Index (biojava 6.0.0 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 _
All Classes All Packages

A

A - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
A - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
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 that 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
ABITrace - Class in org.biojava.nbio.core.sequence.io: Title: ABITrace
ABITrace(byte[]) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace: The byte[] constructor parses an ABI file represented as a byte array.
ABITrace(File) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace: The File constructor opens a local ABI file and parses the content.
ABITrace(URL) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace: The URL constructor opens an ABI file from any URL.
ABITracerCompoundSet - Class in org.biojava.nbio.core.sequence.compound
ABITracerCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet
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
Absorbance_False - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
Absorbance_True - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
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(Map) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation: Create a new Annotation by copying the key-value pairs from a map.
AbstractAnnotation(Annotation) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation: Copy-constructor.
AbstractCifFileSupplier<S> - Class in org.biojava.nbio.structure.io.cif: Convert a BioJava object to a CifFile.
AbstractCifFileSupplier() - Constructor for class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier
AbstractCifFileSupplier.WrappedAtom - Class in org.biojava.nbio.structure.io.cif: Wrapped atoms represent individual atoms enriched with model- and chain-level information.
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(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(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.
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(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment.
AbstractReference - Class in org.biojava.nbio.core.sequence.reference
AbstractReference() - Constructor for class org.biojava.nbio.core.sequence.reference.AbstractReference
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
Ac - org.biojava.nbio.structure.Element
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
acen - org.biojava.nbio.genome.parsers.cytoband.StainType
ACETYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
ACTINOID - org.biojava.nbio.structure.ElementType
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.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.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(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
add(int, int, int, int) - Method in class org.biojava.nbio.structure.align.helper.JointFragments
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(FeatureI) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Add specified feature to the end of the list.
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
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
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[]) - Method in class org.biojava.nbio.structure.contact.Grid: Adds a set of atoms, subsequent call to Grid.getIndicesContacts() or Grid.getAtomContacts() will produce the interatomic contacts.
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) - Method in class org.biojava.nbio.structure.contact.Grid: Adds a set of atoms, subsequent call to Grid.getIndicesContacts() or Grid.getAtomContacts() will produce the interatomic contacts.
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.
addAxis(Matrix4d, int, CESymmParameters.SymmetryType) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes: Adds a new axis of symmetry to the bottom level of the tree
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.EntityInfo: Add new Chain to this EntityInfo
addChain(Chain) - Method in class org.biojava.nbio.structure.Model
addChain(Chain) - Method in interface org.biojava.nbio.structure.Structure: Add a new chain to the first model
addChain(Chain) - Method in class org.biojava.nbio.structure.StructureImpl: Add a new chain to the first model
addChain(Chain, int) - Method in interface org.biojava.nbio.structure.Structure: Add a new chain to the model specified by the given index
addChain(Chain, int) - Method in class org.biojava.nbio.structure.StructureImpl: Add a new chain to the model specified by the given index
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.chem.ChemicalComponentDictionary: Add a new component to the dictionary
addChildElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper: Creates a new element called elementName and adds it to parentElement
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) - 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, C, Iterable<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
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
addCoords(Point3d[]) - Method in class org.biojava.nbio.structure.contact.Grid: Adds a set of coordinates, subsequent call to Grid.getIndicesContacts() will produce the contacts, i.e. the set of points within distance cutoff.
addCoords(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.contact.Grid: Adds the i and j coordinates and fills the grid.
addCoords(Point3d[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid: Adds a set of coordinates, subsequent call to Grid.getIndicesContacts() will produce the contacts, i.e. the set of points within distance cutoff.
addCoords(Point3d[], BoundingBox, Point3d[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid: Adds the i and j coordinates 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.
addDBReference(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addEntityInfo(EntityInfo) - Method in interface org.biojava.nbio.structure.Structure: Add an EntityInfo to this Structure
addEntityInfo(EntityInfo) - Method in class org.biojava.nbio.structure.StructureImpl: Add an EntityInfo to this Structure
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
addGroupsToStructure(Structure, Collection<Group>, int, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Add a list of groups to a new structure.
addGroupToStructure(Structure, Group, int, Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Adds a particular group to a structure.
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
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
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
addNcsEquivalent(StructureInterface, StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Add an interface to the list, possibly defining it as NCS-equivalent to an interface already in the list.
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, double) - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
addPoint(Point3d, T) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
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
addReference(AbstractReference) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
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
addSeqRes(Chain, String) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils: Add the missing groups to the SeqResGroups.
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: The file is read and the bytes stored immediately.
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
addUnknownDataTypeVariable(String, String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
AFFINE - org.biojava.nbio.alignment.template.GapPenalty.Type
AFP - Class in org.biojava.nbio.structure.align.model: A class to represent a FATCAT aligned fragment pair (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(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
Ag - org.biojava.nbio.structure.Element
AgScore - Class in org.biojava.nbio.survival.cox.stats
AgScore() - Constructor for class org.biojava.nbio.survival.cox.stats.AgScore
Al - org.biojava.nbio.structure.Element
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(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 class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
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(List<Subunit>, List<Subunit>, SubunitClustererParameters, QsAlignParameters) - Static method in class org.biojava.nbio.structure.align.quaternary.QsAlign
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeMain
align(Atom[], Atom[]) - 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[]) - 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[], boolean, FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
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[], 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[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
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(Atom[], Atom[], FatCatParameters, boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
align(Atom[], Atom[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Calculate the protein structure superimposition, between two sets of atoms.
align(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
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(Structure, List<Chain>) - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
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, Structure, SubunitClustererParameters, QsAlignParameters) - Static method in class org.biojava.nbio.structure.align.quaternary.QsAlign
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
ALIGNMENT_VIEW - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
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 - 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.
AlignmentCalc(AlignmentGui, Structure, Structure, String, String) - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentCalc: requests an alignment of pdb1 vs pdb 2.
AlignmentCalculationRunnable - Interface in org.biojava.nbio.structure.align.gui
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 - 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 - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
ALIGNMENTS - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
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.
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).
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
AlignUtils - Class in org.biojava.nbio.structure.align.helper: Low level helper methods for CE and FATCAT algorithms.
AlignUtils() - Constructor for class org.biojava.nbio.structure.align.helper.AlignUtils
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
ALKALI_METAL - org.biojava.nbio.structure.ElementType
ALKALINE_EARTH_METAL - org.biojava.nbio.structure.ElementType
ALL - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
ALL_CURRENT_ENDPOINT - Static variable in class org.biojava.nbio.structure.PDBStatus
ALL_POLYMER_TYPES - Static variable in enum org.biojava.nbio.structure.chem.PolymerType: Convenience Set of all polymer types.
ALL_SEQUENCES - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
AllChemCompProvider - Class in org.biojava.nbio.structure.chem: A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.
AllChemCompProvider() - Constructor for class org.biojava.nbio.structure.chem.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
ALN - org.biojava.nbio.core.alignment.template.Profile.StringFormat
ALN - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
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
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
Am - org.biojava.nbio.structure.Element
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 one additional letters - X
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.
AMINOACID - org.biojava.nbio.structure.GroupType: The type for amino acids (L-peptides)
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.
AminoAcidProperties - Class in org.biojava.nbio.aaproperties: This class provides the protein properties at the level of individual amino acids.
AminoAcidProperties() - Constructor for class org.biojava.nbio.aaproperties.AminoAcidProperties
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() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters: This method is the main function call to extract all step parameters, pairing parameters, and sequence information from the Structure object provided to the constructor.
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(Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions: Calculate the rotation angle component of the input unit quaternion.
angle(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: Gets the angle between two vectors
ANGLE - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
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.
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.
antiparallel - org.biojava.nbio.structure.secstruc.BridgeType
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.
ApliphaticIndex - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
App - Class in org.biojava.nbio.genome: Hello world!
App - Class in org.biojava.nbio.ontology: Hello world!
App() - Constructor for class org.biojava.nbio.genome.App
App() - Constructor for class org.biojava.nbio.ontology.App
append(T, Iterable<Fastq>) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter: Append the specified FASTQ formatted sequences to the specified appendable.
append(T, Fastq...) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter: Append the specified FASTQ formatted sequences to the specified appendable.
appendQuality(String) - Method in class org.biojava.nbio.genome.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.genome.io.fastq.ParseListener: Notify this listener of a quality line.
appendSequence(String) - Method in class org.biojava.nbio.genome.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.genome.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<S, T>, Map<T, S>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Applies an alignment k times.
applyAlignment(Map<T, T>, 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
Ar - org.biojava.nbio.structure.Element
Architecture - org.biojava.nbio.structure.cath.CathCategory
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. identity operators) it returns true
arrayLeftDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element left division, C = A.
arrayLeftDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element left division in place, A = A.
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(String, CompoundSet<C>) - 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
arrayRightDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element right division, C = A.
arrayRightDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element right division in place, A = A.
arrayTimes(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element multiplication, C = A.
arrayTimesEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element multiplication in place, A = A.
ARTIFACTUAL - org.biojava.nbio.protmod.ModificationOccurrenceType
As - org.biojava.nbio.structure.Element
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(Point3d[], double, int, int, double) - 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.
AsaCalculator(Structure, double, int, int, boolean) - 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(String, Throwable) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
AssertionFailure(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
assignSecStruc(Structure, List<SecStrucInfo>) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools
Astral - Class in org.biojava.nbio.structure.scop: Provides programmatic access to ASTRAL representative sets.
Astral(String, Reader) - 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(Astral.AstralSet) - 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:
ASYMMETRIC - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass
At - org.biojava.nbio.structure.Element
Atom - Interface in org.biojava.nbio.structure: A simple interface for an Atom.
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.
ATOM_PLANE - org.biojava.nbio.structure.BondType
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(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(Group) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object.
AtomIterator(Structure) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object over all models
AtomIterator(Structure, int) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object over a single model
atomn - org.biojava.nbio.structure.chem.ResidueType
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
atomsToPoints(Collection<Atom>) - Static method in class org.biojava.nbio.structure.Calc: Convert an array of atoms into an array of vecmath points
atomsToPoints(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Convert an array of atoms into an array of vecmath points
ATTACHMENT - org.biojava.nbio.protmod.ModificationCategory
attribute(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
attribute(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Add an un-qualified attribute to an element.
attribute(String, 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.
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.
Au - org.biojava.nbio.structure.Element
AU - org.biojava.nbio.structure.xtal.TransformType
AugmentedResidueRange - Class in org.biojava.nbio.structure: Created by douglas on 1/23/15.
AugmentedResidueRange(String, String, String, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
AugmentedResidueRange(String, ResidueNumber, ResidueNumber, 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
AUTO - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
AutoSuggestProvider - Interface in org.biojava.nbio.structure.align.gui.autosuggest: A class that provides auto-completion suggestions for JAutoSuggest
AV - org.biojava.nbio.phylo.TreeConstructorType: What does this stand for?
available() - Method in class org.biojava.nbio.core.util.UncompressInputStream
available() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
AverageHydropathyValue - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
AVGTM_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
Axis(Matrix4d, int, CESymmParameters.SymmetryType, int, int) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
AxisAligner - Class in org.biojava.nbio.structure.symmetry.axis
AxisAligner() - Constructor for class org.biojava.nbio.structure.symmetry.axis.AxisAligner
axisStroke - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

B

B - org.biojava.nbio.structure.Element
Ba - org.biojava.nbio.structure.Element
BACKGROUND_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
BALL_AND_STICK - org.biojava.nbio.structure.gui.RenderStyle
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
BASE_LIST_DNA - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
BASE_LIST_RNA - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
BASE_MAP - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
BasePairParameters - Class in org.biojava.nbio.structure.basepairs: This module calculates the el Hassan-Calladine Base Pairing and Base-pair Step Parameters for any nucleic acid containing structure that has the information about the core base-pair rings.
BasePairParameters(Structure) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters: This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure for only canonical DNA pairs.
BasePairParameters(Structure, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters: This constructor takes a Structure object, and whether to use the RNA standard bases.
BasePairParameters(Structure, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters: This constructor takes a Structure object, whether to use RNA, and whether to remove duplicate sequences.
BasePairParameters(Structure, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters: This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure.
basePairReferenceFrame(Pair<Group>) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters: This method calculates the central frame (4x4 transformation matrix) of a single base pair.
basicLoad() - Method in class demo.DemoLoadStructure
basicLoad(String) - Method in class demo.DemoDomainsplit
basicLoad(PDBFileReader, String) - Method in class demo.DemoChangeChemCompProvider
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
BCIF - org.biojava.nbio.structure.io.StructureFiletype
BCIF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
BcifFileReader - Class in org.biojava.nbio.structure.io: Parse binary Cif files and provide capabilities to store them locally.
BcifFileReader() - Constructor for class org.biojava.nbio.structure.io.BcifFileReader: Constructs a new BcifFileReader, initializing the extensions member variable.
BcifFileReader(String) - Constructor for class org.biojava.nbio.structure.io.BcifFileReader: Constructs a new BcifFileReader, initializing the extensions member variable.
Be - org.biojava.nbio.structure.Element
bend - org.biojava.nbio.structure.secstruc.SecStrucType
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
BETTER_PERFORMANCE_MORE_MEMORY - org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior: use a built-in HashMap for faster access to memory, at the price of more memory consumption
BETWEEN_11 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
BETWEEN_12 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
BETWEEN_13 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
BETWEEN_22 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
BETWEEN_23 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
BETWEEN_33 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
Bi - org.biojava.nbio.structure.Element
BIO - org.biojava.nbio.structure.align.client.StructureName.Source
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
BioAssemblyIdentifier(PdbId, 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.
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
BitArrayWorker(Sequence<C>) - 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. 2 if using 2bit encoding.
Bk - org.biojava.nbio.structure.Element
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
BLAST_PROGRAM - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
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
blastn - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
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.
blastp - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
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
blastx - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
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(BlockImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl: Copy constructor.
BlockImpl(BlockSet) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl: 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(BlockSetImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl: Copy constructor.
BlockSetImpl(MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl: Constructor.
BLOSUM45 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
BLOSUM50 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
Blosum62 - Static variable in class org.biojava.nbio.ronn.RonnConstraint
BLOSUM62 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
BLOSUM80 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
BLOSUM90 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
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(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
BondLocation(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
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(Point3d[]) - 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
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.
Br - org.biojava.nbio.structure.Element
BRANCHED - org.biojava.nbio.structure.EntityType: The 'branched' type use mainly to represent carbohydrates.
BravaisLattice - Enum in org.biojava.nbio.structure.xtal: An enum to represent the 7 Bravais lattices
Breslow - org.biojava.nbio.survival.cox.CoxMethod
bridge - org.biojava.nbio.structure.secstruc.SecStrucType
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) - Constructor for class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead: Creates a buffering character-input stream that uses a default-sized input buffer.
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.
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.genome.io.fastq.FastqBuilder: Build and return a new FASTQ formatted sequence configured from the properties of this builder.
build() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
build() - Static method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping: Builds the mapping by reading SIFTS the tsv file set in SiftsChainToUniprotMapping.DEFAULT_FILE variable.
builder() - Static method in class org.biojava.nbio.genome.io.fastq.Fastq: Create and return a new FastqBuilder.
builder(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.Fastq: Create and return a new FastqBuilder configured from the specified FASTQ formatted sequence.
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.
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
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 - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange: first allowed c-term
C - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
C - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
C - org.biojava.nbio.structure.Element
C - Static variable in class org.biojava.nbio.aaproperties.Constraints
C_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name for the backbone carbonyl
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
C2_ROTATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod
C2RotationSolver - Class in org.biojava.nbio.structure.symmetry.core
C2RotationSolver(QuatSymmetrySubunits, 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
Ca - org.biojava.nbio.structure.Element
CA_AND_SIDE_CHAIN_ANGLE_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
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
CA_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
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
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, Matrices, Point3d, etc.
Calc() - Constructor for class org.biojava.nbio.structure.Calc
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.
calcCenterOfRotation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
calcGlobalSymmetry(List<Subunit>, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Calculate GLOBAL symmetry results.
calcGlobalSymmetry(Structure, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Calculate GLOBAL symmetry results.
calcGlobalSymmetry(Stoichiometry, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Calculate GLOBAL symmetry results.
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.
calcLocalSymmetries(List<Subunit>, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Returns a List of LOCAL symmetry results.
calcLocalSymmetries(Structure, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Returns a List of LOCAL symmetry results.
calcLocalSymmetries(Stoichiometry, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Returns a List of LOCAL symmetry results.
CalcPoint - Class in org.biojava.nbio.structure.geometry: Utility operations on Point3d.
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(QuatSymmetrySubunits, 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
calculateDsspSecondaryStructure(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils: Generate the secondary structure for a Biojava structure object.
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
calculateTp(Matrix4d) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters: This method calculates pairing and step parameters from 4x4 transformation matrices (used internally) that comes out as a Matrix4d.
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: Simple Callable Class that calculates a pairwise alignment in a different thread, so that multiple pairwise alignments can be run in parallel (examples: all-to-all alignments, DB search alignments).
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
canonical - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
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.
CARTOON - org.biojava.nbio.structure.gui.RenderStyle
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 - org.biojava.nbio.structure.align.client.StructureName.Source
CATH_DOWNLOAD_ALL_RELEASES_DIR - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
CATH_DOWNLOAD_URL - 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() - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
CathInstallation(String) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
CathInstallation(String, boolean, boolean) - 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
Cd - org.biojava.nbio.structure.Element
CDD_SEARCH - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
CDS - Static variable in class org.biojava.nbio.genome.util.ChromosomeMappingTools
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 - org.biojava.nbio.structure.Element
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
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.
CELLTRANSL - org.biojava.nbio.structure.xtal.TransformType
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.geometry.CalcPoint: Center a cloud of points.
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.
centered - Variable in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
centerOfMass(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Returns the center of mass of the set of atoms.
centroid(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint: Calculate the centroid of the point cloud.
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 of a 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(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
Cf - org.biojava.nbio.structure.Element
Chain - Interface in org.biojava.nbio.structure: Defines the interface for a Chain.
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
chainEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
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.
chainName - Variable in class org.biojava.nbio.structure.align.client.StructureName
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(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
changeColumnHeader(ChangeValue) - 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(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
changeRowHeader(ChangeValue) - 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
CHARGE - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
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.chem.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
checkFileExists(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
checkInput(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionAbstract: Check that the input to the superposition algorithms is valid.
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.chem.DownloadChemCompProvider
chem_comp_type - Variable in enum org.biojava.nbio.structure.chem.ResidueType: String value of the type
chemComp - Variable in class org.biojava.nbio.structure.HetatomImpl
ChemComp - Class in org.biojava.nbio.structure.chem: Properties of a chemical component.
ChemComp() - Constructor for class org.biojava.nbio.structure.chem.ChemComp
ChemCompAtom - Class in org.biojava.nbio.structure.chem: Properties of an atom of a chemical component.
ChemCompAtom() - Constructor for class org.biojava.nbio.structure.chem.ChemCompAtom
ChemCompBond - Class in org.biojava.nbio.structure.chem: Properties of a bond in a chemical component.
ChemCompBond() - Constructor for class org.biojava.nbio.structure.chem.ChemCompBond
ChemCompConsumer - Interface in org.biojava.nbio.structure.io.cif: Create the ChemicalComponentDictionary from CIF data.
ChemCompConsumerImpl - Class in org.biojava.nbio.structure.io.cif: Consumes a CCD file to create the ChemicalComponentDictionary.
ChemCompConsumerImpl() - Constructor for class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
ChemCompConverter - Class in org.biojava.nbio.structure.io.cif: Convert CifFiles to chem comps.
ChemCompConverter() - Constructor for class org.biojava.nbio.structure.io.cif.ChemCompConverter
ChemCompDescriptor - Class in org.biojava.nbio.structure.chem: Properties of the chemical component descriptor.
ChemCompDescriptor() - Constructor for class org.biojava.nbio.structure.chem.ChemCompDescriptor
ChemCompDistribution - Class in demo
ChemCompDistribution() - Constructor for class demo.ChemCompDistribution
ChemCompGroupFactory - Class in org.biojava.nbio.structure.chem
ChemCompGroupFactory() - Constructor for class org.biojava.nbio.structure.chem.ChemCompGroupFactory
ChemCompProvider - Interface in org.biojava.nbio.structure.chem: Interface that is implemented by all classes that can provide ChemComp definitions.
ChemCompTools - Class in org.biojava.nbio.structure.chem
ChemCompTools() - Constructor for class org.biojava.nbio.structure.chem.ChemCompTools
CHEMICAL_MODIFICATION - org.biojava.nbio.protmod.ModificationCategory
ChemicalComponentDictionary - Class in org.biojava.nbio.structure.chem: A representation of the Chemical Component Dictionary.
ChemicalComponentDictionary() - Constructor for class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
children() - Method in class org.biojava.nbio.alignment.GuideTree.Node
chiSq(double, int) - Static method in class org.biojava.nbio.survival.cox.stats.ChiSq
ChiSq - Class in org.biojava.nbio.survival.cox.stats
ChiSq() - Constructor for 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
CHROMOSOME - org.biojava.nbio.core.sequence.DNASequence.DNAType
CHROMOSOME - Static variable in class org.biojava.nbio.genome.util.ChromosomeMappingTools
ChromosomeMappingTools - Class in org.biojava.nbio.genome.util: A class that can map chromosomal positions to mRNA (coding sequence) positions.
ChromosomeMappingTools() - Constructor for class org.biojava.nbio.genome.util.ChromosomeMappingTools
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(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>) - 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(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
ChromPos - Class in org.biojava.nbio.genome.parsers.genename: Created by ap3 on 27/10/2014.
ChromPos(int, int) - Constructor for class org.biojava.nbio.genome.parsers.genename.ChromPos
Chsolve2 - Class in org.biojava.nbio.survival.cox.stats
Chsolve2() - Constructor for class org.biojava.nbio.survival.cox.stats.Chsolve2
CIF - org.biojava.nbio.structure.io.StructureFiletype
CIF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.BcifFileReader
CIF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.CifFileReader
CIF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.BcifFileReader
CIF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.CifFileReader
CifBean - Interface in org.biojava.nbio.structure.io.cif: Flag for BioJava beans that resemble categories defined by the mmCIF schema.
CifChainSupplierImpl - Class in org.biojava.nbio.structure.io.cif: Convert a chain to a CifFile.
CifChainSupplierImpl() - Constructor for class org.biojava.nbio.structure.io.cif.CifChainSupplierImpl
CifFileConsumer<S> - Interface in org.biojava.nbio.structure.io.cif: Defines a rather generic interface which allows to populate some data structure with data parsed from a CIF file.
CifFileReader - Class in org.biojava.nbio.structure.io: Parse text Cif files and provide capabilities to store them locally.
CifFileReader() - Constructor for class org.biojava.nbio.structure.io.CifFileReader: Constructs a new CifFileReader, initializing the extensions member variable.
CifFileReader(String) - Constructor for class org.biojava.nbio.structure.io.CifFileReader: Constructs a new CifFileReader, initializing the extensions member variable.
CifFileSupplier<S> - Interface in org.biojava.nbio.structure.io.cif: Create a CifFile instance for a given container of structure data.
CifStructureConsumer - Interface in org.biojava.nbio.structure.io.cif: Defines the categories to consume during CIF parsing.
CifStructureConsumerImpl - Class in org.biojava.nbio.structure.io.cif: An implementation of a CifFileConsumer for BioJava.
CifStructureConsumerImpl(FileParsingParameters) - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
CifStructureConverter - Class in org.biojava.nbio.structure.io.cif: Convert BioJava structures to CifFiles and vice versa.
CifStructureConverter() - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureConverter
CifStructureSupplierImpl - Class in org.biojava.nbio.structure.io.cif: Convert a structure to a CifFile.
CifStructureSupplierImpl() - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureSupplierImpl
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.
Cl - org.biojava.nbio.structure.Element
claFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
Class - org.biojava.nbio.structure.cath.CathCategory
Class - org.biojava.nbio.structure.scop.ScopCategory
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) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil: Removes all whitespace chars in the sequence string
cleanSequence(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils: Returns a new sequence with all invalid characters being replaced by '-'.
cleanup() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc
cleanup() - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
cleanup() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
cleanup() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc
cleanup() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
cleanup(List<Domain>) - Static method in class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
cleanUp() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
cleanUp() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
cleanUp() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
cleanUpAltLocs(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Cleans up the structure's alternate location (altloc) groups.
clear() - Static method in class org.biojava.nbio.core.util.FlatFileCache: Removes all elements from the cache
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
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.chem.ChemCompGroupFactory: Force the in-memory cache to be reset.
clearExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: clear the supported file extensions
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() - 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
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.PdbId
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.internal.CESymmParameters
clone(Object) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache: Subclasses should override clone and use the copy constructor.
cloneAtomArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: Provides an equivalent copy of Atoms in a new array.
cloneAtomsAndBonds(Group) - Method in class org.biojava.nbio.structure.HetatomImpl
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.geometry.CalcPoint: Clone an array of points.
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() - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
close() - Method in interface org.biojava.nbio.core.util.XMLWriter: Close this XMLWriter, and its underlying stream.
close() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitFacade: Closes .2bit file twoBitParser.
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
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.
CLOSED - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
closeParser() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser: Method closes random access file descriptor.
closeTag(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
closeTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Closes an un-qualified element.
closeTag(String, 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
CLUSTALW - org.biojava.nbio.core.alignment.template.Profile.StringFormat
CLUSTALW - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
cluster(List<Subunit>, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.cluster.SubunitClusterer
cluster(List<Domain>, PDPDistanceMatrix) - Static method in class org.biojava.nbio.structure.domain.pdp.ClusterDomains
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(Structure, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.cluster.SubunitClusterer
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
Cm - org.biojava.nbio.structure.Element
CMD - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
Co - org.biojava.nbio.structure.Element
Codon(Table.CaseInsensitiveTriplet) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon
Codon(Table.CaseInsensitiveTriplet, AminoAcidCompound, boolean, boolean) - 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
coil - org.biojava.nbio.structure.secstruc.SecStrucType
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
combine(List<Integer>, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
combine(BiologicalAssemblyTransformation, BiologicalAssemblyTransformation) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Returns the combination (product) of two biological assembly transformations.
combineWith(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup: Combine the ResidueGroup with the alignment block.
combineWith(Stoichiometry) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry: Make a combined Stoichiometry object of this and the other.
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_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(int[], int[]) - Method in class org.biojava.nbio.structure.align.helper.IdxComparator
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(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(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemComp
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(PdbId) - Method in class org.biojava.nbio.structure.PdbId
compareTo(BiologicalAssemblyTransformation) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
compareTo(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber: Compare residue numbers by chain, sequence number, and insertion code
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
compareToPositional(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber: Compare residue numbers by sequence number and insertion code, ignoring the chain
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
complementBase(char, boolean) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters: This method returns the complement of a base.
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. base A will become base T
ComplementSequenceView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.views.ComplementSequenceView
complete() - Method in interface org.biojava.nbio.genome.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. if we have a sequence of length 10 and the location 3..52 we make 4 complete passes through the genome to go from position 3 to position 52.
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. if we have a sequence of length 10 and the location 3..52 we make 4 complete passes through the genome to go from position 3 to position 52.
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.chem.AllChemCompProvider
ComponentXMLConverter - Class in org.biojava.nbio.protmod.io
ComponentXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.ComponentXMLConverter
COMPOSED_OPERATOR_SEPARATOR - Static variable in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder: The character separating operator ids that are composed.
COMPOSITION_BASED_STATISTICS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
Compound - Interface in org.biojava.nbio.core.sequence.template
COMPOUND - org.biojava.nbio.core.alignment.template.AlignedSequence.Step
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(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
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
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() - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
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.
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
CONSTANT - org.biojava.nbio.alignment.template.GapPenalty.Type
constrain(double) - Method in enum org.biojava.nbio.genome.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.
consume(Category) - Method in interface org.biojava.nbio.structure.io.cif.MetalBondConsumer
consume(Category) - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl
consumeAtomSite(AtomSite) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeAtomSite(AtomSite) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeAtomSites(AtomSites) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeAtomSites(AtomSites) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeAuditAuthor(AuditAuthor) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeAuditAuthor(AuditAuthor) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeCell(Cell) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeCell(Cell) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer: Consume a particular Cif category.
consumeChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
consumeChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeChemCompAtom(ChemCompAtom) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer: Consume a particular Cif category.
consumeChemCompAtom(ChemCompAtom) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
consumeChemCompBond(ChemCompBond) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer: Consume a particular Cif category.
consumeChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
consumeChemCompBond(ChemCompBond) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeDatabasePDBRemark(DatabasePDBRemark) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeDatabasePDBRemark(DatabasePDBRemark) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeDatabasePDBRev(DatabasePDBRev) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeDatabasePDBRev(DatabasePDBRev) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeDatabasePDBRevRecord(DatabasePDBRevRecord) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeDatabasePDBRevRecord(DatabasePDBRevRecord) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeEntity(Entity) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeEntity(Entity) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeEntityPoly(EntityPoly) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeEntityPoly(EntityPoly) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeEntityPolySeq(EntityPolySeq) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeEntityPolySeq(EntityPolySeq) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeEntitySrcGen(EntitySrcGen) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeEntitySrcGen(EntitySrcGen) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeEntitySrcNat(EntitySrcNat) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeEntitySrcNat(EntitySrcNat) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeEntitySrcSyn(PdbxEntitySrcSyn) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeEntitySrcSyn(PdbxEntitySrcSyn) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeExptl(Exptl) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeExptl(Exptl) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxAuditRevisionHistory(PdbxAuditRevisionHistory) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxAuditRevisionHistory(PdbxAuditRevisionHistory) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxChemCompIdentifier(PdbxChemCompIdentifier) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxChemCompIdentifier(PdbxChemCompIdentifier) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxDatabaseStatus(PdbxDatabaseStatus) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxDatabaseStatus(PdbxDatabaseStatus) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxEntityBranchDescriptor(PdbxEntityBranchDescriptor) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxEntityBranchDescriptor(PdbxEntityBranchDescriptor) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxMolecule(PdbxMolecule) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxMolecule(PdbxMolecule) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxMoleculeFeatures(PdbxMoleculeFeatures) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxMoleculeFeatures(PdbxMoleculeFeatures) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxNonpolyScheme(PdbxNonpolyScheme) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxNonpolyScheme(PdbxNonpolyScheme) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxReferenceEntityLink(PdbxReferenceEntityLink) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxReferenceEntityLink(PdbxReferenceEntityLink) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxReferenceEntityList(PdbxReferenceEntityList) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxReferenceEntityList(PdbxReferenceEntityList) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxReferenceEntityPolyLink(PdbxReferenceEntityPolyLink) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxReferenceEntityPolyLink(PdbxReferenceEntityPolyLink) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxStructAssembly(PdbxStructAssembly) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxStructAssembly(PdbxStructAssembly) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxStructAssemblyGen(PdbxStructAssemblyGen) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxStructAssemblyGen(PdbxStructAssemblyGen) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxStructModResidue(PdbxStructModResidue) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxStructModResidue(PdbxStructModResidue) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxStructOperList(PdbxStructOperList) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxStructOperList(PdbxStructOperList) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeRefine(Refine) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeRefine(Refine) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStruct(Struct) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStruct(Struct) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructAsym(StructAsym) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructAsym(StructAsym) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructConf(StructConf) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructConf(StructConf) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructConn(StructConn) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructConn(StructConn) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructConnType(StructConnType) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructConnType(StructConnType) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructKeywords(StructKeywords) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructKeywords(StructKeywords) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructNcsOper(StructNcsOper) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructNcsOper(StructNcsOper) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructRef(StructRef) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructRef(StructRef) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructRefSeq(StructRefSeq) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructRefSeq(StructRefSeq) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructRefSeqDif(StructRefSeqDif) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructRefSeqDif(StructRefSeqDif) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructSheetRange(StructSheetRange) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructSheetRange(StructSheetRange) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructSite(StructSite) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructSite(StructSite) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructSiteGen(StructSiteGen) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructSiteGen(StructSiteGen) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeSymmetry(Symmetry) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeSymmetry(Symmetry) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
Contact - Class in org.biojava.nbio.structure.contact: A simple class to store contacts in the form of pairs of indices and a distance associated to them.
Contact(int, int, double) - Constructor for class org.biojava.nbio.structure.contact.Contact
contacts(Point3d[], Point3d[], double) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
contains(Point3d) - Method in class org.biojava.nbio.structure.contact.BoundingBox: Check if a given point falls within this box
contains(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Is the key in the table?
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(ResidueNumber, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange
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(File, File) - Static method in class demo.DemoMmcifToPdbConverter
convert(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.ForesterWrapper: Convert a BioJava MultipleSequenceAlignment to a forester Msa.
convert(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor: Returns the converted sequence.
convert(Fastq) - Method in class org.biojava.nbio.genome.io.fastq.IlluminaFastqWriter
convert(Fastq) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqWriter
convert(Fastq) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqWriter
convert(Fastq, FastqVariant) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools: Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.
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
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
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
convertDNAtoProteinSequence(String) - Static method in class org.biojava.nbio.genome.util.ProteinMappingTools: Converts the DNA sequence to protein sequence.
convertDNAtoProteinSequence(DNASequence) - Static method in class org.biojava.nbio.genome.util.ProteinMappingTools: Converts the DNA sequence to protein sequence.
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.
convertStreamToString(InputStream) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper: Converts an InputStream of text to a String, closing the stream before returning.
convertTo(FastqVariant) - Method in class org.biojava.nbio.genome.io.fastq.Fastq: Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.
convertToDoubleArray(Matrix4d) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils: Convert a four-d matrix to a double array.
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() - Method in class org.biojava.nbio.structure.jama.Matrix: Make a deep copy of a matrix
copy(File, File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Copy the content of file src to dst TODO since java 1.7 this is provided in java.nio.file.Files
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.
copyEmblReference(EmblReference) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference: return copy of EmblReference
copyFile(File, File) - Static method in class org.biojava.nbio.phosphosite.Dataset
copyLigandsByProximity(Structure, Structure) - Static method in class org.biojava.nbio.structure.SubstructureIdentifier: Supplements the reduced structure with ligands from the full structure based on a distance cutoff.
copyLigandsByProximity(Structure, Structure, double, int, int) - Static method in class org.biojava.nbio.structure.SubstructureIdentifier: Supplements the reduced structure with ligands from the full structure based on a distance cutoff.
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(C...) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
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
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
COVALENT - org.biojava.nbio.structure.BondType
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(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(String, String, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
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
Cr - org.biojava.nbio.structure.Element
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.
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
createDNASequence(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools: Create and return a new DNASequence from the specified FASTQ formatted sequence.
createDNASequenceWithErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.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.genome.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.genome.io.fastq.FastqTools: Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence.
createErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.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.
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
createPurelyNonPolyEntities(List<List<Chain>>, List<List<Chain>>, List<EntityInfo>) - Static method in class org.biojava.nbio.structure.io.EntityFinder: Given all chains of all models find entities for the nonpolymers and water chains within them, assigning entity ids, types and descriptions to them.
createQualityScores(Fastq) - Static method in class org.biojava.nbio.genome.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>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
createSequence(Sequence<NucleotideCompound>, Frame) - 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.
createTerm(String) - 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) - Method in class org.biojava.nbio.ontology.Ontology.Impl
createTerm(String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
createTerm(String, String) - Method in interface org.biojava.nbio.ontology.Ontology: Create a new term in this ontology.
createTerm(String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
createTerm(String, String, Object[]) - Method in class org.biojava.nbio.ontology.IntegerOntology
createTerm(String, String, Object[]) - Method in interface org.biojava.nbio.ontology.Ontology: Create a new term in this ontology.
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. this might be needed when working with GLY thanks to Peter Lackner for a python template of this method.
CROSS_LINK_1 - org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_2 - org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_3 - org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_4 - org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_5 - org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_6 - org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_7 - org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_8_OR_LARGE - org.biojava.nbio.protmod.ModificationCategory
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
CrystalBuilder(Structure, Map<String, String>, Map<String, Matrix4d>) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder: Special constructor for NCS-aware 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(CrystalTransform) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform: Copy constructor
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
Cs - org.biojava.nbio.structure.Element
CS_HSV - Static variable in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace: The HSV color space
Cu - org.biojava.nbio.structure.Element
CUBIC - org.biojava.nbio.structure.xtal.BravaisLattice
CURATED - org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
CURRENT - org.biojava.nbio.structure.PDBStatus.Status
CUSTOM - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy: The strategy is defined via an external function, we do not have to do anything.
cut(Atom[], Domain, CutValues, int[][], PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.Cut
Cut - Class in org.biojava.nbio.structure.domain.pdp
Cut() - Constructor for class org.biojava.nbio.structure.domain.pdp.Cut
Cut(int, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.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(Domain, CutSites, PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.CutDomain
CutDomain - Class in org.biojava.nbio.structure.domain.pdp
CutDomain(Atom[], PDPDistanceMatrix) - Constructor for 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
CYCLE - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy: Cycle through the alphabet (e.g., ...xyzABC...)
cyclicPeptide - org.biojava.nbio.structure.chem.PolymerType: cyclic peptides
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 - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

D - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

D - org.biojava.nbio.structure.Element

Deuterium

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.

DATABASE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

DATABASE_PREFIX - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

DATABASE_SORT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

DatabasePDBRevRecord - Class in org.biojava.nbio.structure

Represents revision records for use by PDBHeader.

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

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

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

DatabaseReference(String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference

DatabaseReference(String, 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)

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

dateToIsoString(Date) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Covert a Date object to ISO time format.

DB_GENETIC_CODE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

dBetaPeptideCGammaLinking - org.biojava.nbio.structure.chem.ResidueType

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

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

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

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

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

DDBJ - org.biojava.nbio.core.sequence.DataSource

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

debug(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter

declareNamespace(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

Declare a namespace for current and following elements 'prefixHint' is ignored entirely in this implementation

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_BCIF_FILE_SERVER - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory

The default server to retrieve BinaryCIF files.

DEFAULT_BIOASSEMBLY_STYLE - Static variable in class org.biojava.nbio.structure.align.util.AtomCache

The default output bioassembly style: if true the bioassemblies are multimodel, if false the bioassemblies are flat with renamed chains for symmetry-partners.

DEFAULT_BUFFER_SIZE - Variable in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser

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_CHEMCOMP_PATHURL_TEMPLATE - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

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.URLConnectionTools

The default connection timeout in ms - 15 seconds

DEFAULT_CONTACT_CUTOFF - Static variable in class org.biojava.nbio.structure.contact.InterfaceFinder

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_FILE - Static variable in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

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

Threshold for plausible binding of a ligand to the selected substructure

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_MAX_PROPELLER - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

DEFAULT_MAX_PROPELLER - Static variable in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

DEFAULT_MAX_SHEAR - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

DEFAULT_MAX_STAGGER - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

DEFAULT_MAX_STAGGER - Static variable in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

DEFAULT_MAX_STRETCH - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

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

The default value for number of sphere points to sample.

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_FILE_SERVER - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory

The default server name, prefixed by the protocol string (http://, https:// or ftp://).

DEFAULT_PROBE_SIZE - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

DEFAULT_RANGE_PROBABILITY_THRESHOLD - Static variable in class org.biojava.nbio.ronn.RonnConstraint

DEFAULT_RCSB_DATA_API_SERVER - Static variable in class org.biojava.nbio.structure.PDBStatus

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_URL - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

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_UNIPROT_BASE_URL - Static variable in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

DEFAULT_VARIANT - Static variable in class org.biojava.nbio.genome.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(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable

Delete the key (and paired value) from table.

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

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

Delete an alignment position from the original alignment object.

deleteDirectory(String) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils

Recursively delete a folder & contents

deleteDirectory(Path) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils

Recursively delete a folder & contents

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

Find the alignment position with the highest atomic distance between the equivalent atomic positions of the arrays and remove it from the alignment.

deleteStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Attempts to delete all versions of a structure from the local directory.

deleteStructure(PdbId) - 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

DELETION - org.biojava.nbio.alignment.routines.AlignerHelper.Last

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

DemoBioAssemblies - Class in demo

DemoBioAssemblies() - Constructor for class demo.DemoBioAssemblies

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

DemoMmcifToPdbConverter - Class in demo

An example of how to convert mmCIF file to PDB file

DemoMmcifToPdbConverter() - Constructor for class demo.DemoMmcifToPdbConverter

DemoMmtfReader - Class in demo

Class to show how to read a Biojava structure using MMTF

DemoMmtfReader() - Constructor for class demo.DemoMmtfReader

DemoMmtfWriter - Class in demo

DemoMmtfWriter() - Constructor for class demo.DemoMmtfWriter

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

DemoQsAlign - Class in demo

Demo on how to use programatically QsAlign for the alignment of quaternary structures.

DemoQsAlign() - Constructor for class demo.DemoQsAlign

DemoQuatSymmetryJmol - Class in demo

This demo shows how to display the QuatSymmetryResults of a structure.

DemoQuatSymmetryJmol() - Constructor for class demo.DemoQuatSymmetryJmol

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

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

DemoSymmetry - Class in demo

A demo on how to use the quaternary symmetry detection algorithms.

DemoSymmetry() - Constructor for class demo.DemoSymmetry

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.genome.io.fastq.ParseListener

Notify this parse listener of a description line.

DESCRIPTIONS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

DESCRIPTIONS - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

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() - 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.

dfbeta - org.biojava.nbio.survival.cox.ResidualsCoxph.Type

dfbetas - org.biojava.nbio.survival.cox.ResidualsCoxph.Type

dGammaPeptideCDeltaLinking - org.biojava.nbio.structure.chem.ResidueType

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

DIFFERENT - org.biojava.nbio.structure.align.quaternary.QsRelation

None of the Subunits of one Structure have an equivalent in the other Structure.

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, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay

Display an AFPChain alignment

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(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.

DISPLAY_SORT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

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_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 - org.biojava.nbio.phylo.TreeType

Distance Tree

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.

divideInternally(SubunitClustererParameters) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Analyze the internal symmetry of the SubunitCluster and divide its Subunit into the internal repeats (domains) if they are internally symmetric.

divideStructure(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Method that converts the symmetric units of a structure into different structures, so that they can be individually visualized.

dna - org.biojava.nbio.structure.chem.PolymerType

polydeoxyribonucleotide

DNA_ONLY - Static variable in enum org.biojava.nbio.structure.chem.PolymerType

Convenience Set of polymer types classified as DNA.

dna3PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType

dna5PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType

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

dnaLinking - org.biojava.nbio.structure.chem.ResidueType

dnarna - org.biojava.nbio.structure.chem.PolymerType

polydeoxyribonucleotide/polyribonucleotide hybrid

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

Create a sequence where the actual storage of the sequence data is somewhere else

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

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

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

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

DomainCounter - org.biojava.nbio.structure.cath.CathCategory

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

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.URLConnectionTools

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.URLConnectionTools

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

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

Calculates the dot product of this vector a with b

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

dotProduct(Quat4d, Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

Compute the dot (inner) product of two quaternions.

DOUBLE - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy

Represent every cluster with two symbols from the alphabet, this forces us to specify number of subunits for every subunit (e.g., AA1AB1AC1...).

download() - Method in class org.biojava.nbio.phosphosite.Dataset

DownloadChemCompProvider - Class in org.biojava.nbio.structure.chem

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.chem.DownloadChemCompProvider

DownloadChemCompProvider(String) - Constructor for class org.biojava.nbio.structure.chem.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.chem.AllChemCompProvider

Downloads the components.cif.gz file from the wwPDB site.

downloadFile(URL, File) - Static method in class org.biojava.nbio.core.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.

downloadFile(URL, File) - Method in class org.biojava.nbio.phosphosite.Dataset

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

downloadIfNoTwoBitFileExists(File, String) - Static method in class org.biojava.nbio.genome.parsers.twobit.SimpleTwoBitFileProvider

downloadNodeListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation

downloadStructure(PdbId) - 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.

dpeptide - org.biojava.nbio.structure.chem.PolymerType

polypeptide(D)

dPeptideAminoTerminus - org.biojava.nbio.structure.chem.ResidueType

dPeptideCarboxyTerminus - org.biojava.nbio.structure.chem.ResidueType

dPeptideLinking - org.biojava.nbio.structure.chem.ResidueType

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

dSaccharide - org.biojava.nbio.structure.chem.ResidueType

dSaccharide14and14linking - org.biojava.nbio.structure.chem.ResidueType

dSaccharide14and16linking - org.biojava.nbio.structure.chem.ResidueType

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

Dy - org.biojava.nbio.structure.Element

DYNAMIC - org.biojava.nbio.alignment.template.GapPenalty.Type

E

E - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

E - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

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

ECOD - org.biojava.nbio.structure.align.client.StructureName.Source

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() - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation

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(BufferedReader) - 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(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

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

Interface for carrying out edit operations on a Sequence.

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.

ef - Variable in class org.biojava.nbio.survival.cox.CoxInfo

Efron - org.biojava.nbio.survival.cox.CoxMethod

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.

ELECTRON_CRYSTALLOGRAPHY - org.biojava.nbio.structure.ExperimentalTechnique

ELECTRON_MICROSCOPY - org.biojava.nbio.structure.ExperimentalTechnique

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

One way to model the elements

Element - Enum in org.biojava.nbio.structure

Element is an enumeration of the elements of the periodic table.

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

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.

EMAIL - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

EmblId - Class in org.biojava.nbio.core.sequence.io.embl

This class contains the processed data of embl file Primary accession number Sequence version number Topology: 'circular' or 'linear' Molecule type Data class Taxonomic division Sequence length

EmblId(String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblId

EmblReader - Class in org.biojava.nbio.core.sequence.io.embl

This class should process the data of embl file

EmblReader() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblReader

EmblRecord - Class in org.biojava.nbio.core.sequence.io.embl

this class contains the parsed data of embl file

EmblRecord() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblRecord

EmblReference - Class in org.biojava.nbio.core.sequence.io.embl

This class contains the processed data of embl file that contains the referenceNumber, referenceComment, referencePosition referenceCrossReference, referenceGroup, referenceAuthor referenceTitle, referenceLocation

EmblReference() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblReference

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.

ENA - org.biojava.nbio.core.sequence.DataSource

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

entity_poly_type - Variable in enum org.biojava.nbio.structure.chem.PolymerType

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

Heuristical finding of Entities (called Compounds in legacy PDB format) in a given Structure.

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

EntityInfo - Class in org.biojava.nbio.structure

An object to contain the info from the PDB header for a Molecule.

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

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

Constructs a new EntityInfo copying all data from the given one but not setting the Chains

EntityType - Enum in org.biojava.nbio.structure

The type of entity (polymer, non-polymer, water, macrolide) as defined in the mmCIF dictionary:

entityTypeFromString(String) - Static method in enum org.biojava.nbio.structure.EntityType

Creates a new EntityType from a String value.

ENTREZ_QUERY - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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(boolean, boolean) - Static method in class org.biojava.nbio.core.util.Equals

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(Object, Object) - Static method in class org.biojava.nbio.core.util.Equals

Does not compare class types.

equalLengthSequences(ProteinSequence[]) - Static method in class org.biojava.nbio.core.util.SequenceTools

A method to check whether an array of sequences contains at least two sequences having an equal length.

equals(Object) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence

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.loader.SequenceFileProxyLoader

equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

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.JoiningSequenceReader

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.template.AbstractSequence

equals(Object) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

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(Object) - Method in class org.biojava.nbio.data.sequence.FastaSequence

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.chem.ChemComp

equals(Object) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

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.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(Object) - Method in class org.biojava.nbio.structure.PdbId

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.core.PermutationGroup

equals(Object) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

equals(Object) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

equals(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

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

equals(PDBHeader) - Method in class org.biojava.nbio.structure.PDBHeader

Compare two PDBHeader objects

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

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

equalsPositional(Object) - Method in class org.biojava.nbio.structure.ResidueNumber

Check if the seqNum and insertion code are equivalent, ignoring the chain

equalsToIgnoreEndline(String, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper

Compares two strings in a case-sensitive manner 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

This method is not implemented or used, never returns true and should probably be removed.

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

EQUIVALENT - org.biojava.nbio.structure.align.quaternary.QsRelation

All the Subunits of one Structure have an equivalent in the other Structure.

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.

Er - org.biojava.nbio.structure.Element

error(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter

errorEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter

errorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools

Return the error probabilities from the specified FASTQ formatted sequence.

errorProbabilities(Fastq, double[]) - Static method in class org.biojava.nbio.genome.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.genome.io.fastq.FastqVariant

Convert the specified quality in ASCII format to an error probability.

errorProbability(int) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant

Calculate the error probability given the specified quality score.

Es - org.biojava.nbio.structure.Element

escape(String, boolean) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser

escapeChars - Static variable in class org.biojava.nbio.ontology.obo.OboFileParser

Eu - org.biojava.nbio.structure.Element

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.

expandNcsOps(Structure, Map<String, String>, Map<String, Matrix4d>) - Static method in class org.biojava.nbio.structure.xtal.CrystalBuilder

Apply the NCS operators in the given Structure adding new chains as needed.

expandUserHome(String) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils

Expands ~ in paths to the user's home directory.

EXPECT - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

EXPECT_HIGH - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

EXPECT_LOW - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

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

extended - org.biojava.nbio.structure.secstruc.SecStrucType

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

ExtinctionCoefficient_False - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

ExtinctionCoefficient_True - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

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

extractSubunits(Structure, int, double, int) - Static method in class org.biojava.nbio.structure.cluster.SubunitExtractor

Extract the information of each protein Chain in a Structure and converts them into a List of Subunit.

F

f(Double) - Method in class org.biojava.nbio.survival.cox.StrataInfo

F - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

F - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

F - org.biojava.nbio.structure.Element

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

F_UNCLASSIFIED - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

String for unclassified F-groups

f1Dot2(float) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator

Family - org.biojava.nbio.structure.scop.ScopCategory

FASTA - org.biojava.nbio.core.alignment.template.Profile.StringFormat

FASTA - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat

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(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.

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.

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(File, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser

FastaStructureParser(InputStream, 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(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

TODO Write comment

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(SequencePair<Sequence<AminoAcidCompound>, AminoAcidCompound>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

Provided only for convenience.

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.

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(Fastq) - Method in interface org.biojava.nbio.genome.io.fastq.StreamListener

Notify this listener of a FASTQ formatted sequence.

Fastq - Class in org.biojava.nbio.genome.io.fastq

FASTQ formatted sequence.

FASTQ_ILLUMINA - org.biojava.nbio.genome.io.fastq.FastqVariant

Illumina FASTQ sequence format variant.

FASTQ_SANGER - org.biojava.nbio.genome.io.fastq.FastqVariant

Sanger FASTQ sequence format variant.

FASTQ_SOLEXA - org.biojava.nbio.genome.io.fastq.FastqVariant

Solexa FASTQ sequence format variant.

FastqBuilder - Class in org.biojava.nbio.genome.io.fastq

Fluent builder API for creating FASTQ formatted sequences.

FastqBuilder() - Constructor for class org.biojava.nbio.genome.io.fastq.FastqBuilder

Create a new FASTQ formatted sequence builder.

FastqBuilder(Fastq) - Constructor for class org.biojava.nbio.genome.io.fastq.FastqBuilder

Create a new FASTQ formatted sequence builder configured from the specified FASTQ formatted sequence.

FastqReader - Interface in org.biojava.nbio.genome.io.fastq

Reader for FASTQ formatted sequences.

FastqTools - Class in org.biojava.nbio.genome.io.fastq

Utility methods for FASTQ formatted sequences.

FastqVariant - Enum in org.biojava.nbio.genome.io.fastq

FASTQ sequence format variant.

FastqWriter - Interface in org.biojava.nbio.genome.io.fastq

Writer for FASTQ formatted sequences.

fatal(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter

fatalEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter

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

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

Fe - org.biojava.nbio.structure.Element

Feature - Class in org.biojava.nbio.genome.parsers.gff

A Feature corresponds to a single row in a GFF file.

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(Feature) - Constructor for class org.biojava.nbio.genome.parsers.gff.Feature

Make a copy of the specified feature.

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<C extends Compound> - 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_CURRENT - org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

Fetch the most recent version of the PDB entry.

FETCH_FILES - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Fetch missing files from the server.

FETCH_IF_OUTDATED - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Fetch missing files from the server, also fetch if file present but older than the server file.

FETCH_OBSOLETE - org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

Fetch the obsolete entry from the PDB archives.

FETCH_REMEDIATED - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Fetch missing files from the server.

fh2 - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method

FIBER_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique

figureLineInfoLowerPercentX - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

figureLineInfoLowerPercentY - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

FILE - org.biojava.nbio.structure.align.client.StructureName.Source

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.core.util

FileDownloadUtils() - Constructor for class org.biojava.nbio.core.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

FileProxyRNASequenceCreator - 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.

FileProxyRNASequenceCreator(File, CompoundSet<NucleotideCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator

Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read

FILESPLIT - Static variable in class org.biojava.nbio.structure.cath.CathInstallation

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

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

Fill the aligned Atom arrays with the equivalent residues in the afpChain.

FILTER - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

filterByCathCode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return list of CATH descriptions whose CATH codes (e.g. 1.4.6.10) start with the query.

filterByCathCode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

filterByClassificationId(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Get all scop descriptions that start with a classification ID, e.g. b.1.18

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 interface org.biojava.nbio.structure.scop.ScopDatabase

Get all scop descriptions that start with a certain name. e.g.

filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

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

finalizeStructure() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

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.

findGroup(String, String) - Method in interface org.biojava.nbio.structure.Structure

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.

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.

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.

findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method performs a search for base pairs in the structure.

findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This is an implementation for finding non-canonical base pairs when there may be missing or overhanging bases.

findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

This is an alternative implementation of findPair() that looks for anything that would fit the criteria for a base-pair, useful for the context of tertiary structure of RNA.

findPolyEntities(List<List<Chain>>) - Static method in class org.biojava.nbio.structure.io.EntityFinder

Utility method that employs some heuristics to find the EntityInfos for the polymeric chains given in constructor.

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() - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl

finish() - Method in interface org.biojava.nbio.structure.io.cif.CifFileConsumer

Ultimate setup which can include steps which require several categories to be available and integrate them into the final container.

finish() - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl

finish() - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl

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

FIRST - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION

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

FIRST_QUERY_NUM - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

FIRST25 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION

FIRST50 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION

FIRST75 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION

fixMicroheterogenity(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

This sets all microheterogeneous groups (previously alternate location groups) as separate groups.

flagLoading(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache

flagLoadingFinished(PdbId) - 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.

FlatQueryAnchored - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum

FlatQueryAnchoredNoIdentities - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum

flemingHarrington - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method

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.

floor(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable

Return the largest key in the table <= k.

FLUORESCENCE_TRANSFER - org.biojava.nbio.structure.ExperimentalTechnique

flush() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile

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

Fm - org.biojava.nbio.structure.Element

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

Fold - org.biojava.nbio.structure.scop.ScopCategory

FORCE_DOWNLOAD - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

For every file, force downloading from the server

ForesterWrapper - Class in org.biojava.nbio.phylo

This class contains wrapper methods for communication between BioJava and forester (e.g, Data Structure conversion).

FORMAT_ENTREZ_QUERY - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

FORMAT_OBJECT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

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

URL parameter specifying the file format (PDB or CIF)

FORMAT_TYPE - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

formatExonStructure(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Pretty print the details of a GeneChromosomePosition to a String

formBondsFromStructConn(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 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

formMatrix(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint

FORTY_175 - org.biojava.nbio.structure.scop.Astral.AstralSet

FORTY_175A - org.biojava.nbio.structure.scop.Astral.AstralSet

FORTY_175B - org.biojava.nbio.structure.scop.Astral.AstralSet

FORTY_201 - org.biojava.nbio.structure.scop.Astral.AstralSet

FORTY_202 - org.biojava.nbio.structure.scop.Astral.AstralSet

FORTY_203 - org.biojava.nbio.structure.scop.Astral.AstralSet

FOURBAR - org.biojava.nbio.structure.xtal.TransformType

FourBitArrayWorker(String, CompoundSet<C>) - 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(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

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

Four bit encoding of the bit formats.

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(Sequence<C>) - 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.

FOURFOLD - org.biojava.nbio.structure.xtal.TransformType

FOURFOLDSCREW - org.biojava.nbio.structure.xtal.TransformType

Fr - org.biojava.nbio.structure.Element

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 - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

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

Get frame (aka phase).

Frame - Enum in org.biojava.nbio.core.sequence.transcription

Indicates a way of translating a sequence.

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

fromCifFile(CifFile) - Static method in class org.biojava.nbio.structure.io.cif.ChemCompConverter

Convert CifFile to chem comp dictionary.

fromCifFile(CifFile) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert CifFile to Structure without any FileParsingParameters.

fromCifFile(CifFile, FileParsingParameters) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert CifFile to Structure.

fromConciseAlignmentString(String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

fromInputStream(InputStream) - Static method in class org.biojava.nbio.structure.io.cif.ChemCompConverter

Convert InputStream to chem comp dictionary.

fromInputStream(InputStream) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert InputStream to Structure without any FileParsingParameters.

fromInputStream(InputStream, FileParsingParameters) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert InputStream to Structure.

fromMultiXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

fromPath(Path) - Static method in class org.biojava.nbio.structure.io.cif.ChemCompConverter

Read data from a file and convert to chem comp dictionary.

fromPath(Path) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Read data from a file and convert to Structure without any FileParsingParameters.

fromPath(Path, FileParsingParameters) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Read data from a file and convert to Structure.

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

fromURL(URL) - Static method in class org.biojava.nbio.structure.io.cif.ChemCompConverter

Get data from a URL and convert to chem comp dictionary.

fromURL(URL) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Get data from a URL and convert to Structure without any FileParsingParameters.

fromURL(URL, FileParsingParameters) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Get data from a URL and convert to Structure.

fromXML(String) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter

fromXML(String) - Static method in class org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter

fromXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

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

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(Node) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter

fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.StructureAtomXMLConverter

fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.StructureGroupXMLConverter

FULL_SEQUENCE_DATA - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage

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 - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

G - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

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

Ga - org.biojava.nbio.structure.Element

GAP - org.biojava.nbio.core.alignment.template.AlignedSequence.Step

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.EntityFinder

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

GAPCOSTS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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.

GCG - org.biojava.nbio.core.alignment.template.Profile.StringFormat

GCG - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat

GCStats - Class in org.biojava.nbio.genome.parsers.gff

GCStats() - Constructor for class org.biojava.nbio.genome.parsers.gff.GCStats

Gd - org.biojava.nbio.structure.Element

Ge - org.biojava.nbio.structure.Element

GENBANK - org.biojava.nbio.core.sequence.DataSource

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(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.

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.

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

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

GenbankReference - Class in org.biojava.nbio.core.sequence.reference

For Genbank format file only.

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

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

GENERAL - org.biojava.nbio.core.sequence.DataSource

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. if the Compound C returns 1 from compoundsToIndex then we should find that compound here in position 1

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.

GENETIC_CODE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

GENINFO - org.biojava.nbio.core.sequence.DataSource

get(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence

Returns the window specified at the given index in offsets i.e. asking for position 2 in a moving window sequence of size 3 will get you the window starting at position 4.

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

Gets the interface corresponding to given id.

get(int) - Method in class org.biojava.nbio.structure.math.SparseVector

get a value

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

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

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(Chain) - Method in class org.biojava.nbio.structure.io.cif.CifChainSupplierImpl

get(Structure) - Method in class org.biojava.nbio.structure.io.cif.CifStructureSupplierImpl

get(S) - Method in interface org.biojava.nbio.structure.io.cif.CifFileSupplier

Convert some model instance describing structure information to a CifFile instance.

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.

getA() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

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

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 interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns 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

Gets singleton instance of an AAIndexProvider, always non-null

getABITracerCompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet

getAboutMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator

getAbsoluteMinimumSequenceLength() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.

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 interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns the absorbance (optical density) of sequence.

getAbsorbance(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl

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

getAccessionNumber() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The AC (Accession number) line lists the accession numbers associated with the entry.

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.

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

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.StatusDisplay

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

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.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 Provided for backwards compatibility now that we support both gene and protein aliases via separate methods.

getAligMap() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay

getAligMat() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

getAligMat() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

getAligMat(int, int) - 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_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

getAlignedAtomsForSubunits1(int) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

getAlignedAtomsForSubunits2(int) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

getAlignedAtomsSubunit(int) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

getAlignedAtomsSubunits() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

getAlignedModel(Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

get an artificial List of chains containing the Atoms and groups.

getAlignedResIndex(Group, Chain) - Method in class org.biojava.nbio.structure.EntityInfo

Given a Group g of Chain c (member of this EntityInfo) return the corresponding position in the alignment of all member sequences (1-based numbering), i.e. the index (1-based) in the SEQRES sequence.

getAlignedSequence(int) - 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(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.

getAlignedSequence(S) - Method in class org.biojava.nbio.core.alignment.SimpleProfile

getAlignedSequence(S) - Method in interface org.biojava.nbio.core.alignment.template.Profile

Searches for the given Sequence within this alignment profile.

getAlignedSequences() - 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() - 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.

getAlignedSequences(int...) - Method in class org.biojava.nbio.core.alignment.SimpleProfile

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 class org.biojava.nbio.core.alignment.SimpleProfile

getAlignedSequences(S...) - Method in interface org.biojava.nbio.core.alignment.template.Profile

Returns a List containing some of the individual AlignedSequences of this alignment.

getAlignedStructure(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Get an artificial Structure containing a different model for every input structure, so that the alignment result can be viewed in Jmol.

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.util.AlignmentTools

Get an artifical Structure containing both chains.

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.

getAlignedSubunits1() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

Return the aligned subunits of the first Subunit group, in the alignment order.

getAlignedSubunits2() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

Return the aligned subunits of the second Subunit group, in the alignment order.

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.align.quaternary.QsAlignResult

The alignment that specifies the residue equivalencies of the equivalent Subunits.

getAlignmentAtoms(Structure) - Method in class org.biojava.nbio.structure.align.StructurePairAligner

Returns the atoms that are being used for the alignment.

getAlignmentFromFasta() - Static method in class demo.DemoAlignmentFromFasta

getAlignmentFromSequence() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence

getAlignmentFromSequence() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence

Returns the alignment.

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.

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

Method that returns the value associated with the key given in parameter.

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.

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

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

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

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

getAllAtomArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools

Returns and array of all atoms of the chain, including Hydrogens (if present) and all HETATOMs.

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

Convert all atoms of the structure (all models) into an Atom array

getAllAtomArray(Structure, int) - Static method in class org.biojava.nbio.structure.StructureTools

Convert all atoms of the structure (specified model) into an Atom array

getAllAtoms() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

getAllChains() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

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(InputStream) - Method in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser

getAllCytobands(URL) - 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()

getAllGroupsFromSubset(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools

Expand a set of atoms into all groups from the same structure.

getAllGroupsFromSubset(Atom[], GroupType) - Static method in class org.biojava.nbio.structure.StructureTools

Expand a set of atoms into all groups from the same structure.

getAllInterfaces() - Method in class org.biojava.nbio.structure.contact.InterfaceFinder

Find all inter polymer-chain interfaces in the structure.

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.

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(Structure, boolean, int) - 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.

getAllNonHCoordsArray(Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools

Returns and array of all non-Hydrogen atoms coordinates 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() - Method in class org.biojava.nbio.alignment.GuideTree

Returns a sequence pair score 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.

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

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.cluster.SubunitCluster

A letter that is assigned to this cluster in stoichiometry.

getAlpha() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

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

getAlphabet() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

getAltAligNumber() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

returns the sequential number of this alternative alignment

getAltAtomId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

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

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 other alternate location groups.

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.chem.ChemCompTools

getAminoThreeLetter(Character) - Static method in class org.biojava.nbio.structure.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() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

Returns the pitch angle of the helix

getAngle(Matrix3d) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis

Quickly compute the rotation angle from a rotation matrix.

getAngle(Matrix4d) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis

Quickly compute the rotation angle from a rotation matrix.

getAngle(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis

Calculate the rotation angle for a structure

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(Matrix) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis

Calculate the rotation angle for a given matrix

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

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

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(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties

An adaptor method to return the apliphatic index of sequence.

getApliphaticIndex(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns 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

getAssemblyHeader() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The AH (Assembly Header) line provides column headings for the assembly information.

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

getAssemblyInformation() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The AS (Assembly Information) lines provide information on the composition of a TPA or TSA sequence.

getAssignment() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

getAsymmetryParameter(double) - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

getAtcc() - Method in class org.biojava.nbio.structure.EntityInfo

getAtom() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom

getAtom(int) - Method in interface org.biojava.nbio.structure.Group

Get at atom by position.

getAtom(int) - Method in class org.biojava.nbio.structure.HetatomImpl

Get at atom by position.

getAtom(String) - Method in interface org.biojava.nbio.structure.Group

Get an atom given its PDB name.

getAtom(String) - Method in class org.biojava.nbio.structure.HetatomImpl

Get an atom given its PDB name.

getAtom1() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage

getAtom2() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage

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>) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP

Returns the first atom for each group

getAtomArray(Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

getAtomArray(Chain, String[]) - Static method in class org.biojava.nbio.structure.StructureTools

Returns an array of the requested Atoms from the Chain object.

getAtomArray(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools

Returns an array of the requested Atoms from the Structure 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() - Static method in class org.biojava.nbio.structure.StructureIO

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.Grid

Returns all contacts, i.e. all atoms that are within the cutoff distance.

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. at the present only works with block 0

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

getAtomGroups() - Method in interface org.biojava.nbio.structure.Chain

Return all Groups with observed density in the chain, i.e.

getAtomGroups() - Method in class org.biojava.nbio.structure.ChainImpl

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

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.

getAtomId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getAtomId() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom

getAtomId1() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

getAtomId2() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

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

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() - Method in class org.biojava.nbio.structure.chem.ChemComp

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.symmetry.internal.CeSymmResult

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

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. the contact map.

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

getAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface

getAtomsForGroup(Group) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get a list of atoms for a group.

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. the contact map.

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. the contact map.

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.

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.

getAtomType1() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

getAtomType2() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

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

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.core.sequence.reference.AbstractReference

The authors are a list of Inventors that retrieved from the Reference section.

getAuthors() - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference

getAuthors() - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface

Get the authors that retrieved from Reference section.

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.

getAutoSuggestProvider() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest

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.

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.

getAverageScore() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

Returns the average similarity score between all pairs of members in the cluster

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 interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns the average hydropathy value of sequence.

getAvgHydropathy(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl

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.

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.

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, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler

getAxisAngle(int, AxisAngle4f) - 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

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

Find a segment of the axis that covers the specified set of atoms.

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

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

getBasecalls() - Method in class org.biojava.nbio.core.sequence.io.ABITrace

Returns an int[] array that represents the basecalls - each int in the array corresponds to an x-coordinate point in the graph that is a peak (a base location).

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.

getBiologicalAssemblies(String) - Static method in class org.biojava.nbio.structure.StructureIO

Returns all biological assemblies for the given PDB id, using multiModel=false

getBiologicalAssemblies(String, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns all biological assemblies for given PDB id.

getBiologicalAssemblies(String, boolean) - Static method in class org.biojava.nbio.structure.StructureIO

Returns all biological assemblies for the given PDB id.

getBiologicalAssembly(String) - Static method in class org.biojava.nbio.structure.StructureIO

Returns the first biological assembly that is available for the given PDB id, using multiModel=false

getBiologicalAssembly(String, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the default biological unit (bioassemblyId=1, known in PDB as pdb1.gz).

getBiologicalAssembly(String, boolean) - Static method in class org.biojava.nbio.structure.StructureIO

Returns the first biological assembly that is available for the given PDB id.

getBiologicalAssembly(String, int) - Static method in class org.biojava.nbio.structure.StructureIO

Returns the biological assembly for the given PDB id and bioassembly identifier, using multiModel=false

getBiologicalAssembly(String, int, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()

getBiologicalAssembly(String, int, boolean) - Static method in class org.biojava.nbio.structure.StructureIO

Returns the biological assembly for the given PDB id and bioassembly identifier.

getBiologicalAssembly(PdbId, int, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()

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() - Method in class org.biojava.nbio.structure.EntityInfo

getBioSequences() - Method in class org.biojava.nbio.alignment.io.StockholmStructure

used to retrieve sequences from the structure

getBioSequences(boolean) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

Because some database files have incorrectly small letters (e.g.

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).

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.

getBioUnitTransformationList(PdbxStructAssembly, int, PdbxStructAssemblyGen, 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.

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

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.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) - 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, 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.

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.

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.chem.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. the difference between ASA uncomplexed and ASA complexed

getBsaToAsaRatio() - Method in class org.biojava.nbio.structure.asa.GroupAsa

Returns the bsa/asa(uncomplexed) ratio, i.e. the ratio of burial of a residue upon complexation

getBtype() - Method in class org.biojava.nbio.structure.secstruc.Ladder

getBuckle(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the buckle in degrees for the given base pair

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

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 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

getCacheFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

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

getCalphaCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

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.

getCdsEnd() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

getCDSExonRanges(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Extracts the exon boundaries in CDS coordinates.

getCDSLength(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Get the length of the CDS in nucleotides.

getCDSLengthForward(List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Get the length of the coding sequence

getCDSLengthReverse(List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Get the length of the coding sequence

getCDSPosForChromosomeCoordinate(int, GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

I have a genomic coordinate, where is it on the mRNA

getCDSPosForward(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene living on the forward DNA strand.

getCDSPosReverse(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene living on the reverse DNA strand.

getCDSRegions(List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Extracts the exons boundaries in CDS coordinates corresponding to the forward DNA strand.

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.EntityInfo

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

Get cell value

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.EntityInfo

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.EntityInfo

getCenter(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils

Get the centroid for the set of atoms starting from position 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

getCenterOfMass() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

getCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

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

getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

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

Returns the centroid of the set of atoms.

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

Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first model

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

Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first model

getChain(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the given model index

getChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the given model index

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

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

Retrieve a chain by its index within the Structure .

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

Retrieve a chain by its index within the Structure .

getChainByIndex(int, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a chain by its indices within the Structure and model.

getChainByIndex(int, int) - Method in class org.biojava.nbio.structure.StructureImpl

Retrieve a chain by its indices within the Structure and 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 class org.biojava.nbio.structure.contact.AtomIdentifier

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.cif.AbstractCifFileSupplier.WrappedAtom

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 (asym id) that this transformation should be applied to.

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.EntityInfo

Return the list of member chain ids (asym ids) that are described by this EntityInfo, only unique chain IDs are contained in the list.

getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

This method is provisional and should only be used for coloring Subunits.

getChainIds() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

getChainIdsInEntry(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader

getChainIdToIndexMap() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

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

getChainName() - Method in class org.biojava.nbio.structure.DBRef

The name of the corresponding chain.

getChainName() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom

getChainName() - Method in class org.biojava.nbio.structure.ResidueNumber

getChainName() - Method in class org.biojava.nbio.structure.ResidueRange

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.EntityInfo

Get the list of chains that are part of this EntityInfo.

getChains() - Method in class org.biojava.nbio.structure.Model

Get all chains: polymeric, non-polymeric and water

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 for the first model.

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

Retrieve all chains for 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.

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.chem.ChemCompAtom

getChargeOfAminoAcid(char) - Static method in class org.biojava.nbio.aaproperties.AminoAcidProperties

Returns the charge of amino acid.

getChargesOfAminoAcids(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties

Returns the array of charges of each amino acid in a protein.

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.chem.AllChemCompProvider

Returns a new instance of a chemical component definition.

getChemComp(String) - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory

getChemComp(String) - Method in interface org.biojava.nbio.structure.chem.ChemCompProvider

Returns a new instance of a chemical component definition.

getChemComp(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

getChemComp(String) - Method in class org.biojava.nbio.structure.chem.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.chem.ReducedChemCompProvider

getChemComp(String) - Method in class org.biojava.nbio.structure.chem.ZipChemCompProvider

(non-Javadoc)

getChemCompProvider() - Static method in class org.biojava.nbio.structure.chem.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

getChromosomalRangesForCDS(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Extracts the boundaries of the coding regions in chromosomal coordinates

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

getChromosomePosForCDScoordinate(int, GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Maps the position of a CDS nucleotide back to the genome

getChromosomeSequenceFromDNASequence(LinkedHashMap<String, DNASequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper

getChromPosForward(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Get the CDS position mapped onto the chromosome position

getChromPosReverse(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Get the CDS position mapped on the chromosome position

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

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() - Method in class org.biojava.nbio.structure.scop.ScopDescription

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

getClassificationId(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathDomain

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).

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

getClustererMethod() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

getClustererMethod() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Method to cluster subunits.

getClusterIds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

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() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

getClusters(double) - Method in class org.biojava.nbio.core.util.SingleLinkageClusterer

Get the clusters by cutting the dendrogram at given cutoff

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

Calculate the interface clusters for this StructureInterfaceList using Jaccard contact set scores to measure the similarity of interfaces.

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

Get the interface clusters for this StructureInterfaceList grouped by NCS-equivalence.

getClusterValue() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

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(C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix

getColumn(C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix

getColumn(AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

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

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

getCommonValence() - Method in enum org.biojava.nbio.structure.Element

Returns the common valence for this Element.

getComparator(int) - Method in class org.biojava.nbio.structure.align.gui.MyTableRowSorter

getCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

getCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

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

getComponent(int) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Make a Stoichiometry object that corresponds to a single component.

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(String) - 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, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties

getComposition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties

getComposition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties

getComposition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl

getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties

getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties

getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl

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, 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, IProfeatProperties.GROUPING) - 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

getCompoundAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence

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

getCompoundAt(int, 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 class org.biojava.nbio.core.alignment.SimpleProfile

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.

getCompoundCountsAt(int) - 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 class org.biojava.nbio.core.alignment.SimpleProfile

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. i.e. in the sequence AGGCCT requesting index 1 returns AGG and requesting index 2 return CCT.

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) - 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 class org.biojava.nbio.core.alignment.SimpleProfile

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

getConnectedFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder

getConnectedTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder

getConsAnnotation() - Method in class org.biojava.nbio.alignment.io.StockholmStructure

getConstituents() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound

getConstructedSequence() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

Con(structed) sequences in the CON data classes represent complete chromosomes, genomes and other long sequences constructed from segment entries.

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 Jaccard contact set score (intersection over union) 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

Deprecated.
use Grid.getAtomContacts() instead

getContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface

getContacts() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

getContactsToOtherCell(GridCell) - 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 Contacts containing the indices of the pair and the calculated distance.

getContactsWithinCell() - 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 Contacts containing the indices of the pair and the calculated distance.

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.

getContainer() - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl

getContainer() - Method in interface org.biojava.nbio.structure.io.cif.CifFileConsumer

Retrieve the created container representing a CIF file.

getContainer() - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl

getContainer() - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl

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.

getCoordsAsPoint3d() - Method in interface org.biojava.nbio.structure.Atom

Get the coordinates.

getCoordsAsPoint3d() - 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

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.

getCoverage() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence

getCoverage() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence

Returns the coverage, as a fraction between 0 and 1, of this AlignedSequence with respect to the original sequence.

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

getCreatedDate() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The DT line shows when an entry first appeared in the database

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

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 all current PDB IDs

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

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.xtal.io.TreeMapSpaceGroupWrapper

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.

getDatabaseCrossReference() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The DR (Database Cross-reference) line cross-references other databases which contain information related to the entry in which the DR line appears.

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

getDataClass() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId

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

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

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

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

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

getdCutoff() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

The maximum allowed distance between the centroids of two equivalent Subunits, in A.

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

Return the deposition date of the structure in the PDB.

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.genome.io.fastq.Fastq

Return the description of this FASTQ formatted sequence.

getDescription() - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder

Return the description for this FASTQ formatted sequence builder.

getDescription() - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant

Return the description of this FASTQ sequence format variant.

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.structure.cath.CathNode

getDescription() - Method in class org.biojava.nbio.structure.EntityInfo

getDescription() - Method in class org.biojava.nbio.structure.PDBHeader

Deprecated.
will be removed later. Use PDBHeader.getKeywords() if you use description to keep the keywords.

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.chem.ChemCompDescriptor

getDescriptors() - Method in class org.biojava.nbio.structure.chem.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.DatabasePDBRevRecord

getDetails() - Method in class org.biojava.nbio.structure.EntityInfo

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.AlignUtils

Get distances along diagonal k from coordinate array coords.

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

getDiagonalDistance2() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getDimension() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getDimension() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getDimension() - Method in class org.biojava.nbio.structure.symmetry.axis.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(String) - Static method in class org.biojava.nbio.ronn.Jronn

Calculates the disordered regions of the protein 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(FastaSequence) - Static method in class org.biojava.nbio.ronn.Jronn

Calculates the disordered regions of the sequence.

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.

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(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.

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

getDist() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

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() - Method in interface org.biojava.nbio.alignment.template.Scorer

Returns score as a distance between 0.0 and 1.0.

getDistance() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage

getDistance() - Method in class org.biojava.nbio.structure.contact.AtomContact

getDistance() - Method in class org.biojava.nbio.structure.contact.Contact

getDistance(double) - Method in class org.biojava.nbio.alignment.template.AbstractScorer

getDistance(double) - Method in interface org.biojava.nbio.alignment.template.Scorer

Returns score as a distance between 0.0 and scale.

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

calculate distance between two atoms.

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() - 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() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

The distance matrix this alignment is based on

getDistanceMatrix(Atom[]) - Method in class org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix

A set of Calpha atoms that are representing the protein

getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils

Matrix of all distances between two sets of Atoms.

getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

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

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

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(String) - 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, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - 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(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties

getDistributionPosition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties

getDistributionPosition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl

getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties

getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties

getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl

getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties

getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties

getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl

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, 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, IProfeatProperties.DISTRIBUTION) - 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.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.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.

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 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

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 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

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.EntityInfo

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

getElement() - 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.

getElement(String) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable

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 the operator for 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.

getElementaryAxesObjects() - 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.

getElementaryAxis(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

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.geometry.MomentsOfInertia

The effective value of this distance for a certain body is known as its radius of / gyration with respect to the given axis.

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

Get the email for QBlast.

getEmblId() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The ID (IDentification) line The tokens represent: 1.

getEmblReference() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The Reference (RN, RC, RP, RX, RG, RA, RT, RL) Lines These lines comprise the literature citations within the database.

getEmbTrees() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

getEmptyChemComp() - Static method in class org.biojava.nbio.structure.chem.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() - 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

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.

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.EntityInfo

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(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(ProteinSequence, AminoAcidCompound) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns 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

getEntities() - Method in class org.biojava.nbio.structure.io.sifts.SiftsXMLParser

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

Request a particular entity by its entity id (mol id in legacy PDB format)

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

Request a particular entity by its entity id (mol id in legacy PDB format)

getEntityId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

getEntityInfo() - Method in interface org.biojava.nbio.structure.Chain

Returns the EntityInfo for this chain.

getEntityInfo() - Method in class org.biojava.nbio.structure.ChainImpl

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

Get all the EntityInfo for this Structure.

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

Get all the EntityInfo for this Structure.

getEntityType() - Method in interface org.biojava.nbio.structure.Chain

Returns the EntityType of this chain.

getEntityType() - Method in class org.biojava.nbio.structure.ChainImpl

getEntityType() - Method in enum org.biojava.nbio.structure.EntityType

Returns the type of the Entity as a String

getEnumValuesAsString(Class<T>) - Static method in class org.biojava.nbio.structure.align.util.CliTools

Constructs a comma-separated list of values for an enum.

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(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

getEquivalentCompounds(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

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

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

getExpressionSystem() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemAtccNumber() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemCell() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemCellLine() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemCellularLocation() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemGene() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemOrgan() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemOrganelle() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemOtherDetails() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemPlasmid() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemStrain() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemTaxId() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemTissue() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemVariant() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemVector() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemVectorType() - Method in class org.biojava.nbio.structure.EntityInfo

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 enum org.biojava.nbio.structure.io.StructureFiletype

getExtensions() - Method in interface org.biojava.nbio.structure.io.StructureIOFile

Returns a list of extensions supported by this class

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 interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns 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

getFatCatAligner() - Method in class org.biojava.nbio.structure.align.fatcat.FatCat

getFeatureHeader() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The FH (Feature Header) lines are present only to improve readability of an entry when it is printed or displayed on a terminal screen.

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

getFeatures() - Method in interface org.biojava.nbio.core.sequence.features.FeatureRetriever

getFeatures() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

getFeatures() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

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

getFeatures(int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Return features at a sequence position

getFeatures(String) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

getFeatures(String, int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Return features at a sequence position by type

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

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

getFeatureTable() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The FT (Feature Table) lines provide a mechanism for the annotation of the sequence data.

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.core.util.FileDownloadUtils

Gets the file extension of a file, excluding '.'.

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.BcifFileReader

getFilename(String) - Method in class org.biojava.nbio.structure.io.CifFileReader

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.MMTFFileReader

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.PDBFileParser

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.core.util.FileDownloadUtils

Gets the file name up to and excluding the first '.' character.

getFiletype() - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the currently active file type that will be parsed.

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() - Method in class org.biojava.nbio.structure.AtomPositionMap

getFirst() - Method in class org.biojava.nbio.structure.contact.Pair

getFirst(String) - Method in class org.biojava.nbio.structure.AtomPositionMap

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.

getFirstRepeat() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

Get the index of the first repeat used by this axis

getFirstRepeats(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Get the first repeat index of each axis of a specified level.

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

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

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.QuatSymmetrySubunits

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.chem.ChemComp

getFormulaWeight() - Method in class org.biojava.nbio.structure.chem.ChemComp

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() - Method in class org.biojava.nbio.structure.EntityInfo

getFragment(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils

Get a continue subset of Atoms based by the starting position and the length

getFragmentFromIdxList(Atom[], int[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils

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.AlignUtils

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

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.

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() - Method in class org.biojava.nbio.structure.EntityInfo

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

Get the gene based on accession.

getGeneAliases() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

Pull uniprot gene aliases associated with this sequence

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

getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

Returns a transformation matrix transform polyhedra for Cn structures.

getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

Returns a transformation matrix transform polyhedra for Cn structures.

getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

Returns the geometric center of polyhedron.

getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

Returns the geometric center of polyhedron.

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

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

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.chem.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() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

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

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

Get the name of the groups that are being plotted in the figure

getGroups(boolean) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

getGroups(boolean) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

getGroups(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Returns the List of Groups of the corresponding representative Atom array.

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) - Method in class org.biojava.nbio.structure.ChainImpl

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

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() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

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

getHeaderParser() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

getHeaderVars() - Method in class org.biojava.nbio.structure.EntityInfo

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.axis.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

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

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

getI() - Method in class org.biojava.nbio.structure.contact.Contact

getIAtoms() - Method in class org.biojava.nbio.structure.contact.Grid

getIclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

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.features.DBReferenceInfo

getId() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable

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 'private' asymId (internal chain IDs in mmCif) for this chain.

getId() - Method in class org.biojava.nbio.structure.ChainImpl

getId() - Method in class org.biojava.nbio.structure.chem.ChemComp

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.EntityInfo

get the ID used by Hibernate

getId() - Method in class org.biojava.nbio.structure.HetatomImpl

the Hibernate database ID

getId() - Method in class org.biojava.nbio.structure.PDBHeader

Get the ID used by Hibernate.

getId() - Method in class org.biojava.nbio.structure.PdbId

Get a String representation of this PdbId instance.
By default this function will try to get the PdbId in the short (4 letters) format.

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 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 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

getId(boolean) - Method in class org.biojava.nbio.structure.PdbId

Get a String representation of this PdbId instance, using the passed in behavior.

getID() - Method in class org.biojava.nbio.core.sequence.AccessionID

getID() - Method in class org.biojava.nbio.core.sequence.TaxonomyID

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

Deprecated.
use PDBHeader.getPdbId()

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.cluster.Subunit

The standard identifier of the Subunit.

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

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

Gets identity matrix where matches score 1 and mismatches score -10000

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

getImage(int, int) - Method in class org.biojava.nbio.core.sequence.io.ABITrace

Returns a BufferedImage that represents the entire trace.

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

getIndex() - Method in class org.biojava.nbio.structure.align.helper.GapArray

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

getIndex(TreeNode) - Method in class org.biojava.nbio.alignment.GuideTree.Node

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

getIndexPair() - Method in class org.biojava.nbio.structure.contact.Contact

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.

getIndicesContacts() - Method in class org.biojava.nbio.structure.contact.Grid

Returns all contacts, i.e. all atoms that are within the cutoff distance, as simple Contact objects containing the atom indices pairs and the distance.

getInertiaTensor() - Method in class org.biojava.nbio.structure.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(File) - Method in class org.biojava.nbio.core.util.InputStreamProvider

Get an InputStream for the file.

getInputStream(String) - Static method in class org.biojava.nbio.core.util.FlatFileCache

Gets the cached file as an InputStream.

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(URL) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools

Connect to a URL and return result as an InputStream.

getInputStream(URL, boolean, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools

Open a URL and return an InputStream to it if acceptGzipEncoding == true, use GZIPEncoding to compress communication.

getInputStream(URL, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools

Connect to server and return result as an InputStream.

getInputStream(PdbId) - 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(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties

An adaptor method to return the instability index of sequence.

getInstabilityIndex(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns 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.structure.align.gui.AlignmentGui

getInstance() - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI

getInstance() - Static method in class org.biojava.nbio.structure.gui.util.ScopInstallationInstance

getInstance() - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui

getInstance(int) - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace

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)

getInstance(QuatSymmetryResults) - Static method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

Returns an instance of AxisAligner for differnt type of QuatSymmetryResults (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

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. the residues at the surface with BSA>0

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

getInternal(Structure, List<AbstractCifFileSupplier.WrappedAtom>) - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier

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

getIsoelectricPoint(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties

getIsoelectricPoint(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties

An adaptor method to return the isoelectric point of sequence.

getIsoelectricPoint(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties

getIsoelectricPoint(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl

getIsoelectricPoint(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns the isoelectric point of sequence.

getIsoelectricPoint(ProteinSequence, boolean) - 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

getJ() - Method in class org.biojava.nbio.structure.contact.Contact

getJAtoms() - Method in class org.biojava.nbio.structure.contact.Grid

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(AFPChain, Atom[], Atom[]) - 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.

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

getJournal() - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference

The journal usually contains the Publication Number, Publication Date and Assignee

getJournal() - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference

getJournal() - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface

Get the journal that retrieved from Reference section.

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

getKeyword() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The KW (KeyWord) lines provide information which can be used to generate cross-reference indexes of the sequence entries based on functional, structural, or other categories deemed important.

getKeywords() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

getKeywords() - Method in interface org.biojava.nbio.protmod.ProteinModification

getKeywords() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getKeywords() - Method in class org.biojava.nbio.structure.PDBHeader

Gets the keywords (KEYWODS) record of the structure

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

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

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.QuatSymmetrySubunits

getLast() - Method in class org.biojava.nbio.structure.AtomPositionMap

getLast(String) - 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

getLastUpdatedDate() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The DT (DaTe) line shows when an entry was last updated in the database.

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

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() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the total number of base pairs that were found, used after the call to analyze().

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.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

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.

getLength1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

getLength2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

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.

getLevel() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

getLfrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder

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

getLigandsByProximity(Collection<Group>, Atom[], double) - Static method in class org.biojava.nbio.structure.StructureTools

Finds all ligand groups from the target which fall within the cutoff distance of some atom from the query set.

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

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(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.

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.

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

getLocalFile(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Searches for previously downloaded files

getLocalFileName(String) - Static method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

Returns the file name that contains the definition for this ChemComp

getLocalFiles() - Method in class org.biojava.nbio.phosphosite.Dataset

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

getLocalTimeStart() - 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

getLogger() - Static method in class org.biojava.nbio.structure.chem.ChemCompBond

getLogLevel() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter

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.QuatSymmetrySubunits

getLowerLimit() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

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

Returns the macromolecular size of this biological assembly, i.e.

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>, boolean) - 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() - 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(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.

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

Get a submatrix.

getMatrix(String) - Method in interface org.biojava.nbio.core.alignment.matrices.AAIndexProvider

Gets a substitution matrix by its name.

getMatrix(String) - Method in class org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider

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 . default is 30, which was described to obtained empirically in the CE paper.

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

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.

getMaxOrientationAngle() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

The maximum orientation angle between two equivalent Subunits, in radians.

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

getMaxPropeller() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.

getMaxPropeller() - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.

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

getMaxRmsd() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

The maximum allowed RMSD of the alignment, in A.

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

getMaxRmsd() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

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.

getMaxShear() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method returns the maximum shear between bases used as criteria for the characterization of two bases as being paired.

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

getMaxStagger() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method returns the maximum stagger between bases used as criteria for the characterization of two bases as being paired.

getMaxStagger() - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

This method returns the maximum stagger between bases used as criteria for the characterization of two bases as being paired.

getMaxStretch() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method returns the maximum stretch between bases used as criteria for the characterization of two bases as being paired.

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.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

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

getMetalBondDefinitions() - Static method in class org.biojava.nbio.structure.io.cif.MetalBondConverter

getMethod() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage

getMethod() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

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

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.cluster.SubunitClustererParameters

Get the minimum number of residues of a subunits to be considered in the clusters.

getMinimumSequenceLengthFraction() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.

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

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

getMinLen() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

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.

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

getModDate() - Method in class org.biojava.nbio.structure.PDBHeader

Return the latest modification date of the structure.

getModel() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom

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 .

getModelCartnX() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getModelCartnY() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getModelCartnZ() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getModelNumber() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo

getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

This method is provisional and should only be used for coloring 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

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

getMolecularWeight(Character) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable

getMolecularWeight(String) - 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(String, File, File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties

An adaptor method to return the molecular weight of sequence.

getMolecularWeight(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns the molecular weight of sequence.

getMolecularWeight(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl

getMolecularWeight(ProteinSequence, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns the molecular weight of sequence.

getMolecularWeight(ProteinSequence, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl

getMolecularWeight(ProteinSequence, File, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns the molecular weight of sequence.

getMolecularWeight(ProteinSequence, File, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl

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 interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns the molecular weight of sequence.

getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl

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

getMoleculeType() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId

Molecule type this represents the type of molecule as stored

getMolId() - Method in class org.biojava.nbio.structure.EntityInfo

Return the molecule identifier, called entity_id in mmCIF dictionary.

getMomentsOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getMonNstdFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp

getMonNstdParentCompId() - Method in class org.biojava.nbio.structure.chem.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() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

The multiple alignment is calculated from the equivalent residues in the SubunitCluster.

getMultipleAlignment() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

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

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.EntityInfo

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 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 interface org.biojava.nbio.structure.Chain

Get the 'public' authId (chain ID in PDB file)

getName() - Method in class org.biojava.nbio.structure.ChainImpl

getName() - Method in class org.biojava.nbio.structure.chem.ChemComp

getName() - Method in class org.biojava.nbio.structure.cluster.Subunit

The Name of a Subunit is a free-text field, user defined.

getName() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique

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 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

getNaturalPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

getNavMap() - Method in class org.biojava.nbio.structure.AtomPositionMap

getNcens() - Method in class org.biojava.nbio.survival.cox.StrataInfo

getNclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

getNcsAsArray(Matrix4d[]) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get a list of length N*16 of a list of Matrix4d*N.

getNcsAsMatrix4d(double[][]) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get a list of N 4*4 matrices from a single list of doubles of length 16*N.

getNcsOperators() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Get the NCS operators.

getNcuts() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

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(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties

getNetCharge(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties

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(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties

getNetCharge(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl

getNetCharge(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties

getNetCharge(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl

getNetCharge(ProteinSequence, boolean, double) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties

Returns the net charge of sequence at pH 7.

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

Create a new, empty org.w3c.dom.Document

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.PermutationGenerator

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

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

Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the first model

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

getNonPolyChain(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the given model index

getNonPolyChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

getNonPolyChains() - Method in class org.biojava.nbio.structure.Model

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

Return all non-polymeric chains for the first model

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

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

Return all non-polymeric chains for the given model index.

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

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

Retrieve all non-polymeric Chains corresponding to the given 'public' chain name (authId) for the first model.

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

getNonPolyChainsByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve all non-polymeric Chains corresponding to the 'public' chain name (authId) and the given model index.

getNonPolyChainsByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

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

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

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

getNucleicChains(boolean) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method reports all the nucleic acid chains and has an option to remove duplicates if you are considering an analysis of only unique DNA or RNA helices in the Structure.

getNullValue() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer

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

getNumBonds() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

getNumBondsInGroup(List<Atom>) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Find the number of bonds in a group

getNumericalBondOrder() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

Converts this ChemCompBond's value_order attribute into an int using the conversion:

getNumericRepresentation() - Method in enum org.biojava.nbio.core.sequence.Strand

getNumGapPositions() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence

getNumGapPositions() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence

Returns number of gap positions (gap openings and extensions) in the sequence.

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 (gap openings) in the sequence.

getNumGroups(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Count the total number of groups in the structure

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.PermutationGenerator

getNumLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getNumOperators() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

Gets the number of symmetry operators corresponding to this SpaceGroup (counting the identity operator)

getNumRepeats() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

Return the symmetry order determined by the order detector if the symmetry is significant.

getNumRepeats() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Get the number of repeats.

getNumRes() - Method in class org.biojava.nbio.structure.EntityInfo

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

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.BcifFileReader

getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.CifFileReader

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.MMTFFileReader

getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader

getOccupancy() - Method in interface org.biojava.nbio.structure.Atom

Get occupancy.

getOccupancy() - Method in class org.biojava.nbio.structure.AtomImpl

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

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

getOneLetterCode() - Method in class org.biojava.nbio.structure.chem.ChemComp

getOneLetterCode(ChemComp) - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory

getOneLetterCode(ChemComp, ChemicalComponentDictionary) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools

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

getOpening(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the opening in degrees for the given base pair

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

getOperator() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

Get the transformation operator for this axis as an homogeneous matrix

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.axis.AxisAligner

getOrbits() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getOrbits() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getOrder() - 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.structure.symmetry.internal.SymmetryAxes.Axis

Get the order of this axis (closed symm) or the number of repeats (open symm)

getOrder() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

getOrder(List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

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.EntityInfo

getOrganelle() - Method in class org.biojava.nbio.structure.EntityInfo

getOrGanelle() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The OG (OrGanelle) linetype indicates the sub-cellular location of non-nuclear sequences.

getOrganism() - Method in class org.biojava.nbio.phosphosite.Site

getOrganismClassification() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The OC (Organism Classification) lines contain the taxonomic classification Of the source organism

getOrganismCommon() - Method in class org.biojava.nbio.structure.EntityInfo

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.EntityInfo

getOrganismSpecies() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The OS (Organism Species) line specifies the preferred scientific name of the organism which was the source of the stored sequence.

getOrganismTaxId() - Method in class org.biojava.nbio.structure.EntityInfo

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

getOrientationMatrix() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

The orientation Matrix is a 3x3 Matrix with a column for each principal axis.

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.QuatSymmetrySubunits

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

getOriginalMetaData(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

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.

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

getOutFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

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(String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties

Method that returns the value associated with the key given in parameter.

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

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.

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

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

getPairingNames() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the names of the pairs in terms of A, G, T/U, and C for each base pair group in the list.

getPairingParameters() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method reports all the pair parameters, in the order of: buckle, propeller, opening (in degrees), shear, stagger, stretch (in Å).

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

getPairSequence() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the primary strand's sequence where parameters were found.

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.

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) - Method in class org.biojava.nbio.structure.gui.util.CoordManager

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.

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.gui.SymmetryGui

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 class org.biojava.nbio.structure.DBRef

Get the structure object that this DBRef relates to.

getParent(ChemComp) - Method in class org.biojava.nbio.structure.chem.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 entities 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() - Static method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

Get this provider's cache path

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

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

Deprecated.
use Structure.getPdbId() to get a PdbId object or getPdbId().getId() to get a String

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

Deprecated.
use StructureImpl.getPdbId() to get a PdbId object or getPdbId().getId() to get a String

getPDBCode1() - Method in class org.biojava.nbio.structure.align.client.PdbPair

Deprecated.
use PdbPair.getPDBCode1() instead

getPDBCode2() - Method in class org.biojava.nbio.structure.align.client.PdbPair

Deprecated.
use PdbPair.getPDBCode2() instead

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.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.ecod.EcodDomain

Gets the PdbId object.
Before 6.0.0, this method used to return a String.

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.PDBHeader

Gets the PDB identifier for this protein structure.

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

Gets the PDB identifier for this protein structure.

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

Returns the PDB identifier associated with this StructureIdentifier.

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

Returns the PDB identifier associated with this StructureIdentifier.

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

Get the PDB identifier part of the SubstructureIdentifier

getPdbId1() - Method in class org.biojava.nbio.structure.align.client.PdbPair

getPdbId2() - Method in class org.biojava.nbio.structure.align.client.PdbPair

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

getPDBNameOfPotentialAtomsOnComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage

getPDBNameOfPotentialAtomsOnComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage

getPDBResidueNumber() - Method in class org.biojava.nbio.protmod.structure.StructureGroup

getPdbResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

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

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).

getPDBresnum1() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

getPDBresnum2() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

getPdbSerial() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

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.

getPdbStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

getPdbxAlign() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxAmbiguousFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxAromaticFlag() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxAromaticFlag() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

getPdbxComponentAtomId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxComponentCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxComponentId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxFormalCharge() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxIdealCoordinatesDetails() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxIdealCoordinatesMissingFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxInitialDate() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxLeavingAtomFlag() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxModelCartnXIdeal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxModelCartnYIdeal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxModelCartnZIdeal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxModelCoordinatesDbCode() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxModelCoordinatesDetails() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxModelCoordinatesMissingFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxModifiedDate() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxOrdinal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxOrdinal() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

getPdbxPolymerType() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxProcessingSite() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxRefId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxReleaseStatus() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxReplacedBy() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxReplaces() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxResidueNumbering() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxStereoConfig() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxStereoConfig() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

getPdbxSubcomponentList() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxSynonyms() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxType() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPercentage() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

getPercentageIdentity() - Method in class org.biojava.nbio.core.search.io.Hsp

getPercentageOfIdentity(boolean) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair

Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.

getPercentageOfIdentity(boolean) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair

Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.

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() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

getPermutation(int) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

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

getPhase() - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos

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

getPhi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc

Calculate the phi angle.

getPivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition

Return pivot permutation vector

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

getPolarityOfAminoAcid(char) - Static method in class org.biojava.nbio.aaproperties.AminoAcidProperties

There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.

getPolarityOfAminoAcids(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties

Returns the array of polarity values of each amino acid in a protein sequence.

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

Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the first model

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

getPolyChain(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the given model index

getPolyChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

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

Retrieve a polymeric Chain based on the 'public' chain name (authId) for the first model

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

getPolyChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a polymeric Chain based on the 'public' chain name (authId) for the given model index.

getPolyChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

getPolyChains() - Method in class org.biojava.nbio.structure.Model

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

Return all polymeric chains for the first model

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

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

Return all polymeric chains for the given model index.

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

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

getPolymerType() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPolymerType() - Method in enum org.biojava.nbio.structure.chem.ResidueType

Gets the associated PolymerType, which are less specific

getPolymerType(ResidueType) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools

getPos() - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos

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

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() - Method in interface org.biojava.nbio.structure.Chain

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

getPredominantGroupType() - Method in class org.biojava.nbio.structure.ChainImpl

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

getPrimaryAccession() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId

getPrimitiveMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

getPrincipalAxes() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

The principal axes of intertia

getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

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

getPrincipalMomentsOfInertia() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.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.chem.ChemCompDescriptor

getProgramSpecificParameter(String) - Method in class org.biojava.nbio.core.search.io.Result

getProgramSpecificParametersList() - Method in class org.biojava.nbio.core.search.io.Result

getProgramVersion() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

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

getProjectIdentifier() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

getPropeller(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the propeller ("propeller-twist") in degrees for the given base pair

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

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 interface org.biojava.nbio.structure.Group

Get a single property .

getProperty(String) - Method in class org.biojava.nbio.structure.HetatomImpl

getProtein() - Method in class org.biojava.nbio.phosphosite.Site

getProteinAliases() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

Pull uniprot protein aliases associated with this sequence

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.

getProteinSequence() - Method in class org.biojava.nbio.core.sequence.RNASequence

Get the ProteinSequence from the RNA sequence

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

Get the protein sequence

getProteinSequence() - Method in class org.biojava.nbio.structure.cluster.Subunit

Get the protein sequence of the Subunit.

getProteinSequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.RNASequence

Get the ProteinSequene from the RNA sequence with user defined transcription engine

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() - Method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader

getProteinSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper

getProteinSequenceString() - Method in class org.biojava.nbio.structure.cluster.Subunit

Get the protein sequence of the Subunit as String.

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

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

getPsi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc

Calculate the psi angle.

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

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

getQcalls() - Method in class org.biojava.nbio.core.sequence.io.ABITrace

Returns an int[] array that represents the quality - each int in the array corresponds to an quality value 90-255) in the graph at a base location).

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.genome.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

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() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

Returns the radius for drawing polyhedra

getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

Returns the radius for drawing the minor rotation axis in the xy-plane

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.

getRadiusOfGyration() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

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

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

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

getReducedStructure(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools

Reduce a structure to a single-atom representation (e.g.

getRef() - Method in class org.biojava.nbio.structure.JournalArticle

Get the value of REF field.

getRefAuthor() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference

getRefChainId() - Method in class org.biojava.nbio.structure.EntityInfo

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

getReferenceAuthor() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

The RA (Reference Author) lines list the authors of the paper (or other work) cited.

getReferenceComment() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

The RC (Reference Comment) linetype is an optional linetype which appears if The reference has a comment.

getReferenceCrossReference() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

The RX (reference cross-reference) linetype is an optional linetype which appears if one or more contiguous base spans of the presented sequence can be attributed to the reference in question.

getReferenceFrames() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

getReferenceGroup() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

The RG (Reference Group) lines list the working groups/consortia that produced the record.

getReferenceLocation() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

The RL (Reference Location) line contains the conventional citation information for the reference.

getReferenceNumber() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

The RN (Reference Number) line gives a unique number to each reference Citation within an entry.

getReferencePosition() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

The RP (Reference Position) linetype is an optional linetype which appears if one or more contiguous base spans of the presented sequence can be attributed to the reference in question.

getReferences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

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

getReferenceTitle() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

The RT (Reference Title) lines give the title of the paper (or other work) as exactly as is possible given the limitations of computer character sets.

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

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(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.

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.

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

getRefTitle() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference

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.

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.

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

getRelation() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The quaternary structure relation QsRelation between the two groups of Subunits.

getRelativeAsaC() - Method in class org.biojava.nbio.structure.asa.GroupAsa

Returns the relative (complexed) ASA, i.e. the ASA of the residue with respect to its ASA in an extended tri-peptide conformation (GLY-x-GLY)

getRelativeAsaU() - Method in class org.biojava.nbio.structure.asa.GroupAsa

Returns the relative (uncomplexed) ASA, i.e. the ASA of the residue with respect to its ASA in an extended tri-peptide conformation (GLY-x-GLY)

getRelDate() - Method in class org.biojava.nbio.structure.PDBHeader

Return the release date of the structure in the PDB.

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

Returns the normalised list of sub locations i.e. only those locations which do not have a sub location.

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. those locations which are not complex and define the true Sequence represented

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(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Get the indices of participating repeats in Cauchy two-line form.

getRepeatRelation(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getRepeatRelation(SymmetryAxes.Axis) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getRepeatsCyclicForm(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getRepeatsCyclicForm(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Get the indices of participating repeats in cyclic form.

getRepeatsCyclicForm(List<List<Integer>>, List<?>) - Static method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getRepeatsCyclicForm(SymmetryAxes.Axis) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getRepeatsCyclicForm(SymmetryAxes.Axis, List<?>) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

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 repeat in order to superimpose onto repeat 0.

getRepeatTransform(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Return the transformation that needs to be applied to repeat x in order to superimpose onto repeat y.

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(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

getReplaced(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

If ChemComp is replacing another one, get the old version otherwise return the same ChemComp again.

getReplacer(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

getReplacer(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

If ChemComp is replaced by another one, get the newer version otherwise return the same ChemComp again.

getRepresentative() - Method in class org.biojava.nbio.structure.cath.CathNode

getRepresentative() - Method in class org.biojava.nbio.structure.EntityInfo

Get the representative Chain for this EntityInfo.

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() - Method in class org.biojava.nbio.structure.cluster.Subunit

Get all the representative Atoms of the Subunit.

getRepresentativeAtoms(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the representative atoms for the provided name.

getRepresentativeAtoms(Structure) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Returns the representative Atom Array of the first model, if the structure is NMR, or the Array for each model, if it is a biological assembly with multiple models.

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. the contact map.

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.

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

getRepresentatives(Astral.AstralSet) - Static method in class org.biojava.nbio.structure.scop.Astral

Get a list of representatives' names for the specified ASTRAL cutoff.

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 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.chem.ChemComp

getResidueTypeFromString(String) - Static method in enum org.biojava.nbio.structure.chem.ResidueType

Get ResidueType by chem_comp_type

getResidueTypes() - Method in enum org.biojava.nbio.structure.GroupType

Get a set of ResidueTypes loosely equivalent to this GroupType.

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.EntityInfo

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

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.axis.AxisAligner

getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getRevisionRecords() - Method in class org.biojava.nbio.structure.PDBHeader

getRevNum() - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord

getRfree() - Method in class org.biojava.nbio.structure.PDBHeader

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

getRise(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the rise for the given base pair, relative to the one before it.

getRms() - Method in class org.biojava.nbio.structure.align.helper.JointFragments

getRms() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getRMS(Atom[], Atom[], JointFragments) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

Get the RMS of the JointFragments pair frag

getRmsd() - Method in class org.biojava.nbio.structure.align.model.AFP

getRmsd() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

getRmsd() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The RMSD between the equivalent residues of the equivalent Subunits after superposition of the Subunit groups.

getRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

getRmsd(Point3d[], Point3d[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition

Calculate the RMSD between two arrays of equivalent points that are not superposed.

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

getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQuat

getRmsd(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

Use the SuperPosition.getRmsd(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.

getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionSVD

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(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.

getRmsdAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

Use the SuperPosition.getRmsd(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.

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

getRMSDThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.

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(Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence

Allows the user to pass in the Frame shift.

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(TranscriptionEngine, Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence

getRnaSequenceCreator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

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

getRoll(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the roll for the given base pair, relative to the one before it.

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

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(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

getRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

Get the transformation operator as a rotation axis.

getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup

getRotationJAMA(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices

Convert a transformation matrix into a JAMA rotation matrix.

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() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

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.geometry.Matrices

Convert a transformation matrix into a rotation matrix.

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.axis.AxisAligner

getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.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() - Method in class org.biojava.nbio.structure.align.helper.IndexPair

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(AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

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.

getRscore() - Method in class org.biojava.nbio.survival.cox.CoxInfo

getRscoreLogrankTestpvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo

getRwork() - Method in class org.biojava.nbio.structure.PDBHeader

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

Return the diagonal matrix of singular values

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.util.color.DefaultMatrixMapper

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(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory

Gets an instance of the specified scop version.

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

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

getScope() - Method in class org.biojava.nbio.ontology.Synonym

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

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

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() - 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

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.

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() - 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)

getScores(File) - Method in class org.biojava.nbio.ronn.ORonnModel

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

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.EntityInfo

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).

getSecStrucElements(Structure) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools

Obtain the List of secondary structure elements (SecStrucElement) of a Structure.

getSecStrucInfo(Structure) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools

Obtain the List of secondary structure information (SecStrucInfo) of a Structure.

getSecStructType(Group) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get the secondary structure as defined by DSSP.

getSecStructTypeFromDsspIndex(int) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Set the DSSP type based on a numerical index.

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

getSelfAlignment() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

getSeparatorSequence() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer

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

Gets 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) - Method in class org.biojava.nbio.structure.gui.util.CoordManager

start counting at 0...

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.

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

getSeqResGroups() - Method in interface org.biojava.nbio.structure.Chain

Returns a list of all groups in SEQRES records of the chain, i.e.

getSeqResGroups() - Method in class org.biojava.nbio.structure.ChainImpl

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(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl

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

getSeqResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

getSeqResOneLetterSeq() - Method in class org.biojava.nbio.structure.ChainImpl

Get the one letter sequence so that Sequence is guaranteed to be the same length as seqResGroups.

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

getSeqresStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

getSequence() - Method in class org.biojava.nbio.core.sequence.io.ABITrace

Returns the original programmatically determined (unedited) sequence as a AbstractSequence.

getSequence() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The Sequence Data Line

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.genome.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

getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.FastaSequenceParser

getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

getSequence(BufferedReader, int) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceParserInterface

getSequence(String, int, int) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitFacade

Extract a sequence from a chromosome, using chromosomal coordinates

getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator

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(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(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator

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(String, 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(String, 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(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

Assumes all compounds were uppercase

getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator

Not sure of use case and currently not supported

getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator

getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator

getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator

Not sure of use case and currently not supported

getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator

Not sure of use case and currently not supported

getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator

getSequence(ProxySequenceReader<C>, long) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface

getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

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(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator

getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator

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(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator

Should be able to extend the same concept to a remote URL call or database connection.

getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator

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) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Calculate the sequence alignment Strings for the whole alignment.

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.

getSequenceAsString() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

getSequenceAsString() - 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() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Delegates to SequenceMixin.toList(org.biojava.nbio.core.sequence.template.Sequence)

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

getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getSequenceAsString(List<C>, CompoundSet<C>, Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper

getSequenceCollection() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints

getSequenceCoverageThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

The minimum coverage of the sequence alignment between two subunits to be clustered together.

getSequenceDescription() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The DE (Description) lines contain general descriptive information about the sequence stored.

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

getSequenceFromAlignment() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence

getSequenceFromAlignment() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence

Returns the sequence positions at each alignment index

getSequenceFromString(String) - Method in class org.biojava.nbio.core.util.SequenceTools

Attempts to parse String as a DNA sequence first.
If this fails it tries to parse as a ProteinSequence.

getSequenceHeader() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

The SQ (SeQuence header) line marks the beginning of the sequence data and Gives a summary of its content.

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

getSequenceIdentityThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Sequence identity threshold to consider for the subunits clustering.

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.

getSequenceLength() - Method in class org.biojava.nbio.core.sequence.io.ABITrace

Returns the length of the sequence (number of bases) in this trace.

getSequenceLength() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId

Sequence length The last item on the ID line is the length of the sequence (the total number of bases in the sequence).

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

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.

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

getSequenceUsage() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints

getSequenceVersion() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId

return the sequence version

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

Should sequence conservation be considered as part of the alignment?

getSerialversionuid() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

getSerNum() - Method in class org.biojava.nbio.structure.io.SSBondImpl

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://).

getShear(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the shear in Å for the given base pair

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

getShift(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

Return the shift for the given base pair, relative to the one before it.

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

getShortId() - Method in class org.biojava.nbio.structure.PdbId

Get the PDB Id in the short format.

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

Return the SIFTS mappings by getting the info from individual SIFTS xml files at URL "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/%s.xml.gz"

getSimCount() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

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

Returns the similarity score for the alignment.

getSimilarity(double) - Method in class org.biojava.nbio.alignment.template.AbstractScorer

getSimilarity(double) - Method in interface org.biojava.nbio.alignment.template.Scorer

Returns score as a similarity between 0.0 and scale.

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

Return the one-dimensional array of singular values

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

getSlide(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the slide for the given base pair, relative to the one before it.

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

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

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.

getSpaceGroupAsString(SpaceGroup) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get the string representation of a space group.

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

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.BcifFileReader

getSplitDirPath() - Method in class org.biojava.nbio.structure.io.CifFileReader

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.MMTFFileReader

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

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

getStagger(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the stagger in Å for the given base pair

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

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.survival.cox.StrataInfo

getStatus() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

getStatus(String) - Static method in class org.biojava.nbio.structure.PDBStatus

Get the status of a PDB id.

getStatus(String[]) - Static method in class org.biojava.nbio.structure.PDBStatus

Get the status of a collection of PDB ids (in a single API query).

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

getStdlow() - Method in class org.biojava.nbio.survival.cox.StrataInfo

getStepParameters() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method reports all the base-pair step parameters, in the order of: tilt, roll, twist (in degrees), shift, slide, rise (in Å).

getStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

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.EntityInfo

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

getStrategy() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

getStretch(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the stretch in Å for the given base pair

getString(String) - Method in class org.biojava.nbio.structure.align.util.ResourceManager

getStringForCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

getStringForCompound(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

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

getStringRepresentation() - Method in enum org.biojava.nbio.core.sequence.Strand

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() - Method in interface org.biojava.nbio.structure.Chain

Returns the parent Structure of this chain.

getStructure() - Method in class org.biojava.nbio.structure.ChainImpl

getStructure() - Method in class org.biojava.nbio.structure.cluster.Subunit

The parent Structure from which the Subunit atoms were obtained.

getStructure() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

Gets the structure.

getStructure() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

getStructure(File) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

getStructure(File) - Method in interface org.biojava.nbio.structure.io.StructureIOFile

Read file from File and returns a Structure object.

getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.BcifFileReader

getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.CifFileReader

getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Handles the actual parsing of the file into a Structure object.

getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.MMTFFileReader

getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.PDBFileReader

getStructure(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Request a Structure based on a name.

getStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

getStructure(String) - Method in interface org.biojava.nbio.structure.io.StructureIOFile

Open filename and return 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.

getStructure(URL) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

getStructure(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Get the structure corresponding to the given StructureIdentifier.

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

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

Get the structure for a PDB ID

getStructureById(String) - Method in interface org.biojava.nbio.structure.io.StructureProvider

Get the structure for a PDB ID

getStructureById(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Get the structure for a PDB ID

getStructureById(PdbId) - Method in interface org.biojava.nbio.structure.io.StructureProvider

Get the structure for a PDB ID

getStructureCoverageThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

The minimum coverage of the structure alignment between two subunits to be clustered together.

getStructureFiletype() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

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(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.

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.

getStructureForPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Loads a structure directly by PDB ID

getStructureForPdbId(PdbId) - 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.internal.CeSymmResult

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

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

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

getStructureInfo(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get summary information for the structure.

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.

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.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(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

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

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

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.

getSubunitClusters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

Returns the List of SubunitCluster used to calculate symmetry.

getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

Return the number of Subunits involved in the symmetry.

getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getSubunitMap() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

Map of Subunit equivalencies from the first to the second group.

getSubunitRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

getSubunits() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Subunits contained in the SubunitCluster.

getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

Returns the List of Subunits used to calculate symmetry.

getSubunits1() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

Original Subunits of the first group.

getSubunits2() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

Original Subunits of the second group.

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.ScopDomain

getSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode

getSunID() - Method in class org.biojava.nbio.structure.scop.ScopDescription

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

getSuperpositionAlgorithm() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Method to superpose subunits (i.e., structural aligner).

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.

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

getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

getSymmetryAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Return all symmetry axes of of the structure: the set of axes that describe all parts of the structure.

getSymmetryClass(double) - Method in class org.biojava.nbio.structure.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

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

getSymmType() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

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.EntityInfo

getSynthetic() - Method in class org.biojava.nbio.structure.EntityInfo

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

getTable(Integer) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser

Returns a table by its identifier i.e. 1 means universal codon tables

getTable(String) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser

Returns a table by its name

getTables() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser

Returns a list of all available IUPAC tables

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

getTaxonomicDivision() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId

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

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

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.

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

getThreeLetterCode() - Method in class org.biojava.nbio.structure.chem.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

getTilt(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the tilt for the given base pair, relative to the one before it.

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

getTissue() - Method in class org.biojava.nbio.structure.EntityInfo

getTitle() - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference

The title that retrieved from the Reference section.

getTitle() - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference

getTitle() - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface

Get the title that retrieved from Reference section.

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.EntityInfo

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(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.util.AFPChainScorer

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

Calculate the TM-Score for the superposition.

getTMScore(Atom[], Atom[], int, int, boolean) - Static method in class org.biojava.nbio.structure.Calc

Calculate the TM-Score for the superposition.

getTMThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.

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

getTopology() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId

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.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.

getTrace(String) - Method in class org.biojava.nbio.core.sequence.io.ABITrace

Returns one of the four traces - all of the y-coordinate values, each of which correspond to a single x-coordinate relative to the position in the array, so that if element 4 in the array is 972, then x is 4 and y is 972 for that point.

getTraceLength() - Method in class org.biojava.nbio.core.sequence.io.ABITrace

Returns the length of the trace (number of x-coordinate points in the graph).

getTraceRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

getTraces() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

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

getTranscriptDNASequence(TwoBitFacade, String, List<Integer>, List<Integer>, int, int, Character) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Extracts the DNA sequence transcribed from the input genetic coordinates.

getTranscriptDNASequence(TwoBitFacade, GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

Extracts the DNA sequence transcribed from the input genetic coordinates.

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() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

getTransfAlgebraic(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

Gets a transformation algebraic string given its index.

getTransform() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The transformation 4D matrix that needs to be applied to the second group of Subunits to superimpose them onto the first group of Subunits, given the equivalent residues in the SubunitCluster and the Subunit equivalencies.

getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

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.

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

Convert JAMA rotation and translation to a Vecmath transformation matrix.

getTransformation(Matrix, Matrix) - Static method in class org.biojava.nbio.structure.geometry.Matrices

Convert JAMA rotation and translation to a Vecmath transformation matrix.

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.

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.

getTransformId() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

getTransformMap(BioAssemblyInfo, Map<String, Integer>) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Convert a bioassembly information into a map of transform, chainindices it relates to.

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(String) - 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, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties

getTransition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties

getTransition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties

getTransition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl

getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties

getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties

getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl

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, 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, IProfeatProperties.TRANSITION) - 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() - Method in class org.biojava.nbio.structure.align.util.RotationAxis

getTranslation(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay

getTranslationVector(Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Extract the translational vector as an Atom of a transformation matrix.

getTranslationVector(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices

Extract the translational vector of a transformation matrix.

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.

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 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

getTwist(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the twist for the given base pair, relative to the one before it.

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

getTwoBitURL(String) - Static method in class org.biojava.nbio.genome.parsers.twobit.SimpleTwoBitFileProvider

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 class org.biojava.nbio.structure.chem.ChemComp

getType() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

getType() - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord

getType() - Method in class org.biojava.nbio.structure.EntityInfo

Get the type of entity this EntityInfo describes.

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.sifts.SiftsEntity

getType() - Method in class org.biojava.nbio.structure.NucleotideImpl

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

getTypeField() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

getTypeSymbol() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

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. ligands).

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. www.uniprot.org is load balanced but you can access pir.uniprot.org directly.

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.

getUnitCellAsArray(PDBCrystallographicInfo) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get the length six array of the unit cell information.

getUnitv() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getUnitVectors() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

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

getUpdateFrequency() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

The expected ECOD update frequency determines whether the version "latest" should be re-downloaded

getUpper() - Method in class org.biojava.nbio.survival.cox.StrataInfo

getUpperBound() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getUpperedBase() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

getUpperLimit() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

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

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.utils.SymmetryTools

Find valid symmetry orders for a given stoichiometry.

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(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(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

getValueOrder() - Method in class org.biojava.nbio.structure.chem.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.genome.io.fastq.Fastq

Return the FASTQ sequence format variant for this FASTQ formatted sequence.

getVariant() - Method in class org.biojava.nbio.genome.io.fastq.IlluminaFastqReader

getVariant() - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqReader

getVariant() - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqReader

getVariant() - Method in class org.biojava.nbio.structure.EntityInfo

getVDWRadius() - Method in enum org.biojava.nbio.structure.Element

Returns the van der Waals radius of this Element.

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.

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

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

Retrieve a water Chain based on the 'internal' chain id (asymId) for the first model

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

getWaterChain(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a water chain based on the 'internal' chain id (asymId) for the given model index

getWaterChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

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

Retrieve a water Chain based on the 'public' chain name (authId) for the first model

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

getWaterChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a water Chain based on the 'public' chain name (authId) for the given model index

getWaterChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

getWaterChains() - Method in class org.biojava.nbio.structure.Model

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

Return all water chains for the first model

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

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

Return all water chains for the given model index

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

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

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

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

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

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

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.survival.cox.CoxCoefficient

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

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

GLIDE - org.biojava.nbio.structure.xtal.TransformType

GLOBAL - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType

GLOBAL - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

GLOBAL - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType

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

GLOBAL_CONSENSUS - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType

GLOBAL_IDENTITIES - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

GLOBAL_LINEAR_SPACE - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType

GLOBAL_LINEAR_SPACE - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType

GLOBAL_SIMILARITIES - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

glycine - org.biojava.nbio.structure.chem.ResidueType

gneg - org.biojava.nbio.genome.parsers.cytoband.StainType

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

gpos100 - org.biojava.nbio.genome.parsers.cytoband.StainType

gpos25 - org.biojava.nbio.genome.parsers.cytoband.StainType

gpos50 - org.biojava.nbio.genome.parsers.cytoband.StainType

gpos75 - org.biojava.nbio.genome.parsers.cytoband.StainType

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

GRAPH_COMPONENT - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

GRAPH_COMPONENT - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

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

greenwood - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error

Grid - Class in org.biojava.nbio.structure.contact

A grid to be used for calculating atom contacts through a spatial hashing algorithm.

Grid(double) - Constructor for class org.biojava.nbio.structure.contact.Grid

Creates a Grid, the cutoff is in the same units as the coordinates (Angstroms if they are atom coordinates) and can be specified to a precision of 0.01.

GridCell - Class in org.biojava.nbio.structure.contact

A grid cell to be used in contact calculation via spatial hashing algorithm.

GridCell(Grid) - Constructor for class org.biojava.nbio.structure.contact.GridCell

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

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.

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

group1 - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults

GROUP1 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING

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

GROUP2 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING

group3 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor

GROUP3 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING

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 over all models

GroupIterator(Structure, int) - Constructor for class org.biojava.nbio.structure.GroupIterator

Constructs a GroupIterator object over a specific model

GroupLocation(boolean, 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

GroupLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation

GroupLocation(List<Location>) - 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, List<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, List<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

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.geometry.CalcPoint

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.

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.

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

gvar - org.biojava.nbio.genome.parsers.cytoband.StainType

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 - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

H - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

H - org.biojava.nbio.structure.Element

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

HALOGEN - org.biojava.nbio.structure.ElementType

handleChain(Chain, int, List<AbstractCifFileSupplier.WrappedAtom>) - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier

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

hasAltLoc() - Method in interface org.biojava.nbio.structure.Group

Check if this group has alternate location groups.

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.

hasAnyContact(Collection<Point3d>) - Method in class org.biojava.nbio.structure.contact.Grid

hasAnyContact(Point3d[]) - Method in class org.biojava.nbio.structure.contact.Grid

Fast determination of whether any atoms from a given set fall within the cutoff of iAtoms.

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

Check if the feature has a value defined for the specified key.

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.Feature

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

Check if any feature in list has the specified attribute key/value pair.

hasBond(Atom) - Method in interface org.biojava.nbio.structure.Atom

Test if another atom has a bond to this atom

hasBond(Atom) - Method in class org.biojava.nbio.structure.AtomImpl

Test if another atom has a bond to this atom

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

Check if a chain with the chainId aymId is contained in this structure.

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

Check if a chain with the chainId aymId is contained in this structure.

hasCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

hasCompound(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

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

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(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.

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

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.

hasContactToAtom(Point3d[], Point3d[], Point3d, double) - Method in class org.biojava.nbio.structure.contact.GridCell

Tests whether any atom in this cell has a contact with the specified query atom

hasDeuteratedEquiv(Atom, Group) - Static method in class org.biojava.nbio.structure.StructureTools

Check to see if a Hydrogen has a Deuterated brother in the group.

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, 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, 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, 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, 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.alignment.SimpleAlignedSequence

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.loader.SequenceFileProxyLoader

hashCode() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

hashCode() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

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.JoiningSequenceReader

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.template.AbstractSequence

hashCode() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

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.chem.ChemComp

hashCode() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

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.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.PdbId

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.secstruc.BetaBridge

hashCode() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc

hashCode() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

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

hashCode() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

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 ation.

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

hasNcsOps() - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder

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

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

Check if next window of specified size is available.

hasNonDeuteratedEquiv(Atom, Group) - Static method in class org.biojava.nbio.structure.StructureTools

Check to see if an Deuterated atom has a non deuterated brother in the group.

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

Check if a non polymeric chain with chainId asymId is contained in the structure.

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

Check if a non polymeric chain with chainId asymId is contained in the structure.

hasParent() - Method in class org.biojava.nbio.structure.chem.ChemComp

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

Check if a chain with chain name authId is contained in the structure

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

Check if a chain with chain name authId is contained in the structure

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

HBOND - org.biojava.nbio.structure.BondType

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

He - org.biojava.nbio.structure.Element

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(QuatSymmetrySubunits) - 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

helix3 - org.biojava.nbio.structure.secstruc.SecStrucType

helix4 - org.biojava.nbio.structure.secstruc.SecStrucType

helix5 - org.biojava.nbio.structure.secstruc.SecStrucType

HelixAxisAligner - Class in org.biojava.nbio.structure.symmetry.axis

HelixAxisAligner(QuatSymmetryResults) - Constructor for class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

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

HelixExtender(QuatSymmetrySubunits, 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(QuatSymmetrySubunits, int, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixSolver

HelloWorld - Class in org.biojava.nbio.proteincomparisontool

A dummy class that does nothing.

HelloWorld() - Constructor for class org.biojava.nbio.proteincomparisontool.HelloWorld

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

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

HETATM - org.biojava.nbio.structure.GroupType

The type for hetero groups (everything else)

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. performance.

HEXAGONAL - org.biojava.nbio.structure.xtal.BravaisLattice

hexPropertyNames - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo

Hf - org.biojava.nbio.structure.Element

Hg - org.biojava.nbio.structure.Element

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. to use JSuggestionField like a ComboBox)

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

HITLIST_SIZE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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.

Ho - org.biojava.nbio.structure.Element

Homology - org.biojava.nbio.structure.cath.CathCategory

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

HSP_SORT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

HSVColorSpace - Class in org.biojava.nbio.structure.gui.util.color

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

HTML - org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum

HYDROPHOBIC - org.biojava.nbio.structure.BondType

HYDROPHOBICITY - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE

hypot(double, double) - Static method in class org.biojava.nbio.structure.jama.Maths

sqrt(a^2 + b^2) without under/overflow.

HYPOTHETICAL - org.biojava.nbio.protmod.ModificationOccurrenceType

I

I - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

I - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

I - org.biojava.nbio.structure.Element

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

I_THRESH - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

I_THRESH - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

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

Represents an even coverage of quaternion space by 60 points.

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

IdenticalSequenceFamily - org.biojava.nbio.structure.cath.CathCategory

identify(List<Chain>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

Identify all registered modifications in 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.

identify(Chain) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

Identify all registered modifications in a chain.

identify(Chain, Set<ProteinModification>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

Identify a set of modifications in a a chains.

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.

IDENTITIES - org.biojava.nbio.alignment.Alignments.PairInProfileScorerType

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

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_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.EntityFinder

Identity value for 2 chains to be considered part of same entity

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

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.genome.io.fastq

Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.

IlluminaFastqReader() - Constructor for class org.biojava.nbio.genome.io.fastq.IlluminaFastqReader

IlluminaFastqWriter - Class in org.biojava.nbio.genome.io.fastq

Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences.

IlluminaFastqWriter() - Constructor for class org.biojava.nbio.genome.io.fastq.IlluminaFastqWriter

Impl(String, String) - Constructor for class org.biojava.nbio.ontology.Ontology.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) - Constructor for class org.biojava.nbio.ontology.Variable.Impl

Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.nbio.ontology.Term.Impl

Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.nbio.ontology.Variable.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(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

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.

In - org.biojava.nbio.structure.Element

index - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair

index - Variable in class org.biojava.nbio.structure.align.helper.GapArray

INDEX - Static variable in class org.biojava.nbio.ronn.RonnConstraint

indexOf(String, String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader

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.

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

info(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter

INFRARED_SPECTROSCOPY - org.biojava.nbio.structure.ExperimentalTechnique

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.

initStructure(int, int, int, int, int, String) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

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

INNER - org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection

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

Creates an org.w3c.dom.Document from the content of the inputStream

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. one-of(location, location, location).

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 - 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(String, int, 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(Sequence<C>, int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert

INSERTION - org.biojava.nbio.alignment.routines.AlignerHelper.Last

insertSeqResGroup(Chain, Group, int) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Insert the group in the given position in the sequence.

InstabilityIndex - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

IntegerOntology - Class in org.biojava.nbio.ontology

IntegerOntology.IntTerm - Class in org.biojava.nbio.ontology

InterfaceFinder - Class in org.biojava.nbio.structure.contact

A class containing methods to find interfaces in a given structure.

InterfaceFinder(Structure) - Constructor for class org.biojava.nbio.structure.contact.InterfaceFinder

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 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.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(String, Throwable) - Constructor for exception org.biojava.nbio.ontology.InvalidTermException

InvalidTermException(Throwable) - Constructor for exception org.biojava.nbio.ontology.InvalidTermException

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

Matrix inverse or pseudoinverse

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

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

IONIC - org.biojava.nbio.structure.BondType

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).

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:

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

Ir - org.biojava.nbio.structure.Element

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. replaced by the assembly id

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

isAminoAcid() - Method in interface org.biojava.nbio.structure.Group

Check if this group is an aminoacid group, from the definition in Chemical Component Dictionary

isAminoAcid() - Method in class org.biojava.nbio.structure.HetatomImpl

isAutoFetch() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

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

isChalcogen() - Method in enum org.biojava.nbio.structure.Element

Returns true if Element is a chalcogen (O, S, Se, Te, Po).

isCharged(char) - Static method in class org.biojava.nbio.aaproperties.AminoAcidProperties

At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains), and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).

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.

isClosed() - Method in class org.biojava.nbio.core.sequence.io.GenbankReader

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. if the distance from C to N < 2.5 Angstrom.

isCrossLink() - Method in enum org.biojava.nbio.protmod.ModificationCategory

isCrystallographic() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique

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

Test if this structure is a crystallographic structure, i.e. it is an asymmetric unit from which it is possible to reconstruct the crystal lattice given cell parameters and space group.

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

Whether this Structure is a crystallographic structure or not.

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

isCTerminal() - Method in class org.biojava.nbio.protmod.Component

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

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

isDownloadAll() - Method in class org.biojava.nbio.structure.chem.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.chem.ChemComp

Indicates whether this compound was created with

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

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

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(char) - Static method in class org.biojava.nbio.phylo.Comparison

Method that determines if a character means a gap in the alignment.

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.

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.

isHetAtomInFile() - Method in interface org.biojava.nbio.structure.Group

Tells whether the group is annotated as HETATM in the file.

isHetAtomInFile() - Method in class org.biojava.nbio.structure.HetatomImpl

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

isHighConfidenceScores(double, double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Whether the subunits can be considered "identical" by sequence alignment.

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. homomeric interface), false otherwise (i.e. heteromeric interface)

isHydrogen() - Method in enum org.biojava.nbio.structure.Element

Returns true if this Element is Hydrogen.

isIdenticalByEntityIdTo(SubunitCluster) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Tells whether the other SubunitCluster contains exactly the same Subunit.

isIdenticalTo(SubunitCluster) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Tells whether the other SubunitCluster contains exactly the same Subunit.

isIdentity() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Tells whether this transformation is in identity.

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.genome.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

isInternalSymmetry() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

The internal symmetry option divides each Subunit of each SubunitCluster into its internally symmetric repeats.

isIsologous() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Tell whether the interface is isologous, i.e. it is formed by the same patches of same entity on both sides.

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

A local result means that only a subset of the original Subunits was used for symmetry determination.

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

isLocalLimitsExceeded(Set<?>) - 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.

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() - 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.

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

isNonAmbNucleotideSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!)

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?

isNonStandardCoordFrameConvention() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Whether this structure is non-standard coordinate frame convention, for which our scale matrix calculation and thus the crystal reconstruction will be incorrect.

isNonStandardSg() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Whether this structure has a non-standard space group not supported by Biojava.

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() - Method in interface org.biojava.nbio.structure.Chain

Tell whether given chain is DNA or RNA

isNucleicAcid() - Method in class org.biojava.nbio.structure.ChainImpl

isNucleotide() - Method in interface org.biojava.nbio.structure.Group

Check if this group is a nucleotide group, from the definition in Chemical Component Dictionary

isNucleotide() - Method in class org.biojava.nbio.structure.HetatomImpl

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

IsoelectricPoint - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

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

On-the-fly Jmol bioassembly generation.

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

Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level.

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

Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.

isOptimizeAlignment() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.

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?

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

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

isPFam() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

isPolar(char) - Static method in class org.biojava.nbio.aaproperties.AminoAcidProperties

There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.

isPolymeric() - Method in interface org.biojava.nbio.structure.Group

Check if this group is a polymeric group, from the definition in Chemical Component Dictionary

isPolymeric() - Method in class org.biojava.nbio.structure.HetatomImpl

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() - Method in interface org.biojava.nbio.structure.Chain

Tell whether given chain is a protein chain

isProtein() - Method in class org.biojava.nbio.structure.ChainImpl

isProteinSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

A pseudostoichiometric SubunitCluster was obtained using the SubunitClustererMethod.STRUCTURE similarity, or SubunitClustererMethod.SEQUENCE similarity with low scores.

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. no rotational component and an integer translation vector.

isPureNonPolymer() - Method in interface org.biojava.nbio.structure.Chain

Returns true if the given chain is composed of non-polymeric (including water) groups only.

isPureNonPolymer() - Method in class org.biojava.nbio.structure.ChainImpl

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

isReplaced(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

isReplaced(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

isReplacer(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

isReplacer(ChemComp) - Method in class org.biojava.nbio.structure.chem.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. either pure rotation or screw rotation, but not improper rotation.

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.genome.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

isShortCompatible(String) - Static method in class org.biojava.nbio.structure.PdbId

Checks whether an Extended PDB ID is shortable, assuming it is a valid extended PDB ID.

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, number of repeats higher than 1 and refinement succeeded.

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

isSolexa() - Method in enum org.biojava.nbio.genome.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.chem.ChemComp

isStandardChemComp(ChemComp) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools

isStart() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

isStart() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

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(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.

isSuggestVisible() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest

isSupersededBy(QuatSymmetryResults) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

Determine if this symmetry result is a subset of the other Symmetry result.

isSymRelated() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Tells whether the interface corresponds to one mediated by crystallographic symmetry, i.e. it is between symmetry-related molecules (with same chain identifier)

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.

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

isURLProperty(String) - Method in class org.biojava.nbio.structure.align.gui.SystemInfo

isUseEntityIdForSeqIdentityDetermination() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Whether to use the entity id of subunits to infer that sequences are identical.

isUseGlobalMetrics() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only

isUseRMSD() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use RMSD for evaluating structure similarity

isUseSequenceCoverage() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use sequence coverage for evaluating sequence similarity

isUseStructureCoverage() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use structure coverage for evaluating sequence similarity

isUseTMScore() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use TMScore for evaluating structure similarity

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

isValidExtendedPdbId(String) - Static method in class org.biojava.nbio.structure.PdbId

Check whether id represents a valid PDB ID in the extended format.

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

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

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

isValidShortPdbId(String) - Static method in class org.biojava.nbio.structure.PdbId

Check whether id represents a valid PDB ID in the short format.

isWater() - Method in interface org.biojava.nbio.structure.Group

Determines if this group is water.

isWater() - Method in class org.biojava.nbio.structure.HetatomImpl

isWaterOnly() - Method in interface org.biojava.nbio.structure.Chain

Tests if a chain is consisting of water molecules only

isWaterOnly() - Method in class org.biojava.nbio.structure.ChainImpl

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() - 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

iterator() - Method in class org.biojava.nbio.structure.math.SymbolTable

Return an Iterator for the keys in the table.

iterator() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

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

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(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

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.

JmolLoggerAdapter(Logger) - Constructor for class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter

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

JmolPanel.JmolLoggerAdapter - Class in org.biojava.nbio.structure.align.gui.jmol

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

join(Collection<String>, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper

Joins Strings together with a delimiter to a single

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(List<Sequence<C>>) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

Allows creation of the store from List>.

JoiningSequenceReader(CompoundSet<C>, List<Sequence<C>>) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

JoiningSequenceReader(CompoundSet<C>, Sequence<C>...) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

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

Allows creation of the store from Vargs Sequence objects.

jointFragments(JointFragments[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener

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

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 - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

K - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

K - org.biojava.nbio.structure.Element

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

kaplanMeier - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method

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. triggers copying of stored commands into the current textfield

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.

KMERS - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

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

Kr - org.biojava.nbio.structure.Element

L

L - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

L - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

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

La - org.biojava.nbio.structure.Element

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

LANTHANOID - org.biojava.nbio.structure.ElementType

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

lBetaPeptideCGammaLinking - org.biojava.nbio.structure.chem.ResidueType

LCASE_MASK - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

lDNALinking - org.biojava.nbio.structure.chem.ResidueType

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

LEFT - org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

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() - 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.structure.align.quaternary.QsAlignResult

The length of the alignment is the number of Subunit equivalencies it contains.

length() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

length() - Method in class org.biojava.nbio.survival.data.CompactCharSequence

LENGTH - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature

Sort features by length.

LESS_MEMORY_SLOWER_PERFORMANCE - org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior

Try to minimize memory consumption, at the price of slower speed when accessing atoms by name

lGammaPeptideCDeltaLinking - org.biojava.nbio.structure.chem.ResidueType

Li - org.biojava.nbio.structure.Element

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.

LikeSequenceFamily - org.biojava.nbio.structure.cath.CathCategory

line - Variable in class org.biojava.nbio.ontology.obo.OboFileParser

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

LINEAR - org.biojava.nbio.alignment.template.GapPenalty.Type

LINEAR - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass

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

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

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

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.

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.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

loadStructureFromBcifByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureFromBcifByPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureFromCache() - Method in class demo.DemoLoadStructure

loadStructureFromCifByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureFromCifByPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureFromMmtfByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureFromMmtfByPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Load a Structure from MMTF either from the local file system.

loadStructureFromPdbByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureFromPdbByPdbId(PdbId) - 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

Given a path to an XML file, parses into an org.w3c.dom.Document

LOCAL - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType

LOCAL - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

LOCAL - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType

LOCAL - org.biojava.nbio.core.sequence.DataSource

LOCAL_CONSENSUS - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType

LOCAL_IDENTITIES - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

LOCAL_LINEAR_SPACE - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType

LOCAL_LINEAR_SPACE - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType

LOCAL_ONLY - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Never fetch from the server; Throw errors for missing files

LOCAL_SIMILARITIES - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

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

Superclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and CifFileReader.

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

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

Subclasses should provide default and single-string constructors.

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() - 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(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(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(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>, 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(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 - Class in org.biojava.nbio.genome.parsers.gff

A location on a sequence.

Location - Interface in org.biojava.nbio.core.sequence.location.template

Sets of integers used to represent the location of features on 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_LENGTH - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature

Sort features by start position and then longest length.

Location.Tools - Class in org.biojava.nbio.core.sequence.location.template

Helper methods for use with the Location classes.

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

log - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType

log_log - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType

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

LOWER - org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection

lowercaseName() - Method in enum org.biojava.nbio.genome.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

lPeptideAminoTerminus - org.biojava.nbio.structure.chem.ResidueType

lPeptideCarboxyTerminus - org.biojava.nbio.structure.chem.ResidueType

lPeptideLinking - org.biojava.nbio.structure.chem.ResidueType

lpolysaccharide - org.biojava.nbio.structure.chem.PolymerType

polysaccharide(L)

Lr - org.biojava.nbio.structure.Element

lRNALinking - org.biojava.nbio.structure.chem.ResidueType

lSaccharide - org.biojava.nbio.structure.chem.ResidueType

lSaccharide14and14linking - org.biojava.nbio.structure.chem.ResidueType

lSaccharide14and16linking - org.biojava.nbio.structure.chem.ResidueType

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

LU Decomposition

Lu - org.biojava.nbio.structure.Element

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 - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

M - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

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

MACROLIDE - org.biojava.nbio.structure.EntityType

Macrolide.

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.DemoBioAssemblies

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.DemoMmcifToPdbConverter

main(String[]) - Static method in class demo.DemoMmtfReader

Main function to run the demo

main(String[]) - Static method in class demo.DemoMmtfWriter

main(String[]) - Static method in class demo.DemoMultipleMC

main(String[]) - Static method in class demo.DemoQsAlign

main(String[]) - Static method in class demo.DemoQuatSymmetryJmol

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.DemoSixFrameTranslation

main(String[]) - Static method in class demo.DemoStructureFromFasta

main(String[]) - Static method in class demo.DemoSW3DAligner

main(String[]) - Static method in class demo.DemoSymmetry

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. download ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz and pass in path to local location of file

main(String[]) - Static method in class demo.ParseGO

Parses Biosapiens OBO file and logs name/description at INFO level

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.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.FileDownloadUtils

main(String[]) - Static method in class org.biojava.nbio.core.util.UncompressInputStream

Reads a file, uncompresses it, and sends the result to stdout.

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.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.LocIterator

Deprecated.

main(String[]) - Static method in class org.biojava.nbio.genome.parsers.twobit.SimpleTwoBitFileProvider

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.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.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.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.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.MMTFFileReader

main(String[]) - Static method in class org.biojava.nbio.structure.PDBStatus

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

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

MASK_CHAR - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

MASK_COLOR - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

mat - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

mat - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

match(char, char, boolean) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This returns true if a is the complement of b, false otherwise.

MATCH_SCORES - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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

Matrices - Class in org.biojava.nbio.structure.geometry

Matrices contains static methods to operate and transform matrices used in 3D geometry (transformation matrices and rotation matrices).

matrix - Static variable in class org.biojava.nbio.core.alignment.SimpleProfile

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

Jama = Java Matrix class.

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

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(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_NAME - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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. matrix row column ordering: [m00 m01 m02] [m10 m11 m12] [m20 m21 m22]

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_NUM_SEQ - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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.genome.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

Md - org.biojava.nbio.structure.Element

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

megablast - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum

MEGABLAST - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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

Create the menu for BiojavaJmol

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

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.

mergeIdentical(SubunitCluster) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Merges the other SubunitCluster into this one if it contains exactly the same Subunit.

mergeIdenticalByEntityId(SubunitCluster) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Merges the other SubunitCluster into this one if it contains exactly the same Subunit.

mergeSequence(SubunitCluster, SubunitClustererParameters) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).

mergeSequence(SubunitCluster, SubunitClustererParameters, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<AminoAcidCompound>) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).

mergeStructure(SubunitCluster, SubunitClustererParameters) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (according to the criteria in params).

MESH - org.biojava.nbio.structure.gui.RenderStyle

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) - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo

MetaDataInfo(String, boolean, DiscreteQuantizerInterface) - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo

METAL - org.biojava.nbio.structure.BondType

MetalBondConsumer - Interface in org.biojava.nbio.structure.io.cif

Consume metal bond data.

MetalBondConsumerImpl - Class in org.biojava.nbio.structure.io.cif

Created by andreas on 6/9/16.

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

MetalBondConverter - Class in org.biojava.nbio.structure.io.cif

Created by andreas on 6/6/16.

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

MetalBondDistance - Class in org.biojava.nbio.structure.chem

A bean that contains cutoffs for correctly detecting metal bonds.

MetalBondDistance() - Constructor for class org.biojava.nbio.structure.chem.MetalBondDistance

METALLOID - org.biojava.nbio.structure.ElementType

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

Mg - org.biojava.nbio.structure.Element

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_PDB_FILE_SIZE - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory

Minimum size for a valid structure file (CIF or PDB), in bytes

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

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

min distance between two residues

MINIMAL_SEQUENCE_DATA - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage

MINIMINAL_SEQUENCES - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection

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

minimumLayoutSize(Container) - Method in class org.biojava.nbio.structure.gui.WrapLayout

Returns the minimum dimensions needed to layout the visible components contained in the specified target container.

minimumQualityScore() - Method in enum org.biojava.nbio.genome.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

MismatchedBasePairParameters - Class in org.biojava.nbio.structure.basepairs

This class allows for finding inter-strand base pairs that are not necessarily canonical Watson-Crick pairs.

MismatchedBasePairParameters(Structure, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This constructor is used to create the TertiaryBasePairParameters object.

MITOCHONDRIAL - org.biojava.nbio.core.sequence.DNASequence.DNAType

ML - org.biojava.nbio.phylo.TreeType

Maximum Likelihood Tree

MMCIF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration

MMTF - org.biojava.nbio.structure.io.StructureFiletype

MMTF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration

MMTF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.MMTFFileReader

MMTF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.MMTFFileReader

MmtfActions - Class in org.biojava.nbio.structure.io.mmtf

A class of functions for reading and writing Biojava structures using MMTF

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

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

A class to read MMTF files and cache them locally.

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

Constructs a new MMTFFileReader, initializing the extensions member variable.

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

Constructs a new MMTFFileReader, initializing the extensions member variable.

MmtfStructureReader - Class in org.biojava.nbio.structure.io.mmtf

A biojava specific structure inflator for MMTF.

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

Instantiates a new bio java structure decoder.

MmtfStructureWriter - Class in org.biojava.nbio.structure.io.mmtf

Class to take Biojava structure data and covert to the DataApi for encoding.

MmtfStructureWriter(Structure, StructureAdapterInterface) - Constructor for class org.biojava.nbio.structure.io.mmtf.MmtfStructureWriter

Pass data from Biojava structure to another generic output type.

MmtfSummaryDataBean - Class in org.biojava.nbio.structure.io.mmtf

Class to store the summary data for a given structure.

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

MmtfUtils - Class in org.biojava.nbio.structure.io.mmtf

A utils class of functions needed for Biojava to read and write to mmtf.

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

Mn - org.biojava.nbio.structure.Element

Mo - org.biojava.nbio.structure.Element

Model - Class in org.biojava.nbio.structure

An internal utility class for StructureImpl to make it easier to manage poly and nonpoly chains.

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

Model(int, int) - Constructor for class org.biojava.nbio.ronn.ModelLoader.Model

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. components and atoms.

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

modified - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower

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, Collection<StructureAtomLinkage>) - 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.

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.

MolecularWeight - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

MomentsOfInertia - Class in org.biojava.nbio.structure.geometry

The moment of inertia, otherwise known as the angular mass or rotational inertia, of a rigid body determines the torque needed for a desired angular acceleration about a rotational axis.

MomentsOfInertia() - Constructor for class org.biojava.nbio.structure.geometry.MomentsOfInertia

Creates a new empty instance of MomentsOfInertia

MomentsOfInertia.SymmetryClass - Enum in org.biojava.nbio.structure.geometry

MONOCLINIC - org.biojava.nbio.structure.xtal.BravaisLattice

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.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.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.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.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.util.SequenceMouseListener

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

MSF - org.biojava.nbio.core.alignment.template.Profile.StringFormat

MSF - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat

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.

multiIterator(AtomPositionMap, 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(AFPChain, Atom[], Atom[], boolean) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

Constructor from an AFPChain instance.

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

Copy constructor.

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

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(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.

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

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 - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange

last allowed n-term

N - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

N - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

N - org.biojava.nbio.structure.Element

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

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

The atom name for the backbone amide nitrogen

Na - org.biojava.nbio.structure.Element

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

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

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

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

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

NATURAL - org.biojava.nbio.protmod.ModificationOccurrenceType

Nb - org.biojava.nbio.structure.Element

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

NBRF - org.biojava.nbio.core.sequence.DataSource

NCBI - org.biojava.nbio.core.sequence.DataSource

NCBI_GI - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

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

NCS_CHAINID_SUFFIX_CHAR - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder

Nd - org.biojava.nbio.structure.Element

Ne - org.biojava.nbio.structure.Element

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

NEGATIVE - org.biojava.nbio.core.sequence.Strand

NetCharge_pH_7 - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

NEUTRON_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique

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

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.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.PDBHeader

NEWLINE - Static variable in class org.biojava.nbio.structure.cath.CathInstallation

newNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet

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

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

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

Return next atom.

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

get next Group.

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.

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

Ni - org.biojava.nbio.structure.Element

NINETY_FIVE_175 - org.biojava.nbio.structure.scop.Astral.AstralSet

NINETY_FIVE_175A - org.biojava.nbio.structure.scop.Astral.AstralSet

NINETY_FIVE_175B - org.biojava.nbio.structure.scop.Astral.AstralSet

NINETY_FIVE_201 - org.biojava.nbio.structure.scop.Astral.AstralSet

NINETY_FIVE_202 - org.biojava.nbio.structure.scop.Astral.AstralSet

NINETY_FIVE_203 - org.biojava.nbio.structure.scop.Astral.AstralSet

nIter - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator

nIter - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

NJ - org.biojava.nbio.phylo.TreeConstructorType

Neighbor Joining Algorithm

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

No - org.biojava.nbio.structure.Element

NO_ROTATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod

NOBLE_GAS - org.biojava.nbio.structure.ElementType

nodeListFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation

NOHEADER - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

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 - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType

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.

nonPolymer - org.biojava.nbio.structure.chem.ResidueType

NONPOLYMER - org.biojava.nbio.structure.EntityType

Non-polymeric entities: ligands, metal ions, buffer molecules, etc

nonredundant - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

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_REFINED - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

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.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(CBK, 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(CBK) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener

Np - org.biojava.nbio.structure.Element

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 - org.biojava.nbio.structure.GroupType

The type for nucleotide groups (dna and rna)

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

NUM_OVERVIEW - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

NUM_OVERVIEW - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

numberOfComponents() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

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

O

O - org.biojava.nbio.structure.Element

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

The atom name for the backbone carbonyl oxygen

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

OBLATE - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass

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

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) - 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 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) - 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) - 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.

ONE - org.biojava.nbio.core.sequence.transcription.Frame

ONEBAR - org.biojava.nbio.structure.xtal.TransformType

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(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation

OneOfLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation

Ontology - Interface in org.biojava.nbio.ontology

An ontology.

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

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(String, Throwable) - Constructor for exception org.biojava.nbio.ontology.OntologyException

OntologyException(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

OPEN - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType

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.

openStringInline(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel

openTag(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

openTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter

Open a new unqualified XML tag.

openTag(String, 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.

openURLConnection(URL) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools

Open HttpURLConnection.

openURLConnection(URL, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools

Open HttpURLConnection.

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(int, int, Strand, List<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(List<Location>) - 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, List<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, List<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

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.embl - package org.biojava.nbio.core.sequence.io.embl

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.reference - package org.biojava.nbio.core.sequence.reference

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.io.fastq - package org.biojava.nbio.genome.io.fastq

FASTQ and variants sequence format I/O.

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

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.proteincomparisontool - package org.biojava.nbio.proteincomparisontool

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.structure - package org.biojava.nbio.structure

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.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.quaternary - package org.biojava.nbio.structure.align.quaternary

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.basepairs - package org.biojava.nbio.structure.basepairs

org.biojava.nbio.structure.cath - package org.biojava.nbio.structure.cath

org.biojava.nbio.structure.chem - package org.biojava.nbio.structure.chem

org.biojava.nbio.structure.cluster - package org.biojava.nbio.structure.cluster

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.geometry - package org.biojava.nbio.structure.geometry

org.biojava.nbio.structure.gui - package org.biojava.nbio.structure.gui

org.biojava.nbio.structure.gui.events - package org.biojava.nbio.structure.gui.events

org.biojava.nbio.structure.gui.util - package org.biojava.nbio.structure.gui.util

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.cif - package org.biojava.nbio.structure.io.cif

org.biojava.nbio.structure.io.mmtf - package org.biojava.nbio.structure.io.mmtf

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.scop - package org.biojava.nbio.structure.scop

Parsers and API for SCOP, Structural Classification of Proteins.

org.biojava.nbio.structure.secstruc - package org.biojava.nbio.structure.secstruc

org.biojava.nbio.structure.symmetry.axis - package org.biojava.nbio.structure.symmetry.axis

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.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

orientation(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

The orientation represents the rotation of the principal axes with respect to the axes of the coordinate system (unit vectors [1,0,0], [0,1,0] and [0,0,1]).

orientationAngle(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

The angle of the relative orientation of the two sets of points in 3D.

orientationAngle(Point3d[], Point3d[], boolean) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

The angle of the relative orientation of the two sets of points in 3D.

orientationMetric(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

The orientation metric is obtained by comparing the quaternion orientations of the principal axes of each set of points in 3D.

orientationMetric(Quat4d, Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

The orientation metric is obtained by comparing two unit quaternion orientations.

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

OrthologousSequenceFamily - org.biojava.nbio.structure.cath.CathCategory

ORTHORHOMBIC - org.biojava.nbio.structure.xtal.BravaisLattice

Os - org.biojava.nbio.structure.Element

OTHER_ADVANCED - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

OTHER_NONMETAL - org.biojava.nbio.structure.ElementType

otherChemComp - org.biojava.nbio.structure.chem.ResidueType

otherPolymer - org.biojava.nbio.structure.chem.PolymerType

other

OUTER - org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection

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

Given an org.w3c.dom.Document, writes it to the given outputStream

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. they are within one cutoff distance in one of their 3 dimensions.

OXIGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

P

P - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

P - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

P - org.biojava.nbio.structure.Element

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

Pa - org.biojava.nbio.structure.Element

padding - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

padLeft(String, int) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper

Adds padding to left of supplied string

padRight(String, int) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper

Adds padding to right of supplied string

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.

pairingNames - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

pairingParameters - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

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.

pairParameters - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

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

pairSequence - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

Pairwise - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum

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

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.

PAM250 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum

PAM30 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum

PAM70 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum

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.

parallel - org.biojava.nbio.structure.secstruc.BridgeType

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(BufferedReader, OntologyFactory) - Method in class org.biojava.nbio.ontology.io.TabDelimParser

Parse an ontology from a reader.

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) - Method in class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser

Parse an inputStream that points to an AAINDEX database file

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(Readable, ParseListener) - Method in interface org.biojava.nbio.genome.io.fastq.FastqReader

Parse the specified readable.

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) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser

Main method for parsing a location from a String instance

parse(String) - Static method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser

parses e.g.

parse(String) - Static method in class org.biojava.nbio.structure.ResidueRange

Parse the residue range from a string.

parse(String) - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

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(String, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength

Parses a residue range.

parseBinaryOperatorExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools

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.genome.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(BufferedReader, String, String, OntologyFactory) - Method in class org.biojava.nbio.ontology.io.GOParser

ParseGO - Class in demo

ParseGO() - Constructor for class demo.ParseGO

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

parseInputStream(InputStream, 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.

ParseListener - Interface in org.biojava.nbio.genome.io.fastq

Low-level event based parser callback.

parseMultiple(String) - Static method in class org.biojava.nbio.structure.ResidueRange

parseMultiple(String, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength

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

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) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

parse an ontology file

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

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. matrix multiplication, see below).

parsePDBFile(BufferedReader) - Method in class org.biojava.nbio.structure.io.PDBFileParser

Parse a PDB file and return a datastructure implementing PDBStructure interface.

parsePDBFile(InputStream) - 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(Exception) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException

ParserException(String) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException

ParserException(String, Exception) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException

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.

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(InputStream) - Method in class org.biojava.nbio.structure.io.sifts.SiftsXMLParser

parseXMLfile(String) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser

Creates a list of MultipleAlignment ensembles from an XML file.

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

PARSIMONY - org.biojava.nbio.phylo.TreeType

Parsimony Tree

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

PARTIAL_COMPLETE - org.biojava.nbio.structure.align.quaternary.QsRelation

All the Subunits of one Structure have an equivalent in the other Structure, but the other Structure contains additional non-matched Subunits.

PARTIAL_INCOMPLETE - org.biojava.nbio.structure.align.quaternary.QsRelation

Only a subset of Subunits of one Structure have an equivalent in the other Structure, and the other Structure also contains additional non-matched Subunits.

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

PARTITION_SINGLE - org.biojava.nbio.alignment.Alignments.RefinerType

PARTITION_SINGLE_ALL - org.biojava.nbio.alignment.Alignments.RefinerType

PARTITION_TREE - org.biojava.nbio.alignment.Alignments.RefinerType

PARTITION_TREE_ALL - org.biojava.nbio.alignment.Alignments.RefinerType

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

PATENTS - org.biojava.nbio.core.sequence.DataSource

PATTERN_EXTENDED_PDBID - Static variable in class org.biojava.nbio.structure.PdbId

A regular expression that matches a PDB ID in the extended format.

PATTERN_SHORT_PDBID - Static variable in class org.biojava.nbio.structure.PdbId

A regular expression that matches a PDB ID in the short format.

PATTERN_SHORTABLE_EXTENDED_PDBID - Static variable in class org.biojava.nbio.structure.PdbId

/ * A regular expression that matches an extended PDB ID that is compatible with the short format.

Pb - org.biojava.nbio.structure.Element

Pd - org.biojava.nbio.structure.Element

PDB - org.biojava.nbio.structure.align.client.StructureName.Source

PDB - org.biojava.nbio.structure.io.StructureFiletype

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_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.PDBFileReader

PDB1 - org.biojava.nbio.core.sequence.DataSource

PDB2 - org.biojava.nbio.core.sequence.DataSource

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

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

PDBe - org.biojava.nbio.core.sequence.DataSource

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 - Class in org.biojava.nbio.structure

A wrapper class for the PDB identifier.

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

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

URL parameter specifying the PDB ID

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.

PDBRecord - Interface in org.biojava.nbio.structure

An interface implemented by all classes that represent PDB records.

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, removed, unreleased) 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 a simplified 3 state 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

PDBWEB - org.biojava.nbio.core.alignment.template.Profile.StringFormat

PDBWEB - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat

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

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

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

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

peptide - org.biojava.nbio.structure.chem.PolymerType

polypeptide(L)

peptideLike - org.biojava.nbio.structure.chem.ResidueType

peptideNucleicAcid - org.biojava.nbio.structure.chem.PolymerType

Peptide nucleic acids

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

PERC_IDENT - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

percentageIdentity(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator

BioJava implementation for percentage of identity (PID).

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.

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.

permuteCyclic2(String, int) - Static method in class org.biojava.nbio.core.util.SequenceTools

Improved implementation that is generally 10-100x faster, and fixes some edge-case bugs.

peto - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower

PFAM - org.biojava.nbio.core.sequence.DataSource

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

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

PHI_PATTERN - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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.core.util.FileDownloadUtils

Pings a HTTP URL.

plain - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType

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

PLANAR - org.biojava.nbio.structure.BondType

PLASMID - org.biojava.nbio.core.sequence.DNASequence.DNAType

PLASTID - org.biojava.nbio.core.sequence.DNASequence.DNAType

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(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

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

calculate structure + Matrix coodinates ...

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

A = A + B

Pm - org.biojava.nbio.structure.Element

Po - org.biojava.nbio.structure.Element

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:

POLARITY - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE

POLARIZABILITY - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE

Polyhedron - Interface in org.biojava.nbio.structure.symmetry.geometry

POLYMER - org.biojava.nbio.structure.EntityType

Polymeric entities: poly-peptides and nucleotide chains

polymerType - Variable in enum org.biojava.nbio.structure.chem.ResidueType

The associated PolymerType

PolymerType - Enum in org.biojava.nbio.structure.chem

Enumerates the classification of polymers.

polymerTypeFromString(String) - Static method in enum org.biojava.nbio.structure.chem.PolymerType

POLYNUCLEOTIDE_ONLY - Static variable in enum org.biojava.nbio.structure.chem.PolymerType

Convenience Set of polymer types classified as DNA.

polysaccharide - org.biojava.nbio.structure.chem.PolymerType

polysaccharide(D)

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)

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)

populateMaps() - Method in class org.biojava.nbio.aaproperties.xml.ElementTable

Populate the Maps for quick retrieval

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

POSITIVE - org.biojava.nbio.core.sequence.Strand

POST_TRANSITION_METAL - org.biojava.nbio.structure.ElementType

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<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

postProcessCompoundLists(List<List<NucleotideCompound>>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator

postProcessCompoundLists(List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

POWDER_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique

powerSet(Set<T>) - Method in class org.biojava.nbio.structure.symmetry.utils.PowerSet

PowerSet<T> - Class in org.biojava.nbio.structure.symmetry.utils

In mathematics, the power set (or powerset) of any set S, written P(S), is the set of all subsets of S, including the empty set and S itself.

PowerSet() - Constructor for class org.biojava.nbio.structure.symmetry.utils.PowerSet

Pr - org.biojava.nbio.structure.Element

PredictDisorder - Class in demo

PredictDisorder() - Constructor for class demo.PredictDisorder

PREDICTED - org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType

preferredLayoutSize(Container) - Method in class org.biojava.nbio.structure.gui.WrapLayout

Returns the preferred dimensions for this layout given the visible components in the specified target container.

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).

prepare() - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl

prepare() - Method in interface org.biojava.nbio.structure.io.cif.CifFileConsumer

Setup routine which initializes a new container.

prepare() - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl

prepare() - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl

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

Rotate the Atoms/Groups so they are aligned for the 3D visualisation

prepareURLConnection(String, int) - Static method in class org.biojava.nbio.core.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

PRF - org.biojava.nbio.core.sequence.DataSource

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

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

The prime number used to multiply any calculated hashcode seed by i.e. result = PRIME*result + c Where result is the result of the previous calculation (at first this will be seed) and c is the calculated int to add to result

print() - Method in class org.biojava.nbio.proteincomparisontool.HelloWorld

Prints hello world on command line

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.

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

Print the matrix to stdout.

print(Graphics, PageFormat, int) - Method in class org.biojava.nbio.structure.align.gui.JPrintPanel

print(PrintWriter, int, int) - Method in class org.biojava.nbio.structure.jama.Matrix

Print the matrix to the output stream.

print(PrintWriter, NumberFormat, int) - Method in class org.biojava.nbio.structure.jama.Matrix

Print the matrix to the output stream.

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(String, File) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Prints string to file.

print(NumberFormat, int) - Method in class org.biojava.nbio.structure.jama.Matrix

Print the matrix to stdout.

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

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

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

printScoresInLines(AFPChain, int, int, double, double, int, int, double, double, StringBuffer) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

printSecStruc(Structure) - Static method in class demo.DemoLoadSecStruc

printSymmetryAxes(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay

Generates a String that displays the symmetry axes of a structure.

printSymmetryAxes(CeSymmResult, boolean) - 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, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter

printXMLHeader(PrettyXMLWriter, AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

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() - 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 will return 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() - 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() - Method in class org.biojava.nbio.structure.io.FastaStructureParser

Parses the fasta file and loads it into memory.

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(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(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(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(File) - Static method in class org.biojava.nbio.core.sequence.io.embl.EmblReader

The parsing is done in this method.
This method tries to process all the Embl records in the File , closes the underlying resource, and return the results in object of EmblRecord.

process(File, double, 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) - Method in interface org.biojava.nbio.core.sequence.io.util.IOUtils.ReaderProcessor

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(String, String) - Method in class org.biojava.nbio.genome.uniprot.UniprotToFasta

Convert a Uniprot sequence file to a fasta file.

process(String, String, String, String, String, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM

process(String, String, String, String, String, String, ArrayList<String>, boolean, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxHelper

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(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(LinkedHashMap<String, ArrayList<String>>, LinkedHashMap<String, GeneSequence>, OutputStream) - Method in class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits

process(LinkedHashMap<String, ArrayList<CensorStatus>>, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM

process(CoxInfo) - Static method in class org.biojava.nbio.survival.cox.CoxCC

process(CoxInfo, ResidualsCoxph.Type, boolean, ArrayList<String>) - Static method in class org.biojava.nbio.survival.cox.ResidualsCoxph

process(CoxMethod, ArrayList<SurvivalInfo>, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxMart

process(CoxMethod, ArrayList<SurvivalInfo>, CoxInfo, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxScore

process(CoxMethod, ArrayList<SurvivalInfo>, CoxInfo, boolean) - Static method in class org.biojava.nbio.survival.cox.stats.AgScore

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

process(WorkSheet, String, String, String, String, String, ArrayList<String>, boolean, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxHelper

process(WorkSheet, String, LinkedHashMap<String, String>, String, Double, ArrayList<MetaDataInfo>) - Static method in class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome

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 - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

PROLATE - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass

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.chem.PolymerType

Convenience Set of polymer types classified as protein.

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

ProteinMappingTools - Class in org.biojava.nbio.genome.util

ProteinMappingTools() - Constructor for class org.biojava.nbio.genome.util.ProteinMappingTools

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.

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

PSSM - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

Pt - org.biojava.nbio.structure.Element

Pu - org.biojava.nbio.structure.Element

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

purgeTempFiles(String) - Static method in class org.biojava.nbio.structure.chem.ZipChemCompProvider

Cleanup chemical component (.cif.gz) files downloaded to tmpdir.

put(int, double) - Method in class org.biojava.nbio.structure.math.SparseVector

Setter method (should it be renamed to set?)

put(int, int, double) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix

set A[i][j] = value

put(Double, Color) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper

Adds a gradient endpoint at the specified position.

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(Key, Value) - Method in class org.biojava.nbio.structure.math.SymbolTable

Put key-value pair into the symbol table.

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.

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.

Px - org.biojava.nbio.structure.scop.ScopCategory

Q

Q - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

Q - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

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. provides a data structure to access R and the Householder vectors and compute Q.

QsAlign - Class in org.biojava.nbio.structure.align.quaternary

Quaternary Structure Alignment (QS-Align).

QsAlign() - Constructor for class org.biojava.nbio.structure.align.quaternary.QsAlign

QsAlignParameters - Class in org.biojava.nbio.structure.align.quaternary

The parameter bean for the QsAlign algorithm.

QsAlignParameters() - Constructor for class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

QsAlignResult - Class in org.biojava.nbio.structure.align.quaternary

Result of a Quaternary Structure Alignment QsAlign.

QsAlignResult(List<Subunit>, List<Subunit>) - Constructor for class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The Constructor of the result takes the same inputs as the QsAlign algorithm.

QsRelation - Enum in org.biojava.nbio.structure.align.quaternary

The Quaternary Structure Relation describes the pairwise relation between two quaternary structures.

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.genome.io.fastq.FastqVariant

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

quality(String) - Method in interface org.biojava.nbio.genome.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.genome.io.fastq.FastqVariant

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

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

Convert the specified error probability to a quality score.

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

Return the quality scores from the specified FASTQ formatted sequence.

qualityScores(Fastq, int[]) - Static method in class org.biojava.nbio.genome.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 the symmetry (global, pseudo, internal and local) of protein structures.

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

The QuatSymmetryParameters specify the options used for the detection of quaternary symmetry in structures using the QuatSymmetryDetector.

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 obtained with QuatSymmetryDetector.

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

Constructor for roto-translational symmetries.

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

Constructor for rotational symmetries.

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

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

A bean to represent information about the set of Subunits being considered for symmetry detection.

QuatSymmetrySubunits(List<SubunitCluster>) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

Converts the List of SubunitCluster to a Subunit object.

QUERY - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

QUERY_BELIEVE_DEFLINE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

QUERY_FROM - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

QUERY_TO - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

QueryAnchored - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum

QueryAnchoredNoIdentities - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum

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

QUESTIONMARK - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy

Put '?'

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

Stripped-down QuickSort.

R

R - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

R - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

R - org.biojava.nbio.structure.Element

R-group to represent generic groups that are sometimes present in MDL .sdf files.

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

Ra - org.biojava.nbio.structure.Element

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

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

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

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)

Rb - org.biojava.nbio.structure.Element

Re - org.biojava.nbio.structure.Element

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

Reads a single character.

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

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

Method reads 1 nucleotide from sequence stream.

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

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

Reads characters into a portion of an array.

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

Read a matrix from a stream.

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

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

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

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

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

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

Read a file into a FeatureList.

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

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

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

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

Read a file into a FeatureList.

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

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

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

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

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

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.

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

readFastaRNASequence(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.

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

Read a fasta RNA sequence

readFromFile(Path) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions

Get a Structure object from a mmtf file.

readFromInputStream(InputStream) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions

Read a Biojava structure from an InputStream

readFromWeb(String) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions

Get a Biojava structure from the mmtf REST service.

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

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

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(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(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.

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

readGenbankRNASequence(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.

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

Read a Genbank RNA sequence

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

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>, boolean, boolean) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder

Builds a Structure object containing the quaternary structure built from given asymUnit and transformations, by adding symmetry partners as new models.

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.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.chem

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

ReducedChemCompProvider() - Constructor for class org.biojava.nbio.structure.chem.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. - particular for large structures this increases calc. time a lot.

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

Remove all atoms but the representative atoms (C alphas or phosphates) from the given structure.

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

referenceFrames - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

ReferenceInterface - Interface in org.biojava.nbio.core.sequence.reference

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(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.

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

Refinement procedure based on superposition and dynamic programming.

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

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

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

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.

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.

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

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

relativeOrientation(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

Calculate the relative quaternion orientation of two arrays of points.

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.

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

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

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

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.

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.

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() - 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.core.util.SoftHashMap

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

REMOVED - org.biojava.nbio.structure.PDBStatus.Status

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

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.genome.io.fastq.ParseListener

Notify this parse listener of a repeat description line.

REPEATS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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

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

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

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

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

RESCORE_IDENTITIES - org.biojava.nbio.alignment.Alignments.RefinerType

RESCORE_SIMILARITIES - org.biojava.nbio.alignment.Alignments.RefinerType

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.PermutationGenerator

resetAlphas() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Reassign alpha-strings for each cluster according to the current strategy.

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

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

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

ResidueRange - Class in org.biojava.nbio.structure

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

ResidueRangeAndLength(String, ResidueNumber, ResidueNumber, 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.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

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

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

Returns the equivalent position on the reverse strand

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

REVERSED_ONE - org.biojava.nbio.core.sequence.transcription.Frame

REVERSED_THREE - org.biojava.nbio.core.sequence.transcription.Frame

REVERSED_TWO - org.biojava.nbio.core.sequence.transcription.Frame

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. in a sequence of size 10, if you request base 2 you will get back the base at position 9.

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

Rh - org.biojava.nbio.structure.Element

RIBBON - org.biojava.nbio.structure.gui.RenderStyle

RID - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

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

RIGHT - org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

RING_MAP - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

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.AlignUtils

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

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

Calculate the RMSD of two point arrays, already superposed.

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

Calculate the RMSD of two Atom arrays, already superposed.

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

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

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

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

Rn - org.biojava.nbio.structure.Element

rna - org.biojava.nbio.structure.chem.PolymerType

polyribonucleotide

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

Convenience Set of polymer types classified as RNA.

rna3PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType

rna5PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType

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

rnaLinking - org.biojava.nbio.structure.chem.ResidueType

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

Create a RNA aequence from a proxy reader

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

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, 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

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

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

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

Rotate a single Atom aroud a rotation matrix.

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

Rotate an Atom around a Matrix object.

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

Rotate a Group.

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

Rotate a group object.

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

Rotate a structure.

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

Rotate a structure object.

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

ROTATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod

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

Calculates the rotation axis for an alignment

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.

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

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

RotationAxisAligner(QuatSymmetryResults) - Constructor for class org.biojava.nbio.structure.symmetry.axis.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(QuatSymmetrySubunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.RotationSolver

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

ROTO_TRANSLATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod

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

Ru - org.biojava.nbio.structure.Element

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

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.chem.AllChemCompProvider

Do the actual loading of the dictionary in a thread.

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

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

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

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.

S

S - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

S - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

S - org.biojava.nbio.structure.Element

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

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

saccharide - org.biojava.nbio.structure.chem.ResidueType

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

Reader for FastqVariant.FASTQ_SANGER formatted sequences.

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

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

Writer for FastqVariant.FASTQ_SANGER formatted sequences.

SangerFastqWriter() - Constructor for class org.biojava.nbio.genome.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

Sb - org.biojava.nbio.structure.Element

Sc - org.biojava.nbio.structure.Element

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

Scalar product (dot product).

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

Multiply elements of a by s

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.

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

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

SCOP - org.biojava.nbio.structure.align.client.StructureName.Source

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

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

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

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

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

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

Create a new SCOP installation.

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

Use default MRC location

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

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

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

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

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

score - org.biojava.nbio.survival.cox.ResidualsCoxph.Type

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

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

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

Get score.

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

Se - org.biojava.nbio.structure.Element

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.

SEARCHSP_EFF - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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

Group property key for secondary structure annotation

SECONDARYSTRUCTURE - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE

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

sections start at a line and continue till the first line afterwards with a non-whitespace first character we want to match any of the following as a new section within a section \s{0,8} word \s{0,7} value \s{21} /word = value \s{21} /word

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

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

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.

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

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

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().

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

Gets a list of elements matching xpathExpression.

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

Given an element, searches upwards through ancestor Elements till the first Element matching the requests parentName is found.

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

If xpathExpression is a plain string with no '/' characterr, this is interpreted as a child element name to search for.

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(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

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(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

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

Sends a delete request for given request id.

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

Notify this parse listener of a sequence line.

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 - org.biojava.nbio.structure.cluster.SubunitClustererMethod

The SEQUENCE clustering method uses the residue sequence of the Subunit to calculate sequence alignments.

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

SEQUENCE_CONSERVATION - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

SEQUENCE_FUNCTION - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

SEQUENCE_FUNCTION - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

SEQUENCE_STRUCTURE - org.biojava.nbio.structure.cluster.SubunitClustererMethod

The SEQUENCE_STRUCTURE clustering method uses the residue sequence and the coordinates of its Atom representatives of the Subunit to calculate sequence and structure alignments.

sequenceAndQualityLengthsMatch() - Method in class org.biojava.nbio.genome.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.

SequenceFamily - org.biojava.nbio.structure.cath.CathCategory

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) - 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(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

serverBaseUrl - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

The base URL to which the full path specified via DownloadChemCompProvider.setChemCompPathUrlTemplate(String) is appended.

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

Set a single element.

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

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

Sets the singleton provider.

setAbsoluteMinimumSequenceLength(int) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.

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

setAccessionNumber(List<String>) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

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.StatusDisplay

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

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.

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(int, int, AligMatEl) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setAligMat(AligMatEl[][]) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setAligMat(AligMatEl[][]) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

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(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The alignment that specifies the residue equivalencies of the equivalent Subunits.

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

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

setAllAtoms(List<Atom>) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

setAllChains(List<Chain>) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

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

setAlpha(String) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

A letter that is assigned to this cluster in stoichiometry.

setAlphabet(String) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Change alphabet used for string representation of a stoichiometry.

setAltAligNumber(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setAltAtomId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

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

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.

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

setAngleThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

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

setAsaU(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAssemblyHeader(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setAssemblyId(Long) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setAssemblyInformation(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setAtcc(String) - Method in class org.biojava.nbio.structure.EntityInfo

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) - 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

setAtomicNumber(int) - Method in class org.biojava.nbio.aaproperties.xml.Element

setAtomId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setAtomId1(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setAtomId2(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setAtomInfo(String, int, char, float, float, float, float, float, String, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

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(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.chem.ChemComp

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(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setAtomType1(String) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

setAtomType2(String) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

setAuthorList(List<Author>) - Method in class org.biojava.nbio.structure.JournalArticle

setAuthors(String) - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference

Set The authors are a list of Inventors that retrieved from the Reference section.

setAuthors(String) - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference

setAuthors(String) - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface

Set the authors that retrieved from Reference section.

setAuthors(String) - Method in class org.biojava.nbio.structure.PDBHeader

setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setAutoSuggestProvider(AutoSuggestProvider) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest

setAverageScore(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

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

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

setBioAssemblyTrans(int, int[], double[], String) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

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

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.EntityInfo

setBioStart(Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

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.chem.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

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.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 class org.biojava.nbio.structure.align.pairwise.AlignmentResult

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

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

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(CathDatabase) - Static method in class org.biojava.nbio.structure.cath.CathFactory

Sets the default (singleton) CathDatabase.

setCATH(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setCathDownloadUrl(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setCathVersion(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

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.EntityInfo

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.EntityInfo

setCellularLocation(String) - Method in class org.biojava.nbio.structure.EntityInfo

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.geometry.SuperPositionAbstract

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.

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 class org.biojava.nbio.structure.contact.AtomIdentifier

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 identifier (asym id) that this transformation should be applied to.

setChainID1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setChainID2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setChainIdToIndexMap(Map<String, Integer>) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

setChainInfo(String, String, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

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

setChainName(String) - Method in class org.biojava.nbio.structure.DBRef

The name of the corresponding chain.

setChainName(String) - Method in class org.biojava.nbio.structure.ResidueNumber

setChainOrigNamesMap(Map<String, String>) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Sets a map with mapping from NCS chain names to original chain names.

setChainRmsd(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

The RMSD of the chain of AFPs.

setChains(int, List<Chain>) - Method in interface org.biojava.nbio.structure.Structure

Set the chains for a model

setChains(int, List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the chains for a model

setChains(List<Chain>) - Method in class org.biojava.nbio.structure.EntityInfo

Set the chains for this EntityInfo

setChains(List<Chain>) - Method in class org.biojava.nbio.structure.Model

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(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.

setCharge(int) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

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

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

setChemCompPathUrlTemplate(String) - Static method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

Set the path to append to the serverBaseUrl (settable in DownloadChemCompProvider.setServerBaseUrl(String)).

setChemCompProvider(ChemCompProvider) - Static method in class org.biojava.nbio.structure.chem.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

setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitFacade

Sets a chromosome for TwoBitParser.

setChromosomeNumber(int) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence

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

setClassId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setClassId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

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

setClustererMethod(SubunitClustererMethod) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Method to cluster subunits.

setClusters(List<SubunitCluster>) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

setClusterValue(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

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) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator

setColorSpace(ColorSpace, LinearColorInterpolator.InterpolationDirection[]) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator

Sets the ColorSpace to use for interpolation.

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

setComments(List<String>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Set comments.

setCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

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

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

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

setConstructedSequence(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setContacts(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setContacts(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setContacts(AtomContactSet) - Method in class org.biojava.nbio.structure.contact.StructureInterface

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) - 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 Some uniprot records contain white space in the sequence.

setContents(String) - 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

setContents(String, ArrayList) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

setContents(List<C>) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

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

setCoordinateSystem(int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools

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.

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?

setCreatedDate(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

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

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

setCustomStringGenerator(Function<List<SubunitCluster>, String>) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Let a user-defined function handle the entire string representation of a stoichiometry.

setCut_sites(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

setCutoff(double) - Method in class org.biojava.nbio.structure.contact.InterfaceFinder

Set the contact distance cutoff.

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(TreeMap<Integer, SpaceGroup>) - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

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.

setDatabaseCrossReference(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

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

setDate(Date) - Method in class org.biojava.nbio.structure.cath.CathDomain

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

setDcl(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

setdCutoff(double) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

The maximum allowed distance between the centroids of two equivalent Subunits, in A.

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.

setDefaultSuperPosition(SuperPositionAbstract) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

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

The deposition date of the structure in the PDB

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.EntityInfo

setDescription(String) - Method in class org.biojava.nbio.structure.PDBHeader

Deprecated.
will be removed later. Use PDBHeader.getKeywords() if you use description to keep the keywords.

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.chem.ChemCompDescriptor

setDescriptors(List<ChemCompDescriptor>) - Method in class org.biojava.nbio.structure.chem.ChemComp

setDetails(String) - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord

setDetails(String) - Method in class org.biojava.nbio.structure.EntityInfo

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.FatCatUserArgumentProcessor.FatCatStartupParams

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

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

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

setDomainId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setDomainName(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

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.chem.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.EntityInfo

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

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.

setEmblId(EmblId) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setEmblReference(List<EmblReference>) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband

setEnd(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setEnd(Point) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setEnergy(double) - Method in class org.biojava.nbio.structure.secstruc.HBond

setEngineered(String) - Method in class org.biojava.nbio.structure.EntityInfo

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

setEntityId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

setEntityInfo(int[], String, String, String) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setEntityInfo(EntityInfo) - Method in interface org.biojava.nbio.structure.Chain

Sets the Entity information

setEntityInfo(EntityInfo) - Method in class org.biojava.nbio.structure.ChainImpl

setEntityInfos(List<EntityInfo>) - Method in interface org.biojava.nbio.structure.Structure

Set the EntityInfo

setEntityInfos(List<EntityInfo>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the EntityInfo

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.

setExpressionSystem(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemAtccNumber(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemCell(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemCellLine(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemCellularLocation(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemGene(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemOrgan(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemOrganelle(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemOtherDetails(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemPlasmid(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemStrain(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemTaxId(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemTissue(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemVariant(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemVector(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemVectorType(String) - Method in class org.biojava.nbio.structure.EntityInfo

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

setFeatureHeader(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setFeatureRetriever(FeatureRetriever) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setFeaturesKeyWord(FeaturesKeyWordInterface) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setFeatureTable(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

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.

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.PDBFileParser

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

setFiletype(StructureFiletype) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Set the file type that will be parsed.

setFirstGroupAsa(GroupAsa) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setFirstGroupAsas(Map<ResidueNumber, GroupAsa>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setFirstRepeat(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

setFlexible(boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

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

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.chem.ChemComp

setFormulaWeight(double) - Method in class org.biojava.nbio.structure.chem.ChemComp

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

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

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

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

setFragment(String) - Method in class org.biojava.nbio.structure.EntityInfo

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.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

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

setGapExtension(double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

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

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

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

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.CeUserArgumentProcessor.CeStartupParams

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

setGapOpen(short) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

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

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

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.EntityInfo

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

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.

setGroupBond(int, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setGroupInfo(String, int, char, String, int, int, char, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setGroups(List<Group>) - Method in class org.biojava.nbio.structure.Site

setGroups(Set<StructureGroup>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

setGroups(Set<StructureGroup>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

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

setHeaderInfo(float, float, float, String, String, String, String[]) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

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.EntityInfo

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

setHetAtomInFile(boolean) - Method in interface org.biojava.nbio.structure.Group

Sets the field isHetAtomInFile which is intented only for helping in infering if a polymeric group is in a ligand chain or in a polymeric chain.

setHetAtomInFile(boolean) - Method in class org.biojava.nbio.structure.HetatomImpl

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

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

setId(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setId(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

setId(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

setId(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

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 class org.biojava.nbio.structure.HetatomImpl

the Hibernate database ID

setId(Long) - Method in class org.biojava.nbio.structure.DBRef

Set the ID used by Hibernate.

setId(Long) - Method in class org.biojava.nbio.structure.EntityInfo

set the ID used by Hibernate

setId(String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

setId(String) - Method in interface org.biojava.nbio.structure.Chain

Set the 'private' asymId (internal chain IDs in mmCif) for this chain.

setId(String) - Method in class org.biojava.nbio.structure.ChainImpl

setId(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setId(String) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

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.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

Deprecated.
use PDBHeader.setPdbId(PdbId)

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

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.

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

setInterGroupBond(int, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setInternalSymmetry(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

The internal symmetry option divides each Subunit of each SubunitCluster into its internally symmetric repeats.

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 class org.biojava.nbio.structure.align.pairwise.AlignmentResult

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

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

setJournal(String) - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference

Set The journal usually contains the Publication Number, Publication Date and Assignee

setJournal(String) - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference

setJournal(String) - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface

Set the journal that retrieved from Reference section.

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

setKeyword(List<String>) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setKeywords(List<String>) - Method in class org.biojava.nbio.structure.PDBHeader

Sets the KEYWODS record of the structure.

setKMFigureInfo(KMFigureInfo) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure

setKMFigureInfo(KMFigureInfo) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure

setLastUpdatedDate(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

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(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager

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

setLength1(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setLength2(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setLevel(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

setLigands(Set<String>) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

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

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.

setLowerLimit(float) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

setM(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFP

setMacromolecularSize(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

setMacromolecularSizes() - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser

Set the macromolecularSize fields of the parsed bioassemblies.

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(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.

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

Set a submatrix.

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

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(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).

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

Set the Max gap size parameter.

setMaximumLocalCombinations(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.

setMaxOrientationAngle(double) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

The maximum orientation angle between two equivalent Subunits, in radians.

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

setMaxPropeller(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method sets the maximum propeller allowed for a base pair, prior to analyze() call

setMaxPropeller(double) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

This method sets the maximum propeller allowed for a base pair, prior to analyze() call

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

setMaxRmsd(double) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

The maximum allowed RMSD of the alignment, in A.

setMaxRmsd(double) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

setMaxRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

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

setMaxShear(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method sets the maximum shear allowed for a base pair, prior to analyze() call

setMaxStagger(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method sets the maximum stagger allowed for a base pair, prior to analyze() call

setMaxStagger(double) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

This method sets the maximum stagger allowed for a base pair, prior to analyze() call

setMaxStretch(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method sets the maximum stretch allowed for a base pair, prior to analyze() call.

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(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...

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

set the maximum number of Twists that are allowed...

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

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

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.cluster.SubunitClustererParameters

Set the minimum number of residues of a subunits to be considered in the clusters.

setMinimumSequenceLengthFraction(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.

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

setMinLen(int) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

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

setMinRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

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

setModDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader

The latest modification date of the structure.

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.

setModelCartnX(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setModelCartnY(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setModelCartnZ(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setModelInfo(int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

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

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.EntityInfo

Set the molecule identifier, called entity_id in mmCIF dictionary.

setMonNstdFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setMonNstdParentCompId(String) - Method in class org.biojava.nbio.structure.chem.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.EntityInfo

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 interface org.biojava.nbio.structure.Chain

Set the 'public' authId (chain ID in PDB file)

setName(String) - Method in class org.biojava.nbio.structure.ChainImpl

setName(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setName(String) - Method in class org.biojava.nbio.structure.cluster.Subunit

The Name of a Subunit is a free-text field, user defined.

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.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

setNaturalPos(Integer) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

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

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

setNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setNonStandardCoordFrameConvention(boolean) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the non-standard coordinate frame convention field

setNonStandardSg(boolean) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the non-standard space group field

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

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 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

setNullValue(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer

setNumBonds(int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

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

setNumRepeats(int) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setNumRes(String) - Method in class org.biojava.nbio.structure.EntityInfo

setNumSequences(int) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

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.

setOccupancy(float) - Method in interface org.biojava.nbio.structure.Atom

Set occupancy.

setOccupancy(float) - Method in class org.biojava.nbio.structure.AtomImpl

setOccurrenceType(ModificationOccurrenceType) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

setOffset(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setOmega(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

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

setOneLetterCode(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

On-the-fly Jmol bioassembly generation.

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

setOperator(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

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

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

Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level.

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

Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.

setOptimizeAlignment(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.

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.EntityInfo

setOrganelle(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrGanelle(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setOrganism(String) - Method in class org.biojava.nbio.phosphosite.Site

setOrganismClassification(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setOrganismCommon(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrganismScientific(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrganismSpecies(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setOrganismTaxId(String) - Method in class org.biojava.nbio.structure.EntityInfo

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(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setOutFile(SynchronizedOutFile) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

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

setOutputOption(String, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties

This method forwards to NCBIQBlastOutputProperties.setOutputOption(BlastOutputParameterEnum, String).

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.

setOutputOption(BlastOutputParameterEnum, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties

Sets the value of specified output parameter

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

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(AlignedSequence<S, C>, AlignedSequence<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableSequencePair

Sets both AlignedSequences of the pair.

setPair(Profile<S, C>, Profile<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfilePair

Sets both Profiles 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(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 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. do NOT parse.

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(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(IndexPair[]) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setPath(IndexPair[]) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

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

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

Deprecated.
use #setPDBCode(PdbId)

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

Deprecated.
use #setPDBCode(PdbId)

setPDBDirField(JTextField) - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel

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.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

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.scop.ScopDomain

Deprecated.
use ScopDomain.setPdbId(PdbId)

setPdbId(PdbId) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setPdbId(PdbId) - Method in class org.biojava.nbio.structure.PDBHeader

Sets the PDB identifier code for this protein structure.

setPdbId(PdbId) - Method in class org.biojava.nbio.structure.scop.ScopDomain

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

Sets the PdbId identifier associated with this structure.

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

Sets the PdbId identifier associated with this structure.

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

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

setPdbSerial(int) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

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.

setPdbxAlign(int) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxAmbiguousFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxAromaticFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxAromaticFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setPdbxComponentAtomId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxComponentCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxComponentId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxFormalCharge(int) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxIdealCoordinatesDetails(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxIdealCoordinatesMissingFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxInitialDate(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxLeavingAtomFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxModelCartnXIdeal(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxModelCartnYIdeal(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxModelCartnZIdeal(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxModelCoordinatesDbCode(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxModelCoordinatesDetails(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxModelCoordinatesMissingFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxModifiedDate(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxOrdinal(int) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxOrdinal(int) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setPdbxPolymerType(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxProcessingSite(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxRefId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxReleaseStatus(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxReplacedBy(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxReplaces(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxResidueNumbering(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxStereoConfig(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxStereoConfig(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setPdbxSubcomponentList(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxSynonyms(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxType(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

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

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

setPhase(int) - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos

setPhi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

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.chem.ChemComp

setPos(int) - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos

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

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(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 class org.biojava.nbio.alignment.GuideTree.Node

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.chem.ChemCompDescriptor

setProgramSpecificParameters(HashMap<String, String>) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setProgramVersion(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

setProjectIdentifier(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

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.

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

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.

setPsi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

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.

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(AlignedSequence<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableSequencePair

Sets the first AlignedSequence of the pair.

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

Sets the query Sequence.

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

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.

setRefAuthor(StringBuffer) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference

setRefChainId(String) - Method in class org.biojava.nbio.structure.EntityInfo

Return the ref chain id value.

setReference(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

setReferenceAuthor(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

setReferenceComment(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

setReferenceCrossReference(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

setReferenceGroup(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

setReferenceLocation(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

setReferenceNumber(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

setReferencePosition(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

setReferences(List<AbstractReference>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Set the list of AbstractReference

setReferences(Vector<StockholmFileAnnotation.StockholmFileAnnotationReference>) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

setReferenceTitle(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference

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

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

setRelation(QsRelation) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The quaternary structure relation QsRelation between the two groups of Subunits.

setRelDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader

The release date of the structure in the PDB.

setRemoveCif(boolean) - Method in class org.biojava.nbio.structure.chem.ZipChemCompProvider

Remove downloaded .cif.gz after adding to zip archive?

setRepeatUnits(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

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(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(String, Integer, Character) - Method in class org.biojava.nbio.structure.HetatomImpl

setResidueNumber(ResidueNumber) - Method in interface org.biojava.nbio.structure.Group

Sets the ResidueNumber for this Group

setResidueNumber(ResidueNumber) - 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.chem.ChemComp

setResNames(String) - Method in class org.biojava.nbio.structure.EntityInfo

setResnum1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setResnum2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setResolution(float) - Method in class org.biojava.nbio.structure.PDBHeader

setResolution(Double) - Method in class org.biojava.nbio.structure.cath.CathDomain

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

setRevisionRecords(List<DatabasePDBRevRecord>) - Method in class org.biojava.nbio.structure.PDBHeader

setRevNum(String) - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord

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.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

setRMSDThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.

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

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

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

setRscore(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setRscoreLogrankTestpvalue(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setRwork(float) - Method in class org.biojava.nbio.structure.PDBHeader

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(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

setScale(int) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

setScalevalue(double) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper

setScopDatabase(String) - 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

setScope(int) - Method in class org.biojava.nbio.ontology.Synonym

setScopId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain

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(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 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(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[][][]) - 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

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

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, 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[], 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[], 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, 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, 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, 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, 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, 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

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

Set the scoring strategy to use. 0 is default CE scoring scheme. 1 uses Side chain orientation.

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

setSecondGroupAsas(Map<ResidueNumber, GroupAsa>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setSecretion(String) - Method in class org.biojava.nbio.structure.EntityInfo

setSecStructType(Group, int) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get the secondary structure as defined by DSSP.

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(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 class org.biojava.nbio.structure.gui.JmolViewerImpl

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

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

Sets 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

setSeqResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setSequence(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setSequence(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSequence(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

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

setSequenceCircular(boolean) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser

setSequenceCollection(SequenceOptimizationHints.SequenceCollection) - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints

setSequenceCoverageThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

The minimum coverage of the sequence alignment between two subunits to be clustered together.

setSequenceDescription(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSequenceHeader(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord

setSequenceHeader(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSequenceHeader(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setSequenceIdentityThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Sequence identity threshold to consider for the sequence subunit clustering.

setSequenceLength(long) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser

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

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?

setSerNum(int) - Method in class org.biojava.nbio.structure.io.SSBondImpl

get serial number of this SSBOND in PDB file

setServerBaseUrl(String) - Static method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

Set the base URL for the location of all chemical component CIF files, to which the chemCompPathUrlTemplate is appended, settable in DownloadChemCompProvider.setChemCompPathUrlTemplate(String).

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

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

setSOLID(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

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

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

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

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

setStandardDeviation(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

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

setStartPage(String) - Method in class org.biojava.nbio.structure.JournalArticle

setStartTimestamp(long) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob

setStatus(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

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

setStdError(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

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

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.EntityInfo

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

setStrategy(Stoichiometry.StringOverflowStrategy) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Change string representation of a stoichiometry in case number of clusters exceeds number of letters in the alphabet.

setStringSequence(String) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

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

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

setStructure(Structure) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

setStructure(Structure, boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel

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

setStructureCoverageThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

The minimum coverage of the structure alignment between two subunits to be clustered together.

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.

setSubunitMap(Map<Integer, Integer>) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

Map of Subunit equivalencies from the first to the second group.

setSubunitRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setSunid(int) - Method in class org.biojava.nbio.structure.scop.ScopNode

setSunid(Integer) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setSunID(int) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setSuperfamilyId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setSuperpositionAlgorithm(String) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Method to cluster subunits.

setSurname(String) - Method in class org.biojava.nbio.structure.Author

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

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.

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

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

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

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

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

setSynonyms(List<String>) - Method in class org.biojava.nbio.structure.EntityInfo

setSynonyms(Set<Object>) - Method in class org.biojava.nbio.ontology.Term.Impl

setSynthetic(String) - Method in class org.biojava.nbio.structure.EntityInfo

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

setTarget(AlignedSequence<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableSequencePair

Sets the second AlignedSequence of the pair.

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

Sets the target Sequence.

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

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.

setThreeLetterCode(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setTime(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setTissue(String) - Method in class org.biojava.nbio.structure.EntityInfo

setTitle(String) - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference

Set The title that retrieved from the Reference section.

setTitle(String) - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference

setTitle(String) - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface

Set the title that retrieved from Reference section.

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.EntityInfo

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.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

setTMThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.

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(List<BiologicalAssemblyTransformation>) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

setTransforms(Pair<CrystalTransform>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setTranslation(double[]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

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

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(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setType(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

setType(String) - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord

setType(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

setType(StainType) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband

setType(EntityType) - Method in class org.biojava.nbio.structure.EntityInfo

Set the type of entity this EntityInfo describes.

setType(SecStrucType) - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

setTypeSymbol(String) - Method in class org.biojava.nbio.structure.chem.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

setUpdateFrequency(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

The "latest" version will be re-downloaded if it is older than EcodInstallation.getUpdateFrequency() days.

setUpperLimit(float) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

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

setUseEntityIdForSeqIdentityDetermination(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Whether to use the entity id of subunits to infer that sequences are identical.

setUseGlobalMetrics(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only

setUserCollection(Collection<Object>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setUseRMSD(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use RMSD for evaluating structure similarity

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

setUseSequenceCoverage(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use sequence coverage for evaluating sequence similarity

setUseStructureCoverage(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use structure coverage for evaluating sequence similarity

setUseTMScore(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use TMScore for evaluating structure similarity

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(String) - Method in class org.biojava.nbio.core.sequence.features.Qualifier

setValueOrder(String) - Method in class org.biojava.nbio.structure.chem.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.EntityInfo

setVersion(int) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

setVersion(Integer) - Method in class org.biojava.nbio.core.sequence.AccessionID

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(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

setVolume(String) - Method in class org.biojava.nbio.structure.JournalArticle

setWaldTestInfo(WaldTestInfo) - Method in class org.biojava.nbio.survival.cox.CoxInfo

setWeight(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

setWeighted(boolean) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo

setWinSize(int) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

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

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

setXtalInfo(String, float[], double[][]) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

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(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient

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

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

Shift an array of atoms at once.

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

shift a structure with a vector.

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.util.AlignmentTools

only shift CA positions.

SHORT_QUERY_ADJUST - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

SHORTER - org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

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_CDS_FEATURE - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

SHOW_LINKOUT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

SHOW_OVERVIEW - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

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, String) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP

showAlignmentImage(AFPChain, Atom[], Atom[], Object) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

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

showConsole(boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener

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(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.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

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

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. for using JSuggestionField like a ComboBox)

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.

Si - org.biojava.nbio.structure.Element

SIDE_CHAIN_ANGLE_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

SIDE_CHAIN_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

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

SIMILARITIES - org.biojava.nbio.alignment.Alignments.PairInProfileScorerType

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(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.

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.

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

SimpleLocation(Point, Point) - 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, boolean, boolean) - 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

SimpleLocation(Point, Point, Strand, boolean, List<Location>) - 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, 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, AccessionID) - 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

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(Collection<AlignedSequence<S, C>>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile

Creates a profile for the already aligned sequences.

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(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(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.

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(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(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.

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(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner

Prepares for a profile-profile alignment.

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>, 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.

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.

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>, short, short) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix

Creates an identity substitution matrix from match and replace values.

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.

SimpleTwoBitFileProvider - Class in org.biojava.nbio.genome.parsers.twobit

Created by yana on 4/4/17.

SimpleTwoBitFileProvider() - Constructor for class org.biojava.nbio.genome.parsers.twobit.SimpleTwoBitFileProvider

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(C, CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Build the object with a compound rather than a String

SingleCompoundSequenceReader(String, CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Public constructor to be used with String based constructor

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. if group(1) is null than the feature is on the positive strand, group(2) start position, group(3) end position.

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 - Class in org.biojava.nbio.structure

Holds the data of sites presented in PDB files.

Site() - Constructor for class org.biojava.nbio.phosphosite.Site

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

SIXBAR - org.biojava.nbio.structure.xtal.TransformType

SIXFOLD - org.biojava.nbio.structure.xtal.TransformType

SIXFOLDSCREW - org.biojava.nbio.structure.xtal.TransformType

size() - Static method in class org.biojava.nbio.core.util.FlatFileCache

Returns the number of items in the cache.

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.chem.ChemicalComponentDictionary

Returns the number of ChemComps in this dictionary

size() - Method in class org.biojava.nbio.structure.cluster.Subunit

The size of a Subunit is the number of residues it contains.

size() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

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() - 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 class org.biojava.nbio.structure.Model

Returns the total number of chains in this model: polymeric, non-polymeric and water

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

Return number of polymer Chains in this Structure for first model.

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

size() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

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

Return number of chains of model.

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

return number of chains of model.

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

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

Sm - org.biojava.nbio.structure.Element

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(Map) - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation

Return a new SmallAnnotation that copies all values from a Map.

SmallAnnotation(Annotation) - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation

Return a new SmallAnnotation that copies all values from another annoation.

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 of two structures based on their 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

Sn - org.biojava.nbio.structure.Element

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.genome.io.fastq

Reader for FastqVariant.FASTQ_SOLEXA formatted sequences.

SolexaFastqReader() - Constructor for class org.biojava.nbio.genome.io.fastq.SolexaFastqReader

SolexaFastqWriter - Class in org.biojava.nbio.genome.io.fastq

Writer for FastqVariant.FASTQ_SOLEXA formatted sequences.

SolexaFastqWriter() - Constructor for class org.biojava.nbio.genome.io.fastq.SolexaFastqWriter

SOLID_STATE_NMR - org.biojava.nbio.structure.ExperimentalTechnique

SOLUTION_NMR - org.biojava.nbio.structure.ExperimentalTechnique

SOLUTION_SCATTERING - org.biojava.nbio.structure.ExperimentalTechnique

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

SOLVENTACCESSIBILITY - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE

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.

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. initialize the all 0s vector of length N

Species - org.biojava.nbio.structure.scop.ScopCategory

SPHERES - org.biojava.nbio.structure.gui.RenderStyle

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

Sample possible orientations.

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.

Sr - org.biojava.nbio.structure.Element

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

stalk - org.biojava.nbio.genome.parsers.cytoband.StainType

STANDARD_BASES - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

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.align.gui.jmol.StructureAlignmentJmol

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() - Constructor for class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder

StaticMemberPlaceHolder(Field) - Constructor for class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder

status - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

STATUS_ENDPOINT - Static variable in class org.biojava.nbio.structure.PDBStatus

STATUS_LIST_ENDPOINT - Static variable in class org.biojava.nbio.structure.PDBStatus

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

stepParameters - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

STICKS - org.biojava.nbio.structure.gui.RenderStyle

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

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

A utility object that describes Stoichiometry (composition of a protein assembly), determined via clustering procedure SubunitClusterer, and implements human-readable representation using various strategies.

Stoichiometry(List<SubunitCluster>) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Constructor for Stoichiometry.

Stoichiometry(List<SubunitCluster>, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Constructor for Stoichiometry.

Stoichiometry(List<SubunitCluster>, Function<List<SubunitCluster>, String>) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Constructor for Stoichiometry.

Stoichiometry(List<SubunitCluster>, Stoichiometry.StringOverflowStrategy) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Constructor for Stoichiometry.

Stoichiometry(List<SubunitCluster>, Stoichiometry.StringOverflowStrategy, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Constructor for Stoichiometry.

Stoichiometry.StringOverflowStrategy - Enum in org.biojava.nbio.structure.symmetry.core

What to do when the number of SubunitCluster exceeds the length of the alphabet.

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.genome.io.fastq.FastqReader

Stream the specified readable.

StreamListener - Interface in org.biojava.nbio.genome.io.fastq

Event based parser callback.

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

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 - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

Structure - Interface in org.biojava.nbio.structure

Interface for a structure object.

STRUCTURE - org.biojava.nbio.structure.cluster.SubunitClustererMethod

The STRUCTURE clustering method uses the residue sequence and the coordinates of its Atom representatives of the Subunit to calculate sequence and structure alignments.

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.

StructureFiletype - Enum in org.biojava.nbio.structure.io

An enum of supported file formats.

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(Chain) - Constructor for class org.biojava.nbio.structure.StructureImpl

Construct a Structure object that contains a particular chain

StructureImpl(Group) - Constructor for class org.biojava.nbio.structure.StructureImpl

Construct a Structure object that only contains a single group

StructureInterface - Class in org.biojava.nbio.structure.contact

An interface between 2 molecules (2 sets of atoms).

StructureInterface() - Constructor for class org.biojava.nbio.structure.contact.StructureInterface

Constructs an empty StructureInterface

StructureInterface(Atom[], Atom[], String, String, AtomContactSet, CrystalTransform, CrystalTransform) - Constructor for class org.biojava.nbio.structure.contact.StructureInterface

Constructs a 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

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

SUB_SEQUENCE_DATA - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage

submit(Callable<T>) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Queues up a task and adds a default log entry.

submit(Callable<T>, String) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Queues up a task and adds a 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

SUBSTITUTION - org.biojava.nbio.alignment.routines.AlignerHelper.Last

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

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.

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.

SubstructureIdentifier(PdbId, List<ResidueRange>) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier

Create a new identifier based on a set of ranges.

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

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

subtract two atoms ( a - b).

Subunit - Class in org.biojava.nbio.structure.cluster

A Subunit consists of a set of residues from a Structure, which may correspond to an entire Chain, a Domain, or any subset or combination of residues from them.

Subunit(Atom[], String, StructureIdentifier, Structure) - Constructor for class org.biojava.nbio.structure.cluster.Subunit

A Subunit is solely defined by the coordinates of the representative Atoms of its residues.

SubunitCluster - Class in org.biojava.nbio.structure.cluster

A SubunitCluster contains a set of equivalent QuatSymmetrySubunits, the set of equivalent residues (EQR) between Subunit and a Subunit representative.

SubunitCluster(Subunit) - Constructor for class org.biojava.nbio.structure.cluster.SubunitCluster

A constructor from a single Subunit.

SubunitCluster(SubunitCluster, List<Integer>) - Constructor for class org.biojava.nbio.structure.cluster.SubunitCluster

A copy constructor with the possibility of removing subunits.

SubunitClusterer - Class in org.biojava.nbio.structure.cluster

The SubunitClusterer takes as input a collection of Subunit and returns a collection of SubunitCluster.

SubunitClustererMethod - Enum in org.biojava.nbio.structure.cluster

The SubunitClustererMethod ennummerates all methods that can be used to cluster Subunit in the SubunitCluster.

SubunitClustererParameters - Class in org.biojava.nbio.structure.cluster

The SubunitClustererParameters specifies the options used for the clustering of the subunits in structures using the SubunitClusterer.

SubunitClustererParameters() - Constructor for class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Initialize with "local" metrics by default.

SubunitClustererParameters(boolean) - Constructor for class org.biojava.nbio.structure.cluster.SubunitClustererParameters

"Local" metrics are scoring SubunitClustererMethod.SEQUENCE: sequence identity of a local alignment (normalised by the number of aligned residues) sequence coverage of the alignment (normalised by the length of the longer sequence) SubunitClustererMethod.STRUCTURE: RMSD of the aligned substructures and structure coverage of the alignment (normalised by the length of the larger structure) Two thresholds for each method are required.

SubunitExtractor - Class in org.biojava.nbio.structure.cluster

The SubunitExtractor extracts the information of each protein Chain in a Structure and converts them into a List of 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(Atom[]) - Static method in class org.biojava.nbio.structure.domain.LocalProteinDomainParser

Suggest domains for a set of Calpha atoms

suggestDomains(Structure) - Static method in class org.biojava.nbio.structure.domain.LocalProteinDomainParser

Suggest domains for a protein structure

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

Superfamily - org.biojava.nbio.structure.scop.ScopCategory

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[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition

Obtain the superposition matrix that minimizes the RMSD between two arrays of equivalent points.

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

superpose(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQuat

superpose(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

Use the SuperPosition.superpose(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.

superpose(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionSVD

superposeAfterRmsd() - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP

The QCP method can be used as a two-step calculation: first compute the RMSD (fast) and then compute the superposition.

superposeAndTransform(Point3d[], Point3d[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition

Transform an array of points so that the coordinates of its points minimize the RMSD to the other array of equivalent points, and return the transformation matrix applied.

superposeAndTransform(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionAbstract

superposeAndTransform(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

Use the SuperPosition.superposeAndTransform(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.

superposeAndTransformAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

Use the SuperPosition.superposeAndTransform(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.

superposeAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

Use the SuperPosition.superpose(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.

SuperPosition - Interface in org.biojava.nbio.structure.geometry

The SuperPosition interface defines and documents the required methods for any superpostion algorithm implementation, so that the input and expected output are uniform.

SuperPositionAbstract - Class in org.biojava.nbio.structure.geometry

The SuperPositionAbstract contains common code shared by all SuperPosition algorithm implementations.

SuperPositionAbstract(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionAbstract

SuperPositionQCP - Class in org.biojava.nbio.structure.geometry

Implementation of the Quaternion-Based Characteristic Polynomial algorithm for RMSD and Superposition calculations.

SuperPositionQCP(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionQCP

Default constructor for the quaternion based superposition algorithm.

SuperPositionQCP(boolean, double, double) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionQCP

Constructor with option to set the precision values.

SuperPositionQuat - Class in org.biojava.nbio.structure.geometry

The SuperPositionQuat implements a quaternion based algorithm to superpose arrays of Points in 3D.

SuperPositionQuat(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionQuat

Constructor for the quaternion based superposition algorithm.

SuperPositions - Class in org.biojava.nbio.structure.geometry

SuperPositions is a Class that provides static helper methods and an easy access to the whole family of SuperPosition algorithms.

SuperPositionSVD - Class in org.biojava.nbio.structure.geometry

A class that calculates the superposition between two sets of points using an SVD Matrix Decomposition.

SuperPositionSVD(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionSVD

Constructor for the SVD superposition algorithm.

surf - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor

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

SURFACE - org.biojava.nbio.structure.gui.RenderStyle

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, String, double) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo

SurvivalInfo(double, int, LinkedHashMap<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

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

Swap the row and columns returning a new worksheet

SYM_CHAIN_ID_SEPARATOR - Static variable in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder

The character separating the original chain identifier from the operator id.

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.

SYMMETRIC - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass

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

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.

SymmetryAxes.Axis - Class in org.biojava.nbio.structure.symmetry.internal

Represents an axis of symmetry

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.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

SymmetryPerceptionMethod - Enum in org.biojava.nbio.structure.symmetry.core

Method used for symmetry perception in the QuatSymmetryDetector.

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 symmetry (quaternary and internal) detection and result 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.

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

create a thread safe wrapper for working with this file

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.

Synonym - Class in org.biojava.nbio.ontology

Synonym() - Constructor for class org.biojava.nbio.ontology.Synonym

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

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

SystematicSolver(QuatSymmetrySubunits, 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 - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

T - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

T - org.biojava.nbio.structure.Element

Tritium

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

T0 - org.biojava.nbio.ronn.RonnConstraint.Threshold

T1 - org.biojava.nbio.ronn.RonnConstraint.Threshold

T2 - org.biojava.nbio.ronn.RonnConstraint.Threshold

T3 - org.biojava.nbio.ronn.RonnConstraint.Threshold

T4 - org.biojava.nbio.ronn.RonnConstraint.Threshold

T5 - org.biojava.nbio.ronn.RonnConstraint.Threshold

T6 - org.biojava.nbio.ronn.RonnConstraint.Threshold

T7 - org.biojava.nbio.ronn.RonnConstraint.Threshold

T8 - org.biojava.nbio.ronn.RonnConstraint.Threshold

T9 - org.biojava.nbio.ronn.RonnConstraint.Threshold

Ta - org.biojava.nbio.structure.Element

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(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 - 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.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.

Tabular - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum

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

Tb - org.biojava.nbio.structure.Element

tblastn - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum

tblastx - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum

Tc - org.biojava.nbio.structure.Element

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

TD1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

Te - org.biojava.nbio.structure.Element

techniquesToStringArray(Set<ExperimentalTechnique>) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Converts the set of experimental techniques to an array of strings.

tempBuffer - Variable in class org.biojava.nbio.ontology.obo.OboFileParser

TEMPLATE_LENTH - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

TEMPLATE_TYPE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

Term - Interface in org.biojava.nbio.ontology

A term in an ontology.

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

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

Simple in-memory implementation of an ontology term.

TertiaryBasePairParameters - Class in org.biojava.nbio.structure.basepairs

This class also finds the base pairing and base-pair step parameters but has a broader definition of a base pair so that non-canonical-WC base pairs will be detected and reported.

TertiaryBasePairParameters(Structure, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

TestDNANeedlemanWunsch - Class in demo

TestDNANeedlemanWunsch() - Constructor for class demo.TestDNANeedlemanWunsch

TETRAGONAL - org.biojava.nbio.structure.xtal.BravaisLattice

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 - org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum

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

Th - org.biojava.nbio.structure.Element

thread - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface

THREE - org.biojava.nbio.core.sequence.transcription.Frame

THREEBAR - org.biojava.nbio.structure.xtal.TransformType

THREEFOLD - org.biojava.nbio.structure.xtal.TransformType

THREEFOLDSCREW - org.biojava.nbio.structure.xtal.TransformType

Threshold(int) - Constructor for class org.biojava.nbio.ronn.ModelLoader.Threshold

THRESHOLD - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

THROW_EXCEPTION - org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

Throw a StructureException for obsolete entries.

Ti - org.biojava.nbio.structure.Element

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

Tl - org.biojava.nbio.structure.Element

Tm - org.biojava.nbio.structure.Element

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.geometry.CalcPoint

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. http://zhanglab.ccmb.med.umich.edu/I-TASSER/option4.html

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.

toAtomSite() - Static method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier

Collects AbstractCifFileSupplier.WrappedAtom instances into one AtomSite.

toBinary(Structure) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert a structure to BCIF format.

toBinaryFile(Structure, Path) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Write a structure to a BCIF file.

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.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(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toCE(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

toCIEXYZ(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace

toCifFile(Chain) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert Chain to CifFile

toCifFile(Structure) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert Structure to CifFile.

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

toExtendedId(String) - Static method in class org.biojava.nbio.structure.PdbId

Converts shortId to the PDB ID extended format.

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.

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

Convert this structure to its CIF representation.

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.

toMMCIF(Chain) - Static method in class org.biojava.nbio.structure.io.FileConvert

Convert a chain to its CIF representation.

toMultimodelStructure(MultipleAlignment, List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

TOOL - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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() - 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() - Method in class org.biojava.nbio.structure.io.FileConvert

Convert a structure into a PDB file.

toPDB() - Method in class org.biojava.nbio.structure.io.SSBondImpl

toPDB() - Method in class org.biojava.nbio.structure.PDBHeader

Return a PDB representation of the PDB Header

toPDB() - Method in interface org.biojava.nbio.structure.PDBRecord

Returns a PDB file like representation of this record.

toPDB() - Method in class org.biojava.nbio.structure.ResidueNumber

toPDB() - 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.

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.AtomImpl

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.DBRef

Append the PDB representation of this DBRef to the provided StringBuffer

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.io.SSBondImpl

Append the PDB representation of this SSBOND to the provided StringBuffer

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.PDBHeader

Appends a PDB representation of the PDB header to the provided StringBuffer

toPDB(StringBuffer) - Method in interface org.biojava.nbio.structure.PDBRecord

Appends a PDB file like representation of this record to the provided StringBuffer.

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

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(Atom, StringBuffer) - Static method in class org.biojava.nbio.structure.io.FileConvert

toPDB(Atom, StringBuffer, String) - Static method in class org.biojava.nbio.structure.io.FileConvert

Print ATOM record in the following syntax

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(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.

Topolgy - org.biojava.nbio.structure.cath.CathCategory

toPrettyAlignment(AFPChain, Atom[], Atom[], boolean, boolean) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

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. the angle between the normal vectors of the two plains a-b-c and b-c-d.

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

toShortId(String) - Static method in class org.biojava.nbio.structure.PdbId

Converts extendedId to the PDB ID short format.

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() - 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() - 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() - 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() - 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.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.quaternary.QsAlignResult

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.basepairs.BasePairParameters

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

toString() - Method in class org.biojava.nbio.structure.chem.ChemComp

toString() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

toString() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

toString() - Method in class org.biojava.nbio.structure.cluster.Subunit

toString() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

toString() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

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.GridCell

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.DatabasePDBRevRecord

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.ecod.EcodDomain

toString() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

toString() - Method in class org.biojava.nbio.structure.EntityInfo

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.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.Model

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.PdbId

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() - 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.Helix

toString() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

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.Stoichiometry

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() - 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

toString(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile

toString(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile

Returns a formatted view of the alignment profile.

toString(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Get a string representation of the MSA with a fixed width

toString(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns a formatted view of the alignment profile.

toString(String, String, String) - Method in class org.biojava.nbio.survival.cox.CoxInfo

toString(List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange

toString(Profile.StringFormat) - Method in class org.biojava.nbio.core.alignment.SimpleProfile

toString(Profile.StringFormat) - Method in interface org.biojava.nbio.core.alignment.template.Profile

Returns a formatted view of the alignment profile.

toString(LightweightProfile.StringFormat) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Support for different MSA formats

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.

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

toText(Chain) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert a chain to mmCIF format.

toText(Structure) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert a structure to mmCIF format.

toTextFile(Structure, Path) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Write a structure to a CIF file.

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.core.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() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

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

toXML(PrintWriter) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

convert Configuration to an XML file so it can be serialized

toXML(PrettyXMLWriter) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

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(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(AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

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, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

Convert an afpChain to a simple XML representation

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.

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(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(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

transform(Matrix4d, Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint

Transform all points with a 4x4 transformation matrix.

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. the vecmath library double-precision 4x4 rotation+translation matrix).

transform(Chain, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms a chain object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix).

transform(Group, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms a group object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix).

transform(Structure, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms a structure object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix).

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.

TRANSITION_METAL - org.biojava.nbio.structure.ElementType

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(Matrix4d, Vector3d) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder

translate(Point3i) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

translate(Vector3d) - Method in class org.biojava.nbio.structure.contact.BoundingBox

translate(Vector3d, Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint

Translate all points with a translation vector.

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. the vecmath library double-precision 3-d vector)

translate(Chain, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates a chain object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)

translate(Group, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates a group object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)

translate(Structure, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates a Structure object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)

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(Exception) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException

TranslationException(String) - 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

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

TreeType - Enum in org.biojava.nbio.phylo

The TreeType specifies the optimization criteria used to generate the tree.

TRICLINIC - org.biojava.nbio.structure.xtal.BravaisLattice

triggerMouseOverPosition(int, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener

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 - org.biojava.nbio.structure.xtal.BravaisLattice

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

trimStop(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

Imperfect code.

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

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.

tsiatis - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error

turn - org.biojava.nbio.structure.secstruc.SecStrucType

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

TWO - org.biojava.nbio.core.sequence.transcription.Frame

TWO_HITS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

TWOBAR - org.biojava.nbio.structure.xtal.TransformType

TwoBitArrayWorker(String, CompoundSet<C>) - 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(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

TwoBitFacade - Class in org.biojava.nbio.genome.parsers.twobit

A facade that makes it easier to work with a 2bit file.

TwoBitFacade(File) - Constructor for class org.biojava.nbio.genome.parsers.twobit.TwoBitFacade

Reads a genome from a locally stored .2bit file.

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(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(Sequence<C>) - 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.

TWOFOLD - org.biojava.nbio.structure.xtal.TransformType

TWOFOLDSCREW - org.biojava.nbio.structure.xtal.TransformType

type - Variable in enum org.biojava.nbio.genome.parsers.cytoband.StainType

type - Static variable in class org.biojava.nbio.structure.AminoAcidImpl

this is an Amino acid. type is "amino".

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

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.core.sequence.features.AbstractFeature

Sort features by type

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

U

U - org.biojava.nbio.structure.Element

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

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

Unary minus

uncompress(InputStream, OutputStream) - Static method in class org.biojava.nbio.core.util.UncompressInputStream

Read an input stream and uncompress it to an output stream.

uncompress(String, FileOutputStream) - Static method in class org.biojava.nbio.core.util.UncompressInputStream

Read a named file and uncompress it.

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

UNDEFINED - org.biojava.nbio.core.sequence.Strand

UNDEFINED - org.biojava.nbio.protmod.ModificationCategory

UNDEFINED - org.biojava.nbio.structure.BondType

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.

UNIPROT - org.biojava.nbio.core.sequence.DataSource

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

UnitCellBoundingBox - Class in org.biojava.nbio.structure.xtal

A class to contain the BoundingBoxes of all polymeric molecules in a full unit cell.

UnitCellBoundingBox(int, int) - Constructor for class org.biojava.nbio.structure.xtal.UnitCellBoundingBox

UnitQuaternions - Class in org.biojava.nbio.structure.geometry

UnitQuaternions is a static Class that contains methods for calculating and using unit quaternions.

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

Returns the unit vector of vector a .

unknown - org.biojava.nbio.structure.chem.PolymerType

if all else fails...

UNKNOWN - org.biojava.nbio.core.sequence.DataSource

UNKNOWN - org.biojava.nbio.core.sequence.DNASequence.DNAType

UNKNOWN - org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType

UNKNOWN - org.biojava.nbio.structure.ElementType

UNKNOWN - org.biojava.nbio.structure.io.StructureFiletype

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.

UNRELEASED - org.biojava.nbio.structure.PDBStatus.Status

UP_AC_PATTERN - Static variable in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

update(byte[], int, int) - Method in class org.biojava.nbio.core.util.CRC64Checksum

Updates the CRC-64 checksum with the specified array of bytes.

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

update(int, AlignerHelper.Subproblem, AlignerHelper.Last[][]) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut

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) - 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.

UPGMA - org.biojava.nbio.phylo.TreeConstructorType

Unweighted Pair-Group Method with Arithmetic mean

UPPER - org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection

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 - org.biojava.nbio.structure.align.client.StructureName.Source

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

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

A class that takes care about opening URLConnections and sets the proper timeouts

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

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

URLIdentifier(URL) - Constructor for class org.biojava.nbio.structure.URLIdentifier

urlPropertyNames - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo

useLocalTimeLimit(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

USER_INPUT - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

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.

useRNA - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

usual - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower

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 - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

V - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

V - org.biojava.nbio.structure.Element

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.io.fastq.FastqVariant

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.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.align.quaternary.QsRelation

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.chem.PolymerType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.chem.ResidueType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.cluster.SubunitClustererMethod

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.EntityType

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.geometry.MomentsOfInertia.SymmetryClass

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.StructureFiletype

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.symmetry.core.Stoichiometry.StringOverflowStrategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod

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.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.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.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.align.quaternary.QsRelation

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.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.chem.ResidueType

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.cluster.SubunitClustererMethod

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.EntityType

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.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.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() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

values() - Static method in enum org.biojava.nbio.structure.io.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.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.symmetry.core.Stoichiometry.StringOverflowStrategy

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.core.SymmetryPerceptionMethod

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.

VANDERWAALS - org.biojava.nbio.structure.BondType

Variable - Interface in org.biojava.nbio.ontology

VARIABLE_SEQUENCES - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection

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.multiple.mc.MultipleMcMain

Version history:

version - Static variable in class org.biojava.nbio.structure.symmetry.internal.CeSymm

Version History:

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_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_2_0_6 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_7 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_8 - 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_4_1_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory

VERSION_4_2_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

VOLUME - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE

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

W

W - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

W - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

W - org.biojava.nbio.structure.Element

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

warn(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter

warnEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter

WATER - org.biojava.nbio.structure.EntityType

Water

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

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

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

Weighted superposition.

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

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

WIREFRAME - org.biojava.nbio.structure.gui.RenderStyle

withDescription(String) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified description.

withQuality(String) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified quality scores.

withSequence(String) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified sequence.

withVariant(FastqVariant) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.

WORD_SIZE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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(String[][]) - Constructor for class org.biojava.nbio.survival.data.WorkSheet

WorkSheet(Collection<String>, Collection<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.

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

FlowLayout subclass that fully supports wrapping of components.

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

Constructs a new WrapLayout with a left alignment and a default 5-unit horizontal and vertical gap.

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

Constructs a new FlowLayout with the specified alignment and a default 5-unit horizontal and vertical gap.

WrapLayout(int, int, int) - Constructor for class org.biojava.nbio.structure.gui.WrapLayout

Creates a new flow layout manager with the indicated alignment and the indicated horizontal and vertical gaps.

WrappedAtom(int, String, String, Atom, int) - Constructor for class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom

Construct a new atoms.

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(int) - Method in class org.biojava.nbio.ronn.NullOutputStream

write(File, Iterable<Fastq>) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter

Write the specified FASTQ formatted sequences to the specified file.

write(File, Fastq...) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter

Write the specified FASTQ formatted sequences to the specified file.

write(OutputStream, Iterable<Fastq>) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter

Write the specified FASTQ formatted sequences to the specified output stream.

write(OutputStream, LinkedHashMap<String, ChromosomeSequence>) - Method in class org.biojava.nbio.genome.parsers.gff.GFF3Writer

Output gff3 format for a DNA Sequence

write(OutputStream, Fastq...) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter

Write the specified FASTQ formatted sequences to the specified output stream.

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(String) - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile

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

Write features in FeatureList to file.

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

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

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(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.FastaWriterHelper

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(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.FastaWriterHelper

Write collection of protein sequences to a stream

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(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.FastaWriterHelper

Write a sequence to OutputStream

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.

writeToFile(Structure, Path) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions

Write a Structure object to a file.

writeToOutputStream(Structure, OutputStream) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions

Write a Structure object to an OutputStream

WU_MANBER - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

WWW_BLAST_TYPE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

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

Xe - org.biojava.nbio.structure.Element

xmax - Variable in class org.biojava.nbio.structure.contact.BoundingBox

xmin - Variable in class org.biojava.nbio.structure.contact.BoundingBox

XML - org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum

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

Helper methods to simplify boilerplate XML parsing code for org.w3c.dom XML objects

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

XMLWriter - Interface in org.biojava.nbio.core.util

Simple interface for building XML documents.

XRAY_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique

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

XTALTRANSL - org.biojava.nbio.structure.xtal.TransformType

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 - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

Y - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

Y - org.biojava.nbio.structure.Element

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

Yb - org.biojava.nbio.structure.Element

ymax - Variable in class org.biojava.nbio.structure.contact.BoundingBox

ymin - Variable in class org.biojava.nbio.structure.contact.BoundingBox

Z

ZipChemCompProvider - Class in org.biojava.nbio.structure.chem

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.chem.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

Zn - org.biojava.nbio.structure.Element

Zr - org.biojava.nbio.structure.Element

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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