tools - Class in org.biojava.nbio.core.sequence.location.template: Helper methods for use with the Location classes.
LOCATION_LENGTH - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature: Sort features by start position and then longest length.
LocationHelper - Class in org.biojava.nbio.core.sequence.location: Helper methods for use with the Location classes.
LocationHelper() - Constructor for class org.biojava.nbio.core.sequence.location.LocationHelper
locationParser - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
locationSplitPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser: designed to recursively split a location string in tokens.
LocIterator - Class in org.biojava.nbio.genome.parsers.gff: Move a sliding window over a Location.
LocIterator(Location, int, int) - Constructor for class org.biojava.nbio.genome.parsers.gff.LocIterator: Construct an iterator that slides a window over a Location.
LOCUS_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
LogColorMapper - Class in org.biojava.nbio.structure.gui.util.color: Performs a log10 transform on input before passing the values off to another colorMapper.
LogColorMapper(ContinuousColorMapper) - Constructor for class org.biojava.nbio.structure.gui.util.color.LogColorMapper: Creates a new LogColorMapper with base 10.
LogColorMapper(ContinuousColorMapper, int) - Constructor for class org.biojava.nbio.structure.gui.util.color.LogColorMapper: If logspaceMapper maps values x1 to x2, this creates a mapper for values base^x1 to base^x2
logger - Static variable in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
logger - Static variable in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
logStatus(String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
logStatus(String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
logStatus(String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
LOOP_START - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
lowercaseName() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant: Return the name of this FASTQ sequence format variant in lowercase-with-dashes style.
lp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
lu() - Method in class org.biojava.nbio.structure.jama.Matrix: LU Decomposition
LUDecomposition - Class in org.biojava.nbio.structure.jama: LU Decomposition.
LUDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.LUDecomposition: LU Decomposition provides a data structure to access L, U and piv.

M

M - Static variable in class org.biojava.nbio.aaproperties.Constraints
main(String[]) - Static method in class demo.AFPFromFasta
main(String[]) - Static method in class demo.AlignmentGuiDemo
main(String[]) - Static method in class demo.BioJavaAADemo
main(String[]) - Static method in class demo.ChemCompDistribution
main(String[]) - Static method in class demo.CookBook
main(String[]) - Static method in class demo.CookbookMSA
main(String[]) - Static method in class demo.DemoAlignmentFromFasta
main(String[]) - Static method in class demo.DemoAlignProteins
main(String[]) - Static method in class demo.DemoAsa
main(String[]) - Static method in class demo.DemoAtomCache
main(String[]) - Static method in class demo.DemoBerkeleyScop
main(String[]) - Static method in class demo.DemoCATH
main(String[]) - Static method in class demo.DemoCE
main(String[]) - Static method in class demo.DemoCeSymm
main(String[]) - Static method in class demo.DemoChangeChemCompProvider
main(String[]) - Static method in class demo.DemoCommandLineStartup
main(String[]) - Static method in class demo.DemoContacts
main(String[]) - Static method in class demo.DemoCrystalInterfaces
main(String[]) - Static method in class demo.DemoDistanceTree
main(String[]) - Static method in class demo.DemoDomainsplit
main(String[]) - Static method in class demo.DemoFATCAT
main(String[]) - Static method in class demo.DemoLoadSecStruc
main(String[]) - Static method in class demo.DemoLoadStructure
main(String[]) - Static method in class demo.DemoLoadSubstMax
main(String[]) - Static method in class demo.DemoMMCIFReader
main(String[]) - Static method in class demo.DemoMultipleMC
main(String[]) - Static method in class demo.DemoOrientBioAssembly
main(String[]) - Static method in class demo.DemoRotationAxis
main(String[]) - Static method in class demo.DemoSCOP
main(String[]) - Static method in class demo.DemoSecStrucCalc
main(String[]) - Static method in class demo.DemoShowBiolAssembly
main(String[]) - Static method in class demo.DemoShowCATHDomain
main(String[]) - Static method in class demo.DemoShowLargeAssembly
main(String[]) - Static method in class demo.DemoShowValidationResults
main(String[]) - Static method in class demo.DemoSixFrameTranslation
main(String[]) - Static method in class demo.DemoStructureFromFasta
main(String[]) - Static method in class demo.DemoSW3DAligner
main(String[]) - Static method in class demo.HmmerDemo
main(String[]) - Static method in class demo.NCBIQBlastServiceDemo
main(String[]) - Static method in class demo.ParseFastaFileDemo: e.g.
main(String[]) - Static method in class demo.ParseGO
main(String[]) - Static method in class demo.PredictDisorder
main(String[]) - Static method in class demo.ShowStructureInJmol
main(String[]) - Static method in class demo.TestDNANeedlemanWunsch
main(String[]) - Static method in class demo.WebStartClientDemo
main(String[]) - Static method in class org.biojava.nbio.aaproperties.CommandPrompt: The main method
main(String[]) - Static method in class org.biojava.nbio.core.sequence.DNASequence
main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter
main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.FastaReader
main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper
main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriter
main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReader
main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser
main(String[]) - Static method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
main(String[]) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
main(String[]) - Static method in class org.biojava.nbio.core.sequence.location.InsdcParser
main(String[]) - Static method in class org.biojava.nbio.core.sequence.ProteinSequence
main(String[]) - Static method in class org.biojava.nbio.core.util.UncompressInputStream
main(String[]) - Static method in class org.biojava.nbio.genome.App
main(String[]) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
main(String[]) - Static method in class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser: parses a file from the genenames website
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.Feature: Deprecated.
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Deprecated.
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Reader
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Writer
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.Location: Deprecated.
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Deprecated.
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
main(String[]) - Static method in class org.biojava.nbio.genome.query.BlastXMLQuery
main(String[]) - Static method in class org.biojava.nbio.genome.query.OutputHitsGFF
main(String[]) - Static method in class org.biojava.nbio.genome.uniprot.UniprotToFasta
main(String[]) - Static method in class org.biojava.nbio.genome.util.SplitFasta
main(String[]) - Static method in class org.biojava.nbio.ontology.App
main(String[]) - Static method in class org.biojava.nbio.phosphosite.Dataset
main(String[]) - Static method in class org.biojava.nbio.ronn.ModelLoader
main(String[]) - Static method in class org.biojava.nbio.ronn.ORonn
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeMain: Example Parameters: -pdbFilePath /tmp -autoFetch -printCE -pdb1 1cnv -pdb2 3cna
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
main(String[]) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
main(String[]) - Static method in class org.biojava.nbio.structure.align.FarmJob
main(String[]) - Static method in class org.biojava.nbio.structure.align.fatcat.FatCat: See demo/FatCatDemo.java for an example how to run.
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.AlignmentGui
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.DBResultTable
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.DotPlotPanel
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.MemoryMonitor
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
main(String[]) - Static method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
main(String[]) - Static method in class org.biojava.nbio.structure.align.StructurePairAligner: example usage of this class
main(String[]) - Static method in class org.biojava.nbio.structure.align.webstart.JNLPProxy
main(String[]) - Static method in class org.biojava.nbio.structure.align.webstart.WebStartDBSearch
main(String[]) - Static method in class org.biojava.nbio.structure.align.webstart.WebStartDBSearchResults
main(String[]) - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain: If no arguments, shows AlignmentGui for pairwise alignments.
main(String[]) - Static method in class org.biojava.nbio.structure.Calc
main(String[]) - Static method in class org.biojava.nbio.structure.domain.PDBDomainProvider
main(String[]) - Static method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
main(String[]) - Static method in class org.biojava.nbio.structure.domain.RemotePDPProvider
main(String[]) - Static method in class org.biojava.nbio.structure.ecod.EcodInstallation
main(String[]) - Static method in class org.biojava.nbio.structure.gui.BiojavaJmol
main(String[]) - Static method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
main(String[]) - Static method in class org.biojava.nbio.structure.gui.SequenceDisplay
main(String[]) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
main(String[]) - Static method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
main(String[]) - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
main(String[]) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Prints out the XML representation of an AFPChain from a file containing exactly two FASTA sequences.
main(String[]) - Static method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
main(String[]) - Static method in class org.biojava.nbio.structure.io.MMCIFFileReader
main(String[]) - Static method in class org.biojava.nbio.structure.io.PDBFileReader
main(String[]) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
main(String[]) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils
main(String[]) - Static method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
main(String[]) - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
main(String[]) - Static method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
main(String[]) - Static method in class org.biojava.nbio.structure.symmetry.analysis.ScanSymmetry
main(String[]) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxCC
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxHelper
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxMart
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxR
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxScore
main(String[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
main(String[]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Test client.
main(String[]) - Static method in class org.biojava.nbio.survival.cox.ResidualsCoxph
main(String[]) - Static method in class org.biojava.nbio.survival.cox.stats.AgScore
main(String[]) - Static method in class org.biojava.nbio.survival.cox.stats.ChiSq
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
makeBonds() - Method in class org.biojava.nbio.structure.io.BondMaker: Creates bond objects and corresponding references in Atom objects: peptide bonds: inferred from sequence and distances nucleotide bonds: inferred from sequence and distances intra-group (residue) bonds: read from the chemical component dictionary, via ChemCompProvider
mandatoryArgs - Static variable in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
mapDB - Variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
mapper - Variable in class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform
mapSeqresRecords(Chain, Chain) - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner: Map the seqRes groups to the atomRes chain.
MapToStringTransformer - Class in org.biojava.nbio.ws.alignment.qblast: Transforms Map to String.
MapToStringTransformer() - Constructor for class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer: Creates MapToStringTransformer with defaults:
MapToStringTransformer(String, String, String) - Constructor for class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer: Creates MapToStringTransformer with given values
mark(int) - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead: Marks the present position in the stream.
markMetaDataColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
markMetaDataColumns(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet: marks columns as containing meta data
markMetaDataRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
markSupported() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead: Tells whether this stream supports the mark() operation, which it does.
markSupported() - Method in class org.biojava.nbio.core.util.UncompressInputStream: This stream does not support mark/reset on the stream.
marshal(List<String>) - Method in class org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter
mat - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
mat - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
matches(Group) - Method in interface org.biojava.nbio.structure.AtomPositionMap.GroupMatcher
matchSequenceToStructure(ProteinSequence, Structure) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher: Given a sequence and the corresponding Structure, get the ResidueNumber for each residue in the sequence.
Maths - Class in org.biojava.nbio.structure.jama
Maths() - Constructor for class org.biojava.nbio.structure.jama.Maths
matrix - Static variable in class org.biojava.nbio.core.alignment.SimpleProfile
Matrix - Class in org.biojava.nbio.structure.jama: Jama = Java Matrix class.
Matrix(int, int) - Constructor for class org.biojava.nbio.structure.jama.Matrix: Construct an m-by-n matrix of zeros.
Matrix(int, int, double) - Constructor for class org.biojava.nbio.structure.jama.Matrix: Construct an m-by-n constant matrix.
Matrix(double[][]) - Constructor for class org.biojava.nbio.structure.jama.Matrix: Construct a matrix from a 2-D array.
Matrix(double[][], int, int) - Constructor for class org.biojava.nbio.structure.jama.Matrix: Construct a matrix quickly without checking arguments.
Matrix(double[], int) - Constructor for class org.biojava.nbio.structure.jama.Matrix: Construct a matrix from a one-dimensional packed array
Matrix - Class in org.biojava.nbio.survival.cox.matrix: *********************************************************************** Compilation: javac Matrix.java Execution: java Matrix A bare-bones collection of static methods for manipulating matrices.
Matrix() - Constructor for class org.biojava.nbio.survival.cox.matrix.Matrix
MatrixAligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an Aligner which builds a score matrix during computation.
matrixFromEuler(double, double, double) - Static method in class org.biojava.nbio.structure.Calc: This conversion uses NASA standard aeroplane conventions as described on page: http://www.euclideanspace.com/maths/geometry/rotations/euler/index.htm Coordinate System: right hand Positive angle: right hand Order of euler angles: heading first, then attitude, then bank.
matrixInOptimizer(double[][]) - Method in interface org.biojava.nbio.structure.align.ce.MatrixListener
MatrixListener - Interface in org.biojava.nbio.structure.align.ce
max - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
max() - Method in class org.biojava.nbio.structure.math.SymbolTable: Return the largest key in the table.
MAX_ATOMS - Static variable in class org.biojava.nbio.structure.io.FileParsingParameters: The maximum number of atoms we will add to a structure, this protects from memory overflows in the few really big protein structures.
MAX_CUTS - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
MAX_PEPTIDE_BOND_LENGTH - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc: max distance CA atoms in peptide bond (backbone discontinuity)
MAX_RESOLVER - Static variable in class org.biojava.nbio.core.sequence.location.FuzzyPoint: Always uses the max point to resolve a location
MAX_SCALE - Static variable in class org.biojava.nbio.structure.gui.SequenceDisplay: the maximum value that the scale can get
MAX_WIDTH - Static variable in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat
MAXCONT - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
MAXDOM - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
maxGapSize - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
maxGapSize - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
maximumQualityScore() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant: Return the maximum quality score for this FASTQ sequence format variant.
MAXLEN - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
maxNrIterationsForOptimization - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
maxOptRMSD - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
maxOptRMSD - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
MAXSIZE - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
MC_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
mean - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
mean - Variable in class org.biojava.nbio.structure.validation.BondOutlier
mean - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier
mean - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier
MEAN_RESOLVER - Static variable in class org.biojava.nbio.core.sequence.location.FuzzyPoint: Combines min and max and then gets the mean of it
MeanModelComparator - Class in org.biojava.nbio.survival.cox.comparators
MeanModelComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.MeanModelComparator
MeanQuantizer - Class in org.biojava.nbio.survival.kaplanmeier.metadata
MeanQuantizer() - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MeanQuantizer
MEDLINE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
MemoryMonitor - Class in org.biojava.nbio.structure.align.gui: Tracks Memory allocated & used, displayed in graph form.
MemoryMonitor() - Constructor for class org.biojava.nbio.structure.align.gui.MemoryMonitor
MemoryMonitor.Surface - Class in org.biojava.nbio.structure.align.gui
MenuCreator - Class in org.biojava.nbio.structure.align.gui: Create the menus for structure alignment GUI windows (JFrames).
MenuCreator() - Constructor for class org.biojava.nbio.structure.align.gui.MenuCreator
MenuCreator - Class in org.biojava.nbio.structure.gui.util: Create the menu for BiojavaJmol
MenuCreator() - Constructor for class org.biojava.nbio.structure.gui.util.MenuCreator
MenuCreator.DotPlotListener - Class in org.biojava.nbio.structure.align.gui: Creates a frame to display a DotPlotPanel.
Messages - Class in org.biojava.nbio.core.exceptions
Messages() - Constructor for class org.biojava.nbio.core.exceptions.Messages
MetaDataInfo - Class in org.biojava.nbio.survival.kaplanmeier.metadata
MetaDataInfo(String, boolean, DiscreteQuantizerInterface) - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
MetaDataInfo(String) - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
METHYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
mid - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange: midpoint of the alignment
MIM - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
min - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
min() - Method in class org.biojava.nbio.structure.math.SymbolTable: Return the smallest key in the table.
MIN_DOMAIN_LENGTH - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
MIN_RESOLVER - Static variable in class org.biojava.nbio.core.sequence.location.FuzzyPoint: Always uses the min point to resolve a location
MIN_VALID_CELL_SIZE - Static variable in class org.biojava.nbio.structure.xtal.CrystalCell
minCPLength - Variable in class org.biojava.nbio.structure.align.ce.CECPParameters
minCPLength - Variable in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
mindiff - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier
mindiff - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier
MINDIST - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc: min distance between two residues
MINIMUM_HEIGHT - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
minimumQualityScore() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant: Return the minimum quality score for this FASTQ sequence format variant.
minus() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return location that is in same position on negative strand.
minus(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: C = A - B
minusEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: A = A - B
MMCIF_DEFAULT_VALUE - Static variable in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: The character to be printed out as a default value in mmCIF files, e.g.
MMCIF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
MMCIF_MISSING_VALUE - Static variable in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools: The character to be printed out in cases where a value is not assigned in mmCIF files
MMCIF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.MMCIFFileReader
MMCIF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.MMCIFFileReader
MMCIF_TOP_HEADER - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser: The header appearing at the beginning of a mmCIF file.
MmCifBiolAssemblyProvider - Class in org.biojava.nbio.structure.quaternary.io
MmCifBiolAssemblyProvider() - Constructor for class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
MMcifConsumer - Interface in org.biojava.nbio.structure.io.mmcif: An interface for the events triggered by a MMcifParser.
MMCIFFileReader - Class in org.biojava.nbio.structure.io: How to parse an mmCif file:
MMCIFFileReader() - Constructor for class org.biojava.nbio.structure.io.MMCIFFileReader: Constructs a new MMCIFFileReader, initializing the extensions member variable.
MMCIFFileReader(String) - Constructor for class org.biojava.nbio.structure.io.MMCIFFileReader: Constructs a new PDBFileReader, initializing the extensions member variable.
MMCIFFileTools - Class in org.biojava.nbio.structure.io.mmcif: Some tools for mmCIF file writing.
MMCIFFileTools() - Constructor for class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
MMcifParser - Interface in org.biojava.nbio.structure.io.mmcif: Interface that needs to be implemented by an MMcifParser
MmCifPDBBiolAssemblyProvider - Class in org.biojava.nbio.structure.quaternary.io: A provider for information about biological units for PDB files that is based on reading local MMcif files.
MmCifPDBBiolAssemblyProvider() - Constructor for class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
mmcifProviderClassName - Static variable in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
Model(int, int) - Constructor for class org.biojava.nbio.ronn.ModelLoader.Model
model - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
ModelledSubgroup - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
ModelledSubgroup() - Constructor for class org.biojava.nbio.structure.validation.ModelledSubgroup
modelledSubgroup - Variable in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
ModelLoader - Class in org.biojava.nbio.ronn: Class that loads data from the model files into ModelLoader.Model objects
ModelLoader() - Constructor for class org.biojava.nbio.ronn.ModelLoader
ModelLoader.Model - Class in org.biojava.nbio.ronn: Represent a RONN model
ModelLoader.Threshold - Class in org.biojava.nbio.ronn: Represents a Threshold
ModificationCategory - Enum in org.biojava.nbio.protmod: define modification categories.
ModificationCondition - Interface in org.biojava.nbio.protmod: Conditions of a protein modification, e.g.
ModificationConditionImpl - Class in org.biojava.nbio.protmod
ModificationConditionImpl(List<Component>, List<ModificationLinkage>) - Constructor for class org.biojava.nbio.protmod.ModificationConditionImpl
ModificationLinkage - Class in org.biojava.nbio.protmod
ModificationLinkage(List<Component>, int, int) - Constructor for class org.biojava.nbio.protmod.ModificationLinkage
ModificationLinkage(List<Component>, int, String, int, String) - Constructor for class org.biojava.nbio.protmod.ModificationLinkage
ModificationLinkage(List<Component>, int, List<String>, int, List<String>) - Constructor for class org.biojava.nbio.protmod.ModificationLinkage
ModificationLinkage(List<Component>, int, List<String>, String, int, List<String>, String) - Constructor for class org.biojava.nbio.protmod.ModificationLinkage
ModificationOccurrenceType - Enum in org.biojava.nbio.protmod
ModifiedAminoAcidCompoundSet - Class in org.biojava.nbio.aaproperties.xml
ModifiedAminoAcidCompoundSet(List<AminoAcidComposition>, Map<Character, Double>) - Constructor for class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
ModifiedCompound - Interface in org.biojava.nbio.protmod.structure: Root interface for all modifications in structure.
ModifiedCompoundImpl - Class in org.biojava.nbio.protmod.structure
ModifiedCompoundImpl() - Constructor for class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
ModifiedCompoundImpl(ProteinModification, StructureGroup) - Constructor for class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl: Create a ModifiedCompoundImpl that has only one involved component.
ModifiedCompoundImpl(ProteinModification, Collection<StructureAtomLinkage>) - Constructor for class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
ModifiedCompoundXMLConverter - Class in org.biojava.nbio.protmod.io
ModifiedCompoundXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter
modulateCircularIndex(int, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper: Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base.
modulateCircularIndex(int, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools: Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base.
mogAngleOutlier - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
MogAngleOutlier - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
MogAngleOutlier() - Constructor for class org.biojava.nbio.structure.validation.MogAngleOutlier
mogBondOutlier - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
MogBondOutlier - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
MogBondOutlier() - Constructor for class org.biojava.nbio.structure.validation.MogBondOutlier
mogulIgnore - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
MomentsOfInertia - Class in org.biojava.nbio.structure.symmetry.geometry
MomentsOfInertia() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia: Creates a new instance of MomentsOfInertia
MomentsOfInertia.SymmetryClass - Enum in org.biojava.nbio.structure.symmetry.geometry
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.gui.RasmolCommandListener: Deprecated.
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mouseDragged(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mouseDragged(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mouseDragged(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mouseDragged(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.gui.RasmolCommandListener: Deprecated.
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.gui.RasmolCommandListener: Deprecated.
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mouseMoved(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mouseMoved(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mouseMoved(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mouseMoved(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
mouseOverPosition(AlignedPosition) - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.gui.RasmolCommandListener: Deprecated.
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.gui.RasmolCommandListener: Deprecated.
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mPanel - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
multiIterator(AtomPositionMap, ResidueRange...) - Static method in class org.biojava.nbio.structure.ResidueRange: Returns a new Iterator over every ResidueNumber in the list of ResidueRanges.
multiIterator(AtomPositionMap, List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange: Returns a new Iterator over every ResidueNumber in the list of ResidueRanges.
MULTIPLE_ALIGN - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
MultipleAlignment - Interface in org.biojava.nbio.structure.align.multiple: A MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type.
MultipleAlignmentCalc - Class in org.biojava.nbio.structure.align.gui: A class that obtains structures via DAS and aligns them.
MultipleAlignmentCalc(MultipleAlignmentGUI, List<Structure>, List<StructureIdentifier>) - Constructor for class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc: Requests an alignment of the pdbs.
MultipleAlignmentCoordManager - Class in org.biojava.nbio.structure.align.gui.aligpanel: Generalization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization.
MultipleAlignmentCoordManager(int, int) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Constructor.
MultipleAlignmentDisplay - Class in org.biojava.nbio.structure.align.multiple.util: Utility functions to generalize the visualization of MultipleAlignments in molecular viewers.
MultipleAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay
MultipleAlignmentEnsemble - Interface in org.biojava.nbio.structure.align.multiple: A MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm, version, creation time, etc.).
MultipleAlignmentEnsembleImpl - Class in org.biojava.nbio.structure.align.multiple: A general implementation of a MultipleAlignmentEnsemble.
MultipleAlignmentEnsembleImpl() - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl: Default Constructor.
MultipleAlignmentEnsembleImpl(List<StructureIdentifier>) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl: Constructor using structure identifiers.
MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl: Copy constructor.
MultipleAlignmentEnsembleImpl(AFPChain, Atom[], Atom[], boolean) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl: Constructor from an AFPChain instance.
MultipleAlignmentGUI - Class in org.biojava.nbio.structure.align.gui: A JFrame that allows to trigger a multiple structure alignment, either from files in a directory or after manual upload.
MultipleAlignmentGUI() - Constructor for class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
MultipleAlignmentImpl - Class in org.biojava.nbio.structure.align.multiple: A general implementation of a MultipleAlignment.
MultipleAlignmentImpl() - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl: Default Constructor.
MultipleAlignmentImpl(MultipleAlignmentEnsemble) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl: Constructor linking to an existing ensemble.
MultipleAlignmentImpl(MultipleAlignmentImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl: Copy constructor.
MultipleAlignmentJmol - Class in org.biojava.nbio.structure.align.gui.jmol: A class that provides a 3D visualization Frame in Jmol for MultipleAlignments.
MultipleAlignmentJmol() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol: Default constructor creates an empty JmolPanel window, from where alignments can be made through the align menu.
MultipleAlignmentJmol(MultipleAlignment, List<Atom[]>) - Constructor for class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol: The constructor displays the Mutltiple Alignment in a new JmolPanel Frame.
MultipleAlignmentJmolDisplay - Class in org.biojava.nbio.structure.align.gui: Utility Class that provides helper methods for the visualization of MultipleAlignments.
MultipleAlignmentJmolDisplay() - Constructor for class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
MultipleAlignmentScorer - Class in org.biojava.nbio.structure.align.multiple.util: Utility class for calculating common scores of MultipleAlignments.
MultipleAlignmentScorer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
MultipleAlignmentTools - Class in org.biojava.nbio.structure.align.multiple.util: Utility functions for working with MultipleAlignment.
MultipleAlignmentTools() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
MultipleAlignmentWriter - Class in org.biojava.nbio.structure.align.multiple.util: This class contains functions for the conversion of MultipleAlignment to various String outputs.
MultipleAlignmentWriter() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
MultipleAlignmentXMLConverter - Class in org.biojava.nbio.structure.align.xml: Helper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format.
MultipleAlignmentXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
MultipleAlignmentXMLParser - Class in org.biojava.nbio.structure.align.xml: Parse an XML file representing a MultipleAlignmentEnsemble, so that the original alignment can be recovered.
MultipleAlignmentXMLParser() - Constructor for class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
MultipleAligPanel - Class in org.biojava.nbio.structure.align.gui.aligpanel: A JPanel that can display the sequence alignment of a MultipleAlignment in a nice way and interact with Jmol by selecting the aligned atoms of the sequence selection.
MultipleAligPanel() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel: Default constructor.
MultipleAligPanel(AFPChain, Atom[], Atom[], AbstractAlignmentJmol) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel: Constructor using an afpChain and the atom arrays for pairwise alignments.
MultipleAligPanel(MultipleAlignment, AbstractAlignmentJmol) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel: Constructor using a MultipleAlignment.
MultipleAligPanelMouseMotionListener - Class in org.biojava.nbio.structure.align.gui.aligpanel: Mouse Motion Listener for the MultipleAligPanel, which provides methods to obtain positions of the mouse and connect them to the sequence alignment positions using the information in MultipleAlignmentCoordManager.
MultipleAligPanelMouseMotionListener(MultipleAligPanel) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
multipleFrameTranslation(Sequence<NucleotideCompound>, Frame...) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine: A way of translating DNA in a number of frames
MultipleMcMain - Class in org.biojava.nbio.structure.align.multiple.mc: Main class of the Java implementation of the Combinatorial Extension - Monte Carlo (CEMC) Algorithm, as it was originally described by C.Guda, E.D.Scheeff, P.E.
MultipleMcMain(StructureAlignment) - Constructor for class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain: Default constructor.
MultipleMcOptimizer - Class in org.biojava.nbio.structure.align.multiple.mc: This class takes a MultipleAlignment seed previously generated and runs a Monte Carlo optimization in order to improve the overall score and highlight common structural motifs.
MultipleMcOptimizer(MultipleAlignment, MultipleMcParameters, int) - Constructor for class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer: Constructor.
MultipleMcParameters - Class in org.biojava.nbio.structure.align.multiple.mc: Contains the parameters to be sent to the MC optimization.
MultipleMcParameters() - Constructor for class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters: Constructor with DEFAULT values of the parameters.
MultipleSequenceAlignment<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence: Implements a minimal data structure for reading and writing a sequence alignment.
MultipleSequenceAlignment() - Constructor for class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
MultipleStatusDisplay - Class in org.biojava.nbio.structure.align.gui.aligpanel: This class provides information of the selected positions in the MultipleAligPanel.
MultipleStatusDisplay(MultipleAligPanel) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay: Constructor using an alignment panel as a parent, where the information will be displayed.
MultipleStructureAligner - Interface in org.biojava.nbio.structure.align: Interface for the Multiple Structure Alignment Algorithms.
MultipleSuperimposer - Interface in org.biojava.nbio.structure.align.multiple.util: Interface for Multiple Alignment superposition algorithms.
multiply(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
multiply(double[][], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
multiply(double[], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
MultiThreadedDBSearch - Class in org.biojava.nbio.structure.align: Performs a multi threaded database search for an input protein structure
MultiThreadedDBSearch(String, Structure, String, StructureAlignment, int, boolean) - Constructor for class org.biojava.nbio.structure.align.MultiThreadedDBSearch
MutableAlignedSequence<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a mutable (editable) data structure for an AlignedSequence.
MutableProfile<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a mutable (editable) data structure for a Profile.
MutableProfilePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a mutable (editable) data structure for a ProfilePair.
MutableSequencePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a mutable (editable) data structure for the results of pairwise sequence alignment.
mutate(Structure, String, String, String) - Method in class org.biojava.nbio.structure.Mutator: creates a new structure which is identical with the original one.
mutateResidue(AminoAcid, String) - Method in class org.biojava.nbio.structure.Mutator: create a new residue which is of the new type.
Mutator - Class in org.biojava.nbio.structure: A class that can change one amino acid to another.
Mutator() - Constructor for class org.biojava.nbio.structure.Mutator
MyAlignmentLoadListener - Class in org.biojava.nbio.structure.align.gui: Loads an alignment in an XML format and displays its content in a new Jmol panel.
MyAlignmentLoadListener() - Constructor for class org.biojava.nbio.structure.align.gui.MyAlignmentLoadListener
MyDistMaxListener - Class in org.biojava.nbio.structure.align.gui: Shows the interatomic Distance Matrices of all the Structures aligned in different Frames.
MyDistMaxListener(AbstractAlignmentJmol) - Constructor for class org.biojava.nbio.structure.align.gui.MyDistMaxListener
MyExportListener - Class in org.biojava.nbio.structure.align.gui
MyJmolStatusListener - Class in org.biojava.nbio.structure.align.gui.jmol
MyJmolStatusListener() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
MyOpenPdbFileListener - Class in org.biojava.nbio.structure.align.gui
MyOpenPdbFileListener() - Constructor for class org.biojava.nbio.structure.align.gui.MyOpenPdbFileListener
MySaveFileListener - Class in org.biojava.nbio.structure.align.gui: Save an alignment to a specified File by the user.
MySaveFileListener(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.MySaveFileListener
MySaveFileListener(MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.gui.MySaveFileListener
MySaveFileListener(AFPChain, MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.gui.MySaveFileListener: Constructor to avoid checking which of the two is null before instantiating this class.
MyTableRowSorter - Class in org.biojava.nbio.structure.align.gui
MyTableRowSorter(TableModel) - Constructor for class org.biojava.nbio.structure.align.gui.MyTableRowSorter
MyValidationEventHandler - Class in org.biojava.nbio.aaproperties.xml
MyValidationEventHandler() - Constructor for class org.biojava.nbio.aaproperties.xml.MyValidationEventHandler

N

N - Static variable in class org.biojava.nbio.aaproperties.Constraints
n - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange: last allowed n-term
N_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name for the backbone amide nitrogen
NAME - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
name - Variable in enum org.biojava.nbio.phylo.TreeType: Description name of the Tree Type
name - Variable in class org.biojava.nbio.structure.align.client.StructureName
name - Variable in enum org.biojava.nbio.structure.secstruc.BridgeType
name - Variable in enum org.biojava.nbio.structure.secstruc.SecStrucType
name - Variable in class org.biojava.nbio.structure.validation.Program
Name2Count - Class in org.biojava.nbio.aaproperties.xml
Name2Count() - Constructor for class org.biojava.nbio.aaproperties.xml.Name2Count
Name2Count(String, int) - Constructor for class org.biojava.nbio.aaproperties.xml.Name2Count
NARROW_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
NARROW_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym
natomsEDS - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
nBestTrace - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
nBestTrace - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
nBestTraces - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
nBestTraces - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
NCBIQBlastAlignmentProperties - Class in org.biojava.nbio.ws.alignment.qblast: This class wraps a QBlast search request parameter Map by adding several convenient parameter addition methods.
NCBIQBlastAlignmentProperties() - Constructor for class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
NCBIQBlastOutputProperties - Class in org.biojava.nbio.ws.alignment.qblast: This class wraps a QBlast output parameter Map by adding several convenient parameter addition methods.
NCBIQBlastOutputProperties() - Constructor for class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: This constructor builds the parameters for the output of the GET command sent to the QBlast service with default values:
NCBIQBlastService - Class in org.biojava.nbio.ws.alignment.qblast: Provides a simple way of submitting BLAST request to the QBlast service at NCBI.
NCBIQBlastService() - Constructor for class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Constructs a service object that targets the public NCBI BLAST network service.
NCBIQBlastService(String) - Constructor for class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Constructs a service object which targets a custom NCBI BLAST network service (e.g.: an instance of BLAST in the cloud).
NCBIQBlastServiceDemo - Class in demo: A simple demo showing NCBIQBlastService usage
NCBIQBlastServiceDemo() - Constructor for class demo.NCBIQBlastServiceDemo
ncens - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
NeedlemanWunsch<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
NeedlemanWunsch() - Constructor for class org.biojava.nbio.alignment.NeedlemanWunsch: Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
NeedlemanWunsch(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.NeedlemanWunsch: Prepares for a pairwise global sequence alignment.
needsQuotes() - Method in class org.biojava.nbio.core.sequence.features.Qualifier
nevents - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
newAtomSite(AtomSite) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newAtomSite(AtomSite) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer: A new AtomSite record has been read.
newAtomSite(AtomSite) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newAuditAuthor(AuditAuthor) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newAuditAuthor(AuditAuthor) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer: AuditAuthor contains the info from the PDB-AUTHOR records.
newAuditAuthor(AuditAuthor) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newCell(Cell) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newCell(Cell) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newCell(Cell) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newChemCompAtom(ChemCompAtom) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newChemCompAtom(ChemCompAtom) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newChemCompAtom(ChemCompAtom) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newChemCompBond(ChemCompBond) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newChemCompDescriptor(ChemCompDescriptor) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newChemCompDescriptor(ChemCompDescriptor) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newChemCompDescriptor(ChemCompDescriptor) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newDatabasePDBremark(DatabasePDBremark) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newDatabasePDBremark(DatabasePDBremark) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newDatabasePDBremark(DatabasePDBremark) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newDatabasePDBrev(DatabasePDBrev) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newDatabasePDBrev(DatabasePDBrev) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newDatabasePDBrev(DatabasePDBrev) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newDatabasePDBrevRecord(DatabasePdbrevRecord) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newDatabasePDBrevRecord(DatabasePdbrevRecord) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newDatabasePDBrevRecord(DatabasePdbrevRecord) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newEntity(Entity) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newEntity(Entity) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newEntity(Entity) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newEntityPolySeq(EntityPolySeq) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newEntityPolySeq(EntityPolySeq) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newEntityPolySeq(EntityPolySeq) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer: The EntityPolySeq object provide the amino acid sequence objects for the Entities.
newEntitySrcGen(EntitySrcGen) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newEntitySrcGen(EntitySrcGen) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newEntitySrcGen(EntitySrcGen) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer: Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated.
newEntitySrcNat(EntitySrcNat) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newEntitySrcNat(EntitySrcNat) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newEntitySrcNat(EntitySrcNat) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newEntitySrcSyn(EntitySrcSyn) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newEntitySrcSyn(EntitySrcSyn) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newEntitySrcSyn(EntitySrcSyn) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newExptl(Exptl) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newExptl(Exptl) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newExptl(Exptl) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newGenericData(String, List<String>, List<String>) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newGenericData(String, List<String>, List<String>) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer: This method is called if no particular handler for the provided cif category has been implemented so far.
newGenericData(String, List<String>, List<String>) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newKey(String, String) - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener: found a new key in the file
newKey(String, String) - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
newline - Static variable in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
newline - Static variable in class org.biojava.nbio.structure.align.AbstractStructureAlignment
newline - Static variable in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
newline - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat
newline - Static variable in class org.biojava.nbio.structure.align.model.AFPChain
newline - Static variable in class org.biojava.nbio.structure.align.model.AfpChainWriter
NEWLINE - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
newline - Static variable in class org.biojava.nbio.structure.PDBHeader
NEWLINE - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
newNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.compound.DNACompoundSet
newNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.compound.RNACompoundSet
newNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
newOboFileHeader() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener: parsed a new OBO file header
newOboFileHeader() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
newPdbxChemCompDescriptor(PdbxChemCompDescriptor) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxChemCompDescriptor(PdbxChemCompDescriptor) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxChemCompDescriptor(PdbxChemCompDescriptor) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxChemCompIndentifier(PdbxChemCompIdentifier) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxChemCompIndentifier(PdbxChemCompIdentifier) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxChemCompIndentifier(PdbxChemCompIdentifier) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxEntityNonPoly(PdbxEntityNonPoly) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxEntityNonPoly(PdbxEntityNonPoly) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxEntityNonPoly(PdbxEntityNonPoly) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxNonPolyScheme(PdbxNonPolyScheme) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxNonPolyScheme(PdbxNonPolyScheme) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxNonPolyScheme(PdbxNonPolyScheme) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxPolySeqScheme(PdbxPolySeqScheme) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxPolySeqScheme(PdbxPolySeqScheme) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxPolySeqScheme(PdbxPolySeqScheme) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxStrucAssembly(PdbxStructAssembly) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxStrucAssembly(PdbxStructAssembly) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxStrucAssembly(PdbxStructAssembly) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxStrucAssemblyGen(PdbxStructAssemblyGen) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxStrucAssemblyGen(PdbxStructAssemblyGen) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxStrucAssemblyGen(PdbxStructAssemblyGen) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newPdbxStructOperList(PdbxStructOperList) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newPdbxStructOperList(PdbxStructOperList) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newPdbxStructOperList(PdbxStructOperList) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newRefine(Refine) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newRefine(Refine) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newRefine(Refine) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStanza(String) - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener: parsed a new stanza in the file
newStanza(String) - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
newStructAsym(StructAsym) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructAsym(StructAsym) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructAsym(StructAsym) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructConn(StructConn) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructConn(StructConn) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructConn(StructConn) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructKeywords(StructKeywords) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructKeywords(StructKeywords) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructKeywords(StructKeywords) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructNcsOper(StructNcsOper) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructNcsOper(StructNcsOper) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructNcsOper(StructNcsOper) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructRef(StructRef) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructRef(StructRef) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructRef(StructRef) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructRefSeq(StructRefSeq) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructRefSeq(StructRefSeq) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructRefSeq(StructRefSeq) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer: create a DBRef record from the StrucRefSeq record:
newStructRefSeqDif(StructRefSeqDif) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructRefSeqDif(StructRefSeqDif) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructRefSeqDif(StructRefSeqDif) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructSite(StructSite) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructSite(StructSite) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructSite(StructSite) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newStructSiteGen(StructSiteGen) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newStructSiteGen(StructSiteGen) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newStructSiteGen(StructSiteGen) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newSymmetry(Symmetry) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
newSymmetry(Symmetry) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
newSymmetry(Symmetry) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
newSynonym(Synonym) - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener: a new synonym has been found
newSynonym(Synonym) - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
next() - Method in class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator
next() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Get next window of default size, then increment position by default amount.
next(int, int) - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Get next window of specified size, then increment position by specified amount.
next() - Method in class org.biojava.nbio.structure.AtomIterator: Return next atom.
next() - Method in class org.biojava.nbio.structure.GroupIterator: get next Group.
nextStep(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
nextStep(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
nIter - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator
nIter - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
nnz() - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix: return the number of nonzero entries (not the most efficient implementation)
nnz() - Method in class org.biojava.nbio.structure.math.SparseVector
nodeListFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
NON_AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil: inversion of AA pattern
NON_NUCLEOTIDE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil: Non nucleotide
NONE - Static variable in class org.biojava.nbio.ontology.OntoTools
nonOverlappingKmers(Sequence<C>, int) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: Produces kmers of the specified size e.g.
NONWORD - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil: Non word
norm() - Method in class org.biojava.nbio.structure.math.SparseVector: Calculates the 2-norm
norm(double) - Static method in class org.biojava.nbio.survival.cox.stats.ChiSq
norm1() - Method in class org.biojava.nbio.structure.jama.Matrix: One norm
norm2() - Method in class org.biojava.nbio.structure.jama.Matrix: Two norm
norm2() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Two norm
normalizeMatrix(short) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
normalizeMatrix(short) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
normalizeMatrix(short) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Rescales the matrix so that to SubstitutionMatrix.getMaxValue() - SubstitutionMatrix.getMinValue() = scale.
normF() - Method in class org.biojava.nbio.structure.jama.Matrix: Frobenius norm
normInf() - Method in class org.biojava.nbio.structure.jama.Matrix: Infinity norm
NOT_ALIGNED - Static variable in class org.biojava.nbio.structure.gui.util.AlignedPosition: they can be shown in the same column (for a compact display) , but they are not structurally equivalent
NOT_DOMAIN_ASSEMBLY - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser: String for single-domain assemblies
NOT_REPRESENTATIVE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser: Indicates not a manual representative
notifyCalcFinished() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
notifyCalcFinished() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
notifyCalcFinished() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
notifyCalcFinished() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
notifyCallback(int, Object[]) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
notifyCallback(EnumCallback, Object[]) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
notifyEnabled(int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
notifyEnabled(EnumCallback) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
notifyShutdown() - Method in class org.biojava.nbio.structure.align.util.AtomCache: Send a signal to the cache that the system is shutting down.
NR_BIOL_APPEND - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
NR_BIOL_APPEND - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
nrisk - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
nrModels() - Method in interface org.biojava.nbio.structure.Structure: Return the number of models .
nrModels() - Method in class org.biojava.nbio.structure.StructureImpl: return number of models.
nrOpenWindows - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
nTrace - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
nTrace - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
nTraces - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
nTraces - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
NUC_CARBON_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
NUC_NITROGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
NUCLEOTIDE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil: Nucleotides a, t, g, c, u
NUCLEOTIDE_LETTERS - Static variable in class org.biojava.nbio.core.util.SequenceTools
NUCLEOTIDE_REPRESENTATIVE - Static variable in class org.biojava.nbio.structure.StructureTools: The atom used as representative for nucleotides, equivalent to StructureTools.CA_ATOM_NAME for proteins
NucleotideCompound - Class in org.biojava.nbio.core.sequence.compound
NucleotideCompound(String, CompoundSet<NucleotideCompound>, String) - Constructor for class org.biojava.nbio.core.sequence.compound.NucleotideCompound
NucleotideCompound(String, CompoundSet<NucleotideCompound>, String, NucleotideCompound[]) - Constructor for class org.biojava.nbio.core.sequence.compound.NucleotideCompound
NucleotideImpl - Class in org.biojava.nbio.structure: A nucleotide group is almost the same as a Hetatm group.
NucleotideImpl() - Constructor for class org.biojava.nbio.structure.NucleotideImpl
nullifyComments() - Method in class org.biojava.nbio.structure.scop.ScopInstallation: Removes all of the comments (dir.com file) in order to free memory.
NullOutputStream - Class in org.biojava.nbio.ronn: The stream that void its input
NullOutputStream() - Constructor for class org.biojava.nbio.ronn.NullOutputStream
NumbersAtRiskPanel - Class in org.biojava.nbio.survival.kaplanmeier.figure
NumbersAtRiskPanel() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
numeric - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
numericalEntity(char) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
numFreeReflections - Variable in class org.biojava.nbio.structure.validation.Entry
numHReduce - Variable in class org.biojava.nbio.structure.validation.Entry
numHReduce - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
numMillerIndices - Variable in class org.biojava.nbio.structure.validation.Entry
numobs - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier
numobs - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier

O

O2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone O2' in RNA
O3_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone O3' in RNA
O4_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone O4' in RNA
O5_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone O4' in RNA
O_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name for the backbone carbonyl oxygen
ObjectFactory - Class in org.biojava.nbio.structure.validation: This object contains factory methods for each Java content interface and Java element interface generated in the org.biojava.nbio.structure.validation package.
ObjectFactory() - Constructor for class org.biojava.nbio.structure.validation.ObjectFactory: Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: org.biojava.nbio.structure.validation
OboFileEventListener - Interface in org.biojava.nbio.ontology.obo: an interface for events that occur during parsing of .obo files
OboFileHandler - Class in org.biojava.nbio.ontology.obo: A file handler for .obo files
OboFileHandler(Ontology) - Constructor for class org.biojava.nbio.ontology.obo.OboFileHandler
OboFileParser - Class in org.biojava.nbio.ontology.obo: A class to parse the content of an OBO file.
OboFileParser() - Constructor for class org.biojava.nbio.ontology.obo.OboFileParser
OboFileParser.SOPair - Class in org.biojava.nbio.ontology.obo
OboParser - Class in org.biojava.nbio.ontology.io: Parses an OBO file.
OboParser() - Constructor for class org.biojava.nbio.ontology.io.OboParser
obs - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
obs - Variable in class org.biojava.nbio.structure.validation.BondOutlier
obsval - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier
obsval - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier
obtainAminoAcidCompositionTable(File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File, File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
obtainAminoAcidCompositionTable(File, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
Octahedron - Class in org.biojava.nbio.structure.symmetry.geometry
Octahedron() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Octahedron
of(String) - Static method in class org.biojava.nbio.protmod.Component: Get a Component that does not have to occur at terminals.
of(String, boolean, boolean) - Static method in class org.biojava.nbio.protmod.Component: Get or create a Component.
of(Set<String>) - Static method in class org.biojava.nbio.protmod.Component: Get a Component that does not have to occur at terminals.
of(Set<String>, boolean, boolean) - Static method in class org.biojava.nbio.protmod.Component: Get or create a Component.
offset(int) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
offset(int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
offset(int) - Method in interface org.biojava.nbio.core.sequence.location.template.Point: Returns a new point offset by the given distance
omitOverlapping(String, Location, boolean) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a list of all features that do not overlap the specified location on the specified sequence.
oneDivide(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
oneDivide(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
OneOfLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation
OneOfLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation
ONTOLOGY - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
Ontology - Interface in org.biojava.nbio.ontology: An ontology.
Ontology.Impl - Class in org.biojava.nbio.ontology: A basic in-memory implementation of an ontology
OntologyException - Exception in org.biojava.nbio.ontology: Thrown to indicate an error in an Ontology object
OntologyException() - Constructor for exception org.biojava.nbio.ontology.OntologyException
OntologyException(String) - Constructor for exception org.biojava.nbio.ontology.OntologyException
OntologyException(Throwable) - Constructor for exception org.biojava.nbio.ontology.OntologyException
OntologyException(String, Throwable) - Constructor for exception org.biojava.nbio.ontology.OntologyException
OntologyFactory - Interface in org.biojava.nbio.ontology: A factory for Ontology instances.
OntologyOps - Interface in org.biojava.nbio.ontology: This is an interface for optimizing ontology operators.
OntologyTerm - Interface in org.biojava.nbio.ontology: A term in an ontology which identifies another ontology.
OntologyTerm.Impl - Class in org.biojava.nbio.ontology: Simple in-memory implementation of a remote ontology term.
OntoTools - Class in org.biojava.nbio.ontology: Tools for manipulating ontologies.
OP1_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone O4' in RNA
OP2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone O4' in RNA
openFile(File) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: For a filename this code will check the extension of the file for a .gz extension.
openHttpURLConnection(URL, int) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: open HttpURLConnection.
openHttpURLConnection(URL) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools: open HttpURLConnection.
openStringInline(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
openTag(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
openTag(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
openTag(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Open a new namespace-qualified XML tag.
openTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Open a new unqualified XML tag.
OperatorResolver - Class in org.biojava.nbio.structure.quaternary: A class to resolve the operators for transformations
OperatorResolver() - Constructor for class org.biojava.nbio.structure.quaternary.OperatorResolver
opposite() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return location that is in same position on opposite strand.
OptimalCECPMain - Class in org.biojava.nbio.structure.align.ce: A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.
OptimalCECPMain() - Constructor for class org.biojava.nbio.structure.align.ce.OptimalCECPMain
OptimalCECPParameters - Class in org.biojava.nbio.structure.align.ce: Contains the parameters that can be sent to CE
OptimalCECPParameters() - Constructor for class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
optimize() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer: Optimization method based in a Monte-Carlo approach.
optimize() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmOptimizer: Optimization method based in a Monte-Carlo approach.
optimizeAln(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer: optimize the alignment by dynamic programming
optimizeResult(int[], int, int[][]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer
orange - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
order() - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup: The order of symmetry of the group is the number of connected residues.
OrderDetector - Interface in org.biojava.nbio.structure.symmetry.internal: A method to decide the order of symmetry (number of subunits) given a structure self-alignment, calculated by CE-Symm.
OrderedPair<T> - Class in org.biojava.nbio.structure.quaternary: An ordered pair represents a component of a cartesian product.
OrderLocation(List) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
org.biojava.nbio.aaproperties - package org.biojava.nbio.aaproperties: Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
org.biojava.nbio.aaproperties.profeat - package org.biojava.nbio.aaproperties.profeat: Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
org.biojava.nbio.aaproperties.profeat.convertor - package org.biojava.nbio.aaproperties.profeat.convertor: Set of classes that enable the conversion protein sequences into various attributes.
org.biojava.nbio.aaproperties.xml - package org.biojava.nbio.aaproperties.xml: Set of classes that handles the reading and writing of xml files.
org.biojava.nbio.alignment - package org.biojava.nbio.alignment
org.biojava.nbio.alignment.io - package org.biojava.nbio.alignment.io
org.biojava.nbio.alignment.routines - package org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template - package org.biojava.nbio.alignment.template
org.biojava.nbio.core.alignment - package org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.matrices - package org.biojava.nbio.core.alignment.matrices
org.biojava.nbio.core.alignment.template - package org.biojava.nbio.core.alignment.template
org.biojava.nbio.core.exceptions - package org.biojava.nbio.core.exceptions
org.biojava.nbio.core.search.io - package org.biojava.nbio.core.search.io
org.biojava.nbio.core.search.io.blast - package org.biojava.nbio.core.search.io.blast
org.biojava.nbio.core.sequence - package org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.compound - package org.biojava.nbio.core.sequence.compound
org.biojava.nbio.core.sequence.edits - package org.biojava.nbio.core.sequence.edits
org.biojava.nbio.core.sequence.features - package org.biojava.nbio.core.sequence.features
org.biojava.nbio.core.sequence.io - package org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.io.template - package org.biojava.nbio.core.sequence.io.template
org.biojava.nbio.core.sequence.io.util - package org.biojava.nbio.core.sequence.io.util
org.biojava.nbio.core.sequence.loader - package org.biojava.nbio.core.sequence.loader
org.biojava.nbio.core.sequence.location - package org.biojava.nbio.core.sequence.location
org.biojava.nbio.core.sequence.location.template - package org.biojava.nbio.core.sequence.location.template
org.biojava.nbio.core.sequence.storage - package org.biojava.nbio.core.sequence.storage
org.biojava.nbio.core.sequence.template - package org.biojava.nbio.core.sequence.template
org.biojava.nbio.core.sequence.transcription - package org.biojava.nbio.core.sequence.transcription
org.biojava.nbio.core.sequence.views - package org.biojava.nbio.core.sequence.views
org.biojava.nbio.core.util - package org.biojava.nbio.core.util
org.biojava.nbio.data.sequence - package org.biojava.nbio.data.sequence: Set of classes that responsible for data handling.
org.biojava.nbio.genome - package org.biojava.nbio.genome
org.biojava.nbio.genome.homology - package org.biojava.nbio.genome.homology
org.biojava.nbio.genome.parsers.cytoband - package org.biojava.nbio.genome.parsers.cytoband
org.biojava.nbio.genome.parsers.geneid - package org.biojava.nbio.genome.parsers.geneid
org.biojava.nbio.genome.parsers.genename - package org.biojava.nbio.genome.parsers.genename
org.biojava.nbio.genome.parsers.gff - package org.biojava.nbio.genome.parsers.gff
org.biojava.nbio.genome.parsers.twobit - package org.biojava.nbio.genome.parsers.twobit
org.biojava.nbio.genome.query - package org.biojava.nbio.genome.query
org.biojava.nbio.genome.uniprot - package org.biojava.nbio.genome.uniprot
org.biojava.nbio.genome.util - package org.biojava.nbio.genome.util
org.biojava.nbio.ontology - package org.biojava.nbio.ontology
org.biojava.nbio.ontology.io - package org.biojava.nbio.ontology.io: Tools for loading and saving ontologies.
org.biojava.nbio.ontology.obo - package org.biojava.nbio.ontology.obo
org.biojava.nbio.ontology.utils - package org.biojava.nbio.ontology.utils
org.biojava.nbio.phosphosite - package org.biojava.nbio.phosphosite
org.biojava.nbio.phylo - package org.biojava.nbio.phylo
org.biojava.nbio.protmod - package org.biojava.nbio.protmod
org.biojava.nbio.protmod.io - package org.biojava.nbio.protmod.io
org.biojava.nbio.protmod.structure - package org.biojava.nbio.protmod.structure
org.biojava.nbio.ronn - package org.biojava.nbio.ronn: BioJava provide a module biojava-protein-disorder for prediction disordered regions from a protein sequence.
org.biojava.nbio.sequencing.io.fastq - package org.biojava.nbio.sequencing.io.fastq: FASTQ and variants sequence format I/O.
org.biojava.nbio.structure - package org.biojava.nbio.structure: Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.align - package org.biojava.nbio.structure.align: Classes for the alignment of structures.
org.biojava.nbio.structure.align.ce - package org.biojava.nbio.structure.align.ce: Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.client - package org.biojava.nbio.structure.align.client: This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.nbio.structure.align.events - package org.biojava.nbio.structure.align.events
org.biojava.nbio.structure.align.fatcat - package org.biojava.nbio.structure.align.fatcat: Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
org.biojava.nbio.structure.align.fatcat.calc - package org.biojava.nbio.structure.align.fatcat.calc
org.biojava.nbio.structure.align.gui - package org.biojava.nbio.structure.align.gui
org.biojava.nbio.structure.align.gui.aligpanel - package org.biojava.nbio.structure.align.gui.aligpanel
org.biojava.nbio.structure.align.gui.autosuggest - package org.biojava.nbio.structure.align.gui.autosuggest
org.biojava.nbio.structure.align.gui.jmol - package org.biojava.nbio.structure.align.gui.jmol: Utility methods for better interaction with Jmol.
org.biojava.nbio.structure.align.helper - package org.biojava.nbio.structure.align.helper: Helper classes for structural alignment.
org.biojava.nbio.structure.align.model - package org.biojava.nbio.structure.align.model
org.biojava.nbio.structure.align.multiple - package org.biojava.nbio.structure.align.multiple
org.biojava.nbio.structure.align.multiple.mc - package org.biojava.nbio.structure.align.multiple.mc
org.biojava.nbio.structure.align.multiple.util - package org.biojava.nbio.structure.align.multiple.util
org.biojava.nbio.structure.align.pairwise - package org.biojava.nbio.structure.align.pairwise: Classes for the pairwise alignment of structures.
org.biojava.nbio.structure.align.seq - package org.biojava.nbio.structure.align.seq
org.biojava.nbio.structure.align.util - package org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.align.webstart - package org.biojava.nbio.structure.align.webstart: Classes related to Java Web Start
org.biojava.nbio.structure.align.xml - package org.biojava.nbio.structure.align.xml: Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
org.biojava.nbio.structure.asa - package org.biojava.nbio.structure.asa
org.biojava.nbio.structure.cath - package org.biojava.nbio.structure.cath
org.biojava.nbio.structure.contact - package org.biojava.nbio.structure.contact
org.biojava.nbio.structure.domain - package org.biojava.nbio.structure.domain
org.biojava.nbio.structure.domain.pdp - package org.biojava.nbio.structure.domain.pdp
org.biojava.nbio.structure.ecod - package org.biojava.nbio.structure.ecod
org.biojava.nbio.structure.gui - package org.biojava.nbio.structure.gui: A few convenience classes to view protein structures with Jmol (if it is on the classpath), to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
org.biojava.nbio.structure.gui.events - package org.biojava.nbio.structure.gui.events: Some event classes for the protein structure GUIs.
org.biojava.nbio.structure.gui.util - package org.biojava.nbio.structure.gui.util: Some utility classes for the protein structure GUIs.
org.biojava.nbio.structure.gui.util.color - package org.biojava.nbio.structure.gui.util.color
org.biojava.nbio.structure.io - package org.biojava.nbio.structure.io: Input and Output of Structures
org.biojava.nbio.structure.io.mmcif - package org.biojava.nbio.structure.io.mmcif: Input and Output of mmcif files.
org.biojava.nbio.structure.io.mmcif.chem - package org.biojava.nbio.structure.io.mmcif.chem
org.biojava.nbio.structure.io.mmcif.model - package org.biojava.nbio.structure.io.mmcif.model: Datamodel objects used for processing mmcif files.
org.biojava.nbio.structure.io.sifts - package org.biojava.nbio.structure.io.sifts
org.biojava.nbio.structure.io.util - package org.biojava.nbio.structure.io.util
org.biojava.nbio.structure.jama - package org.biojava.nbio.structure.jama: Matrix package for from JAMA
org.biojava.nbio.structure.math - package org.biojava.nbio.structure.math
org.biojava.nbio.structure.quaternary - package org.biojava.nbio.structure.quaternary
org.biojava.nbio.structure.quaternary.io - package org.biojava.nbio.structure.quaternary.io
org.biojava.nbio.structure.rcsb - package org.biojava.nbio.structure.rcsb
org.biojava.nbio.structure.scop - package org.biojava.nbio.structure.scop: Parsers and API for SCOP, Structural Classification of Proteins.
org.biojava.nbio.structure.scop.server - package org.biojava.nbio.structure.scop.server
org.biojava.nbio.structure.secstruc - package org.biojava.nbio.structure.secstruc
org.biojava.nbio.structure.symmetry.analysis - package org.biojava.nbio.structure.symmetry.analysis
org.biojava.nbio.structure.symmetry.core - package org.biojava.nbio.structure.symmetry.core
org.biojava.nbio.structure.symmetry.geometry - package org.biojava.nbio.structure.symmetry.geometry
org.biojava.nbio.structure.symmetry.gui - package org.biojava.nbio.structure.symmetry.gui
org.biojava.nbio.structure.symmetry.internal - package org.biojava.nbio.structure.symmetry.internal
org.biojava.nbio.structure.symmetry.jmolScript - package org.biojava.nbio.structure.symmetry.jmolScript
org.biojava.nbio.structure.symmetry.misc - package org.biojava.nbio.structure.symmetry.misc
org.biojava.nbio.structure.symmetry.utils - package org.biojava.nbio.structure.symmetry.utils
org.biojava.nbio.structure.validation - package org.biojava.nbio.structure.validation
org.biojava.nbio.structure.xtal - package org.biojava.nbio.structure.xtal
org.biojava.nbio.structure.xtal.io - package org.biojava.nbio.structure.xtal.io
org.biojava.nbio.survival.cox - package org.biojava.nbio.survival.cox
org.biojava.nbio.survival.cox.comparators - package org.biojava.nbio.survival.cox.comparators
org.biojava.nbio.survival.cox.matrix - package org.biojava.nbio.survival.cox.matrix
org.biojava.nbio.survival.cox.stats - package org.biojava.nbio.survival.cox.stats
org.biojava.nbio.survival.data - package org.biojava.nbio.survival.data
org.biojava.nbio.survival.kaplanmeier.figure - package org.biojava.nbio.survival.kaplanmeier.figure
org.biojava.nbio.survival.kaplanmeier.metadata - package org.biojava.nbio.survival.kaplanmeier.metadata
org.biojava.nbio.ws.alignment - package org.biojava.nbio.ws.alignment: This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojava.nbio.ws.alignment.qblast - package org.biojava.nbio.ws.alignment.qblast
org.biojava.nbio.ws.hmmer - package org.biojava.nbio.ws.hmmer
ORGANISM_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
orient() - Method in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
oRmsdThr - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
ORonn - Class in org.biojava.nbio.ronn: Fully re-factored and enhanced version of RONN.
ORonnModel - Class in org.biojava.nbio.ronn: Fully re-factored version of RONN model.
ORonnModel(String, ModelLoader.Model, float) - Constructor for class org.biojava.nbio.ronn.ORonnModel
outputFastaSequenceLengthGFF3(File, File) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper: Output a gff3 feature file that will give the length of each scaffold/chromosome in the fasta file.
OutputHitsGFF - Class in org.biojava.nbio.genome.query
OutputHitsGFF() - Constructor for class org.biojava.nbio.genome.query.OutputHitsGFF
outputToStream(Document, OutputStream) - Static method in class org.biojava.nbio.core.util.XMLHelper
outputToStream(Element, OutputStream) - Static method in class org.biojava.nbio.core.util.XMLHelper
overlappingKmers(Sequence<C>, int) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin: Used to generate overlapping k-mers such i.e.
overlaps(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location and other location overlap.
overlaps(BoundingBox, double) - Method in class org.biojava.nbio.structure.contact.BoundingBox: Returns true if this bounding box overlaps given one, i.e.
overlaps(Subunits) - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
owab - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
OXIGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

P

P - Static variable in class org.biojava.nbio.aaproperties.Constraints
P_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone phosphate in RNA
padding - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
padLeft(String, int) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
padRight(String, int) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
paint(Graphics) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
paint(Graphics) - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.gui.util.color.GradientPanel
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
paintComponent(Graphics) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
paintComponent(Graphics) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
paintComponent(Graphics) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
pair - Variable in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
pair - Variable in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
Pair<T> - Class in org.biojava.nbio.structure.contact: A Pair of objects.
Pair(T, T) - Constructor for class org.biojava.nbio.structure.contact.Pair: Creates a Pair from the specified elements.
PairInProfileScorer<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
PAIRS_ONLY - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
PAIRWISE_ALIGN - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
PairwiseAlignment - Class in org.biojava.nbio.structure.symmetry.core
PairwiseAlignment(SequenceAlignmentCluster, SequenceAlignmentCluster) - Constructor for class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
PairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an Aligner for a pair of Sequences.
PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes a score for a pair of sequences.
pamMLdistance(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The PAM (Point Accepted Mutations) distance is a measure of evolutionary distance in protein sequences.
ParameterGUI - Class in org.biojava.nbio.structure.align.gui: UI for ConfigStrucAligParams, for the AlignmentGUI.
ParameterGUI(ConfigStrucAligParams, String) - Constructor for class org.biojava.nbio.structure.align.gui.ParameterGUI: Constructor for a ParameterGUI.
params - Variable in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
params - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
params - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
params - Variable in class org.biojava.nbio.structure.align.ce.CeMain
params - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
params - Variable in class org.biojava.nbio.structure.align.util.AtomCache
parent - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
parentGeneSequence - Variable in class org.biojava.nbio.core.sequence.StartCodonSequence
parentGeneSequence - Variable in class org.biojava.nbio.core.sequence.StopCodonSequence
parse(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser: Parses a Stockholm file and returns a StockholmStructure object with its content.
This function is meant to be used for single access to specific file and it closes the file after doing its assigned job.
parse(String, int) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser: Parses a Stockholm file and returns a StockholmStructure object with its content.
This function doesn't close the file after doing its assigned job; to allow for further calls of StockholmFileParser.parseNext(int).
parse(InputStream) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser: parses InputStream and returns a the first contained alignment in a StockholmStructure object.
parse(InputStream, int) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser: parses an InputStream and returns at maximum max objects contained in that file.
This method leaves the stream open for further calls of StockholmFileParser.parse(InputStream, int) (same function) or StockholmFileParser.parseNext(int).
parse(InputStream) - Method in class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser: parse an inputStream that points to an AAINDEX database file
parse(String) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser: Main method for parsing a location from a String instance
parse(Reader) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser: Reader based version of the parse methods.
parse(BufferedReader, OntologyFactory) - Method in class org.biojava.nbio.ontology.io.TabDelimParser: Parse an ontology from a reader.
parse(Readable, ParseListener) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqReader: Parse the specified readable.
parse(String) - Static method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser: parses e.g.
parse(BufferedReader) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser: Start the actual parsing.
parse(InputStream) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser: Start the actual parsing.
parse(InputStream) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
parse(BufferedReader) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
parse(String) - Static method in class org.biojava.nbio.structure.ResidueRange: Parse the residue range from a string.
parse(String, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength: Parses a residue range.
parse(String) - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
parseBinaryOperatorExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
parseBlock(Node, BlockSet) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseBlockSet(Node, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseEnsemble(Node) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
ParseFastaFileDemo - Class in demo: Created by andreas on 6/17/15.
ParseFastaFileDemo() - Constructor for class demo.ParseFastaFileDemo
parseFastqVariant(String) - Static method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant: Return the FASTQ sequence format variant with the specified name, if any.
parseFeatures(AbstractSequence<C>) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
parseFile(String, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser: Parse a DSSP output file and return the secondary structure annotation as a List of SecStrucState objects.
ParseGO - Class in demo
ParseGO() - Constructor for class demo.ParseGO
parseGO(BufferedReader, String, String, OntologyFactory) - Method in class org.biojava.nbio.ontology.io.GOParser
parseHeader(String, S) - Method in class org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser: Parse the header and set the values in the sequence
parseHeader(String, S) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser: Parse the header and set the values in the sequence
parseHeader(String, S) - Method in class org.biojava.nbio.core.sequence.io.PlainFastaHeaderParser: Parse the header and set the values in the sequence
parseHeader(String, S) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface
parseHeader(Node, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
ParseListener - Interface in org.biojava.nbio.sequencing.io.fastq: Low-level event based parser callback.
parseMatrix4d(Node) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseMultiple(String) - Static method in class org.biojava.nbio.structure.ResidueRange
parseMultiple(List<String>) - Static method in class org.biojava.nbio.structure.ResidueRange
parseMultiple(List<String>, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength
parseMultiple(String, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength
parseMultipleAlignment(Node, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseMultiXML(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
parseNext(int) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser: Tries to parse and return as maximum as max structures in the last used file or input stream.
Please consider calling either StockholmFileParser.parse(InputStream), StockholmFileParser.parse(InputStream, int), or StockholmFileParser.parse(String, int) before calling this function.
parseOBO(BufferedReader, String, String) - Method in class org.biojava.nbio.ontology.io.OboParser: Parse a OBO file and return its content as a BioJava Ontology object
parseOBO(BufferedReader) - Method in class org.biojava.nbio.ontology.obo.OboFileParser: parse an ontology file
parseOperatorExpressionString(String) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver: Parses the operator expression and save the operators as a list of unary or binary operators (i.e.
parsePDBFile(InputStream) - Method in class org.biojava.nbio.structure.io.PDBFileParser: Parse a PDB file and return a datastructure implementing PDBStructure interface.
parsePDBFile(BufferedReader) - Method in class org.biojava.nbio.structure.io.PDBFileParser: Parse a PDB file and return a datastructure implementing PDBStructure interface.
ParserException - Exception in org.biojava.nbio.core.exceptions: General abstraction of different parsing errors
ParserException(String) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException
ParserException(Exception) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException
ParserException(String, Exception) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException
parseScoresCache(Node, ScoresCache) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseSites(File) - Static method in class org.biojava.nbio.phosphosite.Site
parseSpaceGroup(String) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup: Get the space group for the given international short name, using the PDB format, e.g.
parseSpaceGroupsXML(InputStream) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser: Load all SpaceGroup information from the file spacegroups.xml
parseString(String, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser: Parse a DSSP format String and return the secondary structure annotation as a List of SecStrucState objects.
parseStructures(Node, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
parseSymopLib(InputStream) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser: A parser for the symop.lib file provided by CCP4.
parseUnaryOperatorExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
parseUniprotXMLString(String, CompoundSet<C>) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: The passed in xml is parsed as a DOM object so we know everything about the protein.
parseXMLfile(String) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser: Creates a list of MultipleAlignment ensembles from an XML file.
parseXmlFile(InputStream) - Method in class org.biojava.nbio.structure.io.sifts.SiftsXMLParser
parseXref(String, int, int) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
PART_OF - Static variable in class org.biojava.nbio.ontology.OntoTools
PARTIAL_ORDER - Static variable in class org.biojava.nbio.ontology.OntoTools
PartitionRefiner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning.
PassthroughIdentifier - Class in org.biojava.nbio.structure: A stub StructureIdentifier, representing the full structure in all cases.
PassthroughIdentifier(String) - Constructor for class org.biojava.nbio.structure.PassthroughIdentifier
PDB - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
PDB_AUTHOR_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo: Secondary strucuture assigned by the PDB author
PDB_CACHE_DIR - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
PDB_DIR - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
PDB_FILE_SERVER_PROPERTY - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
pdb_flag - Variable in class org.biojava.nbio.structure.HetatomImpl: stores if 3d coordinates are available.
PDB_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
pdb_name - Variable in class org.biojava.nbio.structure.HetatomImpl: 3 letter name of amino acid in pdb file.
PDB_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.PDBFileReader
pdb_REMARK_350_Handler(String) - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser: Parses REMARK 350 line.
PDB_SERVER_PROPERTY - Static variable in class org.biojava.nbio.structure.PDBStatus
PDB_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.PDBFileReader
PDBBioAssemblyParser - Class in org.biojava.nbio.structure.io: Parses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unit
PDBBioAssemblyParser() - Constructor for class org.biojava.nbio.structure.io.PDBBioAssemblyParser
PDBBioUnitDataProvider - Class in org.biojava.nbio.structure.quaternary.io: A BioUnitDataProvider that extracts the necessary info from PDB files
PDBBioUnitDataProvider() - Constructor for class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
PDBCrystallographicInfo - Class in org.biojava.nbio.structure: A class to hold crystallographic information about a PDB structure.
PDBCrystallographicInfo() - Constructor for class org.biojava.nbio.structure.PDBCrystallographicInfo
PDBDirPanel - Class in org.biojava.nbio.structure.gui.util: A class to define where a structure for the alignment is coming from
PDBDirPanel() - Constructor for class org.biojava.nbio.structure.gui.util.PDBDirPanel: load the PDB files from a local directory
PDBDomainProvider - Class in org.biojava.nbio.structure.domain: Class to fetch domains through the RCSB's REST API.
PDBDomainProvider() - Constructor for class org.biojava.nbio.structure.domain.PDBDomainProvider
PDBDomainProvider(String, int) - Constructor for class org.biojava.nbio.structure.domain.PDBDomainProvider
PDBFileParser - Class in org.biojava.nbio.structure.io: This class implements the actual PDB file parsing.
PDBFileParser() - Constructor for class org.biojava.nbio.structure.io.PDBFileParser
PDBFileReader - Class in org.biojava.nbio.structure.io: The wrapper class for parsing a PDB file.
PDBFileReader() - Constructor for class org.biojava.nbio.structure.io.PDBFileReader: Constructs a new PDBFileReader, initializing the extensions member variable.
PDBFileReader(String) - Constructor for class org.biojava.nbio.structure.io.PDBFileReader: Constructs a new PDBFileReader, initializing the extensions member variable.
PDBHeader - Class in org.biojava.nbio.structure: A class that contains PDB Header information.
PDBHeader() - Constructor for class org.biojava.nbio.structure.PDBHeader
pdbId - Variable in class org.biojava.nbio.structure.align.client.StructureName
PDBID_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier: URL parameter specifying the PDB ID
PdbIdLists - Class in org.biojava.nbio.structure.rcsb: Utility classes for retrieving lists of PDB IDs.
PdbIdLists() - Constructor for class org.biojava.nbio.structure.rcsb.PdbIdLists
PdbPair - Class in org.biojava.nbio.structure.align.client: A pair for structure alignment
PdbPair(String, String) - Constructor for class org.biojava.nbio.structure.align.client.PdbPair
PdbPair(StructureName, StructureName) - Constructor for class org.biojava.nbio.structure.align.client.PdbPair
PdbPairsMessage - Class in org.biojava.nbio.structure.align.xml
PdbPairsMessage() - Constructor for class org.biojava.nbio.structure.align.xml.PdbPairsMessage
PdbPairXMLConverter - Class in org.biojava.nbio.structure.align.xml
PdbPairXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
PDBParseException - Exception in org.biojava.nbio.structure.io: An exception during the parsing of a PDB file.
PDBParseException(String) - Constructor for exception org.biojava.nbio.structure.io.PDBParseException: Constructs a PDBParseException object.
PDBParseException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.io.PDBParseException: Constructs a PDBParseException object.
PDBParseException(Throwable) - Constructor for exception org.biojava.nbio.structure.io.PDBParseException: Constructs a PDBParseException object.
pdbProviderClassName - Static variable in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
PDBRecord - Interface in org.biojava.nbio.structure: An interface implemented by all classes that represent PDB records
pdbRevisionNumber - Variable in class org.biojava.nbio.structure.validation.Entry
PDBServerPanel - Class in org.biojava.nbio.structure.gui.util: A class to define where a structure for the alignment is coming from
PDBServerPanel() - Constructor for class org.biojava.nbio.structure.gui.util.PDBServerPanel: load the PDB files from a local directory
PDBStatus - Class in org.biojava.nbio.structure: Methods for getting the status of a PDB file (current, obsolete, etc) and for accessing different versions of the structure.
PDBStatus() - Constructor for class org.biojava.nbio.structure.PDBStatus
PDBStatus.Status - Enum in org.biojava.nbio.structure: Represents the status of PDB IDs.
PDBTemporaryStorageUtils - Class in org.biojava.nbio.structure.io.util: Internal use only.
PDBTemporaryStorageUtils() - Constructor for class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils
PDBTemporaryStorageUtils.LinkRecord - Class in org.biojava.nbio.structure.io.util: Temporary data storage for LINK records.
PDBUploadPanel - Class in org.biojava.nbio.structure.gui.util: A JPanel to upload 2 custom PDB files.
PDBUploadPanel() - Constructor for class org.biojava.nbio.structure.gui.util.PDBUploadPanel
PDBUploadPanel(boolean) - Constructor for class org.biojava.nbio.structure.gui.util.PDBUploadPanel
PdbxChemCompDescriptor - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxChemCompDescriptor() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
PdbxChemCompIdentifier - Class in org.biojava.nbio.structure.io.mmcif.model: _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier
PdbxChemCompIdentifier() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
PdbxEntityNonPoly - Class in org.biojava.nbio.structure.io.mmcif.model: A bean for the Pdbx_entity_nonpoly category.
PdbxEntityNonPoly() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
PdbxNonPolyScheme - Class in org.biojava.nbio.structure.io.mmcif.model: A bean for the PDBX_NONPOLY_SCHEME category, which provides residue level nomenclature mapping for non-polymer entities.
PdbxNonPolyScheme() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
PdbxPolySeqScheme - Class in org.biojava.nbio.structure.io.mmcif.model: A bean for the PDBX_POLY_SEQ_SCHEME category, which provides residue level nomenclature mapping for polymer entities.
PdbxPolySeqScheme() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
PdbxStructAssembly - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxStructAssembly() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
PdbxStructAssemblyGen - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxStructAssemblyGen() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
PdbxStructAssemblyGenXMLContainer - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxStructAssemblyGenXMLContainer() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
PdbxStructAssemblyXMLContainer - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxStructAssemblyXMLContainer() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
PdbxStructOperList - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxStructOperList() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
PdbxStructOperListXMLContainer - Class in org.biojava.nbio.structure.io.mmcif.model
PdbxStructOperListXMLContainer() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
PDP_DOMAIN_IDENTIFIER - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
PDP_NAME_PATTERN - Static variable in class org.biojava.nbio.structure.domain.PDPDomain
PDPDistanceMatrix - Class in org.biojava.nbio.structure.domain.pdp
PDPDistanceMatrix() - Constructor for class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
PDPDomain - Class in org.biojava.nbio.structure.domain
PDPDomain(String, List<ResidueRange>) - Constructor for class org.biojava.nbio.structure.domain.PDPDomain
PDPParameters - Class in org.biojava.nbio.structure.domain.pdp
PDPParameters() - Constructor for class org.biojava.nbio.structure.domain.pdp.PDPParameters
pdpprovider - Variable in class org.biojava.nbio.structure.align.util.AtomCache
PDPProvider - Interface in org.biojava.nbio.structure.domain: Decomposes a structure into representative PDP domains.
PeptideProperties - Class in org.biojava.nbio.aaproperties: This is an adaptor class which enable the ease of generating protein properties.
PeptideProperties() - Constructor for class org.biojava.nbio.aaproperties.PeptideProperties
PeptideProperties.SingleLetterAACode - Enum in org.biojava.nbio.aaproperties: Enumeration of 20 standard amino acid code
PeptidePropertiesImpl - Class in org.biojava.nbio.aaproperties: This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.
PeptidePropertiesImpl() - Constructor for class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
percentageIdentity(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: BioJava implementation for percentage of identity (PID).
percentFreeReflections - Variable in class org.biojava.nbio.structure.validation.Entry
percentNucleotideSequence(String) - Static method in class org.biojava.nbio.core.util.SequenceTools
percentOverlap(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return percent overlap of two locations.
percentRamaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
percentRotaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
percentRSRZOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
performanceBehavior - Static variable in class org.biojava.nbio.structure.HetatomImpl
PermutationGenerator - Class in org.biojava.nbio.structure.symmetry.utils
PermutationGenerator(int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
PermutationGroup - Class in org.biojava.nbio.structure.symmetry.core
PermutationGroup() - Constructor for class org.biojava.nbio.structure.symmetry.core.PermutationGroup
permuteCyclic(String, int) - Static method in class org.biojava.nbio.core.util.SequenceTools: Cyclically permute the characters in string forward by n elements.
permuteCyclic(T[], T[], int) - Static method in class org.biojava.nbio.core.util.SequenceTools: Cyclically permute array forward by n elements.
PFAM - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure
PFAMB - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
phi - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
PHOSPHOROUS_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
PHOSPHORYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
PHYLOGENETIC_TREE - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
PID(String, String) - Static method in class org.biojava.nbio.phylo.Comparison: this is a gapped PID calculation
PID(String, String, int, int) - Static method in class org.biojava.nbio.phylo.Comparison
ping(String, int) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils: Pings a HTTP URL.
PlainFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io: The plain fasta header takes everything in the header as a single entity.
PlainFastaHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.PlainFastaHeaderParser
playOrientations() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientations
playOrientations() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientations
playOrientations() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
plus() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return location that is in same position on plus strand.
plus(Structure, Matrix) - Static method in class org.biojava.nbio.structure.Calc: calculate structure + Matrix coodinates ...
plus(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: C = A + B
plus(SparseSquareMatrix) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix: return C = A + B
plus(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseVector: Calcualtes return a + b
plusEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: A = A + B
Point - Interface in org.biojava.nbio.core.sequence.location.template: Holds a single point part of a location
Point.Resolver<T extends Point> - Interface in org.biojava.nbio.core.sequence.location.template: Used to resolve a position about a point
poissonDistance(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The Poisson (correction) evolutionary distance (d) is a function of the fractional dissimilarity (D), given by:
Polyhedron - Interface in org.biojava.nbio.structure.symmetry.geometry
PolymerType - Enum in org.biojava.nbio.structure.io.mmcif.chem: Enumerates the classification of polymers.
polymerType - Variable in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType: The associated PolymerType
polymerTypeFromString(String) - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType
POLYNUCLEOTIDE_ONLY - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType: Convenience Set of polymer types classified as DNA.
populate(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: Loops through the Compounds in a Sequence and passes them onto BitSequenceReader.BitArrayWorker.setCompoundAt(Compound, int)
populate(String) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: Loops through the chars in a String and passes them onto BitSequenceReader.BitArrayWorker.setCompoundAt(char, int)
populateMaps() - Method in class org.biojava.nbio.aaproperties.xml.ElementTable: Populate the Maps for quick retrieval
PositionInQueueXMLConverter - Class in org.biojava.nbio.structure.align.xml
PositionInQueueXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.PositionInQueueXMLConverter
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
positionSelected(AlignedPosition) - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
postProcess(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
postProcessAlignment(AFPChain, Atom[], Atom[], CECalculator) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain: Circular permutation specific code to be run after the standard CE alignment
postProcessAlignment(AFPChain, Atom[], Atom[], CECalculator, CECPParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain: Circular permutation specific code to be run after the standard CE alignment
postProcessCompoundLists(List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
postProcessCompoundLists(List<List<NucleotideCompound>>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
postProcessCompoundLists(List<List<AminoAcidCompound>>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator: Performs the trimming of stop codons and the conversion of a valid start amino acid to M
postQuery(String) - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists: post am XML query (PDB XML query format) to the RESTful RCSB web service
PredictDisorder - Class in demo
PredictDisorder() - Constructor for class demo.PredictDisorder
prefetchStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: Download a structure, but don't parse it yet or store it in memory.
prefix(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location: The part of this location before the specified position.
prefix(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: The part of this location before the other location (not inclusive).
prepareGroupsForDisplay(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
prepareGroupsForDisplay(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay: Rotate the Atoms/Groups so they are aligned for the 3D visualisation
prepareURLConnection(String, int) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils: Prepare URLConnection with customised timeouts.
PrettyXMLWriter - Class in org.biojava.nbio.core.util: Implementation of XMLWriter which emits nicely formatted documents to a PrintWriter.
PrettyXMLWriter(PrintWriter) - Constructor for class org.biojava.nbio.core.util.PrettyXMLWriter
PRIME - Static variable in class org.biojava.nbio.core.util.Hashcoder: The prime number used to multiply any calculated hashcode seed by i.e.
print(String, File) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Prints string to file.
print(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
print(String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Prints some textual content in an element.
print(Graphics, PageFormat, int) - Method in class org.biojava.nbio.structure.align.gui.JPrintPanel
PRINT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
print(int, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Print the matrix to stdout.
print(PrintWriter, int, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Print the matrix to the output stream.
print(NumberFormat, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Print the matrix to stdout.
print(PrintWriter, NumberFormat, int) - Method in class org.biojava.nbio.structure.jama.Matrix: Print the matrix to the output stream.
print(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Print an array of doubles to standard output.
print(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Print the M-by-N array of doubles to standard output.
print(int[]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Print an array of ints to standard output.
print(int[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Print the M-by-N array of ints to standard output.
print(boolean[]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Print an array of booleans to standard output.
print(boolean[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Print the M-by-N array of booleans to standard output.
printAboutMe() - Static method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
printAttributeValue(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
printChars(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
printDomainsForPDB() - Method in class demo.DemoSCOP
printDSSP() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc: Generate a DSSP file format ouput String of this SS prediction.
printDSSPline(int) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
printFASTA() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc: Generate a FASTA sequence with the SS annotation letters in the aminoacid sequence order.
printFastaSequence() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
printFastaSequence(long) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
printFull() - Method in class org.biojava.nbio.structure.ResidueNumber
printHelixSummary() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc: Generate a summary of this SS prediction with information about the three types of helix turns in different row sequences.
printHelp() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
printHelp() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
printHelp() - Method in interface org.biojava.nbio.structure.align.ce.UserArgumentProcessor: Print help about the arguments
printHelp() - Method in class org.biojava.nbio.structure.align.FarmJob
println(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
println(String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Prints some textual content, terminated with a newline character.
printRaw(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
printRaw(String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Send raw data to the stream.
PRINTS - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
printSymmetryAxes(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Generates a String that displays the symmetry axes of a structure.
printSymmetryGroup(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Given a symmetry alignment, it draws the symmetry group axes and the polyhedron box around the structure.
printTimeStamps - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
printXMLalignment(PrettyXMLWriter, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
printXMLblock(PrettyXMLWriter, Block) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
printXMLblockSet(PrettyXMLWriter, BlockSet) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
printXMLensemble(PrettyXMLWriter, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
printXMLEQRInferPositions(PrettyXMLWriter, AFPChain, int, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
printXMLHeader(PrettyXMLWriter, AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
printXMLheader(PrettyXMLWriter, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
printXMLmatrix4d(PrettyXMLWriter, Matrix4d) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
printXMLscoresCache(PrettyXMLWriter, ScoresCache) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
Prism - Class in org.biojava.nbio.structure.symmetry.geometry
Prism(int) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Prism
PROBABILITY - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
process() - Method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter
process() - Method in class org.biojava.nbio.core.sequence.io.FastaReader: The parsing is done in this method.
This method tries to process all the available fasta records in the File or InputStream, closes the underlying resource, and return the results in LinkedHashMap.
You don't need to call FastaReader.close() after calling this method.
process(int) - Method in class org.biojava.nbio.core.sequence.io.FastaReader: This method tries to parse maximum max records from the open File or InputStream, and leaves the underlying resource open.
Subsequent calls to the same method continue parsing the rest of the file.
This is particularly useful when dealing with very big data files, (e.g.
process() - Method in class org.biojava.nbio.core.sequence.io.FastaWriter
process() - Method in class org.biojava.nbio.core.sequence.io.GenbankReader: The parsing is done in this method.
This method tries to process all the available Genbank records in the File or InputStream, closes the underlying resource, and return the results in LinkedHashMap.
You don't need to call GenbankReader.close() after calling this method.
process(int) - Method in class org.biojava.nbio.core.sequence.io.GenbankReader: This method tries to parse maximum max records from the open File or InputStream, and leaves the underlying resource open.
Subsequent calls to the same method continue parsing the rest of the file.
This is particularly useful when dealing with very big data files, (e.g.
process() - Method in class org.biojava.nbio.core.sequence.io.GenbankWriter: Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option
process(String) - Method in interface org.biojava.nbio.core.sequence.io.util.IOUtils.ReaderProcessor
process(File, double, LinkedHashMap<String, GeneSequence>, OutputStream) - Method in class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
process(LinkedHashMap<String, ArrayList<String>>, LinkedHashMap<String, GeneSequence>, OutputStream) - Method in class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
process(File, File, File, double, double, boolean, boolean) - Method in class org.biojava.nbio.genome.query.OutputHitsGFF
process(String, String) - Method in class org.biojava.nbio.genome.uniprot.UniprotToFasta: Convert a Uniprot sequence file to a fasta file.
process(String[]) - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
process(String[]) - Method in interface org.biojava.nbio.structure.align.ce.UserArgumentProcessor: Process user arguments that have been provided from the command line
process() - Method in class org.biojava.nbio.structure.io.FastaStructureParser: Parses the fasta file and loads it into memory.
process(CoxInfo) - Static method in class org.biojava.nbio.survival.cox.CoxCC
process(String, String, String, String, String, String, ArrayList<String>, boolean, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxHelper
process(WorkSheet, String, String, String, String, String, ArrayList<String>, boolean, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxHelper
process(CoxMethod, ArrayList<SurvivalInfo>, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxMart
process(ArrayList<String>, ArrayList<SurvivalInfo>, boolean, boolean, boolean, boolean) - Method in class org.biojava.nbio.survival.cox.CoxR
process(ArrayList<String>, ArrayList<SurvivalInfo>, int, CoxMethod, double, double, double[], int, boolean, boolean, boolean, boolean) - Method in class org.biojava.nbio.survival.cox.CoxR
process(CoxMethod, ArrayList<SurvivalInfo>, CoxInfo, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxScore
process(CoxInfo, ResidualsCoxph.Type, boolean, ArrayList<String>) - Static method in class org.biojava.nbio.survival.cox.ResidualsCoxph
process(CoxMethod, ArrayList<SurvivalInfo>, CoxInfo, boolean) - Static method in class org.biojava.nbio.survival.cox.stats.AgScore
process(double[][], int, double) - Static method in class org.biojava.nbio.survival.cox.stats.Cholesky2
process(double[][], int, double[][], int) - Static method in class org.biojava.nbio.survival.cox.stats.Chsolve2
process(double[][], double[], double) - Static method in class org.biojava.nbio.survival.cox.WaldTest
process(double[][], double[][], double) - Static method in class org.biojava.nbio.survival.cox.WaldTest
process(LinkedHashMap<String, ArrayList<CensorStatus>>, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
process(String, String, String, String, String, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
process(String, ArrayList<SurvivalInfo>, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
process(String, ArrayList<SurvivalInfo>, SurvFitKM.Method, SurvFitKM.Error, boolean, double, SurvFitKM.ConfType, SurvFitKM.ConfLower, Double, Double, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
process(WorkSheet, String, LinkedHashMap<String, String>, String, Double, ArrayList<MetaDataInfo>) - Static method in class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
process(WorkSheet, String) - Method in interface org.biojava.nbio.survival.kaplanmeier.metadata.DiscreteQuantizerInterface
process(WorkSheet, String) - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MeanQuantizer
processNucleotides(File, String, File) - Method in class org.biojava.nbio.genome.util.SplitFasta
processReader(BufferedReader, IOUtils.ReaderProcessor) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Takes in a reader and a processor, reads every line from the given file and then invokes the processor.
processStrataInfo(String, ArrayList<SurvivalInfo>, SurvFitKM.Method, SurvFitKM.Error, boolean, double, SurvFitKM.ConfType, SurvFitKM.ConfLower, Double, Double, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
processUnknownCompound(C, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: Since bit encoding only supports a finite number of bases it is more than likely when processing sequence you will encounter a compound which is not covered by the encoding e.g.
ProfeatProperties - Class in org.biojava.nbio.aaproperties.profeat: This is an adaptor class which enable the ease of generating profeat properties.
ProfeatProperties() - Constructor for class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
ProfeatPropertiesImpl - Class in org.biojava.nbio.aaproperties.profeat
ProfeatPropertiesImpl() - Constructor for class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
profile - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Profile<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a data structure for the results of sequence alignment.
Profile.StringFormat - Enum in org.biojava.nbio.core.alignment.template: List of output formats.
ProfilePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a data structure for the results of the alignment of a pair of Profiles.
ProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an Aligner for a pair of Profiles.
ProfileProfileScorer<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes a score for a pairing of alignment profiles.
ProfileView<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a data structure for a view of sequence alignment.
Program - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
Program() - Constructor for class org.biojava.nbio.structure.validation.Program
program - Variable in class org.biojava.nbio.structure.validation.Programs
Programs - Class in org.biojava.nbio.structure.validation: Java class for anonymous complex type.
Programs() - Constructor for class org.biojava.nbio.structure.validation.Programs
programs - Variable in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
properties - Variable in class org.biojava.nbio.structure.validation.Program
propertiesAllocated() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation: A convenience method to see if we have allocated the properties Map.
propertiesAllocated() - Method in class org.biojava.nbio.ontology.utils.SmallAnnotation
PROSITE - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
PROSITE_PROFILE - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
PROTEIN_ONLY - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType: Convenience Set of polymer types classified as protein.
ProteinChainExtractor - Class in org.biojava.nbio.structure.symmetry.core: Extracts information about all the chains in a structure, including chain Ids, sequences, and atoms.
ProteinChainExtractor(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
ProteinComplexSignature - Class in org.biojava.nbio.structure.symmetry.misc
ProteinComplexSignature(String, List<String>, BlastClustReader) - Constructor for class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
proteinCreator(SequenceCreatorInterface<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
ProteinModification - Interface in org.biojava.nbio.protmod: This interface defines information about a specific protein modification.
ProteinModificationIdentifier - Class in org.biojava.nbio.protmod.structure: Identify attachment modification in a 3-D structure.
ProteinModificationIdentifier() - Constructor for class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
ProteinModificationImpl - Class in org.biojava.nbio.protmod: This class contains information about a specific protein modification.
ProteinModificationImpl.Builder - Class in org.biojava.nbio.protmod: Uses Builder pattern to build a ProteinModification.
ProteinModificationRegistry - Class in org.biojava.nbio.protmod: This class serves as a instance registry by maintaining a pool of ProteinModification instances.
ProteinModificationRegistry() - Constructor for class org.biojava.nbio.protmod.ProteinModificationRegistry
ProteinModificationXmlReader - Class in org.biojava.nbio.protmod.io
ProteinSequence - Class in org.biojava.nbio.core.sequence: The representation of a ProteinSequence
ProteinSequence(String) - Constructor for class org.biojava.nbio.core.sequence.ProteinSequence: Create a protein from a string
ProteinSequence(String, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.ProteinSequence: Create a protein from a string with a user defined set of amino acids
ProteinSequence(ProxySequenceReader<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.ProteinSequence: A protein sequence where the storage of the sequence is somewhere else.
ProteinSequence(ProxySequenceReader<AminoAcidCompound>, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.ProteinSequence: A protein sequence where the storage of the sequence is somewhere else with user defined set of amino acids.
ProteinSequenceClusterer - Class in org.biojava.nbio.structure.symmetry.core: Represents a set of non-identical protein sequences.
ProteinSequenceClusterer(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
ProteinSequenceClusterer(Structure, Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
ProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io: Used to create a ProteinSequence from a String to allow for details about the location of the sequence etc.
ProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
ProxySequenceReader<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
psi - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
PUBMED_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
purgeTempFiles(String) - Static method in class org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider: Cleanup chemical component (.cif.gz) files downloaded to tmpdir.
put(K, V) - Method in class org.biojava.nbio.core.util.SoftHashMap: Here we put the key, value pair into the HashMap using a SoftValue object.
put(Object, Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap
put(Object, Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
put(Double, Color) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper: Adds a gradient endpoint at the specified position.
put(int, int, double) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix: set A[i][j] = value
put(int, double) - Method in class org.biojava.nbio.structure.math.SparseVector: Setter method (should it be renamed to set?)
put(Key, Value) - Method in class org.biojava.nbio.structure.math.SymbolTable: Put key-value pair into the symbol table.
putAll(Map<? extends Double, ? extends Color>) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
putCoxInfo(String, CoxInfo) - Method in class org.biojava.nbio.survival.cox.CoxVariables
putScore(String, Double) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
putScore(String, Double) - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache: Add a score to the list of scores.

Q

Q - Static variable in class org.biojava.nbio.aaproperties.Constraints

Q - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc

constant for electrostatic energy

qr() - Method in class org.biojava.nbio.structure.jama.Matrix

QR Decomposition

QRDecomposition - Class in org.biojava.nbio.structure.jama

QR Decomposition.

QRDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.QRDecomposition

QR Decomposition, computed by Householder reflections.

Qualifier - Class in org.biojava.nbio.core.sequence.features

Qualifier(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.Qualifier

Qualifier(String, String, boolean) - Constructor for class org.biojava.nbio.core.sequence.features.Qualifier

QUALIFIER_INDENT - Static variable in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

QUALIFIER_INDENT_STR - Static variable in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

QUALIFIER_INDENT_TMP - Static variable in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

quality(int) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Convert the specified quality score to a quality in ASCII format.

quality(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this listener of a quality line.

QualityFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features

DNA Sequences produced by modern sequencers usually have quality informaion attached to them.

QualityFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.QualityFeature

qualityScore(char) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Convert the specified quality in ASCII format to a quality score.

qualityScore(double) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Convert the specified error probability to a quality score.

qualityScores(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Return the quality scores from the specified FASTQ formatted sequence.

qualityScores(Fastq, int[]) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Copy the quality scores from the specified FASTQ formatted sequence into the specified int array.

QuantityFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features

It is common to have a numerical value or values associated with a feature.

QuantityFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.QuantityFeature

QuatSuperpositionScorer - Class in org.biojava.nbio.structure.symmetry.core

QuatSuperpositionScorer() - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer

QuatSymmetryDetector - Class in org.biojava.nbio.structure.symmetry.core

Detects global and local quaternary protein structure symmetry in a structure.

QuatSymmetryDetector(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector

QuatSymmetryParameters - Class in org.biojava.nbio.structure.symmetry.core

QuatSymmetryParameters() - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

QuatSymmetryResults - Class in org.biojava.nbio.structure.symmetry.core

Holds the results of quaternary symmetry perception.

QuatSymmetryResults(Subunits, RotationGroup, String) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

QuatSymmetryResults(Subunits, HelixLayers, String) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

QuatSymmetryScores - Class in org.biojava.nbio.structure.symmetry.core

QuatSymmetryScores() - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

QuatSymmetrySolver - Interface in org.biojava.nbio.structure.symmetry.core

QueryIndexComparator() - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator

quickSort(String[], int, int) - Static method in class org.biojava.nbio.structure.align.gui.SystemInfo

Stripped-down QuickSort.

R

R - Static variable in class org.biojava.nbio.aaproperties.Constraints

RAINBOW_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper

RAINBOW_INTENSITY_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper

rama - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

random(int, int) - Static method in class org.biojava.nbio.structure.jama.Matrix

Generate matrix with random elements

random(int, int) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix

randomlyDivideSave(double, String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet

Split a worksheet randomly.

randomPick(Collection<Number>) - Static method in class org.biojava.nbio.structure.align.util.CollectionTools

Range(int, int, float) - Constructor for class org.biojava.nbio.ronn.Jronn.Range

RANGE_REGEX - Static variable in class org.biojava.nbio.structure.ResidueRange

rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay

rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

rangeSelected(AlignedPosition, AlignedPosition) - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener

rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener

rank() - Method in class org.biojava.nbio.structure.jama.Matrix

Matrix rank

rank() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition

Effective numerical matrix rank

RasmolCommandListener - Class in org.biojava.nbio.structure.align.gui.jmol

a utility class that listens to Ramsol script commands in the @link BiojavaJmol class

RasmolCommandListener(JmolPanel, JTextField) - Constructor for class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener

RasmolCommandListener - Class in org.biojava.nbio.structure.gui

Deprecated.
use org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener instead

RasmolCommandListener(JmolPanel, JTextField) - Constructor for class org.biojava.nbio.structure.gui.RasmolCommandListener

Deprecated.

RATIO_GAPS_FOR_MISMATCH - Static variable in class org.biojava.nbio.structure.io.CompoundFinder

Above this ratio of mismatching residue types for same residue numbers we consider the 2 chains to have mismatching residue numbers and warn about it

RATIO_RESIDUES_TO_TOTAL - Static variable in class org.biojava.nbio.structure.StructureTools

Below this ratio of aminoacid/nucleotide residues to the sequence total, we use simple majority of aminoacid/nucleotide residues to decide the character of the chain (protein/nucleotide)

RawBioUnitDataProvider - Interface in org.biojava.nbio.structure.quaternary.io

Defines the methods that have to be implemented by a class that provides the data that is necessary to recreate the correct biological assembly of a protein.

RCSBDescription - Class in org.biojava.nbio.structure.rcsb

Corresponds to the wrapper element in an RCSB describeMol XML file.

RCSBDescription() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBDescription

RCSBDescriptionFactory - Class in org.biojava.nbio.structure.rcsb

Fetches information from RCSB's RESTful Web Service Interface.

RCSBDescriptionFactory() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory

RCSBLigand - Class in org.biojava.nbio.structure.rcsb

Corresponds to a ligand in a ligandInfo XML file.

RCSBLigand() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBLigand

RCSBLigands - Class in org.biojava.nbio.structure.rcsb

Corresponds to the wrapper element "ligandInfo" in an RCSB ligandInfo XML file.

RCSBLigands() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBLigands

RCSBLigandsFactory - Class in org.biojava.nbio.structure.rcsb

Fetches information from RCSB's RESTful Web Service Interface.

RCSBLigandsFactory() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory

RCSBMacromolecule - Class in org.biojava.nbio.structure.rcsb

Corresponds to a macromolecule in an RCSB describeMol XML file.

RCSBMacromolecule() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBMacromolecule

RCSBPolymer - Class in org.biojava.nbio.structure.rcsb

Corresponds to a polymer in a describeMol XML file.

RCSBPolymer() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBPolymer

RCSBTaxonomy - Class in org.biojava.nbio.structure.rcsb

Corresponds to a taxonomy in a describeMol XML file.

RCSBTaxonomy(String, int) - Constructor for class org.biojava.nbio.structure.rcsb.RCSBTaxonomy

RCSBUpdates - Class in org.biojava.nbio.structure.rcsb

RCSBUpdates() - Constructor for class org.biojava.nbio.structure.rcsb.RCSBUpdates

read() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Reads a single character.

read(char[], int, int) - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Reads characters into a portion of an array.

read() - Method in class org.biojava.nbio.core.util.UncompressInputStream

read(byte[], int, int) - Method in class org.biojava.nbio.core.util.UncompressInputStream

read(String) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader

Read a file into a FeatureList.

read(String) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader

Read a file into a FeatureList.

read(String, List<String>) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Reader

Read a file into a FeatureList.

read(String) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Reader

read() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser

Method reads 1 nucleotide from sequence stream.

read(File) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqReader

Read zero or more FASTQ formatted sequences from the specified file.

read(URL) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqReader

Read zero or more FASTQ formatted sequences from the specified url.

read(InputStream) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqReader

Read zero or more FASTQ formatted sequences from the specified input stream.

read(BufferedReader) - Static method in class org.biojava.nbio.structure.jama.Matrix

Read a matrix from a stream.

readableFiles - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

readCSV(String, char) - Static method in class org.biojava.nbio.survival.data.WorkSheet

Read a CSV/Tab delimitted file where you pass in the delimiter

readCSV(File, char) - Static method in class org.biojava.nbio.survival.data.WorkSheet

readCSV(InputStream, char) - Static method in class org.biojava.nbio.survival.data.WorkSheet

Read a CSV/Tab delimited file where you pass in the delimiter

readFasta(InputStream) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

Reads fasta sequences from inStream into the list of FastaSequence objects

readFastaDNASequence(File, boolean) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper

Selecting lazySequenceLoad=true will parse the FASTA file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.

readFastaDNASequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper

Read a fasta DNA sequence

readFastaDNASequence(File) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper

readFastaProteinSequence(File) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper

Read a fasta file containing amino acids with setup that would handle most cases.

readFastaProteinSequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper

Read a fasta file containing amino acids with setup that would handle most cases.

readGenbankDNASequence(File, boolean) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.

readGenbankDNASequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

Read a Genbank DNA sequence

readGenbankDNASequence(File) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

readGenbankProteinSequence(File, boolean) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.

readGenbankProteinSequence(File) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

Read a Genbank file containing amino acids with setup that would handle most cases.

readGenbankProteinSequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

Read a Genbank file containing amino acids with setup that would handle most cases.

readLine() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Reads a line of text.

readQuotedString(String, int, int, char, boolean, boolean) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

readResolve() - Method in class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder

readStructure(String, int) - Static method in class demo.DemoShowLargeAssembly

Load a specific biological assembly for a PDB entry

ReadUtils - Class in org.biojava.nbio.structure.rcsb

Package-level static utilities for parsing XML.

ReadUtils() - Constructor for class org.biojava.nbio.structure.rcsb.ReadUtils

ready() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Tells whether this stream is ready to be read.

rebuildAFPChain(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser

replace the PDB res nums with atom positions:

rebuildQuaternaryStructure(Structure, List<BiologicalAssemblyTransformation>) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder

RectangularPrism - Class in org.biojava.nbio.structure.symmetry.geometry

RectangularPrism(double, double, double) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism

RED_BLUE_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper

reduce(Structure) - Method in class org.biojava.nbio.structure.align.client.StructureName

reduce(Structure) - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier

reduce(Structure) - Method in class org.biojava.nbio.structure.cath.CathDomain

reduce(Structure) - Method in class org.biojava.nbio.structure.domain.PDPDomain

reduce(Structure) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

reduce(Structure) - Method in class org.biojava.nbio.structure.PassthroughIdentifier

reduce(Structure) - Method in class org.biojava.nbio.structure.scop.ScopDomain

reduce(Structure) - Method in interface org.biojava.nbio.structure.StructureIdentifier

Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.

reduce(Structure) - Method in class org.biojava.nbio.structure.SubstructureIdentifier

Takes a complete structure as input and reduces it to residues present in the specified ranges

reduce(Structure) - Method in class org.biojava.nbio.structure.URLIdentifier

ReducedChemCompProvider - Class in org.biojava.nbio.structure.io.mmcif

Unlike the DownloadChemCompProvider, this ChemCompProvider does not download any chem comp definitions.

ReducedChemCompProvider() - Constructor for class org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider

reduceFragments(List<FragmentPair>, FragmentPair, Matrix) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

In helices often many similar fragments can be found.

reduceInitialFragments() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

if this is set to false, the time spent to joint the initial fragments (step 2) is increased.

REF_RMSD - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

REFERENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

ReferenceSuperimposer - Class in org.biojava.nbio.structure.align.multiple.util

Superimposes each structure in a MultipleAlignment onto a reference structure.

ReferenceSuperimposer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer

Default Constructor.

ReferenceSuperimposer(int) - Constructor for class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer

Constructor using a specified structure as reference.

refine(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

Refinement procedure based on superposition and dynamic programming.

Refine - Class in org.biojava.nbio.structure.io.mmcif.model

Refine() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Refine

refine(AFPChain, Atom[], int) - Method in class org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner

refine(AFPChain, Atom[], int) - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

refine(AFPChain, Atom[], int) - Method in interface org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner

Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.

RefinerFailedException - Exception in org.biojava.nbio.structure.symmetry.internal

Refinement of the self-alignment failed.

RefinerFailedException() - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

RefinerFailedException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

RefinerFailedException(String) - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

RefinerFailedException(Throwable) - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

refineSymmetry(AFPChain, Atom[], Atom[], int) - Static method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

Refines a CE-Symm alignment so that it is perfectly symmetric.

refineSymmetry(Map<Integer, Integer>, int) - Static method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

Refines a CE-Symm alignment so that it is perfectly symmetric.

REFLEXIVE - Static variable in class org.biojava.nbio.ontology.OntoTools

refmacVersion - Variable in class org.biojava.nbio.structure.validation.Entry

refp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

refRange - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

REFTM_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

register(ProteinModification) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

Register a new ProteinModification.

registerProteinModificationFromXml(InputStream) - Static method in class org.biojava.nbio.protmod.io.ProteinModificationXmlReader

Read protein modifications from XML file and register them.

REGULATORY - Static variable in class org.biojava.nbio.phosphosite.Dataset

REL_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

RELATED_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym

RELATION - Static variable in class org.biojava.nbio.ontology.OntoTools

RELATIONSHIP - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

relativePercentileClashscore - Variable in class org.biojava.nbio.structure.validation.Entry

relativePercentileDCCRfree - Variable in class org.biojava.nbio.structure.validation.Entry

relativePercentilePercentRamaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry

relativePercentilePercentRotaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry

relativePercentilePercentRSRZOutliers - Variable in class org.biojava.nbio.structure.validation.Entry

relativePercentileRNAsuiteness - Variable in class org.biojava.nbio.structure.validation.Entry

reloadFromFile() - Method in class org.biojava.nbio.structure.domain.SerializableCache

remainder() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator

Get portion of bounding location that has not yet been retrieved by next() method.

remark800toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.Site

Appends the REMARK 800 section pertaining to the site onto the end of the StringBuffer provided.

remark800toPDB() - Method in class org.biojava.nbio.structure.Site

Provides REMARK 800 section pertaining to the site as a string.

REMARK_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

RemoteBioUnitDataProvider - Class in org.biojava.nbio.structure.quaternary.io

RemoteBioUnitDataProvider() - Constructor for class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider

RemoteDomainProvider - Class in org.biojava.nbio.structure.domain

A DomainProvider that uses a mixture of SCOP and PDP domains.

RemoteDomainProvider() - Constructor for class org.biojava.nbio.structure.domain.RemoteDomainProvider

RemoteDomainProvider(boolean) - Constructor for class org.biojava.nbio.structure.domain.RemoteDomainProvider

initialize this provider with caching enabled

RemoteHmmerScan - Class in org.biojava.nbio.ws.hmmer

Makes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence.

RemoteHmmerScan() - Constructor for class org.biojava.nbio.ws.hmmer.RemoteHmmerScan

RemotePairwiseAlignmentOutputProperties - Interface in org.biojava.nbio.ws.alignment

RemotePairwiseAlignmentOutputProperties: the simplest representation of an object capable of holding output formatting informations to be fed to a RemotePairwiseAlignmentService-implemented object.

RemotePairwiseAlignmentProperties - Interface in org.biojava.nbio.ws.alignment

RemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties.

RemotePairwiseAlignmentService - Interface in org.biojava.nbio.ws.alignment

This interface specifies minimal information needed to execute a pairwise alignment on a remote service.

RemotePDPProvider - Class in org.biojava.nbio.structure.domain

A class that provided PDP assignments that are loaded from a remote web server

RemotePDPProvider() - Constructor for class org.biojava.nbio.structure.domain.RemotePDPProvider

RemotePDPProvider(boolean) - Constructor for class org.biojava.nbio.structure.domain.RemotePDPProvider

remoteProviderClassName - Static variable in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory

RemoteRawBioUnitDataProvider - Class in org.biojava.nbio.structure.quaternary.io

A BioUnitDataProvider that fetches the symmetry operations via remote calls to servers from RCSB PDB

RemoteRawBioUnitDataProvider() - Constructor for class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider

RemoteScopInstallation - Class in org.biojava.nbio.structure.scop

A class that fetches information about SCOP from a remote data-source.

RemoteScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.RemoteScopInstallation

RemoteTerm - Interface in org.biojava.nbio.ontology

A term in another ontology.

RemoteTerm.Impl - Class in org.biojava.nbio.ontology

Simple in-memory implementation of a remote ontology term.

remove() - Method in class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator

remove(Object) - Method in class org.biojava.nbio.core.util.SoftHashMap

remove() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator

Unsupported.

remove() - Method in class org.biojava.nbio.structure.AtomIterator

does nothing.

remove() - Method in class org.biojava.nbio.structure.GroupIterator

does nothing .

remove(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper

removeAlgorithm(String) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory

Removes the specified algorithm from the list of options

removeAlignedSequence(S) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Remove a sequence

removeAlignmentOption(BlastAlignmentParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

Removes given parameter

removeCDS(String) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

Remove a CDS or coding sequence from the transcript sequence

removeExon(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence

Remove the exon sequence

removeFeature(FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Remove a feature from the sequence

removeGaps(ProteinSequence) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher

Removes all gaps ('-') from a protein sequence

removeGaps(T[][]) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher

Creates a new list consisting of all columns of gapped where no row contained a null value.

removeGeneSequence(String) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence

removeInterfacesBelowArea() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Removes from this interface list all interfaces with areas below the default cutoff area

removeInterfacesBelowArea(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Removes from this interface list all interfaces with areas below the given cutoff area

removeIntron(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence

Remove the intron by accession

removeMMcifConsumer(MMcifConsumer) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser

remove a single consumer from the parser

removeMMcifConsumer(MMcifConsumer) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

removeModels(Structure) - Static method in class org.biojava.nbio.structure.StructureTools

Remove all models from a Structure and keep only the first

removeNote(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

removeOutputOption(BlastOutputParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties

Removes given parameter

removeProperty(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

removeProperty(Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation

Delete a property.

removeRotation(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

removeSynonym(Object) - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm

removeSynonym(Object) - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

removeSynonym(Object) - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl

removeSynonym(Object) - Method in class org.biojava.nbio.ontology.Term.Impl

removeSynonym(Object) - Method in interface org.biojava.nbio.ontology.Term

Remove a synonym for this term.

removeSynonym(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl

removeTranscript(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence

Remove the transcript sequence from the gene

RenderStyle - Enum in org.biojava.nbio.structure.gui

repaint() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl

repaint() - Method in interface org.biojava.nbio.structure.gui.StructureViewer

repeatDescription(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this parse listener of a repeat description line.

replaceColumnValues(String, HashMap<String, String>) - Method in class org.biojava.nbio.survival.data.WorkSheet

Change values in a column where 0 = something and 1 = something different

replaceOptAln(int[][][], AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

It replaces an optimal alignment of an AFPChain and calculates all the new alignment scores and variables.

replaceOptAln(AFPChain, Atom[], Atom[], Map<Integer, Integer>) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Takes an AFPChain and replaces the optimal alignment based on an alignment map

replaceOptAln(AFPChain, Atom[], Atom[], int, int[], int[][][]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

RepresentativeXMLConverter - Class in org.biojava.nbio.structure.align.xml

RepresentativeXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.RepresentativeXMLConverter

requestingAlignmentsFromServer(int) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener

requestingAlignmentsFromServer(int) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener

requestingAlignmentsFromServer(int) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener

requestUserConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain

RescoreRefiner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template

Defines an algorithm which computes a new alignment Profile by rescoring all pairs in an alignment and realigning.

reset() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

Resets output fields; should be overridden to set max and min

reset() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner

reset() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner

reset() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Resets the stream to the most recent mark.

reset() - Method in class org.biojava.nbio.core.util.CRC64Checksum

reset() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser

Method resets current position to the begining of sequence stream.

reset() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

reset() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

reset() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams

Set the parameters to the default.

reset() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

reset() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

reset() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

reset() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

reset() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

reset() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator

reset() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator

resetDisplay() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

Return to the initial state of the alignment visualization.

resetDisplay() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol

resetDisplay() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol

resetModels() - Method in interface org.biojava.nbio.structure.Structure

Resets all models of this Structure

resetModels() - Method in class org.biojava.nbio.structure.StructureImpl

Resets all models of this Structure

ResidualsCoxph - Class in org.biojava.nbio.survival.cox

ResidualsCoxph() - Constructor for class org.biojava.nbio.survival.cox.ResidualsCoxph

ResidualsCoxph.Type - Enum in org.biojava.nbio.survival.cox

ResidueGroup - Class in org.biojava.nbio.structure.symmetry.internal

A ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis.

ResidueGroup(Set<Integer>) - Constructor for class org.biojava.nbio.structure.symmetry.internal.ResidueGroup

Create a ResidueGroup object from a maximally connected component.

residueNumber - Variable in class org.biojava.nbio.structure.HetatomImpl

ResidueNumber - Class in org.biojava.nbio.structure

Everything that is needed to uniquely describe a residue position

ResidueNumber() - Constructor for class org.biojava.nbio.structure.ResidueNumber

ResidueNumber(ResidueNumber) - Constructor for class org.biojava.nbio.structure.ResidueNumber

ResidueNumber(String, Integer, Character) - Constructor for class org.biojava.nbio.structure.ResidueNumber

ResidueRange - Class in org.biojava.nbio.structure

A chain, a start residue, and an end residue.

ResidueRange(String, String, String) - Constructor for class org.biojava.nbio.structure.ResidueRange

ResidueRange(String, ResidueNumber, ResidueNumber) - Constructor for class org.biojava.nbio.structure.ResidueRange

ResidueRangeAndLength - Class in org.biojava.nbio.structure

A chain, a start residue, and an end residue.

ResidueRangeAndLength(String, ResidueNumber, ResidueNumber, int) - Constructor for class org.biojava.nbio.structure.ResidueRangeAndLength

ResidueRangeAndLength(String, String, String, int) - Constructor for class org.biojava.nbio.structure.ResidueRangeAndLength

RESIDUES_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier

URL parameter specifying residue ranges to include, e.g.

ResidueType - Enum in org.biojava.nbio.structure.io.mmcif.chem

Enumerates the possible classifications of residues.

resizeArray(Object, int) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

Reallocates an array with a new size, and copies the contents of the old array to the new array.

resizeArray(Object, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Reallocates an array with a new size, and copies the contents of the old array to the new array.

resizeInnerPanel(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener

resname - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

resnum - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

resolve(T) - Method in interface org.biojava.nbio.core.sequence.location.template.Point.Resolver

resolveInt(int) - Method in class org.biojava.nbio.ontology.IntegerOntology

ResourceManager - Class in org.biojava.nbio.structure.align.util

A class that manages the Strings that are defined in the spice.properties file.

ResourceManager() - Constructor for class org.biojava.nbio.structure.align.util.ResourceManager

restypesNotcheckedForBondAngleGeometry - Variable in class org.biojava.nbio.structure.validation.Entry

Result - Class in org.biojava.nbio.core.search.io

This class models a search result.

Result(String, String, String, String, HashMap<String, String>, int, String, String, int, List<Hit>, Sequence) - Constructor for class org.biojava.nbio.core.search.io.Result

ResultFactory - Interface in org.biojava.nbio.core.search.io

Designed by Paolo Pavan.

reverse(int) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint

reverse(int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

reverse(int, int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

reverse(int) - Method in interface org.biojava.nbio.core.sequence.location.template.Point

Returns the equivalent position on the reverse strand

ReversedSequenceView<C extends Compound> - Class in org.biojava.nbio.core.sequence.views

For a given sequence this class will return the base at the reversed position i.e.

ReversedSequenceView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.views.ReversedSequenceView

reverseSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

Reverses and (if possible) complements the Sequence so as to represent the reverse strand (if one exists).

RFAM - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure

RG - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

RG1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

right - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure

RiskInfo - Class in org.biojava.nbio.survival.cox

RiskInfo() - Constructor for class org.biojava.nbio.survival.cox.RiskInfo

rms_dk_diag(double[], double[], int, int, int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools

Given distance matrix diagonals dk1, dk2, get the rmsd of a fpair.

RMSD - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

rmsd(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

rmsdMin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

rmsdThr - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

rmsdThrJoin - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

RNA_ONLY - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType

Convenience Set of polymer types classified as RNA.

rnaAminoAcidTranslator(RNAToAminoAcidTranslator) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

rnaCompounds(CompoundSet<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

RNACompoundSet - Class in org.biojava.nbio.core.sequence.compound

RNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.RNACompoundSet

rnaCreator(SequenceCreatorInterface<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

RNASequence - Class in org.biojava.nbio.core.sequence

RNASequence where RNACompoundSet are the allowed values

RNASequence(String) - Constructor for class org.biojava.nbio.core.sequence.RNASequence

Create a RNA sequence from a String

RNASequence(ProxySequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.RNASequence

Create a RNA aequence from a proxy reader

RNASequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.RNASequence

Create a RNA sequence from a string with a user defined RNA compound set

RNASequence(ProxySequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.RNASequence

Create a RNA sequence from a proxy reader and user defined RNA compound set

RNASequenceCreator - Class in org.biojava.nbio.core.sequence.io

Used to create a RNA sequence

RNASequenceCreator(CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.RNASequenceCreator

RnaSequenceView - Class in org.biojava.nbio.core.sequence.views

Attempts to do on the fly translation of RNA by not requesting the compounds until asked.

RnaSequenceView(Sequence<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.views.RnaSequenceView

RnaSequenceView(Sequence<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.views.RnaSequenceView

rnaSuiteness - Variable in class org.biojava.nbio.structure.validation.Entry

RNAToAminoAcidTranslator - Class in org.biojava.nbio.core.sequence.transcription

Takes a Sequence of NucleotideCompound which should represent an RNA sequence (RNASequence is good for this) and returns a list of Sequence which hold AminoAcidCompound.

RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound>, CompoundSet<NucleotideCompound>, CompoundSet<Table.Codon>, CompoundSet<AminoAcidCompound>, Table, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

Deprecated.
Retained for backwards compatability, setting RNAToAminoAcidTranslator.stopAtStopCodons to false

RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound>, CompoundSet<NucleotideCompound>, CompoundSet<Table.Codon>, CompoundSet<AminoAcidCompound>, Table, boolean, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

Deprecated.

RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound>, CompoundSet<NucleotideCompound>, CompoundSet<Table.Codon>, CompoundSet<AminoAcidCompound>, Table, boolean, boolean, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

RonnConstraint - Class in org.biojava.nbio.ronn

A collection of various constrain values used by RONN

RonnConstraint() - Constructor for class org.biojava.nbio.ronn.RonnConstraint

RonnConstraint.Threshold - Enum in org.biojava.nbio.ronn

rota - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

rotate(Atom[], double) - Method in class org.biojava.nbio.structure.align.util.RotationAxis

rotate(Atom, double[][]) - Static method in class org.biojava.nbio.structure.Calc

Rotate a single Atom aroud a rotation matrix.

rotate(Structure, double[][]) - Static method in class org.biojava.nbio.structure.Calc

Rotate a structure.

rotate(Group, double[][]) - Static method in class org.biojava.nbio.structure.Calc

Rotate a Group.

rotate(Atom, Matrix) - Static method in class org.biojava.nbio.structure.Calc

Rotate an Atom around a Matrix object.

rotate(Group, Matrix) - Static method in class org.biojava.nbio.structure.Calc

Rotate a group object.

rotate(Structure, Matrix) - Static method in class org.biojava.nbio.structure.Calc

Rotate a structure object.

rotate(Atom[], Matrix) - Static method in class org.biojava.nbio.structure.Calc

rotateHue(Color, float) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils

Rotate a color through HSB space

rotateJmol(Matrix) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel

Rotation - Class in org.biojava.nbio.structure.symmetry.core

Rotation() - Constructor for class org.biojava.nbio.structure.symmetry.core.Rotation

RotationAxis - Class in org.biojava.nbio.structure.align.util

Calculates the rotation axis for an alignment

RotationAxis(AFPChain) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis

Calculate the rotation axis for the first block of an AFPChain

RotationAxis(Atom, Atom, double) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis

Create a rotation axis from a vector, a point, and an angle.

RotationAxis(Matrix, Atom) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis

Determine the location of the rotation axis based on a rotation matrix and a translation vector

RotationAxis(Matrix4d) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis

Create a rotation axis from a Matrix4d containing a rotational component and a translational component.

RotationAxisAligner - Class in org.biojava.nbio.structure.symmetry.core

RotationAxisAligner(QuatSymmetryResults) - Constructor for class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner

RotationGroup - Class in org.biojava.nbio.structure.symmetry.core

RotationGroup() - Constructor for class org.biojava.nbio.structure.symmetry.core.RotationGroup

RotationSolver - Class in org.biojava.nbio.structure.symmetry.core

RotationSolver(Subunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.RotationSolver

rotMatrixToString(Matrix4d) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

roundToDecimals(double, int) - Static method in class org.biojava.nbio.aaproperties.Utils

Returns a value with the desired number of decimal places.

row - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

rscc - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

rsr - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

rsrz - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

run(String[]) - Static method in class org.biojava.nbio.aaproperties.CommandPrompt

run() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable

run() - Method in class org.biojava.nbio.structure.align.FarmJob

run() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc

run() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB

run() - Method in class org.biojava.nbio.structure.align.gui.GUIFarmJobRunnable

run() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface

run() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc

run() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

run() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc

run() - Method in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider

Do the actual loading of the dictionary in a thread.

run() - Method in class org.biojava.nbio.structure.symmetry.analysis.ScanSymmetry

run() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc

runOptimization(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer

run the optimization

runPairwiseScorers(List<PairwiseSequenceScorer<S, C>>) - Static method in class org.biojava.nbio.alignment.Alignments

Factory method to run a list of scorers concurrently.

runPDB(String, int) - Static method in class demo.DemoOrientBioAssembly

S

S - Static variable in class org.biojava.nbio.aaproperties.Constraints

s_min - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues

said - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

SandboxStyleStructureProvider - Class in org.biojava.nbio.structure.io

The "Sandbox" style of organizing files is to have a directory structure like below, i.e.

SandboxStyleStructureProvider() - Constructor for class org.biojava.nbio.structure.io.SandboxStyleStructureProvider

SangerFastqReader - Class in org.biojava.nbio.sequencing.io.fastq

Reader for FastqVariant.FASTQ_SANGER formatted sequences.

SangerFastqReader() - Constructor for class org.biojava.nbio.sequencing.io.fastq.SangerFastqReader

SangerFastqWriter - Class in org.biojava.nbio.sequencing.io.fastq

Writer for FastqVariant.FASTQ_SANGER formatted sequences.

SangerFastqWriter() - Constructor for class org.biojava.nbio.sequencing.io.fastq.SangerFastqWriter

save(OutputStream, char, boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet

SAVE_ALIGNMENT_XML - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator

saveCSV(String) - Method in class org.biojava.nbio.survival.data.WorkSheet

Save the worksheet as a csv file

savePNG(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure

savePNG(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure

savePNGKMNumRisk(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure

Combine the KM and Num risk into one image

saveSurvivalData(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure

Save data from survival curve to text file

saveTXT(String) - Method in class org.biojava.nbio.survival.data.WorkSheet

scalarProduct(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Scalar product (dot product).

scale(Atom, double) - Static method in class org.biojava.nbio.structure.Calc

Multiply elements of a by s

scale(double) - Method in class org.biojava.nbio.structure.math.SparseVector

Calculates alpha * a

scale(double[][], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix

scale(double[][], double) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix

SCALE_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel

ScaleableMatrixPanel - Class in org.biojava.nbio.structure.gui

A JPanel that can display the underlying distance matrix data of the protein structure alignment algorithm.

ScaleableMatrixPanel() - Constructor for class org.biojava.nbio.structure.gui.ScaleableMatrixPanel

ScaleableMatrixPanel.GradientRenderer - Class in org.biojava.nbio.structure.gui

A renderer for the the gradient dropdown menu at the top of scaleableMatrixPanes.

scaleAdd(double, Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Perform linear transformation s*X+B, and store the result in b

ScaledSubstitutionMatrix - Class in org.biojava.nbio.core.alignment.matrices

The biojava-alignment module represents substitution matrices with short values.

ScaledSubstitutionMatrix() - Constructor for class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

scaleEquals(Atom, double) - Static method in class org.biojava.nbio.structure.Calc

Multiply elements of a by s (in place)

scan(ProteinSequence) - Method in interface org.biojava.nbio.ws.hmmer.HmmerScan

scan(ProteinSequence) - Method in class org.biojava.nbio.ws.hmmer.RemoteHmmerScan

scan(ProteinSequence, URL) - Method in class org.biojava.nbio.ws.hmmer.RemoteHmmerScan

Scans a protein sequence for Pfam profile matches.

ScanSymmetry - Class in org.biojava.nbio.structure.symmetry.analysis

ScanSymmetry() - Constructor for class org.biojava.nbio.structure.symmetry.analysis.ScanSymmetry

SchemaGenerator - Class in org.biojava.nbio.aaproperties.xml

SchemaGenerator(String) - Constructor for class org.biojava.nbio.aaproperties.xml.SchemaGenerator

scid - Variable in class org.biojava.nbio.structure.validation.SymmClash

SCOP - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference

SCOP_DOWNLOAD - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation

SCOP_DOWNLOAD_ALTERNATE - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation

SCOP_VERSION - Static variable in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB

SCOPAutoSuggestProvider - Class in org.biojava.nbio.structure.align.gui.autosuggest

SCOPAutoSuggestProvider() - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider

ScopCategory - Enum in org.biojava.nbio.structure.scop

The various categories provided by SCOP.

ScopDatabase - Interface in org.biojava.nbio.structure.scop

General API how to interact with SCOP

ScopDescription - Class in org.biojava.nbio.structure.scop

Contains data from dir.des.scop.txt_1.75

ScopDescription() - Constructor for class org.biojava.nbio.structure.scop.ScopDescription

ScopDescriptions - Class in org.biojava.nbio.structure.scop.server

ScopDescriptions() - Constructor for class org.biojava.nbio.structure.scop.server.ScopDescriptions

ScopDomain - Class in org.biojava.nbio.structure.scop

Container for the information for a domain.

ScopDomain() - Constructor for class org.biojava.nbio.structure.scop.ScopDomain

ScopDomains - Class in org.biojava.nbio.structure.scop.server

ScopDomains() - Constructor for class org.biojava.nbio.structure.scop.server.ScopDomains

ScopFactory - Class in org.biojava.nbio.structure.scop

Controls the global ScopDatabase being used.

ScopFactory() - Constructor for class org.biojava.nbio.structure.scop.ScopFactory

ScopInstallation - Class in org.biojava.nbio.structure.scop

This class provides access to the SCOP protein structure classification.

ScopInstallation(String) - Constructor for class org.biojava.nbio.structure.scop.ScopInstallation

Create a new SCOP installation.

ScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.ScopInstallation

Create a new SCOP installation, downloading the file to "the right place".

ScopInstallationInstance - Class in org.biojava.nbio.structure.gui.util

ScopIOException - Exception in org.biojava.nbio.structure.scop

Indicates that an I/O error occurred with SCOP lazy initialization.

ScopIOException() - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException

ScopIOException(String) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException

ScopIOException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException

ScopIOException(Throwable) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException

ScopMirror - Class in org.biojava.nbio.structure.scop

Helper class to store paths to the four SCOP files The string "%s" is replaced with the version number.

ScopMirror(String, String, String, String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror

Specify all keys individually

ScopMirror(String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror

Specify a common root URL which is concatenated with individual filenames

ScopMirror(String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror

ScopMirror() - Constructor for class org.biojava.nbio.structure.scop.ScopMirror

Use default MRC location

ScopNode - Class in org.biojava.nbio.structure.scop

ScopNode() - Constructor for class org.biojava.nbio.structure.scop.ScopNode

ScopNodes - Class in org.biojava.nbio.structure.scop.server

ScopNodes() - Constructor for class org.biojava.nbio.structure.scop.server.ScopNodes

ScopSelectPanel - Class in org.biojava.nbio.structure.gui.util

ScopSelectPanel() - Constructor for class org.biojava.nbio.structure.gui.util.ScopSelectPanel

ScopSelectPanel(boolean) - Constructor for class org.biojava.nbio.structure.gui.util.ScopSelectPanel

scopVersion - Variable in class org.biojava.nbio.structure.scop.ScopInstallation

score - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

score() - Method in class org.biojava.nbio.genome.parsers.gff.Feature

Get score.

score - Variable in class org.biojava.nbio.ronn.Jronn.Range

Scorer - Interface in org.biojava.nbio.alignment.template

Defines an algorithm which computes a score.

scores - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

Dynamic programming score matrix The first dimension has the length of the first (query) sequence + 1 The second has the length of the second (target) sequence + 1 The third has length 1 for linear gap penalty and 3 for affine/constant gap (one each for match/substitution, deletion, insertion)

ScoresCache - Interface in org.biojava.nbio.structure.align.multiple

Interface for classes which implement a temporary cache for various numeric scores, e.g.

scoresToRanges(float[], float) - Static method in class org.biojava.nbio.ronn.Jronn

Convert raw scores to ranges.

scoringStrategy - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

scoringStrategy - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

scroll - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel

SearchIO - Class in org.biojava.nbio.core.search.io

Designed by Paolo Pavan.

SearchIO(File) - Constructor for class org.biojava.nbio.core.search.io.SearchIO

Build a SearchIO reader and tries to select the appropriate parser inspecting file extension.

SearchIO(File, ResultFactory) - Constructor for class org.biojava.nbio.core.search.io.SearchIO

Build a SearchIO reader and specify a ResultFactory object to be used for parsing

SearchIO(File, ResultFactory, double) - Constructor for class org.biojava.nbio.core.search.io.SearchIO

Build a SearchIO reader, specify a ResultFactory object to be used for parsing and filter hsp retrieved by a e-value threshold.

SEC_STRUC - Static variable in interface org.biojava.nbio.structure.Group

Group property key for secondary structure annotation

SecStrucCalc - Class in org.biojava.nbio.structure.secstruc

Calculate and assign the secondary structure (SS) to the Groups of a Structure object.

SecStrucCalc() - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucCalc

SecStrucElement - Class in org.biojava.nbio.structure.secstruc

A secondary structure element (SSE) is an object representing a block of sequential residues that share the same secondary structure type.

SecStrucElement(SecStrucType, ResidueNumber, ResidueNumber, int, int, String) - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucElement

Create a new SSE object.

SecStrucInfo - Class in org.biojava.nbio.structure.secstruc

Container for the secondary structure information of a single residue.

SecStrucInfo(Group, String, SecStrucType) - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucInfo

SecStrucState - Class in org.biojava.nbio.structure.secstruc

This class extends the basic container for secondary structure annotation, including all the information used in the DSSP algorithm.

SecStrucState(Group, String, SecStrucType) - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucState

SecStrucTools - Class in org.biojava.nbio.structure.secstruc

This class contains methods for obtaining and converting secondary structure information from BioJava Structures.

SecStrucTools() - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucTools

SecStrucType - Enum in org.biojava.nbio.structure.secstruc

This enum contains all of the secondary structure types found in the DSSP output.

SECTIONKEYNULL - Static variable in class org.biojava.nbio.core.exceptions.Messages

sectp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

SEED - Static variable in class org.biojava.nbio.core.util.Hashcoder

An initial value for a hashCode, to which we add contributions from fields.

Segment - Class in org.biojava.nbio.structure.domain.pdp

Segment() - Constructor for class org.biojava.nbio.structure.domain.pdp.Segment

SegmentComparator - Class in org.biojava.nbio.structure.domain.pdp

SegmentComparator() - Constructor for class org.biojava.nbio.structure.domain.pdp.SegmentComparator

select(WorkSheet, String) - Method in interface org.biojava.nbio.survival.kaplanmeier.figure.CensorStatusSelect

SELECT_EQR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator

selectByAttribute(String, String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Create a list of all features that include the specified attribute key/value pair.

selectByAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Create a list of all features that include the specified attribute key.

selectByGroup(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Create a list of all features that have the specified group id, as defined by the group() method of the features.

selectByType(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Create a list of all features that are of the specified type, as defined by the type() method of the features.

selectByUserData(String, Object) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Create a list of all features that include the specified key/value pair in their userMap().

selectByUserData(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Create a list of all features that include the specified key in their userMap().

selectElements(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper

Selection - Interface in org.biojava.nbio.structure.gui

SelectionImpl - Class in org.biojava.nbio.structure.gui

SelectionImpl() - Constructor for class org.biojava.nbio.structure.gui.SelectionImpl

selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay

selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

selectionLocked() - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener

selectionLocked() - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener

selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay

selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

selectionUnlocked() - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener

selectionUnlocked() - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener

SelectMultiplePanel - Class in org.biojava.nbio.structure.gui.util

A Text Panel that allows the user to specify multiple structure identifiers, space separated.

SelectMultiplePanel() - Constructor for class org.biojava.nbio.structure.gui.util.SelectMultiplePanel

SelectMultiplePanel(boolean) - Constructor for class org.biojava.nbio.structure.gui.util.SelectMultiplePanel

selectOverlapping(String, Location, boolean) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Create a list of all features that overlap the specified location on the specified sequence.

selectParentElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper

SelectPDBPanel - Class in org.biojava.nbio.structure.align.gui

A Panel that allows user to specify PDB & chain ID, as well as sub-ranges

SelectPDBPanel() - Constructor for class org.biojava.nbio.structure.align.gui.SelectPDBPanel

SelectPDBPanel(boolean) - Constructor for class org.biojava.nbio.structure.align.gui.SelectPDBPanel

selectSingleElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper

sendAFPChainToServer(String, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient

sendAlignmentRequest(Sequence<Compound>, RemotePairwiseAlignmentProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService

Converts given sequence to String and calls NCBIQBlastService.sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)

sendAlignmentRequest(int, RemotePairwiseAlignmentProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService

Converts given GenBank GID to String and calls NCBIQBlastService.sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)

sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService

Sends the Blast request via the Put command of the CGI-BIN interface.

sendAlignmentRequest(Sequence<Compound>, RemotePairwiseAlignmentProperties) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService

Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object

sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService

Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object

sendDeleteRequest(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService

Sends a delete request for given request id.

sendMultiAFPChainToServer(String, String, String) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient

sendMultiAFPChainToServer(String, String, String, String) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient

sendResultsToServer(List<String>) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable

sentResultsToServer(int, String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener

sentResultsToServer(int, String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener

sentResultsToServer(int, String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener

seq - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

seqArraySize(int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

seqFont - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel

SeqMisMatch - Interface in org.biojava.nbio.structure

Created by andreas on 9/11/15.

SeqMisMatchImpl - Class in org.biojava.nbio.structure

Created by andreas on 9/11/15.

SeqMisMatchImpl() - Constructor for class org.biojava.nbio.structure.SeqMisMatchImpl

seqname() - Method in class org.biojava.nbio.genome.parsers.gff.Feature

Get the sequence name.

seqname() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI

Get the sequence name.

SeqRes2AtomAligner - Class in org.biojava.nbio.structure.io

Aligns the SEQRES residues to the ATOM residues.

SeqRes2AtomAligner() - Constructor for class org.biojava.nbio.structure.io.SeqRes2AtomAligner

SEQRESRECORD - Static variable in interface org.biojava.nbio.structure.AminoAcid

Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.

Sequence<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template

Main interface for defining a collection of Compounds and accessing them using biological indexes

sequence(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this parse listener of a sequence line.

SEQUENCE_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel

SequenceAlignmentCluster - Class in org.biojava.nbio.structure.symmetry.core

Represents a cluster of equivalent sequences

SequenceAlignmentCluster(QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster

sequenceAndQualityLengthsMatch() - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length.

SequenceAsStringHelper<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage

This is a common method that can be used across multiple storage/proxy implementations to handle Negative strand and other interesting elements of sequence data.

SequenceAsStringHelper() - Constructor for class org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper

SequenceComparator - Class in org.biojava.nbio.core.sequence

Used to sort sequences

SequenceComparator() - Constructor for class org.biojava.nbio.core.sequence.SequenceComparator

SequenceCreatorInterface<C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template

SequenceDisplay - Class in org.biojava.nbio.structure.gui

A sequence display that can show the results of a protein structure alignment.

SequenceDisplay(StructurePairAligner) - Constructor for class org.biojava.nbio.structure.gui.SequenceDisplay

sequenceEquality(Sequence<C>, Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

A case-sensitive manner of comparing two sequence objects together.

sequenceEqualityIgnoreCase(Sequence<C>, Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

A case-insensitive manner of comparing two sequence objects together.

SequenceFileProxyLoader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader

This class represents the storage container of a sequence stored in a fasta file where the initial parsing of the file we store the offset and length of the sequence.

SequenceFileProxyLoader(File, SequenceParserInterface, long, int, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

SequenceFunctionOrderDetector - Class in org.biojava.nbio.structure.symmetry.internal

Calls Spencer's method for determining order.

SequenceFunctionOrderDetector() - Constructor for class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector

SequenceFunctionOrderDetector(int, float) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector

SequenceFunctionRefiner - Class in org.biojava.nbio.structure.symmetry.internal

Creates a refined alignment with the CE-Symm alternative self-alignment.

SequenceFunctionRefiner() - Constructor for class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

SequenceHeaderParserInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template

SequenceIterator(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator

SequenceLocation<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.location

A location in a sequence that keeps a reference to its parent sequence

SequenceLocation(int, int, S) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation

SequenceLocation(int, int, S, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation

SequenceLocation(int, int, S, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation

SequenceLocation(Point, Point, S, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation

SequenceMixin - Class in org.biojava.nbio.core.sequence.template

Provides a set of static methods to be used as static imports when needed across multiple Sequence implementations but inheritance gets in the way.

SequenceMixin() - Constructor for class org.biojava.nbio.core.sequence.template.SequenceMixin

SequenceMixin.SequenceIterator<C extends Compound> - Class in org.biojava.nbio.core.sequence.template

A basic sequence iterator which iterates over the given Sequence by biological index.

SequenceMouseListener - Class in org.biojava.nbio.structure.gui.util

a mouse listener for the AbstractChainRenderer class it listens to all mouse events and triggeres appropriate SequenceListener and FeatureListener events

SequenceMouseListener(SequenceDisplay) - Constructor for class org.biojava.nbio.structure.gui.util.SequenceMouseListener

SequenceOptimizationHints - Class in org.biojava.nbio.core.sequence

A static class that provides optimization hints for memory or performance handling of sequence data.

SequenceOptimizationHints() - Constructor for class org.biojava.nbio.core.sequence.SequenceOptimizationHints

SequenceOptimizationHints.SequenceCollection - Enum in org.biojava.nbio.core.sequence

SequenceOptimizationHints.SequenceUsage - Enum in org.biojava.nbio.core.sequence

SequencePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template

Defines a data structure for the results of pairwise sequence alignment.

SequenceParserInterface - Interface in org.biojava.nbio.core.sequence.io.template

SequenceProxyView<C extends Compound> - Class in org.biojava.nbio.core.sequence.template

SequenceProxyView() - Constructor for class org.biojava.nbio.core.sequence.template.SequenceProxyView

SequenceProxyView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceProxyView

SequenceProxyView(Sequence<C>, Integer, Integer) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceProxyView

Main constructor for working with SequenceProxyViews

SequenceReader<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template

SequenceScalePanel - Class in org.biojava.nbio.structure.gui.util

A class that draws a Sequence as a rectangle, a scale display over it.

SequenceScalePanel(int) - Constructor for class org.biojava.nbio.structure.gui.util.SequenceScalePanel

SequenceTools - Class in org.biojava.nbio.core.util

SequenceTools() - Constructor for class org.biojava.nbio.core.util.SequenceTools

SequenceUtil - Class in org.biojava.nbio.data.sequence

Utility class for operations on sequences

SequenceView<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template

seqWeight - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

SerializableCache<K,V> - Class in org.biojava.nbio.structure.domain

A class that provides all that is necessary to create a Serializable Cache

SerializableCache(String) - Constructor for class org.biojava.nbio.structure.domain.SerializableCache

set cacheFileName to null to disable caching

serialize(File) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

serializedCache - Variable in class org.biojava.nbio.structure.domain.SerializableCache

serialVersionUID - Static variable in class org.biojava.nbio.structure.align.gui.ChooseDirAction

serialVersionUID - Static variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor

serialVersionUID - Static variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface

serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathDomain

serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathFragment

serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathNode

serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathSegment

serialVersionUID - Static variable in exception org.biojava.nbio.structure.io.PDBParseException

serialVersionUID - Static variable in exception org.biojava.nbio.structure.StructureException

serialVersionUID - Static variable in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties

serialVersionUID - Static variable in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties

SERVER_LOCATION - Static variable in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider

SERVICELOCATION - Static variable in class org.biojava.nbio.structure.rcsb.PdbIdLists

set(int, int, double) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a single element.

set(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP

set(Point3d[], Point3d[], double[]) - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP

setA(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setAAIndexProvider(AAIndexProvider) - Static method in class org.biojava.nbio.core.alignment.matrices.AAindexFactory

setAbsoluteMinimumSequenceLength(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setAbsolutePercentialRNAsuiteness(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

setAbsolutePercentileClashscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the absolutePercentileClashscore property.

setAbsolutePercentileDCCRfree(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

setAbsolutePercentilePercentRamaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the absolutePercentilePercentRamaOutliers property.

setAbsolutePercentilePercentRotaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the absolutePercentilePercentRotaOutliers property.

setAbsolutePercentilePercentRSRZOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the absolutePercentilePercentRSRZOutliers property.

setAbsorpt_coefficient_mu(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setAbsorpt_correction_T_max(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setAbsorpt_correction_T_min(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setAbsorpt_correction_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setAbsorpt_process_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setAcc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

setAccept1(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setAccept2(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setAcceptedAtomNames(String[]) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

By default the parser will read in all atoms (unless using the CAonly switch).

setAccession(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

The last accession passed to this routine will always be the one used.

setAccession(AccessionID) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setAccession(AccessionID) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setAccessionNr(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setAcentricOutliers(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the acentricOutliers property.

setAddress(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor

setAfpAftIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpBefIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAFPChain(AFPChain) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager

setAFPChain(AFPChain) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

setAfpChain(AFPChain) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

setAfpChainLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainList(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainTwiBin(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainTwiList(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainTwiNum(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpDisCut(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setAfpDisCut0(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setAfpIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpSet(List<AFP>) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Set the set of AFPs for this alignment.

setAlgorithm(StructureAlignment) - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB

setAlgorithm(StructureAlignment) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Caution has to be made when changing the algorithmName of an AFPChain, since downstream analysis methods (scores, display, etc) behave differently if the alignment is flexible (created with FatCat).

setAlgorithmName(String) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.

setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setAligMap(List<AlignedPosition>) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel

setAligMat(AligMatEl[][]) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setAligMat(int, int, AligMatEl) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setAligMat(AligMatEl[][]) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setAlign_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setAlign_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setAlign_se1(int[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setAlign_se1(int[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setAlign_se2(int[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setAlign_se2(int[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setAlignementOption(String, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

This method forwards to NCBIQBlastAlignmentProperties.setAlignmentOption(BlastAlignmentParameterEnum, String).

setAlignementOption(String, String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties

Method to set the value for a specific alignment parameter using a key to store in a map.

setAlignment(int[][][]) - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment

setAlignment1(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList

setAlignment2(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList

setAlignmentFractionThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setAlignmentJmol(AbstractAlignmentJmol) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

setAlignmentLengthFraction(double) - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment

setAlignmentMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setAlignmentNumber(int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties

Set the number of alignments to fetch

setAlignmentOption(BlastAlignmentParameterEnum, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

Sets the value of specified parameter

setAlignmentOutputFormat(BlastOutputAlignmentFormatEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties

Sets the alignment output format to get from the QBlast service

setAlignments(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

we only keep the first alternative...

setAlignPairs(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setAlignRes(List<List<Integer>>) - Method in interface org.biojava.nbio.structure.align.multiple.Block

Set the double List containing the aligned residues for each structure.

setAlignRes(List<List<Integer>>) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

setAlignScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlignScoreUpdate(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlignSeqRes(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.

setAliLenth(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

setAlnbeg1(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnbeg2(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnLength(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnseq1(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnseq2(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnsymb(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlpha(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setAlt_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setAltAligNumber(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setAltcode(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the altcode property.

setAlternativeAlignment(AlternativeAlignment) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay

setAlternativeAlignments(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame

setAlternativeAligs(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel

setAlternativeAligs(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel

setAltLoc(Character) - Method in interface org.biojava.nbio.structure.Atom

Set alternate Location.

setAltLoc(Character) - Method in class org.biojava.nbio.structure.AtomImpl

Set alternate Location.

setAltShortSymbol(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setAminoacid(List<AminoAcidComposition>) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable

setAminoType(Character) - Method in interface org.biojava.nbio.structure.AminoAcid

Set the name of the AA, in single letter code .

setAminoType(Character) - Method in class org.biojava.nbio.structure.AminoAcidImpl

Set the name of the AA, in single letter code .

setAnchors(int[]) - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner

Sets the starting list of anchors before running the alignment routine.

setAngle_alpha(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setAngle_alpha_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setAngle_beta(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setAngle_beta_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setAngle_gamma(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setAngle_gamma_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setAngleDiff(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setAngleThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setAniso_B(String[][]) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setAnnotation(Annotation) - Method in class org.biojava.nbio.ontology.Term.Impl

setAnnotationType(AbstractSequence.AnnotationType) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setApprovedName(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setApprovedSymbol(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setArchitectureId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setArchitectureName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setAsaC(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAsas(double[], double[], int, int, int) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setAsaU(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAssembly_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen

setAssemblyId(Long) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setAssignments(Map<String, String>) - Method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer

setAsym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setAsym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setAsym_id_list(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen

setAsymUnit(Structure) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider

setAsymUnit(Structure) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider

setAsymUnit(Structure) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider

setAsymUnit(Structure) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider

setAsymUnit(Structure) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider

setAtcc(String) - Method in class org.biojava.nbio.structure.Compound

setAtom(String) - Method in class org.biojava.nbio.structure.validation.Clash

Sets the value of the atom property.

setAtom(String) - Method in class org.biojava.nbio.structure.validation.SymmClash

Sets the value of the atom property.

setAtom0(String) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the atom0 property.

setAtom0(String) - Method in class org.biojava.nbio.structure.validation.BondOutlier

Sets the value of the atom0 property.

setAtom1(String) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the atom1 property.

setAtom1(String) - Method in class org.biojava.nbio.structure.validation.BondOutlier

Sets the value of the atom1 property.

setAtom2(String) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the atom2 property.

setAtom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setAtom_id_1(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setAtom_id_2(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setAtomArrays(List<Atom[]>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Sets the List of Atom arrays.

setAtomArrays(List<Atom[]>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setAtomAsaCs(List<Double>) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAtomAsaUs(List<Double>) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

setAtomCache(AtomCache) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider

Set an AtomCache to use when fetching asymmetric units.

setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider

setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider

setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider

setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider

setAtomCache(AtomCache) - Static method in class org.biojava.nbio.structure.StructureIO

setAtomCaThreshold(int) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.

setAtomGroups(List<Group>) - Method in interface org.biojava.nbio.structure.Chain

Set all Groups with observed density in the chain, i.e.

setAtomGroups(List<Group>) - Method in class org.biojava.nbio.structure.ChainImpl

Set all Groups with observed density in the chain, i.e.

setAtomicNumber(int) - Method in class org.biojava.nbio.aaproperties.xml.Element

setAtomLinkages(Set<StructureAtomLinkage>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

Set atom linkages

setAtomLinkages(Set<StructureAtomLinkage>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

setAtomName(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo

setAtoms(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

Create and set a new structure from a given atom array.

setAtoms(List<Atom>) - Method in interface org.biojava.nbio.structure.Group

Set the atoms of this group.

setAtoms(List<Atom>) - Method in class org.biojava.nbio.structure.HetatomImpl

Set the atoms of this group.

setAtoms(List<ChemCompAtom>) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setAtoms(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setAtoms(String) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the atoms property.

setAtoms(String) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the atoms property.

setAttemptedValidationSteps(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the attemptedValidationSteps property.

setAuth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setAuth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setAuth_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setAuth_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setAuth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setAuth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setAuth_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setAuth_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setAuth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setAuth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setAuth_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setAuth_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setAuthorList(List<Author>) - Method in class org.biojava.nbio.structure.JournalArticle

setAuthors(String) - Method in class org.biojava.nbio.structure.PDBHeader

setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Deprecated.
Use AtomCache.getFetchBehavior()

setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

Deprecated.
Use UserConfiguration.getFetchBehavior()

setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Deprecated.
Use #setFetchBehavior()

setAutoSuggestProvider(AutoSuggestProvider) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest

setAverageScore(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

setAvgoccu(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the avgoccu property.

setAxes(SymmetryAxes) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setAxisAngle(AxisAngle4d) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setAxisTransformation(RotationAxisAligner) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup

setAxisTypes(int[]) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setB(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setB_iso_max(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setB_iso_mean(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setB_iso_min(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setB_iso_or_equiv(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setB_iso_or_equiv_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setBadRmsd(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setBbs(Structure, Matrix4d[], boolean) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox

setBend(boolean) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setBeta(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setBetweenCompounds(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setBinaryOperators(List<OrderedPair<String>>) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver

setBioAssemblies(Map<Integer, BioAssemblyInfo>) - Method in class org.biojava.nbio.structure.PDBHeader

setBioBegin(Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setBioEnd(Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setBioEnd(Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

setBiol_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setBiologicalAssembly(boolean) - Method in interface org.biojava.nbio.structure.Structure

Set a flag to indicate if this structure is a biological assembly

setBiologicalAssembly(boolean) - Method in class org.biojava.nbio.structure.StructureImpl

Sets a flag to indicate if this structure is a biological assembly

setBiologicalUnit(String) - Method in class org.biojava.nbio.structure.Compound

setBioStart(Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

setBioUnitDataProvider(Class<? extends BioUnitDataProvider>) - Static method in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory

Set the type of provider to be created

setBioUnitDataProvider(String) - Static method in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory

Sets the data provider to the specified class name.

setBlastAdvancedOptions(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

This method is to be used if a request is to use non-default values at submission.

setBlastDatabase(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

Sets the database to be used with blastall

setBlastExpect(double) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

Sets the EXPECT parameter to be use with blastall

setBlastFromToPosition(int, int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

Sets the QUERY_FROM and QUERY_TO parameters to be use by blast.

setBlastGapCosts(int, int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

Sets the GAPCOSTS parameter

setBlastMatrix(BlastMatrixEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

Sets the value for the MATRIX parameter to use for blastall

setBlastProgram(BlastProgramEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

Sets the program to be used with blastall

setBlastWordSize(int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

Sets the WORD_SIZE parameter to be use with blastall

setBlock2Afp(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockGap(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockNum(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockNumClu(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockNumIni(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockNumSpt(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockResList(int[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockResSize(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockRmsd(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockRotationMatrix(Matrix[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlocks(List<Block>) - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Set the List of alignment Blocks of the BlockSet.

setBlocks(List<Block>) - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

setBlockScore(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockSet(BlockSet) - Method in interface org.biojava.nbio.structure.align.multiple.Block

Set the back-reference to its parent BlockSet.

setBlockSet(BlockSet) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

setBlockSets(List<BlockSet>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Sets the List of BlockSet List of the specified alignment.

setBlockSets(List<BlockSet>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

setBlockShiftVector(Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockSize(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setbondLengthTolerance(double) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

setBonds(List<Bond>) - Method in interface org.biojava.nbio.structure.Atom

Sets the bonds

setBonds(List<Bond>) - Method in class org.biojava.nbio.structure.AtomImpl

Sets the bonds

setBonds(List<ChemCompBond>) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setBravLattice(BravaisLattice) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setBridge1(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setBridge2(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setBulkSolventB(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the bulkSolventB property.

setBulkSolventK(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the bulkSolventK property.

setC(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setC1(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

setCa1Length(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setCa2(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

setCa2(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

setCa2Length(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setCache(AtomCache) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setCacheDoubleValues(boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet

setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setCacheLocation(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setCacheLocation(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Set an alternate download location for files

setCacheLocation(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

setCachePath(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

set the location at which utility data should be cached.

setCalculationTime(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setCalculationTime(Long) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the running time spent to calculate this alignment.

setCalculationTime(Long) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setCalculationTime(long) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setCallbackFunction(String, String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener

setCartn_x(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setCartn_x_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setCartn_y(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setCartn_y_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setCartn_z(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setCartn_z_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setCategory(String) - Method in class org.biojava.nbio.ontology.Synonym

setCategory(ModificationCategory) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

setCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setCATH(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setCath(CathDatabase) - Static method in class org.biojava.nbio.structure.cath.CathFactory

Sets the default (singleton) CathDatabase.

setCathDownloadUrl(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setCathVersion(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setCCP4Version(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the ccp4Version property.

setCdsEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

setCdsStart(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

setCell(String) - Method in class org.biojava.nbio.structure.Compound

setCell_setting(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry

setCellColor(ContinuousColorMapper) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel

setCellColor(ContinuousColorMapper) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel

setCellLine(String) - Method in class org.biojava.nbio.structure.Compound

setCellularLocation(String) - Method in class org.biojava.nbio.structure.Compound

setCenter1(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setCenter2(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setCentered(boolean) - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP

setCentricOutliers(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the centricOutliers property.

setChain(Chain) - Method in interface org.biojava.nbio.structure.Group

Sets the back-reference to its parent Chain.

setChain(Chain) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener

setChain(Chain) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel

setChain(Chain) - Method in class org.biojava.nbio.structure.HetatomImpl

Sets the back-reference to its parent Chain.

setChain(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the chain property.

setChain1(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setChain2(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setChainId(String) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

setChainId(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo

setChainID(String) - Method in interface org.biojava.nbio.structure.Chain

Sets the name of this chain (Chain id in PDB file ).

setChainID(String) - Method in class org.biojava.nbio.structure.ChainImpl

Sets the name of this chain (Chain id in PDB file ).

setChainId(String) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

setChainId(String) - Method in class org.biojava.nbio.structure.DBRef

The chain ID of the corresponding chain.

setChainId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setChainId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setChainId(String) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Sets the chain identified this transformation should be applied to.

setChainId(String) - Method in class org.biojava.nbio.structure.ResidueNumber

setChainID1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setChainID2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setChainLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setChainRmsd(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

The RMSD of the chain of AFPs.

setChains(List<Chain>) - Method in class org.biojava.nbio.structure.Compound

Set the chains for this Compound

setChains(List<Chain>) - Method in interface org.biojava.nbio.structure.Structure

Set the chains of a structure, if this is a NMR structure, this will only set model 0.

setChains(int, List<Chain>) - Method in interface org.biojava.nbio.structure.Structure

Set the chains for a model

setChains(List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the chains of a structure, if this is a NMR structure, this will only set model 0.

setChains(int, List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the chains for a model

setCharge(short) - Method in interface org.biojava.nbio.structure.Atom

Set the charge of this atom

setCharge(short) - Method in class org.biojava.nbio.structure.AtomImpl

setCharge(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.Group

Set the Chemical Component that closer describes this group.

setChemComp(ChemComp) - Method in class org.biojava.nbio.structure.HetatomImpl

setChemCompProvider(ChemCompProvider) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory

The new ChemCompProvider will be set in the static variable, so this provider will be used from now on until it is changed again.

setChildren(List<Integer>) - Method in class org.biojava.nbio.structure.scop.ScopNode

setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

Set the children features

setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Set the children features

setChrLoc(String) - Method in class org.biojava.nbio.phosphosite.Site

setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband

setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setChromosomeNumber(int) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence

setCid(BigInteger) - Method in class org.biojava.nbio.structure.validation.Clash

Sets the value of the cid property.

setCircular(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

Set the radius of a circumscribed sphere, that goes through all vertices

setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Set the radius of a circumscribed sphere, that goes through all vertices

setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

Set the radius of a circumscribed sphere, that goes through all vertices

setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Set the radius of a circumscribed sphere, that goes through all vertices

setClashmag(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Clash

Sets the value of the clashmag property.

setClashmag(BigDecimal) - Method in class org.biojava.nbio.structure.validation.SymmClash

Sets the value of the clashmag property.

setClashscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the clashscore property.

setClassId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setClassId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setClassification(String) - Method in class org.biojava.nbio.structure.PDBHeader

setClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setCluster(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

set the number of the cluster this alignment belongs to.

setCluster(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setCluster(StructureInterfaceCluster) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setClusterValue(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setCode(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper

setCoeff(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

setCoefficient(String, CoxCoefficient) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setCol(short) - Method in class org.biojava.nbio.structure.align.helper.IndexPair

setColor(Color) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl

setColor(Color) - Method in interface org.biojava.nbio.structure.gui.StructureViewer

Apply this color to the current Selection

setColorByBlocks(boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol

setColorSpace(ColorSpace, LinearColorInterpolator.InterpolationDirection[]) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator

Sets the ColorSpace to use for interpolation.

setColorSpace(ColorSpace) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator

setCols(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

setComment(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

setComment(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setCommon_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor

setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier

setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly

setComplexFeaturesAppendMode(InsdcParser.complexFeaturesAppendEnum) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser

setCompositionId(String) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

setCompound(Compound) - Method in interface org.biojava.nbio.structure.Chain

Sets the Compound

setCompound(Compound) - Method in class org.biojava.nbio.structure.ChainImpl

Sets the Compound

setCompoundAt(char, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Converts from char to Compound and sets it at the given biological index

setCompoundAt(C, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Sets the compound at the specified biological index

setCompounds(List<Compound>) - Method in interface org.biojava.nbio.structure.Structure

Set the Compounds

setCompounds(List<Compound>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the Compounds

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Class is immutable & so this is unsupported

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Unsupported

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setCompoundSet(CompoundSet<C>) - Method in interface org.biojava.nbio.core.sequence.template.SequenceReader

setCompoundSet(CompoundSet<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView

setCondition(ModificationCondition) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

setConn(Double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setConn_type_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setConnections(List<Map<String, Integer>>) - Method in interface org.biojava.nbio.structure.Structure

Deprecated.
use Atom.addBond(Bond) instead

setConnections(List<Map<String, Integer>>) - Method in class org.biojava.nbio.structure.StructureImpl

sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:

setContacts(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setContacts(AtomContactSet) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setContacts(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setContents(String) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

setContents(String) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

setContents(String, ArrayList) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

setContents(String) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

Once the sequence is retrieved set the contents and make sure everything this is valid

setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

setContents(List<C>) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Class is immutable & so this is unsupported

setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Unsupported

setContents(String) - Method in interface org.biojava.nbio.core.sequence.template.SequenceReader

setContents(String) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView

setContig(int) - Method in class org.biojava.nbio.structure.align.helper.AligMatEl

setConvergenceSteps(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setCoords(double[]) - Method in interface org.biojava.nbio.structure.Atom

Set the coordinates.

setCoords(double[]) - Method in class org.biojava.nbio.structure.AtomImpl

Set the coordinates.

setCorrelation_coeff_Fo_to_Fc(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setCorrelation_coeff_Fo_to_Fc_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setCovered(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setCoxInfo(ArrayList<String>, CoxInfo, String, LinkedHashMap<String, String>, Boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure

setCPPoint(Integer) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

setCreate_co(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setCreateAtomBonds(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should we create bonds between atoms when parsing a file.

setCreateAtomCharges(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should we create charges on atoms when parsing a file?

setCrystalCell(CrystalCell) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the crystal cell

setCrystallographicInfo(PDBCrystallographicInfo) - Method in class org.biojava.nbio.structure.PDBHeader

setCrystallographicInfo(PDBCrystallographicInfo) - Method in interface org.biojava.nbio.structure.Structure

Set crystallographic information for this structure

setCrystallographicInfo(PDBCrystallographicInfo) - Method in class org.biojava.nbio.structure.StructureImpl

Sets crystallographic information for this structure

setCrystals_number(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setCurrentSequence(String) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser

Method open nucleotide stream for sequence with given name.

setCurrentSequencePosition(long) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser

setCustomChain1(String) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

sets a chain in a custom, user provided file

setCustomFile1(String) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

set the file path for a custom, user provided file, not a standard PDB file.

setCut_sites(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

setCuts(int, AlignerHelper.Subproblem, AlignerHelper.Last[][], AlignerHelper.Cut[]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

setCutsPerSection(int) - Method in class org.biojava.nbio.alignment.routines.GuanUberbacher

Sets the number of cuts added to each section during each pass.

setData(List<String>) - Method in class org.biojava.nbio.structure.scop.server.ListStringWrapper

setData(TreeSet<String>) - Method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper

setData(TreeMap<Integer, SpaceGroup>) - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

setDataAnisotropy(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the dataAnisotropy property.

setDatabase(String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

setDatabase(String) - Method in class org.biojava.nbio.structure.DBRef

Specifies the database value.

setDatabaseReferences(List<Sequence>) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser

Intended for use with run module.

setDatabaseReferences(List<Sequence>) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser

setDatabaseReferences(List<Sequence>) - Method in interface org.biojava.nbio.core.search.io.ResultFactory

Specify the collection of sequences objects used as database in the Search run.

setDatabaseReferences(DatabaseReferenceInterface) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setDataCompleteness(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the dataCompleteness property.

setDate(Date) - Method in class org.biojava.nbio.structure.cath.CathDomain

setDate(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

setDate_original(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

setDb_align_beg(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setDb_align_end(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setDb_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setDb_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setDb_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setDbAccession(String) - Method in class org.biojava.nbio.structure.DBRef

Sequence database accession code.

setDbComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setDbFile(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setDbIdCode(String) - Method in class org.biojava.nbio.structure.DBRef

Sequence database identification code.

setDbReferences(Set<StockholmStructure.DatabaseReference>) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setDBRefs(List<DBRef>) - Method in interface org.biojava.nbio.structure.Structure

Set the list of database references for this structure

setDBRefs(List<DBRef>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the list of database references for this structure

setDbSeqBegin(int) - Method in class org.biojava.nbio.structure.DBRef

Initial sequence number of the database seqment.

setDbSeqEnd(int) - Method in class org.biojava.nbio.structure.DBRef

The begin of the sequence position in the database

setDCCR(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the dccr property.

setDCCRefinementProgram(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the dccRefinementProgram property.

setDCCRfree(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the dccRfree property.

setDcl(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

setDebug(boolean) - Method in class org.biojava.nbio.structure.align.StructurePairAligner

Deprecated.

setDefault() - Method in class org.biojava.nbio.structure.align.gui.ParameterGUI

setDefault() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

setDefaultColoring(String) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator

Sets a default Jmol script used for coloring.

setDefaultColoring(String) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH

setDefaultColoring(String) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup

setDefaultCutsPerSection(int) - Static method in class org.biojava.nbio.alignment.routines.GuanUberbacher

Sets the default number of cuts added to each section during each pass.

setDefaultExtensionPenalty(int) - Static method in class org.biojava.nbio.alignment.SimpleGapPenalty

Sets the default gap extension penalty.

setDefaultOpenPenalty(int) - Static method in class org.biojava.nbio.alignment.SimpleGapPenalty

Sets the default gap open penalty.

setDefaultText(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest

setDegreeFreedom(double) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setDensityCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDepDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader

setDesc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

setDescription(String) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

setDescription(String) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix

setDescription(String) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix

Sets the description of this matrix.

setDescription(String) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

setDescription(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

setDescription(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setDescription(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Set the description that can be used to describe the feature

setDescription(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

setDescription(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

setDescription(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setDescription(String) - Method in interface org.biojava.nbio.core.sequence.template.Compound

setDescription(String) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

setDescription(String) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

setDescription(String) - Method in class org.biojava.nbio.ontology.AbstractTerm

setDescription(String) - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm

setDescription(String) - Method in class org.biojava.nbio.ontology.IntegerOntology

setDescription(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl

setDescription(String) - Method in interface org.biojava.nbio.ontology.Ontology

set the description of this ontology

setDescription(String) - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

setDescription(String) - Method in interface org.biojava.nbio.ontology.Term

set the description of the term;

setDescription(String) - Method in class org.biojava.nbio.ontology.Triple.Impl

setDescription(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

setDescription(String) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

setDescription(String) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

setDescription(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setDescription(String) - Method in class org.biojava.nbio.structure.PDBHeader

setDescription(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setDescription(String) - Method in class org.biojava.nbio.structure.Site

sets the REMARK 800 description of the site

setDescription(String) - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface

setDescription(String) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator

setDescription2(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Set the textual description for protein 2.

setDescriptionNumber(int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties

Sets the number of descriptions to fetch

setDescriptor(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

setDescriptors(List<ChemCompDescriptor>) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setDetails(String) - Method in class org.biojava.nbio.structure.Compound

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setDetails(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setDetails(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setDf(int) - Method in class org.biojava.nbio.survival.cox.WaldTestInfo

setDiagonalDistance(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDiagonalDistance2(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDirection(int) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setDiscreteValues(WorkSheet) - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo

setDisCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setDisCut(double) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setDisFilter(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setDisSmooth(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setDist(int[][]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

setDist(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Clash

Sets the value of the dist property.

setDist(BigDecimal) - Method in class org.biojava.nbio.structure.validation.SymmClash

Sets the value of the dist property.

setDist1(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setDist1(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setDist2(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setDist2(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setDisTable1(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setDisTable2(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContact

setDistanceCutoff(Double) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setDistanceCutoff(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setDistanceIncrement(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setDistanceMatrix(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain

A matrix with ca1length rows and ca2length columns.

setDistanceMatrix(Matrix) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

The distance matrix this alignment is based on

setDNAType(DNASequence.DNAType) - Method in class org.biojava.nbio.core.sequence.DNASequence

setDoAngleCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDoDensityCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDoDistanceCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDoi(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of doi

setDomainCounter(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setDomainId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setDomainId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setDomainName(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setDomainProvider(DomainProvider) - Static method in class org.biojava.nbio.structure.domain.DomainProviderFactory

setDomains(SortedSet<HmmerDomain>) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

setDomainSplit(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setDonor1(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setDonor2(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setDoRMSCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDownloadAll(boolean) - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider

By default this provider will download only some of the ChemComp files.

setDuplicationHint(CECPParameters.DuplicationHint) - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

setDuplicationHint(CECPParameters.DuplicationHint) - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

setDVar(Double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setEcNums(List<String>) - Method in class org.biojava.nbio.structure.Compound

setEcodDatabase(String) - Static method in class org.biojava.nbio.structure.ecod.EcodFactory

Updates the default version

setEditorList(List<Author>) - Method in class org.biojava.nbio.structure.JournalArticle

setEDSR(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the edsr property.

setEDSResolution(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the edsResolution property.

setEDSResolutionLow(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the edsResolutionLow property.

setElement(List<Element>) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable

setElement(Element) - Method in interface org.biojava.nbio.structure.Atom

Set element of the atom name, e.g.

setElement(Element) - Method in class org.biojava.nbio.structure.AtomImpl

Set element of the atom name, e.g.

setElement1(T) - Method in class org.biojava.nbio.structure.quaternary.OrderedPair

Sets the first element of an ordered pair.

setElement2(T) - Method in class org.biojava.nbio.structure.quaternary.OrderedPair

Sets the second element of an ordered pair.

setEmail(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService

Set the email for QBlast.

setEnd(Point) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband

setEnd(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setEnergy(double) - Method in class org.biojava.nbio.structure.secstruc.HBond

setEngineered(String) - Method in class org.biojava.nbio.structure.Compound

setEnsemble(MultipleAlignmentEnsemble) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Set the back-reference to its parent Ensemble.

setEnsemble(MultipleAlignmentEnsemble) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

setEnsemblGeneId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setEnt(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the ent property.

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym

setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setEntityId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

setEntry(Entry) - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation

Sets the value of the entry property.

setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords

setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry

setEquivalent(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition

setEvalCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setEvalue(Float) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

setEvalue(Float) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

setEvCode(String) - Method in class org.biojava.nbio.structure.Site

sets the REMARK 800 EVIDENCE CODE for the site.

setExonCount(int) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

setExonEnds(List<Integer>) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

setExonStarts(List<Integer>) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

setExpectedExecutionTime(long) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob

setExperimentalTechnique(String) - Method in class org.biojava.nbio.structure.PDBHeader

Adds the experimental technique to the set of experimental techniques of this header.

setExpression_system_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setExpressionSystem(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemAtccNumber(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemCell(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemCellLine(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemCellularLocation(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemGene(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemOrgan(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemOrganelle(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemOtherDetails(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemPlasmid(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemStrain(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemTaxId(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemTissue(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemVariant(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemVector(String) - Method in class org.biojava.nbio.structure.Compound

setExpressionSystemVectorType(String) - Method in class org.biojava.nbio.structure.Compound

setExtensionPenalty(int) - Method in class org.biojava.nbio.alignment.SimpleGapPenalty

setExtensionPenalty(int) - Method in interface org.biojava.nbio.alignment.template.GapPenalty

Sets penalty given when an already open gap elongates by a single element

setFalseDiscoveryRate(float) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setFamilyId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setFarmJob(FarmJob) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener

setFeatureRetriever(FeatureRetriever) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setFeaturesKeyWord(FeaturesKeyWordInterface) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Set the behavior for fetching files from the server

setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Set the behavior for fetching files from the server.

setFetchCurrent(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Deprecated.
Use FileParsingParameters#setObsoleteBehavior() instead (4.0.0)

setFetchCurrent(boolean) - Method in class org.biojava.nbio.structure.io.PDBFileReader

Deprecated.
Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)

setFetchFileEvenIfObsolete(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Deprecated.
Use FileParsingParameters#setObsoleteBehavior() instead (4.0.0)

setFetchFileEvenIfObsolete(boolean) - Method in class org.biojava.nbio.structure.io.PDBFileReader

Deprecated.
Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)

setFGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setFGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setFigureLineInfo(ArrayList<String>) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure

setFigureLineInfo(ArrayList<String>) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure

setFile(File) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser

setFile(File) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser

setFile(File) - Method in interface org.biojava.nbio.core.search.io.ResultFactory

setFile1(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setFile2(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setFileFormat(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setFileLocation(String) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider

setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer

setFileParsingParameters(FileParsingParameters) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer

setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer

setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.PDBFileParser

setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider

setFileParsingParameters(FileParsingParameters) - Method in interface org.biojava.nbio.structure.io.StructureProvider

Set the parameters that should be used for file parsing

setFileParsingParams(FileParsingParameters) - Method in class org.biojava.nbio.structure.align.util.AtomCache

setFirstGroupAsa(GroupAsa) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setFlexible(boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setFlippableSidechain(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the flippableSidechain property.

setFocusAfpList(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFocusAfpn(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFocusRes1(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFocusRes2(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFocusResn(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFoFcCorrelation(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the foFcCorrelation property.

setFold(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setFold(int) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setFoldId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setFormat(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setFormat(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setFormula(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the residue formula.

setFormula(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setFormula(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setFormula_weight(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setFormula_weight(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setFragCompat(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setFragLen(Integer) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setFragLen(int) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setFragLen(int) - Method in class org.biojava.nbio.structure.align.model.AFP

setFragLenSq(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setFragment(String) - Method in class org.biojava.nbio.structure.Compound

setFragmentId(Integer) - Method in class org.biojava.nbio.structure.cath.CathFragment

setFragmentLength(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setFragmentMiniDistance(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.align.StructurePairAligner

setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel

setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel

setFragScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setFrom(Integer) - Method in class org.biojava.nbio.structure.domain.pdp.Segment

setFromFtp(JCheckBox) - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel

setGamma(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setGapCreate(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setGapExtCol(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setGapExtCol(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setGapExtend(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setGapExtend(Short) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

setGapExtend(short) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

setGapExtension(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setGapExtension(double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setGapExtension(Double) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setGapExtension(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setGapExtRow(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setGapExtRow(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setGapLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setGapOpen(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setGapOpen(double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setGapOpen(Double) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setGapOpen(Short) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

setGapOpen(short) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

setGapOpen(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setGapOpenCol(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setGapOpenCol(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setGapOpenRow(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setGapOpenRow(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setGapPenalty(GapPenalty) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

Sets the gap penalties.

setGaps(Boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setGenbankDirectoryCache(String) - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

setGene(String) - Method in class org.biojava.nbio.structure.Compound

setGene_src_common_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_dev_stage(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_genus(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_species(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_strain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_tissue(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGene_src_tissue_fraction(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setGenebankId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

setGeneName(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

setGeneSymb(String) - Method in class org.biojava.nbio.phosphosite.Site

setGenus(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setGFAccessionNumber(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFAuthors(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFClan(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFDBComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFDefinition(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFGatheringThreshs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFIdentification(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFKeywords(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFLocation(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFMembership(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFNoiseCutoffs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFNumSequences(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFPfamAccession(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFPreviousIDs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFRefComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFSearchMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFSourceSeed(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFSourceStructure(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFTrustedCutoffs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFTypeField(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGFWikipediaLink(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setGroup(String) - Method in class org.biojava.nbio.phosphosite.Site

setGroup(Group) - Method in interface org.biojava.nbio.structure.Atom

Set the back-reference to its parent Group.

setGroup(Group) - Method in class org.biojava.nbio.structure.AtomImpl

Set the back-reference to its parent Group.

setGroup_PDB(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setGroups(Set<StructureGroup>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

setGroups(Set<StructureGroup>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

setGroups(List<Group>) - Method in class org.biojava.nbio.structure.Site

setHazardRatio(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

setHazardRatioHiCI(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

setHazardRatioLoCI(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

setHeaderOnly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Parse only the PDB file header out of the files

setHeaderVars(String) - Method in class org.biojava.nbio.structure.Compound

setHeight(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

setHelixRmsdThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setHelixRmsdToRiseRatio(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setHetero(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq

setHetero(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setHgncId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setHGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setHGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setHide(boolean) - Method in class org.biojava.nbio.survival.data.HeaderInfo

setHitAccession(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder

setHitDef(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder

setHitId(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder

setHitLen(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder

setHitNum(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder

setHits(List<Hit>) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setHitSequence(Sequence) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder

setHmmAcc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

setHmmDesc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

setHmmFrom(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

setHmmName(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

setHmmTo(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

setHomologyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setHost_org_common_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setHost_org_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setHost_org_genus(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setHost_org_species(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setHost_org_strain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setHspAlignLen(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspBitScore(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspEvalue(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspGaps(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspHitFrame(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspHitFrom(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspHitTo(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspHseq(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspIdentity(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspIdentityString(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspNum(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspPositive(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspQseq(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspQueryFrame(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspQueryFrom(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHspQueryTo(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setHsps(List<Hsp>) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder

setHspScore(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setIclose(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

setIcode(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the icode property.

setId(String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

setId(long) - Method in class org.biojava.nbio.structure.align.model.AFP

setId(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setId(Long) - Method in interface org.biojava.nbio.structure.Chain

Set the ID used by Hibernate.

setId(Long) - Method in class org.biojava.nbio.structure.ChainImpl

Set the ID used by Hibernate.

setId(Long) - Method in class org.biojava.nbio.structure.Compound

set the ID used by Hibernate

setId(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setId(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

setId(Long) - Method in class org.biojava.nbio.structure.DBRef

Set the ID used by Hibernate.

setId(String) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setId(long) - Method in class org.biojava.nbio.structure.HetatomImpl

the Hibernate database ID

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setId(int) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setId(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

setId(String) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Sets the identifier for this biological assembly transformation.

setId(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setId(Long) - Method in interface org.biojava.nbio.structure.Structure

set the ID used by Hibernate

setId(Long) - Method in class org.biojava.nbio.structure.StructureImpl

set the ID used by Hibernate

setId(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setId(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setId(String) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob

setIdbnsBegin(char) - Method in class org.biojava.nbio.structure.DBRef

Insertion code of initial residue of the segment, if PDB is the reference.

setIdbnsEnd(char) - Method in class org.biojava.nbio.structure.DBRef

Insertion code of the ending residue of the segment, if PDB is the reference.

setIdCode(String) - Method in class org.biojava.nbio.structure.DBRef

Set the idCode for this entry.

setIdCode(String) - Method in class org.biojava.nbio.structure.PDBHeader

The PDB code for this protein structure.

setIdenticalSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setIdentifier(String) - Method in class org.biojava.nbio.core.sequence.AccessionID

setIdentifier(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

setIdentifier(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor

setIdentifier(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier

setIdentity(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setIdxlist(List<int[]>) - Method in class org.biojava.nbio.structure.align.helper.JointFragments

Stores the alignment between the residues of several fragments.

setInChI(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setInChIKey(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setIndex(int) - Method in class org.biojava.nbio.structure.align.helper.GapArray

setIndex(Integer) - Method in class org.biojava.nbio.survival.data.HeaderInfo

setIndexColumnName(String) - Method in class org.biojava.nbio.survival.data.WorkSheet

setInitialK(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setInitials(String) - Method in class org.biojava.nbio.structure.Author

setInsCode(Character) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

setInsCode(Character) - Method in class org.biojava.nbio.structure.ResidueNumber

setInsCode(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setInsCode(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setInsCode1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setInsCode2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

Sets the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces

setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Sets the radius of an inscribed sphere, that is tangent to each of the octahedron's faces

setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

Sets the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces

setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Sets the radius of an inscribed sphere, that is tangent to each of the tetrahedron's faces

setInsertBegin(char) - Method in class org.biojava.nbio.structure.DBRef

Initial insertion code of the PDB sequence segment.

setInsertEnd(char) - Method in class org.biojava.nbio.structure.DBRef

Ending insertion code of the PDB sequence segment.

setInstalledDomainDescription(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setInstalledDomainList(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setInstalledDomall(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setInstalledNodeList(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setInt_Tables_number(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry

setInternalChainID(String) - Method in interface org.biojava.nbio.structure.Chain

Sets the internal chain ID that is used in mmCif files

setInternalChainID(String) - Method in class org.biojava.nbio.structure.ChainImpl

setInterpolationDirection(int, LinearColorInterpolator.InterpolationDirection) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator

setInterpolator(ColorInterpolator) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper

setIoTime(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setIoTime(Long) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the IO time to load this object

setIoTime(Long) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setIoTime(long) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setIoverSigma(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the ioverSigma property.

setIsAminoAcid(boolean) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

setIsotopes(List<Isotope>) - Method in class org.biojava.nbio.aaproperties.xml.Element

setIsPublished(Boolean) - Method in class org.biojava.nbio.structure.JournalArticle

Sets the publication state of a JournalArticle - TO BE PUBLISHED == false

setIterationNumber(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setJclose(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

setJmolPanel(JmolPanel) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

Set the jmolPanel of the AlignmentJmol instance.

setJoinFast(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setJoinPlo(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setJoinRMSCutoff(double) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setJournalArticle(JournalArticle) - Method in class org.biojava.nbio.structure.PDBHeader

Set the associated publication as defined by the JRNL records in a PDB file.

setJournalArticle(JournalArticle) - Method in interface org.biojava.nbio.structure.Structure

Set the associated publication as defined by the JRNL records in a PDB file.

setJournalArticle(JournalArticle) - Method in class org.biojava.nbio.structure.StructureImpl

set the associated publication as defined by the JRNL records in a PDB file.

setJournalName(String) - Method in class org.biojava.nbio.structure.JournalArticle

setKaplanMeierFigure(KaplanMeierFigure) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel

Pick up needed info and details from the KM Figure

setKappa(float) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setKMFigureInfo(KMFigureInfo) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure

setKMFigureInfo(KMFigureInfo) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure

setLabel_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setLabel_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setLabel_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setLabel_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setLabel_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setLabel_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setLabel_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setLabel_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setLabel_entity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setLabel_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setLabel_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setLcmp(int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setLcmp(int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setLength(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathFragment

setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathSegment

setLength(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager

setLength1(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setLength2(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setLength_a(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setLength_a_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setLength_b(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setLength_b_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setLength_c(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setLength_c_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setLigands(Set<String>) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setLigRSRnbrMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the ligRSRnbrMean property.

setLigRSRnbrStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the ligRSRnbrStdev property.

setLigRSRnumnbrs(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the ligRSRnumnbrs property.

setLigRSRZ(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the ligRSRZ property.

setLikeSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setLinearPredictor(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setLineLength(int) - Method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter

setLineLength(int) - Method in class org.biojava.nbio.core.sequence.io.FastaWriter

setLineLength(int) - Method in class org.biojava.nbio.core.sequence.io.GenbankWriter

setLineSeparator(String) - Method in class org.biojava.nbio.core.sequence.io.FastaWriter

Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option

setLocal(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

setLocalSymmetry(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setLocalTimeLimit(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setLocation(AbstractLocation) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.

setLocation(AbstractLocation) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setLocation(AbstractLocation) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

The new location for this feature.

setLocationInAlignment(Location) - Method in interface org.biojava.nbio.core.alignment.template.MutableAlignedSequence

Sets the position of the AlignedSequence to the given Location (start, gaps, end).

setLocus(String) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband

setLongName(String) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

setLongName(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

setLongName(String) - Method in interface org.biojava.nbio.core.sequence.template.Compound

setLongName(String) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

setLongName(String) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

setLookAndFeel() - Static method in class org.biojava.nbio.structure.align.webstart.AligUIManager

setLowercaseToNull(ProteinSequence, Object[]) - Static method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

Takes a ProteinSequence which was created by a CasePreservingProteinSequenceCreator.

setLs_d_res_high(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_d_res_low(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_matrix_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_number_parameters(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_number_reflns_all(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_number_reflns_obs(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_number_reflns_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_number_reflns_R_work(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_number_restraints(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_percent_reflns_obs(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_percent_reflns_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_R_factor_all(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_R_factor_obs(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_R_factor_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_R_factor_R_free_error(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_R_factor_R_free_error_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_R_factor_R_work(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_redundancy_reflns_obs(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_wR_factor_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setLs_wR_factor_R_work(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setM(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFP

setMacromolecularSize(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

setManual(Boolean) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setMappingSequence(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer

setMapProperty(TreeMap<Integer, SpaceGroup>) - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot

setMass(double) - Method in class org.biojava.nbio.aaproperties.xml.Element

setMass(double) - Method in class org.biojava.nbio.aaproperties.xml.Isotope

setMatMatrix(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setMatMatrix(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setMatrix(short[][]) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

setMatrix(Matrix) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel

sets the distance matrix to be displayed

setMatrix(Matrix) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel

setMatrix(Matrix) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix(int, int, int, int, Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a submatrix.

setMatrix(int[], int[], Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a submatrix.

setMatrix(int[], int, int, Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a submatrix.

setMatrix(int, int, int[], Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a submatrix.

setMatrix11(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix12(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix13(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix21(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix22(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix23(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix31(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix32(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatrix33(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setMatTransform(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

setMax(short) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

setMaxAtoms(int) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

The maximum numbers of atoms to load in a protein structure (prevents memory overflows)

setMaxGap(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMaxGapFrag(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMaxGapSize(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Set the Max gap size parameter.

setMaxGapSize(int) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

CE specific parameter: set the Max gap size parameter G (during AFP extension).

setMaximumLocalCombinations(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMaximumLocalResults(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMaximumLocalSubunits(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMaxIter(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setMaxNrIterationsForOptimization(int) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Set the maximum nr of times the (slow) optimiziation of alignment should iterate.

setMaxNrSuggestions(int) - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider

set the maximum number of suggestions to return

setMaxNrSuggestions(int) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider

setMaxNrSuggestions(int) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider

setMaxOptRMSD(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

set the maximum RMSD cutoff to be applied during alignment optimization.

setMaxOptRMSD(Double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

(jCE specific): maximum RMSD that shall be calculated for the alignment.

setMaxPenalty(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMaxrefine(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setMaxRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setMaxSequenceIdentity(double) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster

setMaxSymmOrder(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setMaxTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setMaxTra(Integer) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

set the maximum number of Twists that are allowed...

setMaxTra(int) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setMaxTra(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Set the maximum number of Twists that are allowed...

setMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the mean property.

setMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.BondOutlier

Sets the value of the mean property.

setMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the mean property.

setMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the mean property.

setMean(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

setMembers(List<StructureInterface>) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

setMetaDataColumns(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet

Clears existing meta data columns and sets new ones

setMetaDataColumnsAfterColumn() - Method in class org.biojava.nbio.survival.data.WorkSheet

setMetaDataColumnsAfterColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet

setMetaDataFilter(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setMetaDataRows(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet

setMetaDataRowsAfterRow() - Method in class org.biojava.nbio.survival.data.WorkSheet

setMetaDataRowsAfterRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet

setMethod(String) - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage

setMethod(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setMethod_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl

setMethod_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

Sets the radius of radius of a sphere, that is tangent to each of the icosahedron's edges

setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Sets the radius of radius of a sphere, that is tangent to each of the octahedron's edges

setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Sets the radius of radius of a sphere, that is tangent to each of the tetrahedron's edges

setMin(short) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

setMinAlignedStructures(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setMinBlockLen(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setMinCoreLength(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setMinCPLength(Integer) - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

setMinCPLength(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

setMindiff(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the mindiff property.

setMindiff(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the mindiff property.

setMinimumHelixAngle(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMinimumHelixRise(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMinimumSequenceLength(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMinimumSequenceLengthFraction(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMinLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setMinRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setMinSequenceIdentity(double) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster

setMinTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setMisCut(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMisLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setMismatchCount(Integer) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setMisScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMod_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

setModDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader

setModel(int, List<Chain>) - Method in interface org.biojava.nbio.structure.Structure

A convenience function if one wants to edit and replace the models in a structure.

setModel(int, List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl

A convenience function if one wants to edit and replace the models in a structure.

setModel(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the model property.

setModel_Cartn_x(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setModel_Cartn_y(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setModel_Cartn_z(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setModelNumber(int) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo

setModification(ProteinModification) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

setModification(ProteinModification) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

setModType(String) - Method in class org.biojava.nbio.phosphosite.Site

setMogulIgnore(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the mogulIgnore property.

setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

setMolecularWeight(Float) - Method in interface org.biojava.nbio.core.sequence.template.Compound

setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

setMoleculeIds(Pair<String>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setMolecules(Pair<Atom[]>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setMolId(int) - Method in class org.biojava.nbio.structure.Compound

Set the molecule identifier, called entity_id in mmCIF dictionary.

setMolName(String) - Method in class org.biojava.nbio.structure.Compound

setMon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq

setMon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setMon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setMon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setMon_nstd_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setMon_nstd_parent_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setMultipleAlignment(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Set the back-reference to its parent MultipleAlignment.

setMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

setMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setMultipleAlignments(List<MultipleAlignment>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the List of MultipleAlignments in the ensemble.

setMultipleAlignments(List<MultipleAlignment>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setMultiplicity(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setMutation(String) - Method in class org.biojava.nbio.structure.Compound

setNaiveVariance(double[][]) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setName(String) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition

setName(String) - Method in class org.biojava.nbio.aaproperties.xml.Element

setName(String) - Method in class org.biojava.nbio.aaproperties.xml.Isotope

setName(String) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

setName(String) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix

setName(String) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix

Sets the name (short description) of this matrix.

setName(String) - Method in class org.biojava.nbio.core.sequence.features.Qualifier

setName(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

setName(String) - Method in class org.biojava.nbio.ontology.IntegerOntology

setName(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl

setName(String) - Method in interface org.biojava.nbio.ontology.Ontology

Set the name for this ontology

setName(String) - Method in class org.biojava.nbio.ontology.Synonym

setName(String) - Method in interface org.biojava.nbio.structure.Atom

Set atom name, e.g.

setName(String) - Method in class org.biojava.nbio.structure.AtomImpl

Set atom name, e.g.

setName(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setName(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor

setName(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setName(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly

setName(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setName(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setName(String) - Method in interface org.biojava.nbio.structure.Structure

Set biological name of Structure .

setName(String) - Method in class org.biojava.nbio.structure.StructureImpl

Set biological name of Structure .

setName(String) - Method in class org.biojava.nbio.structure.validation.Program

Sets the value of the name property.

setName(String) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

setName(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

setName1(String) - Method in class org.biojava.nbio.structure.align.client.PdbPair

setName1(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setName2(String) - Method in class org.biojava.nbio.structure.align.client.PdbPair

setName2(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setnAtom(int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setnAtom(int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setNatomsEDS(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the natomsEDS property.

setNaturalPos(Integer) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setNcbi_taxonomy_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn

setNclose(int) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

setNcsOperators(Matrix4d[]) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the NCS operators.

setNcuts(int) - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

setNdb_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setNdb_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setNdom(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

setNeedsQuotes(boolean) - Method in class org.biojava.nbio.core.sequence.features.Qualifier

setNeutronsNum(int) - Method in class org.biojava.nbio.aaproperties.xml.Isotope

setNmr(boolean) - Method in interface org.biojava.nbio.structure.Structure

Deprecated.

setNmr(boolean) - Method in class org.biojava.nbio.structure.StructureImpl

Deprecated.

setNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setNormAlignScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setNotesList(ArrayList<String>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setNotObserved(Boolean) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setNrAlignments(int) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setNrCPU(int) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setNrCPUs(int) - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc

does not do anything here...

setNrCPUs(int) - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB

setNrCPUs(int) - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable

setNrCPUs(int) - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc

setNrCPUs(int) - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc

setNreported(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

setNrThreads(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setNseg(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setnStart(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setNucleicAcidChainCount(int) - Method in class org.biojava.nbio.structure.symmetry.core.Subunits

setNullValue(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer

setNum(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

setNum(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq

setNumCells(int) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder

Set the number of neighboring crystal cells that will be used in the search for contacts

setNumFreeReflections(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the numFreeReflections property.

setNumHReduce(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the numHReduce property.

setNumHReduce(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the numHReduce property.

setNumMillerIndices(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the numMillerIndices property.

setNumobs(BigInteger) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the numobs property.

setNumobs(BigInteger) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the numobs property.

setNumRes(String) - Method in class org.biojava.nbio.structure.Compound

setNumSequences(int) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setObs(BigDecimal) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the obs property.

setObs(BigDecimal) - Method in class org.biojava.nbio.structure.validation.BondOutlier

Sets the value of the obs property.

setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.align.util.AtomCache

[Optional] This method changes the behavior when obsolete entries are requested.

setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

[Optional] This method changes the behavior when obsolete entries are requested.

setObsval(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the obsval property.

setObsval(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the obsval property.

setOccupancy(float) - Method in interface org.biojava.nbio.structure.Atom

Set occupancy.

setOccupancy(float) - Method in class org.biojava.nbio.structure.AtomImpl

setOccupancy(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setOccupancy_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setOccupancy_max(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOccupancy_min(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOccurrenceType(ModificationOccurrenceType) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

setOffset(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setOligomeric_count(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

setOligomeric_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

setOmega(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setOmimId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setOne_letter_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator

Sets the type of bioassembly to be colored.

setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH

setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup

setOpenPenalty(int) - Method in class org.biojava.nbio.alignment.SimpleGapPenalty

setOpenPenalty(int) - Method in interface org.biojava.nbio.alignment.template.GapPenalty

Sets penalty given when a deletion or insertion gap first opens

setOper_expression(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen

setOperator(Matrix4d) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper

setOptAln(int[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setOptimization(Boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setOptimizationSteps(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setOptLen(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setOptLength(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

The length of the optimal alignment.

setOptRmsd(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setOrder(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setOrderDetectorMethod(CESymmParameters.OrderDetectorMethod) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setOrgan(String) - Method in class org.biojava.nbio.structure.Compound

setOrganelle(String) - Method in class org.biojava.nbio.structure.Compound

setOrganism(String) - Method in class org.biojava.nbio.phosphosite.Site

setOrganism_common_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn

setOrganism_scientific(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn

setOrganismCommon(String) - Method in class org.biojava.nbio.structure.Compound

setOrganismScientific(String) - Method in class org.biojava.nbio.structure.Compound

setOrganismTaxId(String) - Method in class org.biojava.nbio.structure.Compound

setOrientation(Character) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

setOrigGroup(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setOrigGroup(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setOriginalHeader(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setORmsdThr(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Set the Original RMSD threshold from which the alignment optimization is started

setOrthologousSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setOutFile(SynchronizedOutFile) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setOutFile(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setOutFile(String) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

setOutputDir(File) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setOutputFormat(BlastOutputFormatEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties

Sets the stream output format to get from the QBlast service
If HTML format is selected, also adds the following parameters (which are removed if another output format is chosen):

setOutputOption(String, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties

This method forwards to NCBIQBlastOutputProperties.setOutputOption(BlastOutputParameterEnum, String).

setOutputOption(BlastOutputParameterEnum, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties

Sets the value of specified output parameter

setOutputOption(String, String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties

Method to set the value for a specific output parameter using a key to store in a map.

setOutputPDB(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

When writing the results to a file, don;t write as XML but write aligned PDB file

setOverall_FOM_free_R_set(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOverall_FOM_work_R_set(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOverall_SU_B(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOverall_SU_ML(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOverall_SU_R_Cruickshank_DPI(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOverall_SU_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setOwab(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the owab property.

setP1(int) - Method in class org.biojava.nbio.structure.align.model.AFP

setP2(int) - Method in class org.biojava.nbio.structure.align.model.AFP

setPaintDefaults(Graphics2D) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel

set some default rendering hints, like text antialiasing on

setPair(Profile<S, C>, Profile<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfilePair

Sets both Profiles of the pair.

setPair(AlignedSequence<S, C>, AlignedSequence<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableSequencePair

Sets both AlignedSequences of the pair.

setPair(PdbPair) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setPair(Pair<Atom>) - Method in class org.biojava.nbio.structure.contact.AtomContact

setPair(Pair<Group>) - Method in class org.biojava.nbio.structure.contact.GroupContact

setPairs(SortedSet<PdbPair>) - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.CeMain

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

setParameters(ConfigStrucAligParams) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner

Set the parameters for this algorithm to use.

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

setParameters(ConfigStrucAligParams) - Method in interface org.biojava.nbio.structure.align.StructureAlignment

Set the default parameters for this algorithm to use

setParams(FarmJobParameters) - Method in class org.biojava.nbio.structure.align.FarmJob

setParams(StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner

set the parameters to be used for the algorithm

setParams(CESymmParameters) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setParent(Structure) - Method in interface org.biojava.nbio.structure.Chain

Deprecated.
use setStructure instead

setParent(Structure) - Method in class org.biojava.nbio.structure.ChainImpl

Deprecated.

setParent(Structure) - Method in class org.biojava.nbio.structure.DBRef

Set the structure object that this DBRef relates to.

setParentDNASequence(AbstractSequence<NucleotideCompound>, Integer, Integer) - Method in class org.biojava.nbio.core.sequence.ProteinSequence

A Protein sequence can be stand alone or loaded from a transcript sequence.

setParentFeature(FeatureInterface<S, C>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

A feature can be the child or contained by a parent feature.

setParentFeature(FeatureInterface<S, C>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setParentFeature(FeatureInterface<S, C>) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Set the parent feature

setParentId(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setParentSequence(AbstractSequence<?>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setParentSunid(int) - Method in class org.biojava.nbio.structure.scop.ScopNode

setParseBioAssembly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should the biological assembly info (REMARK 350) be parsed from the PDB file?

setParseCAOnly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Flag if only the C-alpha atoms of the structure should be parsed.

setParseSecStruc(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

A flag to tell the parser to parse the Author's secondary structure assignment from the file default is set to false, i.e.

setParsingConsistency(BlastTabularParser.PARSING_CONSISTENCY) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser

Tries to define a different level of consistency during parsing.

setPartialOn3prime(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setPartialOn5prime(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setPartner(int) - Method in class org.biojava.nbio.structure.secstruc.HBond

setPath(IndexPair[]) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setPath(IndexPair[]) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setPath(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Set the path that is used to cache PDB files.

setPath(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Sets the path for the directory where PDB files are read/written

setPath(String) - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider

directory where to find PDB files

setPathSize(int) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setPathSize(int) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setPdb1(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

mandatory argument to set the first PDB (and optionally chain ID) to be aligned.

setPdb1(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setPdb2(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

mandatory argument to set the second PDB (and optionally chain ID) to be aligned.

setPdb2(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setPdb_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setPdb_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setPdb_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setPdb_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setPdb_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setPdb_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setPdb_strand_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setPdb_strand_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setPdbAln(String[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setPdbccId(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the Protein Data Bank Chemical Component ID.

setPdbccName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the Protein Data Bank Chemical Component name.

setPDBCode(String) - Method in interface org.biojava.nbio.structure.Structure

Set PDB code of structure .

setPDBCode(String) - Method in class org.biojava.nbio.structure.StructureImpl

Set PDB code of structure .

setPDBDirField(JTextField) - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel

setPdbDirSplit(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

Deprecated.
Ignored (4.0.0)

setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

mandatory argument to set the location of PDB files.

setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setPDBFlag(boolean) - Method in interface org.biojava.nbio.structure.Group

Flag if group has 3D data .

setPDBFlag(boolean) - Method in class org.biojava.nbio.structure.HetatomImpl

flag if group has 3D data.

setPdbGroup(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setPdbGroup(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setPDBHeader(PDBHeader) - Method in interface org.biojava.nbio.structure.Structure

Set the the header information for this PDB file

setPDBHeader(PDBHeader) - Method in class org.biojava.nbio.structure.StructureImpl

Set the the header information for this PDB file

setPdbId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setPdbId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setPdbId(String) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider

setPdbId(String) - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider

Tell the provider for which PDB ID the quaternary structure should be returned.

setPdbId(String) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider

setPdbId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setPDBName(String) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

setPDBName(String) - Method in class org.biojava.nbio.structure.AminoAcidImpl

set three character name of AminoAcid.

setPDBName(String) - Method in interface org.biojava.nbio.structure.Group

Set the PDB 3-letter name for this group.

setPDBName(String) - Method in class org.biojava.nbio.structure.HetatomImpl

Set three character name of Group .

setPdbPath(String) - Static method in class org.biojava.nbio.structure.StructureIO

Utility method to set the location where PDB files can be found

setPDBResidueNumber(ResidueNumber) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

setPdbResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setPdbResNum(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setPdbResNum(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setPdbResNum(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setPDBresnum1(String[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setPDBresnum2(String[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setPDBRevisionNumber(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the pdbRevisionNumber property.

setPDBserial(int) - Method in interface org.biojava.nbio.structure.Atom

Set PDB atom number.

setPDBserial(int) - Method in class org.biojava.nbio.structure.AtomImpl

Set PDB atom number.

setPdbSerial(int) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

setPdbx_align(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_align_begin(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setPdbx_alt_source_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_alt_source_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_ambiguous_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_aromatic_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_aromatic_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setPdbx_atcc(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_auth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setPdbx_auth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setPdbx_auth_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setPdbx_auth_seq_align_beg(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_auth_seq_align_end(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_auth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setPdbx_auth_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_beg_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_beg_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_blank_PDB_chainid_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym

setPdbx_CASP_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

setPdbx_cell(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_cell_line(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_cellular_location(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_component_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_component_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_component_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_data_cutoff_high_absF(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_data_cutoff_high_rms_absF(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_data_cutoff_low_absF(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_db_accession(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setPdbx_db_accession(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_db_align_beg_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_db_align_end_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_description(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setPdbx_description(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_descriptor(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

setPdbx_diffrn_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_dist_value(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ec(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setPdbx_end_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_end_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_evidence_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setPdbx_formal_charge(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setPdbx_formal_charge(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_fragment(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setPdbx_fragment(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_full_space_group_name_H_M(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry

setPdbx_gene_src_atcc(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_cell(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_cell_line(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_cellular_location(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_fragment(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_gene(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_ncbi_taxonomy_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_organ(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_organelle(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_plasmid(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_plasmid_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_scientific_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_gene_src_variant(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_atcc(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_cell(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_cell_line(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_cellular_location(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_culture_collection(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_gene(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_ncbi_taxonomy_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_organ(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_organelle(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_scientific_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_strain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_tissue(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_tissue_fraction(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_variant(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_vector(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_host_org_vector_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_ideal_coordinates_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_ideal_coordinates_missing_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_initial_date(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_isotropic_thermal_model(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_keywords(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords

setPdbx_leaving_atom_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_leaving_atom_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_leaving_atom_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ls_cross_valid_method(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_ls_sigma_F(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_ls_sigma_I(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_method_to_determine_struct(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_model_Cartn_x_ideal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_model_Cartn_y_ideal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_model_Cartn_z_ideal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_model_coordinates_db_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_model_coordinates_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_model_coordinates_missing_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_model_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

setPdbx_model_type_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

setPdbx_modified(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym

setPdbx_modified_date(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_mutation(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setPdbx_ncbi_taxonomy_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_num_res(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setPdbx_num_residues(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite

setPdbx_number_of_molecules(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setPdbx_ordinal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor

setPdbx_ordinal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_ordinal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setPdbx_ordinal(Integer) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_organ(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_organelle(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_organism_scientific(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_overall_ESU_R(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_overall_ESU_R_Free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_overall_phase_error(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_overall_SU_R_Blow_DPI(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_overall_SU_R_free_Blow_DPI(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_overall_SU_R_free_Cruickshank_DPI(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_PDB_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_PDB_id_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_pdb_id_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_PDB_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setPdbx_pdb_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_PDB_model_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setPdbx_pdb_strand_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_plasmid_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_plasmid_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_polymer_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_processing_site(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_ptnr1_label_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr1_PDB_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr1_standard_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr2_label_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr2_PDB_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr3_label_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr3_label_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr3_label_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr3_label_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr3_label_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_ptnr3_PDB_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_R_Free_selection_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_ref_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_refine_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_release_status(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_replaced_by(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_replaces(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_residue_numbering(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_secretion(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_seq_align_beg_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_seq_align_end_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_seq_db_accession_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_seq_db_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_seq_db_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setPdbx_seq_one_letter_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef

setPdbx_seq_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_solvent_ion_probe_radii(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_solvent_shrinkage_radii(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_solvent_vdw_probe_radii(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_src_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPdbx_src_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbx_starting_model(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_stereo_config(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setPdbx_stereo_config(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setPdbx_stereochem_target_val_spec_case(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_stereochemistry_target_values(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_strand_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setPdbx_subcomponent_list(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_synonyms(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_TLS_residual_ADP_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setPdbx_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPdbx_unique_axis(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setPdbx_value_order(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPdbx_variant(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setPdbxStructAssemblies(List<PdbxStructAssemblyGen>) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer

setPdbxStructAssemblies(List<PdbxStructAssembly>) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer

setPdbxStructOperLists(List<PdbxStructOperList>) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer

setPdpprovider(PDPProvider) - Method in class org.biojava.nbio.structure.align.util.AtomCache

setPercentage(Double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

setPercentageIdentity(Double) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

setPercentFreeReflections(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the percentFreeReflections property.

setPercentRamaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the percentRamaOutliers property.

setPercentRotaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the percentRotaOutliers property.

setPercentRSRZOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the percentRSRZOutliers property.

setPercId(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setPermutationSize(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setPhi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setPhi(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the phi property.

setPlasmid_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPlasmid_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setPmid(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of pmid

setPolyhedron(Polyhedron) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup

setPolymerType(PolymerType) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setPos(int, int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition

setPos1(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setPos1(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition

setPos2(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setPos2(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition

setPosition(int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

setPreferredResult(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

setPreferredSize() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel

setPreviousNames(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setPreviousSymbols(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setPrimitiveMultiplicity(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setPrintCE(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

Display the output string in CE style

setPrintConnections(boolean) - Method in class org.biojava.nbio.structure.io.FileConvert

enable/disable printing of connections connections are sometimes buggy in PDB files so there are some cases where one might turn this off.

setPrintFatCat(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setPrintXML(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setProbability(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setProfile(Profile<S, C>) - Method in class org.biojava.nbio.alignment.GuideTree.Node

setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner

setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.SimpleProfileProfileAligner

setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.SmithWaterman

setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

setProfile(Profile<S, C>) - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode

Stores the given profile.

setProfileFuture(Future<ProfilePair<S, C>>) - Method in class org.biojava.nbio.alignment.GuideTree.Node

setProfileFuture(Future<ProfilePair<S, C>>) - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode

Stores the given profile future.

setProgram(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setProgram(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

setProgram(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor

setProgram(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier

setProgram_version(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

setProgram_version(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor

setProgram_version(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier

setPrograms(Programs) - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation

Sets the value of the programs property.

setProgramSpecificParameters(HashMap<String, String>) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setProperties(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

setProperties(Map<String, Object>) - Method in interface org.biojava.nbio.structure.Group

Properties of this amino acid.

setProperties(Map<String, Object>) - Method in class org.biojava.nbio.structure.HetatomImpl

Properties of this amino acid.

setProperties(String) - Method in class org.biojava.nbio.structure.validation.Program

Sets the value of the properties property.

setProperty(Object, Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

setProperty(Object, Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation

Set the value of a property.

setProperty(String, Object) - Method in interface org.biojava.nbio.structure.Group

set a single property .

setProperty(String, Object) - Method in class org.biojava.nbio.structure.HetatomImpl

set a single property .

setProtein(String) - Method in class org.biojava.nbio.phosphosite.Site

setProxySequenceReader(SequenceReader<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Very important method that allows external mappings of sequence data and features.

setPseudoSymmetric(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.Subunits

setPsi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setPsi(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the psi property.

setPsimodId(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the PSI-MOD ID.

setPsimodName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the PSI-MOD name.

setPtnr1_auth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_auth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_auth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_label_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_label_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_label_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_label_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr1_symmetry(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_auth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_auth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_auth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_label_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_label_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_label_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_label_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPtnr2_symmetry(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn

setPublicationDate(int) - Method in class org.biojava.nbio.structure.JournalArticle

setPublished(boolean) - Method in class org.biojava.nbio.structure.JournalArticle

setPublisher(String) - Method in class org.biojava.nbio.structure.JournalArticle

setPvalue(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

setPvalue(Double) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

setPx(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setQualifiers(Map<String, List<Qualifier>>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

setQualifiers(Map<String, List<Qualifier>>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setQualifiers(Map<String, List<Qualifier>>) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Set the qualifiers

setQualities(List<Number>) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature

setQuantities(List<Number>) - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature

setQuery(S) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner

Sets the query Sequence.

setQuery(Profile<S, C>) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner

Sets the query Profile.

setQuery(Profile<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfilePair

Sets the first Profile of the pair.

setQuery(AlignedSequence<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableSequencePair

Sets the first AlignedSequence of the pair.

setQueryDef(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setQueryID(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setQueryLength(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setQueryReferences(List<Sequence>) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser

Intended for use with run module.

setQueryReferences(List<Sequence>) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser

setQueryReferences(List<Sequence>) - Method in interface org.biojava.nbio.core.search.io.ResultFactory

Specify the collection of sequences objects used as queries in the Search run.

setQuerySequence(Sequence) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setRama(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the rama property.

setRandomSeed(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setRange(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setRanges(List<String>) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setRecordAdditionalAttachments(boolean) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

setRecordType(String) - Method in interface org.biojava.nbio.structure.AminoAcid

Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.

setRecordType(String) - Method in class org.biojava.nbio.structure.AminoAcidImpl

Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.

setRecordUnidentifiableCompounds(boolean) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

setReduceInitialFragments(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setRef(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of the ref.

setRef_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setRefAuthor(StringBuffer) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference

setRefChainId(String) - Method in class org.biojava.nbio.structure.Compound

Return the ref chain id value.

setReference(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setReferences(Vector<StockholmFileAnnotation.StockholmFileAnnotationReference>) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setRefined(boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setRefinedScoreThreshold(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setRefineMethod(CESymmParameters.RefineMethod) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setRefineResult(boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

Deprecated.

setRefLocation(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference

setRefmacVersion(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the refmacVersion property.

setRefMedline(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference

setRefn(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of the refn

setRefseqIds(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setRefTitle(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference

setRelativePercentileClashscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the relativePercentileClashscore property.

setRelativePercentileDCCRfree(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

setRelativePercentilePercentRamaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the relativePercentilePercentRamaOutliers property.

setRelativePercentilePercentRotaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the relativePercentilePercentRotaOutliers property.

setRelativePercentilePercentRSRZOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the relativePercentilePercentRSRZOutliers property.

setRelativePercentileRNAsuiteness(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

setRemoveCif(boolean) - Method in class org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider

Remove downloaded .cif.gz after adding to zip archive? Default is true.

setRepeatUnits(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setReplaces(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

setRepresentative(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setResidId(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the RESID ID.

setResidName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the RESID name.

setResidual(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setResidualVariable(String, Double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

Set the residual value for the variable for this sample.

setResidue(String) - Method in class org.biojava.nbio.phosphosite.Site

setResidueName(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo

Including insertion code

setResidueNumber(int) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

setResidueNumber(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo

setResidueNumber(ResidueNumber) - Method in interface org.biojava.nbio.structure.Group

sets the ResidueNumber for this Group

setResidueNumber(String, Integer, Character) - Method in interface org.biojava.nbio.structure.Group

Utility method to temporarily set a chainID for a group, if a parent chain object does not exist yet.

setResidueNumber(ResidueNumber) - Method in class org.biojava.nbio.structure.HetatomImpl

setResidueNumber(String, Integer, Character) - Method in class org.biojava.nbio.structure.HetatomImpl

setResidues(List<SiftsResidue>) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setResidueType(ResidueType) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setResname(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the resname property.

setResNames(String) - Method in class org.biojava.nbio.structure.Compound

setResnum(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the resnum property.

setResnum1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setResnum2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setResolution(Double) - Method in class org.biojava.nbio.structure.cath.CathDomain

setResolution(float) - Method in class org.biojava.nbio.structure.PDBHeader

setResScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setRestypesNotcheckedForBondAngleGeometry(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the restypesNotcheckedForBondAngleGeometry property.

setResultFile(File) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

setRev_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord

setRevisionRecords(List<DatabasePdbrevRecord>) - Method in class org.biojava.nbio.structure.PDBHeader

setRfree(float) - Method in class org.biojava.nbio.structure.PDBHeader

setRise(double) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setRms(double) - Method in class org.biojava.nbio.structure.align.helper.JointFragments

setRms(double) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

the rms in the structurally equivalent regions

setRms(double) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setRmsd(double) - Method in class org.biojava.nbio.structure.align.model.AFP

setRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment

setRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setRmsdCenters(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setRmsdCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

The cutoff to be used during AFP detection

setRmsdCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setRmsdIntra(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setRmsdThr(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setRmsdThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setRmsdThrJoin(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setRnaSuiteness(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

setRndSeed(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setRobustStdError(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

setRot(Matrix) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setRota(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the rota property.

setRotationGroup(RotationGroup) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup

setRotationMatrix(double[][]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

setRow(short) - Method in class org.biojava.nbio.structure.align.helper.IndexPair

setRowHeader(String) - Method in class org.biojava.nbio.survival.data.WorkSheet

setRows(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

setRscc(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the rscc property.

setRscore(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setRscoreLogrankTestpvalue(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setRsr(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the rsr property.

setRsrz(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the rsrz property.

setRunBackground(boolean) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setSaid(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the said property.

setSaturation(float) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel

Deprecated.

setSaturation(float) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper

setSaveOutputDir(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setScale(int) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

setScale(float) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel

setScale(float) - Method in class org.biojava.nbio.structure.gui.util.CoordManager

setScale(float) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel

setScalevalue(float) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel

Deprecated.

setScalevalue(double) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper

setScid(BigInteger) - Method in class org.biojava.nbio.structure.validation.SymmClash

Sets the value of the scid property.

setScopDatabase(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory

Set the default scop version

setScopDatabase(String, boolean) - Static method in class org.biojava.nbio.structure.scop.ScopFactory

Set the default scop version

setScopDatabase(ScopDatabase) - Static method in class org.biojava.nbio.structure.scop.ScopFactory

Set the default scop version and instance

setScopDescription(List<ScopDescription>) - Method in class org.biojava.nbio.structure.scop.server.ScopDescriptions

setScopDomain(List<ScopDomain>) - Method in class org.biojava.nbio.structure.scop.server.ScopDomains

setScopDownloadURL(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

Deprecated.
Use ScopInstallation.addMirror(java.lang.String) instead

setScope(int) - Method in class org.biojava.nbio.ontology.Synonym

setScopId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setScopNode(List<ScopNode>) - Method in class org.biojava.nbio.structure.scop.server.ScopNodes

setScopVersion(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation

setScopVersion(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation

setScopVersion(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Sets the scop version used.

setScopVersion(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

setScore(double) - Method in class org.biojava.nbio.structure.align.model.AFP

setScore(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setScore(float) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setScore(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setScore(double) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setScore(double) - Method in class org.biojava.nbio.structure.domain.pdp.Segment

setScore(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setScore(Float) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

setScoreLogrankTest(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setScoreLogrankTestpvalue(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setScorePoint(int, int, int, int, int, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Calculate the optimal alignment score for the given sequence positions with an affine or constant gap penalty

setScorePoint(int, int, int, int, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Calculates the optimal alignment score for the given sequence positions and a linear gap penalty

setScores(QuatSymmetryScores) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setScores(QuatSymmetryScores) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setScoreVector(int, AlignerHelper.Subproblem, int, int, int[], boolean, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Score global alignment for a given position in the query sequence

setScoreVector(int, int, int, int, int, int, int[], boolean, int[][][], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Score global alignment for a given position in the query sequence

setScoreVector(int, AlignerHelper.Subproblem, int, int[], boolean, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Score global alignment for a given position in the query sequence for a linear gap penalty

setScoreVector(int, int, int, int, int, int[], boolean, int[][][], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Score global alignment for a given position in the query sequence for a linear gap penalty

setScoreVector(int, int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Score local alignment for a given position in the query sequence

setScoreVector(int, int, int, int, int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Score local alignment for a given position in the query sequence

setScoreVector(int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Score local alignment for a given position in the query sequence for a linear gap penalty

setScoreVector(int, int, int, int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Score local alignment for a given position in the query sequence for a linear gap penalty

setScoringStrategy(CeParameters.ScoringStrategy) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Set the scoring strategy to use.

setScoringStrategy(CeParameters.ScoringStrategy) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setSearchFile(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setSecondGroupAsa(GroupAsa) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setSecretion(String) - Method in class org.biojava.nbio.structure.Compound

setSeedFragmentLength(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setSeedRmsdCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setSegId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setSegmentId(Integer) - Method in class org.biojava.nbio.structure.cath.CathSegment

setSegments(List<CathSegment>) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSegments(List<Segment>) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setSegments(List<SiftsSegment>) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

setSelectedAlignmentPos(int) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel

setSelectedAlignmentPos(int) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel

setSelection(Selection) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl

setSelection(List<AtomInfo>) - Method in interface org.biojava.nbio.structure.gui.Selection

setSelection(List<AtomInfo>) - Method in class org.biojava.nbio.structure.gui.SelectionImpl

setSelection(Selection) - Method in interface org.biojava.nbio.structure.gui.StructureViewer

setSelfAlignment(AFPChain) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setSeparatorSequence(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer

setSeq(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup

Sets the value of the seq property.

setSeq_align_beg(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setSeq_align_end(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

setSeq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme

setSeq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme

setSeq_num(Integer) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

setSeqBegin(int) - Method in class org.biojava.nbio.structure.DBRef

Initial sequence number of the PDB sequence segment.

setSeqEnd(int) - Method in class org.biojava.nbio.structure.DBRef

Ending sequence number of the PDB sequence segment.

setSeqIdRange(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setSeqMisMatches(List<SeqMisMatch>) - Method in interface org.biojava.nbio.structure.Chain

Set annotated sequence mismatches for this chain.

setSeqMisMatches(List<SeqMisMatch>) - Method in class org.biojava.nbio.structure.ChainImpl

setSeqNum(Integer) - Method in class org.biojava.nbio.structure.ResidueNumber

setSeqNum(Integer) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setSeqNum(Integer) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setSeqResGroups(List<Group>) - Method in interface org.biojava.nbio.structure.Chain

Sets the list of SeqResGroups for this chain.

setSeqResGroups(List<Group>) - Method in class org.biojava.nbio.structure.ChainImpl

Sets the list of SeqResGroups for this chain.

setSeqResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

setSequence(S) - Method in class org.biojava.nbio.core.sequence.location.SequenceLocation

setSequence(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSequence(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setSequenceCollection(SequenceOptimizationHints.SequenceCollection) - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints

setSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSequenceHeader(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSequenceHeader(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setSequenceIdentity(double) - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment

setSequenceIdentityThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

setSequenceIdentityThresholds(double[]) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setSequencePseudoSymmetryThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setSequences(List<AlignedSequence<S, C>>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfile

Sets entirely new set of AlignedSequences.

setSequenceScore(Double) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setSequenceString(String) - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList

setSequenceUsage(SequenceOptimizationHints.SequenceUsage) - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints

setSequentialAlignment(boolean) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Set whether this alignment has the normal topology, ie the residues aligned in each block increase sequentially over the original protein.

setSeqWeight(double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.

setSerNum(int) - Method in class org.biojava.nbio.structure.io.SSBondImpl

get serial number of this SSBOND in PDB file

setServer(String) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setServer(String) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider

setServer(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation

setShortAlign(boolean) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setShortDescription(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

setShortDescription(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setShortDescription(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Set the short description that can be used to describe the feature

setShortName(String) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition

setShortName(String) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

setShortName(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

setShortName(String) - Method in interface org.biojava.nbio.core.sequence.template.Compound

setShortName(String) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

setShortName(String) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

setShortSymbol(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setShow3d(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setShowAFPRanges(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setShowAFPRanges(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setShowDBresult(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setShowMenu(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setSimCount(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

setSimilarity(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setSite_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setSiteID(String) - Method in class org.biojava.nbio.structure.Site

setSites(List<Site>) - Method in interface org.biojava.nbio.structure.Structure

setSites(List<Site>) - Method in class org.biojava.nbio.structure.StructureImpl

setSize(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setSmiles(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setSOLID(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSolvent_model_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setSolvent_model_param_bsol(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setSolvent_model_param_ksol(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine

setSource(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

Set the feature source

setSource(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setSource(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Change the source of the FeatureInterface.

setSource(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Added support for the source of this sequence for GFF3 export

setSource(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSpace_group_name_H_M(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry

setSpace_group_name_Hall(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry

setSpaceGroup(SpaceGroup) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the SpaceGroup

setSparse(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setSpecies(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setSpeciesId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setSqFrom(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

setSqTo(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

setSrc_method(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setSSBonds(List<Bond>) - Method in interface org.biojava.nbio.structure.Structure

Set the list of SSBonds for this structure

setSSBonds(List<Bond>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the list of SSBonds for this structure

setSSEThreshold(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setStandard(boolean) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setStandardDeviation(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

setStart(Point) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setStart(Integer) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband

setStart(String) - Method in class org.biojava.nbio.structure.cath.CathFragment

setStart(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setStart(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setStart_construct_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen

setStartPage(String) - Method in class org.biojava.nbio.structure.JournalArticle

setStartTimestamp(long) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob

setStatus(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setStatus(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

setStatus(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setStdError(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

setStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the stdev property.

setStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.BondOutlier

Sets the value of the stdev property.

setStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the stdev property.

setStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the stdev property.

setStdlow(ArrayList<Double>) - Method in class org.biojava.nbio.survival.cox.StrataInfo

setSteps(AlignerHelper.Last[][][], boolean, int[], AlignerHelper.Last, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Find alignment path through traceback matrix

setSteps(AlignerHelper.Last[][][], int[][][], List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Find global alignment path through traceback matrix

setSteps(AlignerHelper.Last[][][], int[], List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

Find local alignment path through traceback matrix

setStepSize(int) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setStop(String) - Method in class org.biojava.nbio.structure.cath.CathFragment

setStop(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setStoringScoreMatrix(boolean) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

Sets choice to cache the score matrix or to save memory by deleting score matrix after alignment.

setStrain(String) - Method in class org.biojava.nbio.structure.Compound

setStrain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setStrain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn

setStrand(Strand) - Method in class org.biojava.nbio.core.sequence.GeneSequence

setStrand(Strand) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setStrata(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setStrataInfoHashMap(LinkedHashMap<String, StrataInfo>) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo

setStrictSCOP(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Deprecated.
Removed in 4.2.0

setStringSequence(String) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

setStruct(Struct) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer

setStruct(Struct) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer

setStruct(Struct) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer

setStructure(Structure) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

Set a new Structure to visualize in the AlignmentJmol window.

setStructure(Structure) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel

setStructure(Structure) - Method in interface org.biojava.nbio.structure.Chain

Sets the back-reference to its parent Structure.

setStructure(Structure) - Method in class org.biojava.nbio.structure.ChainImpl

Sets the back-reference to its parent Structure.

setStructure(Structure) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol

setStructure(Structure) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl

setStructure(Structure) - Method in interface org.biojava.nbio.structure.gui.StructureViewer

setStructure1(Structure) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener

setStructure1(Structure) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay

setStructure2(Structure) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener

setStructure2(Structure) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay

setStructureAlignmentJmol(AbstractAlignmentJmol) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

setStructureId(StructureIdentifier) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setStructureIdentifier(StructureIdentifier) - Method in interface org.biojava.nbio.structure.Structure

Set the identifier corresponding to this structure

setStructureIdentifier(StructureIdentifier) - Method in class org.biojava.nbio.structure.StructureImpl

setStructureIdentifiers(List<StructureIdentifier>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).

setStructureIdentifiers(List<StructureIdentifier>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setStructurePairAligner(StructurePairAligner) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay

setStructurePairAligner(StructurePairAligner) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame

setStyle(RenderStyle) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl

setStyle(RenderStyle) - Method in interface org.biojava.nbio.structure.gui.StructureViewer

Apply this style to the current selection

setSubLocations(List<Location>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setSubstitutionMatrix(SubstitutionMatrix<C>) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

Sets the substitution matrix.

setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound>) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.

setSubunitRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setSunID(int) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setSunid(Integer) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setSunid(int) - Method in class org.biojava.nbio.structure.scop.ScopNode

setSuperfamilyId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setSurname(String) - Method in class org.biojava.nbio.structure.Author

setSurvivalData(ArrayList<String>, SurvFitInfo, Double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure

Allow setting of points in the figure where weighted correction has been done and percentage has already been calculated.

setSurvivalData(ArrayList<String>, LinkedHashMap<String, ArrayList<CensorStatus>>, Boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure

The data will set the max time which will result in off time points for tick marks

setSurvivalData(ArrayList<String>, LinkedHashMap<String, ArrayList<CensorStatus>>, Double, Boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure

setSurvivalInfo(ArrayList<String>, ArrayList<SurvivalInfo>, String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure

setSurvivalInfoList(ArrayList<SurvivalInfo>) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setSwissprotId(String) - Method in interface org.biojava.nbio.structure.Chain

Sets the Swissprot id of this chain.

setSwissprotId(String) - Method in class org.biojava.nbio.structure.ChainImpl

set the Swissprot id of this chains .

setSymbol(String) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition

setSymbol(String) - Method in class org.biojava.nbio.aaproperties.xml.Element

setSymDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setSymmetry(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

setSymmetryDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

setSymmetryDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

setSymmGroup(String) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setSymmLevels(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setSymmLevels(int) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setSymmOrder(int) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setSymmType(CESymmParameters.SymmetryType) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setSymop(String) - Method in class org.biojava.nbio.structure.validation.SymmClash

Sets the value of the symop property.

setSynonyms(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setSynonyms(Set<Object>) - Method in class org.biojava.nbio.ontology.Term.Impl

setSynonyms(List<String>) - Method in class org.biojava.nbio.structure.Compound

setSynthetic(String) - Method in class org.biojava.nbio.structure.Compound

setSystematicName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the systematic name.

setT(double[]) - Method in class org.biojava.nbio.structure.align.model.AFP

setTabPane(JTabbedPane) - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI

setTarget(S) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner

Sets the target Sequence.

setTarget(Profile<S, C>) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner

Sets the target Profile.

setTarget(Profile<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfilePair

Sets the second Profile of the pair.

setTarget(AlignedSequence<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableSequencePair

Sets the second AlignedSequence of the pair.

setTaxonomy(TaxonomyID) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setTempFactor(float) - Method in interface org.biojava.nbio.structure.Atom

Set temp factor .

setTempFactor(float) - Method in class org.biojava.nbio.structure.AtomImpl

setText(String) - Method in class org.biojava.nbio.structure.align.gui.AlignmentTextPanel

setText(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark

setText(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords

setTextField(JTextField) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener

setTextOutput(boolean) - Method in class org.biojava.nbio.structure.align.gui.MySaveFileListener

If true, the alignment format saved will be a text output (FASTA for MultipleAlignments and FatCat for pairwise alignments)

setTGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setThreadPool(ThreadPoolExecutor) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Sets thread pool to any given ThreadPoolExecutor to allow use of an alternative execution style.

setThreadPoolCPUsAvailable(int) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Sets thread pool to reserve a given number of processor cores for foreground or other use.

setThreadPoolCPUsFraction(float) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Sets thread pool to a given fraction of the available processors.

setThreadPoolDefault() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Sets thread pool to default of 1 background thread for each processor core.

setThreadPoolSingle() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Sets thread pool to a single background thread.

setThreadPoolSize(int) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Sets thread pool to given size.

setThreads(int) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setThree_letter_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setTime(int) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setTime(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setTimeout(int) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider

setTissue(String) - Method in class org.biojava.nbio.structure.Compound

setTissue(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setTissue_fraction(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat

setTitle(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

Set the title of the AlignmentJmol window.

setTitle(String) - Method in class org.biojava.nbio.structure.Compound

setTitle(String) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol

setTitle(String) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl

setTitle(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

setTitle(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of title

setTitle(String) - Method in class org.biojava.nbio.structure.PDBHeader

setTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setTmIntra(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setTMScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setTo(Integer) - Method in class org.biojava.nbio.structure.domain.pdp.Segment

setTool(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService

Set the tool identifier for QBlast.

setTopologyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setTorsionPenalty(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setTotalArea(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setTotalLenIni(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setTotalLenOpt(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setTotalRmsdIni(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

this is the init-RMSD, not the final RMSD after refinement.

setTotalRmsdOpt(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

The RMSD of the final alignment.

setTraceRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setTraceTmScoreMin(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setTrans(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setTranscriptionEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

setTranscriptionStart(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

setTransfAlgebraic(List<String>) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setTransformation(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setTransformation(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setTransformationMatrix(Matrix4d) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Sets the transformation using a 4x4 transformation matrix

setTransformations(List<Matrix4d>) - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Set a new superposition for the structures.

setTransformations(List<Matrix4d>) - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

setTransformId(int) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

setTransforms(Pair<CrystalTransform>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setTransforms(List<BiologicalAssemblyTransformation>) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

setTranslation(double[]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

setTransNCS(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the transNCS property.

setTryAllCPs(Boolean) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

setTurn(char, int) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

Set the turn column corresponding to 3,4 or 5 helix patterns.

setTwi(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setTwinFraction(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the twinFraction property.

setTwinL(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the twinL property.

setTwinL2(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the twinL2 property.

setTwistedGroups(Group[]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner

setType(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

Set the feature type

setType(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setType(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Change the type of this feature.

setType(StainType) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier

setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setType(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

setType(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setType(SecStrucType) - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

setType(CESymmParameters.SymmetryType) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setType_symbol(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite

setType_symbol(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

setUid(Long) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setUnaryOperators(List<String>) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver

setUncertain(boolean) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

setUniprot(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

setUniprot(String) - Method in class org.biojava.nbio.phosphosite.Site

setUniProtAccessionId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setUniprotbaseURL(String) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

setUniprotDirectoryCache(String) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

setUniProtId(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setUniProtId(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setUniProtPos(Integer) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setUniProtResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setUnitv(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setUnknown(boolean) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

setUnrefinedScoreThreshold(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setUnweightedStrataInfoHashMap(LinkedHashMap<String, StrataInfo>) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo

setUpdateRemediatedFiles(boolean) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setUpdateRemediatedFiles(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Deprecated.
Properties which impact downloading and caching behavior have been moved to the StructureIOFile implementations. See LocalPDBDirectory.setFetchBehavior(LocalPDBDirectory.FetchBehavior)

setUrl(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Specify a different mirror for the ECOD server.

setUsed(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setUsedAtomNames(String[]) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setUseInternalChainId(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Set the useInternalChainId parsing mode.

setUseMmCif(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

setUserCollection(Collection<Object>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setUsername(String) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setUserObject(Object) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

Allow the user to associate an object with the feature.

setUserObject(Object) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setUserObject(Object) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

setUserOrder(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setValue(String) - Method in class org.biojava.nbio.core.sequence.features.Qualifier

setValue(int) - Method in class org.biojava.nbio.structure.align.helper.AligMatEl

setValue(int) - Method in class org.biojava.nbio.structure.align.helper.GapArray

setValue_order(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

setVariableResiduals(double[][]) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setVariance(double[][]) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setVariant(String) - Method in class org.biojava.nbio.structure.Compound

setVector(double[]) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

setVerbose(boolean) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

setVerbose(boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel

setVerbose(boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener

setVerbose(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setVersion(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setVersion(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setVersion(Integer) - Method in class org.biojava.nbio.core.sequence.AccessionID

setVersion(int) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

setVersion(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setVersion(String) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Sets the version of the algorithm used to generate the MultipleAlignment objects.

setVersion(String) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setVersion(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setVersion(String) - Method in class org.biojava.nbio.structure.validation.Program

Sets the value of the version property.

setVolume(String) - Method in class org.biojava.nbio.structure.JournalArticle

setWaitForAlignments(boolean) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable

setWaldTestInfo(WaldTestInfo) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setWeight(Double) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand

setWeight(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setWeighted(boolean) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo

setWilsonBaniso(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the wilsonBaniso property.

setWilsonBestimate(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the wilsonBestimate property.

setWinSize(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setWinSize(int) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setX(double) - Method in interface org.biojava.nbio.structure.Atom

Set the X coordinate.

setX(double) - Method in class org.biojava.nbio.structure.AtomImpl

setXGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setXGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setXMLcreationDate(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the xmLcreationDate property.

setXtriageInputColumns(String) - Method in class org.biojava.nbio.structure.validation.Entry

Sets the value of the xtriageInputColumns property.

setY(double) - Method in interface org.biojava.nbio.structure.Atom

Set the Y coordinate.

setY(double) - Method in class org.biojava.nbio.structure.AtomImpl

setZ(double) - Method in interface org.biojava.nbio.structure.Atom

Set the Z coordinate.

setZ(double) - Method in class org.biojava.nbio.structure.AtomImpl

setZ(BigDecimal) - Method in class org.biojava.nbio.structure.validation.AngleOutlier

Sets the value of the z property.

setZ(BigDecimal) - Method in class org.biojava.nbio.structure.validation.BondOutlier

Sets the value of the z property.

setZ(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

setZ_PDB(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell

setZoom(int) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl

setZoom(int) - Method in interface org.biojava.nbio.structure.gui.StructureViewer

Set the Zoom level

setZscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier

Sets the value of the zscore property.

setZscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier

Sets the value of the zscore property.

shift(Structure, Atom) - Static method in class org.biojava.nbio.structure.Calc

shift a structure with a vector.

shift(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Shift a vector.

shift(Group, Atom) - Static method in class org.biojava.nbio.structure.Calc

Shift a Group with a vector.

shift(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc

Shift an array of atoms at once.

shiftAtAlignmentLocation(Location, int) - Method in interface org.biojava.nbio.core.alignment.template.MutableAlignedSequence

Slides a part of the AlignedSequence.

shiftAtSequenceLocation(Location, int) - Method in interface org.biojava.nbio.core.alignment.template.MutableAlignedSequence

Slides a part of the AlignedSequence.

shiftCA2(AFPChain, Atom[], Matrix, Atom, Group[]) - Static method in class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay

only shift CA positions.

ShortSegmentRemover - Class in org.biojava.nbio.structure.domain.pdp

ShortSegmentRemover() - Constructor for class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover

shouldCreateAtomBonds() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should we create bonds between atoms when parsing a file?

shouldCreateAtomCharges() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should we create charges on atoms when parsing a file?

show(BufferedReader, UserConfiguration) - Method in class org.biojava.nbio.structure.align.gui.DBResultTable

show(File, UserConfiguration) - Method in class org.biojava.nbio.structure.align.gui.DBResultTable

show(URL, UserConfiguration) - Method in class org.biojava.nbio.structure.align.gui.DBResultTable

showAboutDialog() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator

Show some info about this GUI

showAFPRanges - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

showAFPRanges - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

showAlignmentGUI() - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

showAlignmentImage(AFPChain, Atom[], Atom[], Object) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

showAlignmentImage(AFPChain, String) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP

showAlignmentImage(MultipleAlignment, String) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay

Creates a new Frame with the String output representation of the MultipleAlignment.

showAlignmentPanel(AFPChain, Atom[], Atom[], AbstractAlignmentJmol) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP

showAlternative(int) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame

showAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator

Returns a Jmol script to show axes

showAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH

Returns a Jmol script to show axes

showAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup

showCompound() - Method in class org.biojava.nbio.structure.Compound

showConsole(boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener

showDBResults(StartupParameters) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

showDialog() - Method in class org.biojava.nbio.structure.align.gui.AboutDialog

showDialog() - Static method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel

showDialog() - Method in class org.biojava.nbio.structure.align.gui.HelpDialog

showDialog() - Method in class org.biojava.nbio.structure.align.gui.SystemInfo

showDistanceMatrix(int) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame

showDocument(URL) - Static method in class org.biojava.nbio.structure.align.webstart.BrowserOpener

open a URL in the browser that was used to launch SPICE

showDocument(String) - Static method in class org.biojava.nbio.structure.align.webstart.BrowserOpener

open a URL in the browser that was used to launch SPICE

showDocument(URL) - Static method in class org.biojava.nbio.structure.align.webstart.JNLPProxy

showHeader() - Method in class org.biojava.nbio.structure.Compound

Print some debug statements to System.out

showMemoryMonitor() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator

showMultipleAligmentPanel(MultipleAlignment, AbstractAlignmentJmol) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay

Creates a new Frame with the MultipleAlignment Sequence Panel.

ShowPDBIDListener - Class in org.biojava.nbio.structure.align.gui

ShowPDBIDListener() - Constructor for class org.biojava.nbio.structure.align.gui.ShowPDBIDListener

showPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator

showPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH

showPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup

showProgressBar() - Static method in class org.biojava.nbio.structure.align.gui.StructureLoaderThread

showSource() - Method in class org.biojava.nbio.structure.Compound

showStructure(Structure) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

Shows a structure in Jmol

ShowStructureInJmol - Class in demo

Demo how to load and display a structure in Jmol

ShowStructureInJmol() - Constructor for class demo.ShowStructureInJmol

showSuggest() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest

Force the suggestions to be displayed (Useful for buttons e.g.

showSystemInfo() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator

showUrl(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener

shuffle(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Implements sequence shuffling by first materializing the given Sequence into a List, applying Collections.shuffle(List) and then returning the shuffled elements in a new instance of SequenceBackingStore which behaves as a Sequence.

shuffleColumnsAndThenRows(ArrayList<String>, ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet

Randomly shuffle the columns and rows.

shuffleColumnValues(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet

Need to shuffle column values to allow for randomized testing.

shuffleRowValues(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet

Need to shuffle rows values to allow for randomized testing.

shutdown() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Disables new tasks from being submitted and closes the thread pool cleanly.

shutdownAndAwaitTermination() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Closes the thread pool.

sideChainScoringType - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

SiftsChainEntry - Class in org.biojava.nbio.structure.io.sifts

An entry in the chain-level SIFTS mapping between UniProt and the PDB.

SiftsChainEntry(String, String, String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

SiftsChainToUniprotMapping - Class in org.biojava.nbio.structure.io.sifts

A mapping between UniProt entries and PDB chains.

SiftsEntity - Class in org.biojava.nbio.structure.io.sifts

SiftsEntity() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsEntity

SiftsEntity(String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsEntity

SiftsMappingProvider - Class in org.biojava.nbio.structure.io.sifts

SiftsMappingProvider() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider

SiftsResidue - Class in org.biojava.nbio.structure.io.sifts

SiftsResidue() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsResidue

SiftsSegment - Class in org.biojava.nbio.structure.io.sifts

SiftsSegment() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsSegment

SiftsSegment(String, String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsSegment

SiftsXMLParser - Class in org.biojava.nbio.structure.io.sifts

SiftsXMLParser() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsXMLParser

SigEva - Class in org.biojava.nbio.structure.align.fatcat.calc

SigEva() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.SigEva

signatureName - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults

SIMILARITY_COLOR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator

SimpleAlignedSequence<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.core.alignment

Implements a data structure for a Sequence within an alignment.

SimpleAlignedSequence(S, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleAlignedSequence

Creates an AlignedSequence for the given Sequence in a global alignment.

SimpleAlignedSequence(S, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.core.alignment.SimpleAlignedSequence

Creates an AlignedSequence for the given Sequence in a local alignment.

SimpleAlignedSequence(AlignedSequence<S, C>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleAlignedSequence

Creates a new AlignedSequence for the given AlignedSequence in a global alignment.

SimpleAlignedSequence(AlignedSequence<S, C>, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.core.alignment.SimpleAlignedSequence

Creates a new AlignedSequence for the given AlignedSequence in a local alignment.

SimpleGapPenalty - Class in org.biojava.nbio.alignment

Implements a data structure for the gap penalties used during a sequence alignment routine.

SimpleGapPenalty() - Constructor for class org.biojava.nbio.alignment.SimpleGapPenalty

Creates a new set of gap penalties using the defaults.

SimpleGapPenalty(int, int) - Constructor for class org.biojava.nbio.alignment.SimpleGapPenalty

Creates a new set of gap penalties.

SimpleLocation - Class in org.biojava.nbio.core.sequence.location

Very basic implementation of the Location interface which defines a series of simple constructors.

SimpleLocation(int, int) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(int, int, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, boolean, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleMMcifConsumer - Class in org.biojava.nbio.structure.io.mmcif

A MMcifConsumer implementation that builds an in-memory representation of the content of a mmcif file as a BioJava Structure object.

SimpleMMcifConsumer() - Constructor for class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer

SimpleMMcifParser - Class in org.biojava.nbio.structure.io.mmcif

A simple mmCif file parser Usage:

SimpleMMcifParser() - Constructor for class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

SimplePoint - Class in org.biojava.nbio.core.sequence.location

Basic implementation of the Point interface.

SimplePoint() - Constructor for class org.biojava.nbio.core.sequence.location.SimplePoint

SimplePoint(int) - Constructor for class org.biojava.nbio.core.sequence.location.SimplePoint

SimplePoint(int, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.SimplePoint

SimpleProfile<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.core.alignment

Implements a data structure for the results of sequence alignment.

SimpleProfile(AlignedSequence<S, C>, AlignedSequence<S, C>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile

Creates a pair profile for the given already aligned sequences.

SimpleProfile(S) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile

Creates a profile from a single sequence.

SimpleProfile(S, S, List<AlignedSequence.Step>, int, int, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile

Creates a pair profile for the given sequences.

SimpleProfile(Profile<S, C>, Profile<S, C>, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile

Creates a pair profile for the given profiles.

SimpleProfile(Collection<AlignedSequence<S, C>>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile

Creates a profile for the already aligned sequences.

SimpleProfilePair<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.core.alignment

Implements a data structure for the results of the alignment of a pair of Profiles.

SimpleProfilePair(Profile<S, C>, Profile<S, C>, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfilePair

Creates a pair profile for the given profiles.

SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment

Implements a simple (naive) Aligner for a pair of Profiles.

SimpleProfileProfileAligner() - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner

Before running a profile-profile alignment, data must be sent in via calls to AbstractProfileProfileAligner.setQuery(Profile), AbstractProfileProfileAligner.setTarget(Profile), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).

SimpleProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner

Prepares for a profile-profile alignment.

SimpleProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner

Prepares for a profile-profile alignment run concurrently.

SimpleProfileProfileAligner(Profile<S, C>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner

Prepares for a profile-profile alignment run concurrently.

SimpleProfileProfileAligner(Future<ProfilePair<S, C>>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner

Prepares for a profile-profile alignment run concurrently.

SimpleSequencePair<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.core.alignment

Implements a data structure for the results of pairwise sequence alignment.

SimpleSequencePair(AlignedSequence<S, C>, AlignedSequence<S, C>) - Constructor for class org.biojava.nbio.core.alignment.SimpleSequencePair

Creates a pair profile for the given already aligned sequences.

SimpleSequencePair(S, S, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleSequencePair

Creates a pair profile for the given sequences with a global alignment.

SimpleSequencePair(S, S, List<AlignedSequence.Step>, int, int, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.core.alignment.SimpleSequencePair

Creates a pair profile for the given sequences with a local alignment.

SimpleSubstitutionMatrix<C extends Compound> - Class in org.biojava.nbio.core.alignment.matrices

Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.

SimpleSubstitutionMatrix(CompoundSet<C>, File) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix

Creates a substitution matrix by reading in a file.

SimpleSubstitutionMatrix(CompoundSet<C>, Reader, String) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix

Creates a substitution matrix by parsing some input.

SimpleSubstitutionMatrix(CompoundSet<C>, String, String) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix

Creates a substitution matrix by parsing a String.

SimpleSubstitutionMatrix(CompoundSet<C>, short, short) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix

Creates an identity substitution matrix from match and replace values.

SingleCompoundSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage

An implementation of the SequenceReader interface which for every call will return only 1 compound (given to it during construction; a String is also valid but will require a CompoundSet).

SingleCompoundSequenceReader(String, CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Public constructor to be used with String based constructor

SingleCompoundSequenceReader(C, CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Build the object with a compound rather than a String

SingleLinkageClusterer - Class in org.biojava.nbio.core.util

An implementation of a single linkage clusterer See http://en.wikipedia.org/wiki/Single-linkage_clustering

SingleLinkageClusterer(double[][], boolean) - Constructor for class org.biojava.nbio.core.util.SingleLinkageClusterer

Constructs a new SingleLinkageClusterer Subsequently use SingleLinkageClusterer.getDendrogram() to get the full tree or SingleLinkageClusterer.getClusters(double) to get the clusters at a certain cutoff in the tree Please note that the matrix will be altered during the clustering procedure.

singleLocationPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser

parse a location.

SingularValueDecomposition - Class in org.biojava.nbio.structure.jama

Singular Value Decomposition.

SingularValueDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.SingularValueDecomposition

Construct the singular value decomposition.

Site - Class in org.biojava.nbio.phosphosite

Created by ap3 on 31/10/2014.

Site() - Constructor for class org.biojava.nbio.phosphosite.Site

Site - Class in org.biojava.nbio.structure

Holds the data of sites presented in PDB files.

Site() - Constructor for class org.biojava.nbio.structure.Site

Site(String, List<Group>) - Constructor for class org.biojava.nbio.structure.Site

site2 - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues

size() - Method in class org.biojava.nbio.core.util.FlatFileCache

size() - Method in class org.biojava.nbio.core.util.SoftHashMap

size() - Method in class org.biojava.nbio.ontology.utils.SmallMap

size() - Method in interface org.biojava.nbio.structure.align.multiple.Block

Returns the number of aligned structures (rows) in the Block.

size() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

size() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Returns the number of aligned structures in the BlockSet.

size() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

size() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the number of aligned structures in the MultipleAlignment.

size() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Returns the number of aligned structures in the MultipleAlignments.

size() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

size() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

size() - Method in class org.biojava.nbio.structure.contact.AtomContactSet

size() - Method in class org.biojava.nbio.structure.contact.GroupContactSet

size() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

size() - Method in interface org.biojava.nbio.structure.Group

Get number of atoms.

size() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper

SIZE - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel

size() - Method in class org.biojava.nbio.structure.HetatomImpl

Get number of atoms.

size() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

Returns the number of mapped entries.

size() - Method in class org.biojava.nbio.structure.math.SparseVector

size() - Method in class org.biojava.nbio.structure.math.SymbolTable

How many keys are in the table?

size() - Method in interface org.biojava.nbio.structure.Structure

Return number of Chains in this Structure.

size(int) - Method in interface org.biojava.nbio.structure.Structure

Return number of chains of model.

size() - Method in class org.biojava.nbio.structure.StructureImpl

return number of chains , if NMR return number of chains of first model .

size(int) - Method in class org.biojava.nbio.structure.StructureImpl

return number of chains of model.

size() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

skip(long) - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Skips characters.

skip(long) - Method in class org.biojava.nbio.core.util.UncompressInputStream

skip(long) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser

Method skips n nucleotides in sequence stream.

sleepAmount - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface

slider - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel

SLIDER_STEPS - Static variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel

SmallAnnotation - Class in org.biojava.nbio.ontology.utils

Annotation that is optimized for memory usage.

SmallAnnotation() - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation

Return a new SmallAnnotation optimised for small sets of properties.

SmallAnnotation(Annotation) - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation

Return a new SmallAnnotation that copies all values from another annoation.

SmallAnnotation(Map) - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation

Return a new SmallAnnotation that copies all values from a Map.

SmallMap - Class in org.biojava.nbio.ontology.utils

Lightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability.

SmallMap() - Constructor for class org.biojava.nbio.ontology.utils.SmallMap

SmallMap(int) - Constructor for class org.biojava.nbio.ontology.utils.SmallMap

SmallMap(Map) - Constructor for class org.biojava.nbio.ontology.utils.SmallMap

SMART - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference

smartAdapter - Static variable in class org.biojava.nbio.structure.gui.BiojavaJmol

smartAdapter - Static variable in class org.biojava.nbio.structure.gui.JmolViewerImpl

SmithWaterman<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment

Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence).

SmithWaterman() - Constructor for class org.biojava.nbio.alignment.SmithWaterman

Before running a pairwise local sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).

SmithWaterman(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SmithWaterman

Prepares for a pairwise local sequence alignment.

SmithWaterman3Daligner - Class in org.biojava.nbio.structure.align.seq

provides a 3D superimposition based on the sequence alignment

SmithWaterman3Daligner() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

SmithWaterman3DParameters - Class in org.biojava.nbio.structure.align.seq

SmithWaterman3DParameters() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

SmithWatermanStartupParams() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

SmithWatermanUserArgumentProcessor - Class in org.biojava.nbio.structure.align.seq

SmithWatermanUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor

SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams - Class in org.biojava.nbio.structure.align.seq

SoftHashMap<K,V> - Class in org.biojava.nbio.core.util

A in memory cache using soft references.

SoftHashMap() - Constructor for class org.biojava.nbio.core.util.SoftHashMap

SoftHashMap(int) - Constructor for class org.biojava.nbio.core.util.SoftHashMap

SolexaFastqReader - Class in org.biojava.nbio.sequencing.io.fastq

Reader for FastqVariant.FASTQ_SOLEXA formatted sequences.

SolexaFastqReader() - Constructor for class org.biojava.nbio.sequencing.io.fastq.SolexaFastqReader

SolexaFastqWriter - Class in org.biojava.nbio.sequencing.io.fastq

Writer for FastqVariant.FASTQ_SOLEXA formatted sequences.

SolexaFastqWriter() - Constructor for class org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriter

solve(Matrix) - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition

Solve A*X = B

solve(Matrix) - Method in class org.biojava.nbio.structure.jama.LUDecomposition

Solve A*X = B

solve(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Solve A*X = B

solve(Matrix) - Method in class org.biojava.nbio.structure.jama.QRDecomposition

Least squares solution of A*X = B

solveTranspose(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Solve X*A = B, which is also A'*X' = B'

SOPair(String, int) - Constructor for class org.biojava.nbio.ontology.obo.OboFileParser.SOPair

SOPair(String, int, int) - Constructor for class org.biojava.nbio.ontology.obo.OboFileParser.SOPair

sort() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Sorts the interface list and reassigns ids based on new sorting

sortAfps(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator

sortBlocks(List<Block>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Sort blocks so that the specified row is in sequential order.

sortByFoldDecending() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

sortByStart() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Create a new list that is ordered by the starting index of the features' locations.

sortSequenceClustersBySize(List<SequenceAlignmentCluster>) - Static method in class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer

source() - Method in class org.biojava.nbio.genome.parsers.gff.Feature

Get source (aka method).

SOURCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

SpaceGroup - Class in org.biojava.nbio.structure.xtal

A crystallographic space group.

SpaceGroup(int, int, int, String, String, BravaisLattice) - Constructor for class org.biojava.nbio.structure.xtal.SpaceGroup

SpaceGroupMapElements - Class in org.biojava.nbio.structure.xtal.io

SpaceGroupMapElements(Integer, SpaceGroup) - Constructor for class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements

SpaceGroupMapRoot - Class in org.biojava.nbio.structure.xtal.io

SpaceGroupMapRoot() - Constructor for class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot

SparseSquareMatrix - Class in org.biojava.nbio.structure.math

A sparse, square matrix, implementing using two arrays of sparse vectors, one representation for the rows and one for the columns.

SparseSquareMatrix(int) - Constructor for class org.biojava.nbio.structure.math.SparseSquareMatrix

initialize an N-by-N matrix of all 0s

SparseVector - Class in org.biojava.nbio.structure.math

A sparse vector, implemented using a symbol table.

SparseVector(int) - Constructor for class org.biojava.nbio.structure.math.SparseVector

Constructor.

SphereSampler - Class in org.biojava.nbio.structure.symmetry.geometry

splice(DNASequence) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Concatenate successive portions of the specified sequence using the feature locations in the list.

splitBlocksByTopology(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

SplitFasta - Class in org.biojava.nbio.genome.util

Utility to write each Fasta entry to a unique file

SplitFasta() - Constructor for class org.biojava.nbio.genome.util.SplitFasta

sqrt(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix

sqrt(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix

SqrtColorMapper - Class in org.biojava.nbio.structure.gui.util.color

Performs a sqrt transform on input before passing the values off to another colorMapper.

SqrtColorMapper(ContinuousColorMapper) - Constructor for class org.biojava.nbio.structure.gui.util.color.SqrtColorMapper

Creates a new SqrtColorMapper.

SSBondImpl - Class in org.biojava.nbio.structure.io

A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.

SSBondImpl() - Constructor for class org.biojava.nbio.structure.io.SSBondImpl

StainType - Enum in org.biojava.nbio.genome.parsers.cytoband

standardAASet - Static variable in class org.biojava.nbio.aaproperties.PeptideProperties

Contains the 20 standard AA code in a set

StandardAminoAcid - Class in org.biojava.nbio.structure

A class that provides a set of standard amino acids.

StandardRescoreRefiner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment

StandardRescoreRefiner(Alignments.PairInProfileScorerType, Alignments.ProfileProfileAlignerType) - Constructor for class org.biojava.nbio.alignment.StandardRescoreRefiner

start() - Method in class org.biojava.nbio.genome.parsers.gff.Location

Get starting index (origin 0).

start() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface

START_SEQUENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

StartCodonSequence - Class in org.biojava.nbio.core.sequence

Used to map the start codon feature on a gene

StartCodonSequence(TranscriptSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.StartCodonSequence

startElement(String, String, String, Attributes) - Method in class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler

startingAlignment(String, Atom[], String, Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener

startsAfter(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location

Check if this location starts after the other location starts.

startsBefore(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location

Check if this location starts before other location starts.

StartupParameters - Class in org.biojava.nbio.structure.align.ce

a simple bean that contains the parameters that can get set at startup

StartupParameters() - Constructor for class org.biojava.nbio.structure.align.ce.StartupParameters

stateChanged(ChangeEvent) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel

stateChanged(ChangeEvent) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay

StaticMemberPlaceHolder - Class in org.biojava.nbio.ontology.utils

StaticMemberPlaceHolder(Field) - Constructor for class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder

StaticMemberPlaceHolder() - Constructor for class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder

status - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

StatusDisplay - Class in org.biojava.nbio.structure.align.gui.aligpanel

StatusDisplay() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

StdArrayIO - Class in org.biojava.nbio.survival.cox.matrix

Standard array IO.

StdArrayIO() - Constructor for class org.biojava.nbio.survival.cox.matrix.StdArrayIO

stdev - Variable in class org.biojava.nbio.structure.validation.AngleOutlier

stdev - Variable in class org.biojava.nbio.structure.validation.BondOutlier

stdev - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier

stdev - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier

StockholmFileAnnotation - Class in org.biojava.nbio.alignment.io

Stores all the content parsed from the #=GF lines

StockholmFileAnnotation() - Constructor for class org.biojava.nbio.alignment.io.StockholmFileAnnotation

StockholmFileAnnotation.StockholmFileAnnotationReference - Class in org.biojava.nbio.alignment.io

StockholmFileAnnotationReference() - Constructor for class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference

StockholmFileParser - Class in org.biojava.nbio.alignment.io

Stockholm file parser.
for more information about the format refer to ftp://ftp.sanger.ac.uk/pub/databases /Pfam/current_release/userman.txt. ftp://ftp.sanger.ac.uk/pub/databases/Rfam/CURRENT /USERMAN. http://sonnhammer.sbc.su.se/Stockholm.html.

StockholmFileParser() - Constructor for class org.biojava.nbio.alignment.io.StockholmFileParser

StockholmStructure - Class in org.biojava.nbio.alignment.io

Stores all the content of a Stockholm file.

StockholmStructure() - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure

StockholmStructure.DatabaseReference - Class in org.biojava.nbio.alignment.io

stop() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider

Interrupt searching for suggestions

stop() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider

stop() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider

stop() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface

stopAtStopCodons(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

If set, then the last codon translated in the resulting peptide sequence will be the stop codon

StopCodonSequence - Class in org.biojava.nbio.core.sequence

Used to map the stop codon sequence on a gene

StopCodonSequence(TranscriptSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.StopCodonSequence

storeObjects(List<Result>) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser

storeObjects(List<Result>) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser

storeObjects(List<Result>) - Method in interface org.biojava.nbio.core.search.io.ResultFactory

The factory that implements this method will be able to save the Search results to a file in the same format that it is able to read.

storeParameters() - Method in class org.biojava.nbio.structure.align.gui.ParameterGUI

storeUnAlignedSeqRes(Structure, List<Chain>, boolean) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner

Storing unaligned SEQRES groups in a Structure.

str - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair

Strand - Enum in org.biojava.nbio.core.sequence

Provides a way of representing the strand of a sequence, location hit or feature.

StrataInfo - Class in org.biojava.nbio.survival.cox

Information needed to represent a survival curve

StrataInfo() - Constructor for class org.biojava.nbio.survival.cox.StrataInfo

StrCompAlignment - Class in org.biojava.nbio.structure.align.pairwise

StrCompAlignment(int, int) - Constructor for class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

stream(Readable, StreamListener) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqReader

Stream the specified readable.

StreamListener - Interface in org.biojava.nbio.sequencing.io.fastq

Event based parser callback.

STRING_LIMIT - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

Quoting character ; (multi-line quoting)

StringManipulationHelper - Class in org.biojava.nbio.core.util

A utility class for common String manipulation tasks.

StringProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader

An example of a ProxySequenceReader that is created from a String.

StringProxySequenceReader() - Constructor for class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

StringProxySequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

stringToFloats(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

StrucAligParameters - Class in org.biojava.nbio.structure.align

A class that contains all the parameters of the structure alignment algorithm.

StrucAligParameters() - Constructor for class org.biojava.nbio.structure.align.StrucAligParameters

Struct - Class in org.biojava.nbio.structure.io.mmcif.model

a bean to contain the data of the _struct lines

Struct() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Struct

StructAsym - Class in org.biojava.nbio.structure.io.mmcif.model

Contains the data for _struct_asym

StructAsym() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructAsym

StructConn - Class in org.biojava.nbio.structure.io.mmcif.model

A bean that stores data from the mmcif category _struct_conn

StructConn() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructConn

StructKeywords - Class in org.biojava.nbio.structure.io.mmcif.model

StructKeywords() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructKeywords

StructNcsOper - Class in org.biojava.nbio.structure.io.mmcif.model

A class containing the _struct_ncs_oper data

StructNcsOper() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper

StructRef - Class in org.biojava.nbio.structure.io.mmcif.model

A class to containt the _struct_ref field data

StructRef() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructRef

StructRefSeq - Class in org.biojava.nbio.structure.io.mmcif.model

StructRefSeq() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq

StructRefSeqDif - Class in org.biojava.nbio.structure.io.mmcif.model

A class to store sequence mismatch annotations

StructRefSeqDif() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif

StructSite - Class in org.biojava.nbio.structure.io.mmcif.model

Created by Matt on 11/1/2015.

StructSite() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructSite

StructSiteGen - Class in org.biojava.nbio.structure.io.mmcif.model

Created by Matt on 10/31/2015.

StructSiteGen() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen

structuralDistance(double[][], double, double, double) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator

The structural distance (d_S) uses the structural similarity (or dissimilarity) from a the structural alignment of two protein strutures.

structure - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

Structure - Interface in org.biojava.nbio.structure

Interface for a structure object.

StructureAlignment - Interface in org.biojava.nbio.structure.align

StructureAlignmentDisplay - Class in org.biojava.nbio.structure.align.gui

StructureAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay

StructureAlignmentFactory - Class in org.biojava.nbio.structure.align

StructureAlignmentFactory() - Constructor for class org.biojava.nbio.structure.align.StructureAlignmentFactory

StructureAlignmentJmol - Class in org.biojava.nbio.structure.align.gui.jmol

A class that provides a simple GUI for Jmol

StructureAlignmentJmol() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol

StructureAlignmentJmol(AFPChain, Atom[], Atom[]) - Constructor for class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol

StructureAlignmentOptimizer - Class in org.biojava.nbio.structure.align.fatcat.calc

StructureAlignmentOptimizer(int, int, Atom[], int, int, Atom[], int, int[][]) - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer

optimize the structural alignment by update the equivalent residues and then run dynamic programming input: len1 the length of structure 1; c1: the structure information of 1 len2 the length of structure 2; c2: the structure information of 2 iniLen and iniSet is the length and list of initial equivalent residues

StructureAtom - Class in org.biojava.nbio.protmod.structure

Everything that is needed to uniquely describe a atom.

StructureAtom(StructureGroup, String) - Constructor for class org.biojava.nbio.protmod.structure.StructureAtom

StructureAtomLinkage - Class in org.biojava.nbio.protmod.structure

StructureAtomLinkage(StructureAtom, StructureAtom, double) - Constructor for class org.biojava.nbio.protmod.structure.StructureAtomLinkage

StructureAtomXMLConverter - Class in org.biojava.nbio.protmod.io

StructureAtomXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.StructureAtomXMLConverter

StructureException - Exception in org.biojava.nbio.structure

An exception during the parsing of a PDB file.

StructureException(String) - Constructor for exception org.biojava.nbio.structure.StructureException

Constructs a StructureException object.

StructureException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.StructureException

Constructs a StructureException object.

StructureException(Throwable) - Constructor for exception org.biojava.nbio.structure.StructureException

Constructs a StructureException object.

StructureGroup - Class in org.biojava.nbio.protmod.structure

Information of a group (residue or ligand) involved in a modification.

StructureGroup() - Constructor for class org.biojava.nbio.protmod.structure.StructureGroup

StructureGroup(ResidueNumber, String, boolean) - Constructor for class org.biojava.nbio.protmod.structure.StructureGroup

StructureGroupXMLConverter - Class in org.biojava.nbio.protmod.io

StructureGroupXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.StructureGroupXMLConverter

StructureIdentifier - Interface in org.biojava.nbio.structure

An identifier that uniquely identifies a whole Structure or arbitrary substructure.

StructureImpl - Class in org.biojava.nbio.structure

Implementation of a PDB Structure.

StructureImpl() - Constructor for class org.biojava.nbio.structure.StructureImpl

Constructs a StructureImpl object.

StructureImpl(Group) - Constructor for class org.biojava.nbio.structure.StructureImpl

construct a Structure object that only contains a single group

StructureImpl(Chain) - Constructor for class org.biojava.nbio.structure.StructureImpl

construct a Structure object that contains a particular chain

StructureInterface - Class in org.biojava.nbio.structure.contact

An interface between 2 molecules (2 sets of atoms).

StructureInterface(Atom[], Atom[], String, String, AtomContactSet, CrystalTransform, CrystalTransform) - Constructor for class org.biojava.nbio.structure.contact.StructureInterface

Constructs a StructureInterface

StructureInterface() - Constructor for class org.biojava.nbio.structure.contact.StructureInterface

Constructs an empty StructureInterface

StructureInterfaceCluster - Class in org.biojava.nbio.structure.contact

StructureInterfaceCluster() - Constructor for class org.biojava.nbio.structure.contact.StructureInterfaceCluster

StructureInterfaceList - Class in org.biojava.nbio.structure.contact

A list of interfaces between 2 molecules (2 sets of atoms)

StructureInterfaceList() - Constructor for class org.biojava.nbio.structure.contact.StructureInterfaceList

StructureIO - Class in org.biojava.nbio.structure

A class that provides static access methods for easy lookup of protein structure related components

StructureIO() - Constructor for class org.biojava.nbio.structure.StructureIO

StructureIO.StructureFiletype - Enum in org.biojava.nbio.structure

StructureIOFile - Interface in org.biojava.nbio.structure.io

StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem.

StructureLoaderThread - Class in org.biojava.nbio.structure.align.gui

StructureName - Class in org.biojava.nbio.structure.align.client

A utility class that makes working with names of structures, domains and ranges easier.

StructureName(String) - Constructor for class org.biojava.nbio.structure.align.client.StructureName

Create a new StructureName from the given identifier, which may be a domain name, a substructure identifier, etc.

StructureName.Source - Enum in org.biojava.nbio.structure.align.client

StructurePairAligner - Class in org.biojava.nbio.structure.align

Perform a pairwise protein structure superimposition.

StructurePairAligner() - Constructor for class org.biojava.nbio.structure.align.StructurePairAligner

StructurePairSelector - Interface in org.biojava.nbio.structure.gui.util

To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.

StructureProvider - Interface in org.biojava.nbio.structure.io

A class that can provide a protein structure object from somewhere.

StructureSequenceMatcher - Class in org.biojava.nbio.structure.io

A utility class with methods for matching ProteinSequences with Structures.

StructureSequenceMatcher() - Constructor for class org.biojava.nbio.structure.io.StructureSequenceMatcher

StructureTools - Class in org.biojava.nbio.structure

A class that provides some tool methods.

StructureTools() - Constructor for class org.biojava.nbio.structure.StructureTools

StructureUtil - Class in org.biojava.nbio.protmod.structure

StructureViewer - Interface in org.biojava.nbio.structure.gui

submit(Callable<T>, String) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Queues up a task and adds a log entry.

submit(Callable<T>) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Queues up a task and adds a default log entry.

Subproblem(int, int, int, int) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem

Subproblem(int, int, int, int, boolean) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem

subSequence(int, int) - Method in class org.biojava.nbio.survival.data.CompactCharSequence

SUBSET - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

Substitute(String, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Substitute

Substitute(Sequence<C>, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Substitute

SubstitutionMatrix<C extends Compound> - Interface in org.biojava.nbio.core.alignment.template

Defines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.

substitutionMatrix - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

SubstitutionMatrixHelper - Class in org.biojava.nbio.core.alignment.matrices

Static utility to access substitution matrices that come bundled with BioJava.

SubstitutionMatrixScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment

Scores using a substitution matrix.

SubstitutionMatrixScorer(SequencePair<S, C>, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SubstitutionMatrixScorer

SubstructureIdentifier - Class in org.biojava.nbio.structure

This is the canonical way to identify a part of a structure.

SubstructureIdentifier(String) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier

Create a new identifier from a string.

SubstructureIdentifier(String, List<ResidueRange>) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier

Create a new identifier based on a set of ranges.

subtract(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

subtract two atoms ( a - b).

subtract(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix

SubunitGraph - Class in org.biojava.nbio.structure.symmetry.core

SubunitGraph(List<Point3d[]>) - Constructor for class org.biojava.nbio.structure.symmetry.core.SubunitGraph

Subunits - Class in org.biojava.nbio.structure.symmetry.core

A bean to represent info about the set of subunits being considered for a QuatSymmetryDetector alignment.

Subunits(List<Point3d[]>, List<Integer>, List<Boolean>, List<Double>, List<Double>, List<Integer>, List<String>, List<Integer>) - Constructor for class org.biojava.nbio.structure.symmetry.core.Subunits

All inputs should contain one element per subunit.

suffix(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location

The part of this location after the specified position.

suffix(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location

The part of this location after the other location (not inclusive).

suggestDomains(Structure) - Static method in class org.biojava.nbio.structure.domain.LocalProteinDomainParser

Suggest domains for a protein structure

suggestDomains(Atom[]) - Static method in class org.biojava.nbio.structure.domain.LocalProteinDomainParser

Suggest domains for a set of Calpha atoms

SULFUR_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

SUMMARY_POS - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager

Position at which the alignment summary is printed

SUMMARY_POS - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager

Position at which the alignment summary is printed

SUMOYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset

superimpose(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer

superimpose(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer

Superimpose all structures from a MultipleAlignment.

superimpose(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer

superpose(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

superposeAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

superposeAtOrigin(Point3d[], Point3d[], AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

superposeWithTranslation(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

SuperPosition - Class in org.biojava.nbio.structure.symmetry.geometry

SuperPosition() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

SuperPositionQCP - Class in org.biojava.nbio.structure.symmetry.geometry

SuperPositionQCP() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP

surf - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor

Surface() - Constructor for class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface

SurvFitInfo - Class in org.biojava.nbio.survival.cox

Contains info for graphing km figures

SurvFitInfo() - Constructor for class org.biojava.nbio.survival.cox.SurvFitInfo

SurvFitKM - Class in org.biojava.nbio.survival.kaplanmeier.figure

Ported from survfitKM.S When combining multiple entries with same time not sure how the weighting adds up

SurvFitKM() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM

SurvFitKM.ConfLower - Enum in org.biojava.nbio.survival.kaplanmeier.figure

SurvFitKM.ConfType - Enum in org.biojava.nbio.survival.kaplanmeier.figure

SurvFitKM.Error - Enum in org.biojava.nbio.survival.kaplanmeier.figure

SurvFitKM.Method - Enum in org.biojava.nbio.survival.kaplanmeier.figure

SurvivalInfo - Class in org.biojava.nbio.survival.cox

Data class to represent a single sample where time and event/censor status is required Additionally each variable and data associated with that variable.

SurvivalInfo(double, int) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo

SurvivalInfo(double, int, LinkedHashMap<String, Double>) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo

SurvivalInfo(double, int, String, double) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo

SurvivalInfoComparator - Class in org.biojava.nbio.survival.cox.comparators

SurvivalInfoComparator() - Constructor for class org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator

SurvivalInfoHelper - Class in org.biojava.nbio.survival.cox

Used to work with SurvivalInfo

SurvivalInfoHelper() - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoHelper

SurvivalInfoIndex - Class in org.biojava.nbio.survival.cox

Not used and probably should be deleted

SurvivalInfoIndex(double, int, int) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoIndex

SurvivalInfoIndex(double, int, int, double[]) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoIndex

SurvivalInfoIndex(double, int, int, double) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoIndex

SurvivalInfoValueComparator - Class in org.biojava.nbio.survival.cox.comparators

SurvivalInfoValueComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator

svd() - Method in class org.biojava.nbio.structure.jama.Matrix

Singular Value Decomposition

SVDSuperimposer - Class in org.biojava.nbio.structure

A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class...

SVDSuperimposer(Atom[], Atom[]) - Constructor for class org.biojava.nbio.structure.SVDSuperimposer

Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.

swapRowAndColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet

Swap the row and columns returning a new worksheet

SymbolTable<Key extends Comparable<Key>,Value> - Class in org.biojava.nbio.structure.math

Sorted symbol table implementation using a java.util.TreeMap.

SymbolTable() - Constructor for class org.biojava.nbio.structure.math.SymbolTable

Create an empty symbol table.

symmClash - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

SymmClash - Class in org.biojava.nbio.structure.validation

Java class for anonymous complex type.

SymmClash() - Constructor for class org.biojava.nbio.structure.validation.SymmClash

SYMMETRIC - Static variable in class org.biojava.nbio.ontology.OntoTools

Symmetry - Class in org.biojava.nbio.structure.io.mmcif.model

Symmetry() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Symmetry

SymmetryAxes - Class in org.biojava.nbio.structure.symmetry.internal

Data Structure that stores all the symmetry axis that describe the symmetry of a structure.

SymmetryAxes() - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Constructor.

SymmetryCalc - Class in org.biojava.nbio.structure.symmetry.gui

Calculates a symmetry analysis and displays the results.

SymmetryCalc(SymmetryGui, Structure) - Constructor for class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc

Requests for a structure to analyze.

symmetryCoefficient() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia

SymmetryDisplay - Class in org.biojava.nbio.structure.symmetry.gui

Class that provides visualizations methods for symmetry alignments.

SymmetryDisplay() - Constructor for class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay

SymmetryGui - Class in org.biojava.nbio.structure.symmetry.gui

A JFrame that allows to trigger a symmetry analysis, either from files in a directory or after manual upload Adapted from the AlignmentGui class in biojava.

SymmetryListener - Class in org.biojava.nbio.structure.symmetry.gui

Action Listener for the symmetry menu.

SymmetryListener(MultipleAlignmentJmol, CeSymmResult) - Constructor for class org.biojava.nbio.structure.symmetry.gui.SymmetryListener

SymmetryRefiner - Interface in org.biojava.nbio.structure.symmetry.internal

Interface for all symmetry refinement implementations.

SymmetryTools - Class in org.biojava.nbio.structure.symmetry.utils

Utility methods for the internal symmetry identification and manipulation.

SymmOptimizer - Class in org.biojava.nbio.structure.symmetry.internal

Optimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment.

SymmOptimizer(CeSymmResult) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmOptimizer

Constructor with a seed MultipleAligment storing a refined symmetry alignment of the repeats.

symop - Variable in class org.biojava.nbio.structure.validation.SymmClash

SymoplibParser - Class in org.biojava.nbio.structure.xtal

A class containing static methods to parse the symop.lib file from the CCP4 package.

SymoplibParser() - Constructor for class org.biojava.nbio.structure.xtal.SymoplibParser

SynchronizedOutFile - Class in org.biojava.nbio.structure.align.util

SynchronizedOutFile(File, boolean) - Constructor for class org.biojava.nbio.structure.align.util.SynchronizedOutFile

Create a thread safe wrapper for writing to this file, the file will be gzip compressed.

SynchronizedOutFile(File) - Constructor for class org.biojava.nbio.structure.align.util.SynchronizedOutFile

create a thread safe wrapper for working with this file

SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

Synonym - Class in org.biojava.nbio.ontology

Synonym() - Constructor for class org.biojava.nbio.ontology.Synonym

SystematicSolver - Class in org.biojava.nbio.structure.symmetry.core

SystematicSolver(Subunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.SystematicSolver

SystemInfo - Class in org.biojava.nbio.structure.align.gui

SystemInfo() - Constructor for class org.biojava.nbio.structure.align.gui.SystemInfo

T

T - Static variable in class org.biojava.nbio.aaproperties.Constraints

TabDelimParser - Class in org.biojava.nbio.ontology.io

Parse tab-delimited ontology files into Ontology objects.

TabDelimParser() - Constructor for class org.biojava.nbio.ontology.io.TabDelimParser

Table - Interface in org.biojava.nbio.core.sequence.transcription

Provides a way of separating us from the specific IUPACParser.IUPACTable even though this is the only implementing class for the interface.

table(Integer) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by ID.

table(String) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by its String name

table(Table) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

Table.CaseInsensitiveTriplet - Class in org.biojava.nbio.core.sequence.transcription

Class used to hold three nucleotides together and allow for equality to be assessed in a case insensitive manner.

Table.Codon - Class in org.biojava.nbio.core.sequence.transcription

Instance of a Codon which is 3 NucleotideCompounds, its corresponding AminoAcidCompound and if it is a start or stop codon.

TaxonomyID - Class in org.biojava.nbio.core.sequence

A sequence can be associated with a species or Taxonomy ID

TaxonomyID(String, DataSource) - Constructor for class org.biojava.nbio.core.sequence.TaxonomyID

TD - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

TD1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

tempBuffer - Variable in class org.biojava.nbio.ontology.obo.OboFileParser

TERM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

Term - Interface in org.biojava.nbio.ontology

A term in an ontology.

Term.Impl - Class in org.biojava.nbio.ontology

Simple in-memory implementation of an ontology term.

terminate() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable

Send signal to terminate calculations

terminate() - Method in class org.biojava.nbio.structure.align.FarmJob

TestDNANeedlemanWunsch - Class in demo

TestDNANeedlemanWunsch() - Constructor for class demo.TestDNANeedlemanWunsch

TETRAHEDRAL_CARBON_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

TETRAHEDRAL_NITROGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

Tetrahedron - Class in org.biojava.nbio.structure.symmetry.geometry

Tetrahedron() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

text - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

TEXT_ONLY - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator

TEXT_SCALE_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel

TextFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features

A implmentation of AbstractFeature

TextFeature(String, String, String, String) - Constructor for class org.biojava.nbio.core.sequence.features.TextFeature

thread - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface

Threshold(int) - Constructor for class org.biojava.nbio.ronn.ModelLoader.Threshold

time - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

time - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

Timer - Class in org.biojava.nbio.ronn

A simple timer, calculates the time interval between two events.

Timer() - Constructor for class org.biojava.nbio.ronn.Timer

Timer(TimeUnit) - Constructor for class org.biojava.nbio.ronn.Timer

times(double) - Method in class org.biojava.nbio.structure.jama.Matrix

Multiply a matrix by a scalar, C = s*A

times(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Linear algebraic matrix multiplication, A * B

times(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix

timeScale - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

timesEquals(double) - Method in class org.biojava.nbio.structure.jama.Matrix

Multiply a matrix by a scalar in place, A = s*A

TITLE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

titleHeight - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

TMP_DIR - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration

TMScore(Point3d[], Point3d[], int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

Returns the TM-Score for two superimposed sets of coordinates Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)

to - Variable in class org.biojava.nbio.ronn.Jronn.Range

The range ending position includes the last residue.

to3DFormat(MultipleAlignment, int, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Outputs a pairwise alignment in I-TASSER's 3D Format for target-template alignment.

toAlignedPairs(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

Prints the alignment in the simplest form: a list of aligned residues.

toAlignedResidues(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts the alignment to its simplest form: a list of groups of aligned residues.

toCanonical() - Method in class org.biojava.nbio.structure.align.client.StructureName

toCanonical() - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier

toCanonical() - Method in class org.biojava.nbio.structure.cath.CathDomain

toCanonical() - Method in class org.biojava.nbio.structure.domain.PDPDomain

toCanonical() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

toCanonical() - Method in class org.biojava.nbio.structure.PassthroughIdentifier

toCanonical() - Method in class org.biojava.nbio.structure.scop.ScopDomain

toCanonical() - Method in interface org.biojava.nbio.structure.StructureIdentifier

Convert to a canonical SubstructureIdentifier.

toCanonical() - Method in class org.biojava.nbio.structure.SubstructureIdentifier

Return itself.

toCanonical() - Method in class org.biojava.nbio.structure.URLIdentifier

toCE(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

toCE(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toCIEXYZ(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace

toConciseAlignmentString(Map<S, T>, Map<T, S>) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Print an alignment map in a concise representation.

toConciseAlignmentString(Map<T, T>) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

toDASStructure(XMLWriter) - Method in class org.biojava.nbio.structure.io.FileConvert

Convert a protein Structure to a DAS Structure XML response .

toDBSearchResult() - Method in class org.biojava.nbio.structure.align.model.AFPChain

toDBSearchResult(AFPChain) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toDoubleArray(Collection<Number>) - Static method in class org.biojava.nbio.structure.align.util.CollectionTools

toFASTA(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts the MultipleAlignment into a multiple sequence alignment String in FASTA format.

toFatcat(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

toFatCat(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toFatCat(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts the MultipleAlignment into a FatCat String format.

toFatCatCore(AFPChain, Atom[], Atom[], boolean, boolean, boolean, boolean) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

Output in FatCatCore format

toFullAlignment(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Method that converts a repeats symmetric alignment into an alignment of whole structures.

toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay

toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

toggleSelection(AlignedPosition) - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener

toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener

toHexColor(Color) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils

toIndex(int) - Method in class org.biojava.nbio.core.sequence.views.ReversedSequenceView

toIntArray(Collection<Number>) - Static method in class org.biojava.nbio.structure.align.util.CollectionTools

toList(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

For the given Sequence this will return a List filled with the Compounds of that Sequence.

toLoopMmCifHeaderString(String, String) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Produces a mmCIF loop header string for the given categoryName and className.

toMMCIF() - Method in interface org.biojava.nbio.structure.Chain

Convert this Chain to a String in mmCIF format

toMMCIF() - Method in class org.biojava.nbio.structure.ChainImpl

toMMCIF() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Return a String representing the 2 molecules of this interface in mmCIF format.

toMMCIF() - Method in class org.biojava.nbio.structure.io.FileConvert

toMMCIF(Chain, String, String, boolean) - Static method in class org.biojava.nbio.structure.io.FileConvert

toMMCIF(Chain, boolean) - Static method in class org.biojava.nbio.structure.io.FileConvert

toMMCIF(String, Object) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Converts a mmCIF bean (see org.biojava.nbio.structure.io.mmcif.model to a String representing it in mmCIF (single-record) format.

toMMCIF(List<Object>) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Converts a list of mmCIF beans (see org.biojava.nbio.structure.io.mmcif.model to a String representing them in mmCIF loop format with one record per line.

toMMCIF() - Method in interface org.biojava.nbio.structure.Structure

Create a String that contains this Structure's contents in MMCIF file format.

toMMCIF() - Method in class org.biojava.nbio.structure.StructureImpl

Create a String that contains this Structure's contents in MMCIF file format.

Tools() - Constructor for class org.biojava.nbio.core.sequence.location.template.Location.Tools

top - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure

toPDB(Structure, Structure) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

converts the alignment to a PDB file each of the structures will be represented as a model.

toPDB() - Method in class org.biojava.nbio.structure.AtomImpl

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.AtomImpl

toPDB() - Method in interface org.biojava.nbio.structure.Chain

Convert this Chain to a String in PDB format

toPDB() - Method in class org.biojava.nbio.structure.ChainImpl

toPDB() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Return a String representing the 2 molecules of this interface in PDB format.

toPDB() - Method in class org.biojava.nbio.structure.DBRef

Convert the DBRef object to a DBREF record as it is used in PDB files

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.DBRef

Append the PDB representation of this DBRef to the provided StringBuffer

toPDB() - Method in class org.biojava.nbio.structure.io.FileConvert

Convert a structure into a PDB file.

toPDB(Atom) - Static method in class org.biojava.nbio.structure.io.FileConvert

Prints the content of an Atom object as a PDB formatted line.

toPDB(Atom, String) - Static method in class org.biojava.nbio.structure.io.FileConvert

toPDB(Chain) - Static method in class org.biojava.nbio.structure.io.FileConvert

Convert a Chain object to PDB representation

toPDB(Group) - Static method in class org.biojava.nbio.structure.io.FileConvert

Convert a Group object to PDB representation

toPDB(Atom, StringBuffer, String) - Static method in class org.biojava.nbio.structure.io.FileConvert

Print ATOM record in the following syntax

toPDB(Atom, StringBuffer) - Static method in class org.biojava.nbio.structure.io.FileConvert

toPDB() - Method in class org.biojava.nbio.structure.io.SSBondImpl

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.io.SSBondImpl

Append the PDB representation of this SSBOND to the provided StringBuffer

toPDB() - Method in class org.biojava.nbio.structure.PDBHeader

Return a PDB representation of the PDB Header

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.PDBHeader

Appends a PDB representation of the PDB header to the provided StringBuffer

toPDB() - Method in interface org.biojava.nbio.structure.PDBRecord

Returns a PDB file like representation of this record.

toPDB(StringBuffer) - Method in interface org.biojava.nbio.structure.PDBRecord

Appends a PDB file like representation of this record to the provided StringBuffer.

toPDB() - Method in class org.biojava.nbio.structure.ResidueNumber

toPDB() - Method in class org.biojava.nbio.structure.Site

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.Site

toPDB() - Method in interface org.biojava.nbio.structure.Structure

Create a String that contains this Structure's contents in PDB file format.

toPDB() - Method in class org.biojava.nbio.structure.StructureImpl

Create a String that contains this Structure's contents in PDB file format.

toProteinMSA(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid residues.

toRepeatsAlignment(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Method that converts a symmetry alignment into an alignment of the repeats only, as new independent structures.

toRGB(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace

toRotMat() - Method in class org.biojava.nbio.structure.align.model.AFPChain

toRotMat(AFPChain) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

torsionAngle(Atom, Atom, Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Calculate the torsion angle, i.e.

toScoresList(AFPChain) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toSDF() - Method in interface org.biojava.nbio.structure.Group

Function to get the Group as an MDL molblock

toSDF() - Method in class org.biojava.nbio.structure.HetatomImpl

toSsBond(Bond) - Static method in class org.biojava.nbio.structure.io.SSBondImpl

Converts the given Bond object into a SSBondImpl.

toStartIndex(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence

Calculates start index according to the equation start = ( (index-1) - windowSize) +1

toString() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition

toString() - Method in class org.biojava.nbio.aaproperties.xml.Element

toString() - Method in class org.biojava.nbio.alignment.GuideTree

toString() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference

toString() - Method in class org.biojava.nbio.alignment.io.StockholmStructure

toString() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

Returns in a format similar to the standard NCBI files.

toString() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix

Returns in a format similar to the standard NCBI files.

toString() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence

Provides standard Java language access to results of SimpleAlignedSequence.getSequenceAsString().

toString(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile

toString(Profile.StringFormat) - Method in class org.biojava.nbio.core.alignment.SimpleProfile

toString() - Method in class org.biojava.nbio.core.alignment.SimpleProfile

toString() - Method in interface org.biojava.nbio.core.alignment.template.Profile

Returns a simple view of the alignment profile.

toString(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile

Returns a formatted view of the alignment profile.

toString(Profile.StringFormat) - Method in interface org.biojava.nbio.core.alignment.template.Profile

Returns a formatted view of the alignment profile.

toString() - Method in class org.biojava.nbio.core.sequence.AccessionID

toString() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

toString() - Method in class org.biojava.nbio.core.sequence.features.Qualifier

toString() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

toString() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

toString() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

toString() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

toString() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

toString(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Get a string representation of the MSA with a fixed width

toString(LightweightProfile.StringFormat) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Support for different MSA formats

toString() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

String representation of the MSA

toString() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

toString() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

toString() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns a simple view of the alignment profile.

toString(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns a formatted view of the alignment profile.

toString(LightweightProfile.StringFormat) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns a formatted view of the alignment profile.

toString(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Shortcut to SequenceMixin.toStringBuilder(org.biojava.nbio.core.sequence.template.Sequence) which calls toString() on the resulting object.

toString() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

toString() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet

toString() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

toString() - Method in class org.biojava.nbio.core.util.CRC64Checksum

Returns a zero-padded 16 character wide string containing the current value of this checksum in uppercase hexadecimal format.

toString() - Method in class org.biojava.nbio.data.sequence.FastaSequence

Same as oneLineFasta

toString() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband

toString() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

toString() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

toString() - Method in class org.biojava.nbio.genome.parsers.gff.Feature

toString() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI

A string representation of the feature.

toString() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Return a string representation of all features in this list.

toString() - Method in class org.biojava.nbio.genome.parsers.gff.Location

Return a string representation of location.

toString() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator

Get string representation of iterator.

toString() - Method in class org.biojava.nbio.ontology.Ontology.Impl

toString() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

toString() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl

toString() - Method in class org.biojava.nbio.ontology.Synonym

toString() - Method in class org.biojava.nbio.ontology.Term.Impl

toString() - Method in class org.biojava.nbio.ontology.Triple.Impl

toString() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

toString() - Method in class org.biojava.nbio.phosphosite.Site

toString() - Method in class org.biojava.nbio.protmod.Component

toString() - Method in enum org.biojava.nbio.protmod.ModificationCategory

toString() - Method in class org.biojava.nbio.protmod.ModificationConditionImpl

toString() - Method in class org.biojava.nbio.protmod.ModificationLinkage

toString() - Method in enum org.biojava.nbio.protmod.ModificationOccurrenceType

toString() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

toString() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

toString() - Method in class org.biojava.nbio.protmod.structure.StructureAtom

toString() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage

toString() - Method in class org.biojava.nbio.protmod.structure.StructureGroup

toString() - Method in class org.biojava.nbio.ronn.Jronn.Range

toString() - Method in class org.biojava.nbio.ronn.ModelLoader.Model

toString() - Method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

toString() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

toString() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

toString() - Method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

toString() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

toString() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

toString() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

toString() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

toString() - Method in class org.biojava.nbio.structure.align.client.CountProgressListener

toString() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters

toString() - Method in class org.biojava.nbio.structure.align.client.PdbPair

toString() - Method in class org.biojava.nbio.structure.align.client.StructureName

toString() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

toString() - Method in class org.biojava.nbio.structure.align.fatcat.FatCat

toString() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo

toString() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl

toString() - Method in class org.biojava.nbio.structure.align.helper.IndexPair

toString() - Method in class org.biojava.nbio.structure.align.helper.JointFragments

toString() - Method in class org.biojava.nbio.structure.align.model.AFP

toString() - Method in class org.biojava.nbio.structure.align.model.AFPChain

toString() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

toString() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

toString() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

toString() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Return a summary of the MultipleAlignment, containing the structures, the lengths and the cached scores.

toString() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

toString() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

toString() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

print the idx positions of this alignment

toString() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

toString() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

toString() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

toString() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage

toString() - Method in class org.biojava.nbio.structure.AminoAcidImpl

string representation.

toString() - Method in class org.biojava.nbio.structure.AtomImpl

toString() - Method in class org.biojava.nbio.structure.Author

toString() - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier

toString() - Method in class org.biojava.nbio.structure.BondImpl

toString() - Method in enum org.biojava.nbio.structure.cath.CathCategory

toString() - Method in class org.biojava.nbio.structure.cath.CathDomain

toString() - Method in class org.biojava.nbio.structure.cath.CathNode

toString() - Method in class org.biojava.nbio.structure.cath.CathSegment

toString() - Method in interface org.biojava.nbio.structure.Chain

toString() - Method in class org.biojava.nbio.structure.ChainImpl

String representation.

toString() - Method in class org.biojava.nbio.structure.Compound

toString() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

toString() - Method in class org.biojava.nbio.structure.contact.BoundingBox

toString() - Method in class org.biojava.nbio.structure.contact.GroupContact

toString() - Method in class org.biojava.nbio.structure.contact.Pair

toString() - Method in class org.biojava.nbio.structure.contact.StructureInterface

toString() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

toString() - Method in class org.biojava.nbio.structure.DBRef

String representation of a DBRef.

toString() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

toString() - Method in class org.biojava.nbio.structure.domain.pdp.CutValues

toString() - Method in class org.biojava.nbio.structure.domain.pdp.Domain

toString() - Method in class org.biojava.nbio.structure.domain.pdp.Segment

toString() - Method in class org.biojava.nbio.structure.domain.PDPDomain

toString() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

toString() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

toString() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique

toString() - Method in enum org.biojava.nbio.structure.GroupType

toString() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition

toString() - Method in class org.biojava.nbio.structure.HetatomImpl

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.AbstractBean

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

toString() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct

toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

toString() - Method in class org.biojava.nbio.structure.io.SSBondImpl

toString() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

toString() - Method in class org.biojava.nbio.structure.jama.Matrix

toString() - Method in class org.biojava.nbio.structure.JournalArticle

toString() - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix

toString() - Method in class org.biojava.nbio.structure.math.SparseVector

toString() - Method in class org.biojava.nbio.structure.NucleotideImpl

toString() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

toString() - Method in class org.biojava.nbio.structure.PDBHeader

String representation

toString() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

toString() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

toString() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair

toString() - Method in class org.biojava.nbio.structure.ResidueNumber

toString() - Method in class org.biojava.nbio.structure.ResidueRange

toString(List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange

toString() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

toString() - Method in enum org.biojava.nbio.structure.scop.ScopCategory

toString() - Method in class org.biojava.nbio.structure.scop.ScopDescription

toString() - Method in class org.biojava.nbio.structure.scop.ScopDomain

toString() - Method in class org.biojava.nbio.structure.scop.ScopNode

toString() - Method in enum org.biojava.nbio.structure.secstruc.BridgeType

toString() - Method in class org.biojava.nbio.structure.secstruc.HBond

toString() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc

toString() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement

toString() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

toString() - Method in enum org.biojava.nbio.structure.secstruc.SecStrucType

toString() - Method in interface org.biojava.nbio.structure.SeqMisMatch

toString() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

toString() - Method in class org.biojava.nbio.structure.Site

toString() - Method in interface org.biojava.nbio.structure.Structure

String representation of object.

toString() - Method in class org.biojava.nbio.structure.StructureImpl

string representation.

toString() - Method in class org.biojava.nbio.structure.SubstructureIdentifier

toString() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer

toString() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

toString() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

toString() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment

toString() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

toString() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

toString() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

toString() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

toString() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

toString() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

toString() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster

toString() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList

toString() - Method in class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus

toString() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

toString() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

toString() - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector

toString() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

toString() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

toString() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

toString() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

toString() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

toString() - Method in class org.biojava.nbio.survival.cox.CoxInfo

toString(String, String, String) - Method in class org.biojava.nbio.survival.cox.CoxInfo

toString() - Method in class org.biojava.nbio.survival.cox.CoxVariables

toString() - Method in class org.biojava.nbio.survival.cox.StrataInfo

toString() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo

toString() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

toString() - Method in class org.biojava.nbio.survival.cox.SurvivalInfoIndex

toString() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo

toString() - Method in class org.biojava.nbio.survival.data.CompactCharSequence

toString() - Method in class org.biojava.nbio.survival.data.HeaderInfo

toString() - Method in class org.biojava.nbio.survival.data.WorkSheet

toString() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

toString() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob

toString() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

toString() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

toStringBuilder(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

For the given Sequence this will return a StringBuilder object filled with the results of Compound#toString().

toStrings(List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange

totalSize - Variable in class org.biojava.nbio.ontology.obo.OboFileParser

toTransformMatrices(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts the transformation Matrices of the alignment into a String output.

toUnixPath(String) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils

Converts path to Unix convention and adds a terminating slash if it was omitted

toWebSiteDisplay(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.

toWebSiteDisplay(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.

toXML(Component) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter

toXML(Component, PrettyXMLWriter) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter

toXML(ModifiedCompound) - Static method in class org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter

toXML(StructureAtom) - Static method in class org.biojava.nbio.protmod.io.StructureAtomXMLConverter

toXML(StructureAtom, PrettyXMLWriter) - Static method in class org.biojava.nbio.protmod.io.StructureAtomXMLConverter

toXML(StructureGroup, PrettyXMLWriter) - Static method in class org.biojava.nbio.protmod.io.StructureGroupXMLConverter

toXML(MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts all the information of a multiple alignment ensemble into an XML String format.

toXML(PrintWriter) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

convert Configuration to an XML file so it can be serialized

toXML(XMLWriter) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

convert Configuration to an XML file so it can be serialized add to an already existing xml file.

toXML(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

Convert an afpChain to a simple XML representation

toXML(AFPChain, StringWriter, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

Write the XML representation to a StringWriter

toXML(AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

toXML(boolean) - Method in class org.biojava.nbio.structure.align.xml.HasResultXMLConverter

return flag if the server has a result

toXML(int) - Method in class org.biojava.nbio.structure.align.xml.PositionInQueueXMLConverter

toXML(SortedSet<String>) - Static method in class org.biojava.nbio.structure.align.xml.RepresentativeXMLConverter

toXML() - Method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer

toXML() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer

toXML() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer

toXML() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer

toXML() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

toXML(PrettyXMLWriter) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

toXML() - Method in class org.biojava.nbio.structure.scop.server.ListStringWrapper

toXML() - Method in class org.biojava.nbio.structure.scop.server.ScopDescriptions

toXML() - Method in class org.biojava.nbio.structure.scop.server.ScopDomains

toXML() - Method in class org.biojava.nbio.structure.scop.server.ScopNodes

toXML() - Method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper

toXML() - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot

toXML() - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

toXML() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

toXYZString() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

Expresses this transformation in terms of x,y,z fractional coordinates.

trace() - Method in class org.biojava.nbio.structure.jama.Matrix

Matrix trace.

trace1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

trace1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

trace2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

trace2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

tracebackToString(AlignerHelper.Last[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

traceFragmentMatrix(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

traceFragmentMatrix(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

TranscriptionEngine - Class in org.biojava.nbio.core.sequence.transcription

Used as a way of encapsulating the data structures required to parse DNA to a Protein sequence.

TranscriptionEngine.Builder - Class in org.biojava.nbio.core.sequence.transcription

This class is the way to create a TranslationEngine.

TranscriptSequence - Class in org.biojava.nbio.core.sequence

This is the sequence if you want to go from a gene sequence to a protein sequence.

TranscriptSequence(GeneSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.TranscriptSequence

TransfAlgebraicAdapter - Class in org.biojava.nbio.structure.xtal.io

TransfAlgebraicAdapter() - Constructor for class org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter

transform(Atom[], Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transform an array of atoms at once.

transform(Atom, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms an atom object, given a Matrix4d (i.e.

transform(Group, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms a group object, given a Matrix4d (i.e.

transform(Structure, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms a structure object, given a Matrix4d (i.e.

transform(Chain, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms a chain object, given a Matrix4d (i.e.

transform(double) - Method in class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform

An arbitrary transform over reals

transform(double) - Method in class org.biojava.nbio.structure.gui.util.color.LogColorMapper

Apply log transform.

transform(double) - Method in class org.biojava.nbio.structure.gui.util.color.SqrtColorMapper

Return sqrt(value).

transform(Matrix4d, Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

transform(Map<?, ?>) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer

Transforms Map to String, representing every entry as key mappingSequence value , joined by separatorSequence

transformAtoms(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Transforms atoms according to the superposition stored in the alignment.

transformPoint(double[]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Applies the transformation to given point.

TransformType - Enum in org.biojava.nbio.structure.xtal

transfToCrystal(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Transform given Matrix4d in orthonormal basis to the crystal basis using the PDB axes convention (NCODE=1)

transfToCrystal(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Transforms the given orthonormal basis coordinates into crystal coordinates.

transfToOriginCell(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Converts the coordinates in pt so that they occur within the (0,0,0) unit cell

transfToOriginCell(Tuple3d[], Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Converts a set of points so that the reference point falls in the unit cell.

transfToOriginCellCrystal(Matrix4d[], Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

transfToOriginCellOrthonormal(Matrix4d[], Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

transfToOrthonormal(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Transform given Matrix4d in crystal basis to the orthonormal basis using the PDB axes convention (NCODE=1)

transfToOrthonormal(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Transforms the given crystal basis coordinates into orthonormal coordinates.

TRANSITIVE - Static variable in class org.biojava.nbio.ontology.OntoTools

translate(F) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

translate(F) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator

translate(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

Quick method to let you go from a CDS to a Peptide quickly.

translate(Atom, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates an atom object, given a Vector3d (i.e.

translate(Group, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates a group object, given a Vector3d (i.e.

translate(Chain, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates a chain object, given a Vector3d (i.e.

translate(Structure, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates a Structure object, given a Vector3d (i.e.

translate(Vector3d) - Method in class org.biojava.nbio.structure.contact.BoundingBox

translate(Point3d, Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

translate(Matrix4d, Vector3d) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder

translate(Point3i) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

translateMany(F) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

translateMany(F) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator

translateNCodons() - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

Indicates if we want to force exact translation of compounds or not i.e.

translateNCodons(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

TranslationException - Exception in org.biojava.nbio.core.exceptions

Thrown from AbstractCompundTranslator

TranslationException(String) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException

TranslationException(Exception) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException

TranslationException(String, Exception) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException

translVecToString(Matrix4d) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

transNCS - Variable in class org.biojava.nbio.structure.validation.Entry

transpose() - Method in class org.biojava.nbio.structure.jama.Matrix

Matrix transpose.

transpose(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix

traverseHierarchy() - Method in class demo.DemoSCOP

Traverse throught the SCOP hierarchy

TreeConstructor - Class in org.biojava.nbio.phylo

The TreeConstructor uses the forester library to build different types of phylogenetic trees.

TreeConstructorType - Enum in org.biojava.nbio.phylo

The TreeConstructorType specifies the aligorithm used to construct the tree (clustering algorithm).

TreeMapSpaceGroupWrapper - Class in org.biojava.nbio.structure.xtal.io

TreeMapSpaceGroupWrapper() - Constructor for class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

TreeSetStringWrapper - Class in org.biojava.nbio.structure.scop.server

TreeSetStringWrapper() - Constructor for class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper

TreeType - Enum in org.biojava.nbio.phylo

The TreeType specifies the optimization criteria used to generate the tree.

triggerDocumentEnd() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerDocumentStart() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerGeneric(String, List<String>, List<String>) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerMouseOverPosition(int, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener

triggerNewChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewChemCompDescriptor(ChemCompDescriptor) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewEntity(Entity) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewEntityPolySeq(EntityPolySeq) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewEntitySrcGen(EntitySrcGen) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewEntitySrcNat(EntitySrcNat) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewEntitySrcSyn(EntitySrcSyn) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewPdbxEntityNonPoly(PdbxEntityNonPoly) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewPdbxStructOper(PdbxStructOperList) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewRefine(Refine) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewStructAsym(StructAsym) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewStructKeywords(StructKeywords) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerNewStructNcsOper(StructNcsOper) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

triggerSelectionLocked(boolean) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener

triggerSelectionLocked(boolean) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener

TRIGONAL_CARBON_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

TRIGONAL_NITROGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

trimStop(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

Imperfect code.

trimStop(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

trimToSize() - Method in interface org.biojava.nbio.structure.Group

attempts to reduce the memory imprint of this group by trimming all internal Collection objects to the required size.

trimToSize() - Method in class org.biojava.nbio.structure.HetatomImpl

attempts to reduce the memory imprint of this group by trimming all internal Collection objects to the required size.

trimToValidResidues(ResidueRange) - Method in class org.biojava.nbio.structure.AtomPositionMap

Trims a residue range so that both endpoints are contained in this map.

Triple - Interface in org.biojava.nbio.ontology

A triple in an ontology.

Triple.Impl - Class in org.biojava.nbio.ontology

Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple

tryAllCPs - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

If true, ignores OptimalCECPParameters.cpPoint and tries all possible cp points.

twinFraction - Variable in class org.biojava.nbio.structure.validation.Entry

twinL - Variable in class org.biojava.nbio.structure.validation.Entry

twinL2 - Variable in class org.biojava.nbio.structure.validation.Entry

twistOptimized(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.AFPTwister

superimposing according to the optimized alignment

twistPDB(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.AFPTwister

calculate the total rmsd of the blocks output a merged pdb file for both proteins protein 1, in chain A protein 2 is twisted according to the twists detected, in chain B

TwoBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker

TwoBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker

TwoBitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker

TwoBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker

TwoBitParser - Class in org.biojava.nbio.genome.parsers.twobit

downloaded from http://storage.bioinf.fbb.msu.ru/~roman/TwoBitParser.java Class is a parser of UCSC Genome Browser file format .2bit used to store nucleotide sequence information.

TwoBitParser(File) - Constructor for class org.biojava.nbio.genome.parsers.twobit.TwoBitParser

TwoBitSequenceReader<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.storage

Implementation of the 2bit encoding.

TwoBitSequenceReader(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader

TwoBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader

TwoBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader

TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader

TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader

TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.storage

Extension of the BitArrayWorker which provides the 2bit implementation code.

TYPE - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature

Sort features by type

type - Variable in enum org.biojava.nbio.genome.parsers.cytoband.StainType

type() - Method in class org.biojava.nbio.genome.parsers.gff.Feature

Get feature type, such as "exon" or "CDS".

type() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI

Get the feature type, for example, "exon", "CDS", etc.

type - Static variable in class org.biojava.nbio.structure.AminoAcidImpl

this is an Amino acid.

type - Static variable in class org.biojava.nbio.structure.HetatomImpl

The GroupType is HETATM

type - Static variable in class org.biojava.nbio.structure.NucleotideImpl

this is a "nucleotide", a special occurance of a Hetatom.

type - Variable in enum org.biojava.nbio.structure.secstruc.BridgeType

type - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo

type - Variable in enum org.biojava.nbio.structure.secstruc.SecStrucType

TYPEDEF - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

U

UBIQUITINATION - Static variable in class org.biojava.nbio.phosphosite.Dataset

uminus() - Method in class org.biojava.nbio.structure.jama.Matrix

Unary minus

uncompress(String, FileOutputStream) - Static method in class org.biojava.nbio.core.util.UncompressInputStream

UncompressInputStream - Class in org.biojava.nbio.core.util

This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant).

UncompressInputStream(InputStream) - Constructor for class org.biojava.nbio.core.util.UncompressInputStream

UNDERSCORE - Static variable in class org.biojava.nbio.structure.align.util.AtomCache

unescape(String) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

unescape(String, char, int, boolean) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

unescape(String, char, int, int, boolean) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

unescapeChars - Static variable in class org.biojava.nbio.ontology.obo.OboFileParser

union(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location

Return the union.

unionWorkSheetsRowJoin(String, String, char, boolean) - Static method in class org.biojava.nbio.survival.data.WorkSheet

Combine two work sheets where you join based on rows.

unionWorkSheetsRowJoin(WorkSheet, WorkSheet, boolean) - Static method in class org.biojava.nbio.survival.data.WorkSheet

* Combine two work sheets where you join based on rows.

uniProtEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

UniprotProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader

Pass in a Uniprot ID and this ProxySequenceReader when passed to a ProteinSequence will get the sequence data and other data elements associated with the ProteinSequence by Uniprot.

UniprotProxySequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

The UniProt id is used to retrieve the UniProt XML which is then parsed as a DOM object so we know everything about the protein.

UniprotProxySequenceReader(Document, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

The xml is passed in as a DOM object so we know everything about the protein.

UniprotToFasta - Class in org.biojava.nbio.genome.uniprot

UniprotToFasta() - Constructor for class org.biojava.nbio.genome.uniprot.UniprotToFasta

UniqueSequenceList - Class in org.biojava.nbio.structure.symmetry.core

Bean for a single sequence.

UniqueSequenceList(Atom[], String, int, int, String) - Constructor for class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList

UnitCellBoundingBox - Class in org.biojava.nbio.structure.xtal

A class to contain the BoundingBoxes of all molecules in a full unit cell

UnitCellBoundingBox(int, int) - Constructor for class org.biojava.nbio.structure.xtal.UnitCellBoundingBox

unitVector(Atom) - Static method in class org.biojava.nbio.structure.Calc

Returns the unit vector of vector a .

UNKNOWN_ALGORITHM - Static variable in class org.biojava.nbio.structure.align.model.AFPChain

UNKNOWN_DNA - Static variable in interface org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface

UNKNOWN_GROUP_LABEL - Static variable in class org.biojava.nbio.structure.StructureTools

The character to use for unknown compounds in sequence strings

UNKNOWN_SCOPE - Static variable in class org.biojava.nbio.ontology.Synonym

unknownGroup - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor

unmarshal(String[]) - Method in class org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter

unregister(ProteinModification) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

Remove a modification from registry.

UP_AC_PATTERN - Static variable in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

update(int, AlignerHelper.Subproblem, AlignerHelper.Last[][]) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut

update(int) - Method in class org.biojava.nbio.core.util.CRC64Checksum

update(byte[], int, int) - Method in class org.biojava.nbio.core.util.CRC64Checksum

update(String) - Method in class org.biojava.nbio.core.util.CRC64Checksum

updateAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

Force the atom arrays to regenerate based on MultipleAlignmentEnsembleImpl.getStructureIdentifiers().

updateAxis(Integer, Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Updates an axis of symmetry, after the superposition changed.

updateCache() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

updateCache() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

Updates all cached properties

updateContinousVariable(String, Double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

updateCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

updateCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

updateCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

Force recalculation of the core length (ungapped columns) based on the BlockSet core lengths.

updateDisplay() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay

updateDistanceMatrix() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

Force recalculation of the distance matrices.

updateLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

updateLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

Force recalculation of the length (aligned columns) based on the BlockSet lengths.

updateMatrixWithSequenceConservation(double[][], Atom[], Atom[], CeParameters) - Static method in class org.biojava.nbio.structure.align.ce.CECalculator

Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.

updateMatrixWithSequenceConservation(double[][], Atom[], Atom[], CeParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.

updateScore(FatCatParameters, AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer

to update the chaining score after block delete and merge processed the blockScore value is important for significance evaluation

updateSuperposition(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

After the alignment changes (optAln, optLen, blockNum, at a minimum), many other properties which depend on the superposition will be invalid.

updateSymmetryScores(MultipleAlignment) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Update the scores (TM-score and RMSD) of a symmetry multiple alignment.

updateSymmetryTransformation(SymmetryAxes, MultipleAlignment, Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Calculates the set of symmetry operation Matrices (transformations) of the new alignment, based on the symmetry relations in the SymmetryAxes object.

upstream(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location

Return the adjacent location of specified length directly upstream of this location.

URL - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference

url - Variable in class org.biojava.nbio.structure.domain.RemoteDomainProvider

URLIdentifier - Class in org.biojava.nbio.structure

Represents a structure loaded from a URL (including a file URL) A few custom query parameters are supported: format=[pdb|cif] Specify the file format (will otherwise be guessed from the extension) pdbId=[String] Specify the PDB ID (also guessed from the filename) chainID=[String] A single chain from the structure residues=[String] Residue ranges, in a form understood by SubstructureIdentifier

URLIdentifier(URL) - Constructor for class org.biojava.nbio.structure.URLIdentifier

URLIdentifier(String) - Constructor for class org.biojava.nbio.structure.URLIdentifier

urlPropertyNames - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo

USERAGENT - Static variable in class org.biojava.nbio.structure.align.util.HTTPConnectionTools

UserArgumentProcessor - Interface in org.biojava.nbio.structure.align.ce

UserConfiguration - Class in org.biojava.nbio.structure.align.util

A container to persist config to the file system

UserConfiguration() - Constructor for class org.biojava.nbio.structure.align.util.UserConfiguration

Default UserConfiguration: split directory autofetch files default download location.

userData() - Method in class org.biojava.nbio.genome.parsers.gff.Feature

Get HashMap of user data.

userData() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI

Get HashMap of user data.

Utils - Class in org.biojava.nbio.aaproperties

This is a utility class that contains utility methods which will facilitates the coding of other methods

Utils() - Constructor for class org.biojava.nbio.aaproperties.Utils

V

V - Static variable in class org.biojava.nbio.aaproperties.Constraints

value - Variable in class org.biojava.nbio.structure.align.helper.GapArray

value - Variable in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements

value - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.PairInProfileScorerType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.RefinerType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.alignment.routines.AlignerHelper.Last

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.alignment.template.GapPenalty.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.alignment.template.AlignedSequence.Step

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.alignment.template.Profile.StringFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.DataSource

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.DNASequence.DNAType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.Strand

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.phylo.TreeConstructorType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.phylo.TreeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.protmod.ModificationCategory

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.align.client.StructureName.Source

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.BondType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.Element

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.ElementType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.GroupType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.gui.RenderStyle

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.PDBStatus.Status

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.scop.ScopCategory

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.StructureIO.StructureFiletype

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia.SymmetryClass

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.xtal.TransformType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.survival.cox.CoxMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.survival.cox.ResidualsCoxph.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum

Returns the enum constant of this type with the specified name.

valueOfIgnoreCase(String) - Static method in enum org.biojava.nbio.structure.Element

Returns the Element that corresponds to the specified element symbol.

values() - Static method in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.alignment.Alignments.PairInProfileScorerType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.alignment.Alignments.RefinerType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.alignment.routines.AlignerHelper.Last

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.alignment.template.GapPenalty.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.alignment.template.AlignedSequence.Step

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.alignment.template.Profile.StringFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.DataSource

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.DNASequence.DNAType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.Strand

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.phylo.TreeConstructorType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.phylo.TreeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.protmod.ModificationCategory

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.align.client.StructureName.Source

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.BondType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.cath.CathCategory

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.Element

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.ElementType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.GroupType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.gui.RenderStyle

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper

values() - Static method in enum org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

values() - Static method in enum org.biojava.nbio.structure.PDBStatus.Status

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.scop.ScopCategory

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.StructureIO.StructureFiletype

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia.SymmetryClass

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.xtal.TransformType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.survival.cox.CoxMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.survival.cox.ResidualsCoxph.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum

Returns an array containing the constants of this enum type, in the order they are declared.

Variable - Interface in org.biojava.nbio.ontology

Variable.Impl - Class in org.biojava.nbio.ontology

vectorProduct(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Vector product (cross product).

verbose - Static variable in class org.biojava.nbio.structure.domain.pdp.CutDomain

version - Static variable in class org.biojava.nbio.structure.align.ce.CeCPMain

version history: 1.5 - Added more parameters to the command line, including -maxOptRMSD 1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain 1.3 - Short CPs are now discarded 1.2 - now supports check AlignmentTools.isSequentialAlignment.

version - Static variable in class org.biojava.nbio.structure.align.ce.CeMain

version history: 1.2 - Added more parameters to the command line, including -maxOptRMSD 1.1 - Additional parameters 1.0 - Initial port from C code

version - Static variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

version history: 1.0 - Initial version

VERSION - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat

version history: 1.1 - Added more parameters to the command line 1.0 - Initial version

version - Static variable in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

Version history:

version - Static variable in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry

version - Static variable in class org.biojava.nbio.structure.symmetry.internal.CeSymm

Version History:

version - Variable in class org.biojava.nbio.structure.validation.Program

VERSION_1_55 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_57 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_59 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_61 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_63 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_65 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_67 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_69 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_71 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_73 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_75 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_75A - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_75B - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_75C - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_1 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_2 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_3 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_4 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_5 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_3_5_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory

VERSION_4_0_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory

VERSION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

viewer - Static variable in class org.biojava.nbio.structure.gui.BiojavaJmol

viewer - Static variable in class org.biojava.nbio.structure.gui.JmolViewerImpl

vp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

W

W - Static variable in class org.biojava.nbio.aaproperties.Constraints

WAIT_INCREMENT - Static variable in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService

Number of milliseconds by which expected job execution time is incremented if it is not finished yet.

waitForStartCodon(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

If set, then translation will not start until a start codon is encountered

WaldTest - Class in org.biojava.nbio.survival.cox

WaldTest() - Constructor for class org.biojava.nbio.survival.cox.WaldTest

WaldTestInfo - Class in org.biojava.nbio.survival.cox

WaldTestInfo() - Constructor for class org.biojava.nbio.survival.cox.WaldTestInfo

WATERNAMES - Static variable in enum org.biojava.nbio.structure.GroupType

The 3-letter codes used in the PDB to identify water molecules

WeakValueHashMap - Class in org.biojava.nbio.ontology.utils

Map implementation which keeps weak references to values.

WeakValueHashMap() - Constructor for class org.biojava.nbio.ontology.utils.WeakValueHashMap

WebStartClientDemo - Class in demo

WebStartClientDemo() - Constructor for class demo.WebStartClientDemo

WebStartDBSearch - Class in org.biojava.nbio.structure.align.webstart

A Web Start wrapper for a FarmJobRunnable.

WebStartDBSearch() - Constructor for class org.biojava.nbio.structure.align.webstart.WebStartDBSearch

WebStartDBSearchResults - Class in org.biojava.nbio.structure.align.webstart

WebStartDBSearchResults() - Constructor for class org.biojava.nbio.structure.align.webstart.WebStartDBSearchResults

WebStartMain - Class in org.biojava.nbio.structure.align.webstart

WebStartMain() - Constructor for class org.biojava.nbio.structure.align.webstart.WebStartMain

weight - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

WHITE_BLACK_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper

WHITE_SPACE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil

A whitespace character: [\t\n\x0B\f\r]

width - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

wilsonBaniso - Variable in class org.biojava.nbio.structure.validation.Entry

wilsonBestimate - Variable in class org.biojava.nbio.structure.validation.Entry

window(int, int) - Method in class org.biojava.nbio.genome.parsers.gff.Location

Enable a "sliding window" iteration over a location to use with Java's "for" loop construct.

windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay

windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay

windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay

windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay

windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay

windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

WindowedSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence.views

A sliding window view of a sequence which does not implement any interfaces like Sequence because they do not fit how this works.

WindowedSequence(Sequence<C>, int) - Constructor for class org.biojava.nbio.core.sequence.views.WindowedSequence

windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay

windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay

windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

winSize - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

winSize - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

withDescription(String) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified description.

withQuality(String) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified quality scores.

withSequence(String) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified sequence.

withVariant(FastqVariant) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.

workingListToSequences(List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

WorkSheet - Class in org.biojava.nbio.survival.data

Need to handle very large spreadsheets of expression data so keep memory footprint low

WorkSheet() - Constructor for class org.biojava.nbio.survival.data.WorkSheet

WorkSheet(Collection<String>, Collection<String>) - Constructor for class org.biojava.nbio.survival.data.WorkSheet

WorkSheet(String[][]) - Constructor for class org.biojava.nbio.survival.data.WorkSheet

WorkSheet(CompactCharSequence[][]) - Constructor for class org.biojava.nbio.survival.data.WorkSheet

wrap(Sequence<C>) - Method in enum org.biojava.nbio.core.sequence.transcription.Frame

Optionally wraps a Sequence in a reverse complementing view (if the frame is on the reverse strand) and creates a sub sequence view if it is required.

wrapToRna(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator

Takes in the given DNA Sequence and returns an instance of RNASequence which is using RnaSequenceView as a ProxySequenceReader.

write(Appendable, Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Used as a way of sending a Sequence to a writer without the cost of converting to a full length String and then writing the data out

write(FeatureList, String) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader

Write features in FeatureList to file.

write(OutputStream, LinkedHashMap<String, ChromosomeSequence>) - Method in class org.biojava.nbio.genome.parsers.gff.GFF3Writer

Output gff3 format for a DNA Sequence

write(int) - Method in class org.biojava.nbio.ronn.NullOutputStream

write(File, Fastq...) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter

Write the specified FASTQ formatted sequences to the specified file.

write(File, Iterable<Fastq>) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter

Write the specified FASTQ formatted sequences to the specified file.

write(OutputStream, Fastq...) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter

Write the specified FASTQ formatted sequences to the specified output stream.

write(OutputStream, Iterable<Fastq>) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter

Write the specified FASTQ formatted sequences to the specified output stream.

write(String) - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile

writeFasta(OutputStream, List<FastaSequence>, int) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line

writeFasta(OutputStream, List<FastaSequence>) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

Writes FastaSequence in the file, each sequence will take one line only

writeGeneSequence(File, Collection<GeneSequence>, boolean) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence

writeGeneSequence(OutputStream, Collection<GeneSequence>, boolean) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence

writeIndent() - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

writeNucleotideSequence(File, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write a collection of NucleotideSequences to a file

writeNucleotideSequence(OutputStream, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write a collection of NucleotideSequences to a file

writeNucleotideSequence(File, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write a collection of NucleotideSequences to a file

writeNucleotideSequence(OutputStream, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write a collection of NucleotideSequences to a file

writeNucleotideSequence(OutputStream, Collection<DNASequence>, String) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write a collection of NucleotideSequences to a file

writeProteinSequence(File, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write collection of protein sequences to a file

writeProteinSequence(OutputStream, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write collection of protein sequences to a stream

writeProteinSequence(File, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write collection of protein sequences to a file

writeProteinSequence(OutputStream, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write collection of protein sequences to a stream

writeResults() - Method in class org.biojava.nbio.core.search.io.SearchIO

used to write a search report using the guessed or specified factory

writeSequence(File, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write a sequence to a file

writeSequence(OutputStream, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write a sequence to OutputStream

writeSequence(File, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write a sequence to a file

writeSequence(OutputStream, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write a sequence to OutputStream

writeSequences(OutputStream, Collection<Sequence<?>>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Method which will write your given Sequences to the specified OutputStream.

writeSequences(OutputStream, Collection<Sequence<?>>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Method which will write your given Sequences to the specified OutputStream.

WwPDBValidationInformation - Class in org.biojava.nbio.structure.validation

Java class for anonymous complex type.

WwPDBValidationInformation() - Constructor for class org.biojava.nbio.structure.validation.WwPDBValidationInformation

X

xAxisLabels - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

xAxisLegend - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

xaxisPercentIncrement - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

xmax - Variable in class org.biojava.nbio.structure.contact.BoundingBox

xmin - Variable in class org.biojava.nbio.structure.contact.BoundingBox

xmLcreationDate - Variable in class org.biojava.nbio.structure.validation.Entry

XMLHelper - Class in org.biojava.nbio.core.util

XMLHelper() - Constructor for class org.biojava.nbio.core.util.XMLHelper

XMLUtil - Class in org.biojava.nbio.structure.scop.server

Utility classes for the XML serialization and de-serialization of SCOP.

XMLUtil() - Constructor for class org.biojava.nbio.structure.scop.server.XMLUtil

XMLWriter - Interface in org.biojava.nbio.core.util

Simple interface for building XML documents.

XREF_ANALOG - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

xtriageInputColumns - Variable in class org.biojava.nbio.structure.validation.Entry

xyMax - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

End position of the aligned sequence in the query and target respectively

xyStart - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

Start position of the aligned sequence in the query and target respectively

Y

Y - Static variable in class org.biojava.nbio.aaproperties.Constraints

yAxisLegend - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

yaxisPercentIncrement - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

ymax - Variable in class org.biojava.nbio.structure.contact.BoundingBox

ymin - Variable in class org.biojava.nbio.structure.contact.BoundingBox

Z

z - Variable in class org.biojava.nbio.structure.validation.AngleOutlier

z - Variable in class org.biojava.nbio.structure.validation.BondOutlier

ZipChemCompProvider - Class in org.biojava.nbio.structure.io.mmcif

This chemical component provider retrieves and caches chemical component definition files from a zip archive specified in its construction.

ZipChemCompProvider(String, String) - Constructor for class org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider

ZipChemCompProvider is a Chemical Component provider that stores chemical components in a zip archive.

zmax - Variable in class org.biojava.nbio.structure.contact.BoundingBox

zmin - Variable in class org.biojava.nbio.structure.contact.BoundingBox

zscore - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier

zscore - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier

zscore - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

zStrAlign(int, int, double, int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

zStrAlign(int, int, double, int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

zThr - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator

zThr - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

_

_split_multi_line(String, int) - Method in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

Returns a list of strings.

_write_feature(FeatureInterface<AbstractSequence<C>, C>, int) - Method in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

Write a single SeqFeature object to features table.

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