Index (biojava 7.1.4 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 and Interfaces|All Packages|Constant Field Values|Serialized Form

A

A - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
A - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
Absorbance_True - Enum constant in enum 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> - Class in org.biojava.nbio.core.sequence.template
AbstractCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
AbstractCompoundTranslator<F,T> - 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,C> - 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,C> - 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> - Class in org.biojava.nbio.core.sequence.template
AbstractNucleotideCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
AbstractPairwiseSequenceAligner<S,C> - 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,C> - 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> - 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 - Enum constant in enum 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 identifier.
AccessionID() - Constructor for class org.biojava.nbio.core.sequence.AccessionID: Default constructor sets id t empty string
AccessionID(String) - Constructor for class org.biojava.nbio.core.sequence.AccessionID: Creates an id with default DataSource.LOCAL source
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 - Enum constant in enum org.biojava.nbio.genome.parsers.cytoband.StainType
ACETYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
ACTINOID - Enum constant in enum 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(Map<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(Map<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(Map<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
addGmodGFF3GeneFeatures(Map<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: Sets the start codon sequence at given begin / end location.
addStopCodonSequence(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence: Sets the stop codon sequence at given begin / end location.
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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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,C> - 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,C> - 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
ALIGNMENTS - Enum constant in enum 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<K,V> 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 - Enum constant in enum org.biojava.nbio.structure.ElementType
ALKALINE_EARTH_METAL - Enum constant in enum org.biojava.nbio.structure.ElementType
ALL - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.core.alignment.template.Profile.StringFormat
ALN - Enum constant in enum org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
AlreadyExistsException - Exception Class 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 class org.biojava.nbio.ontology.AlreadyExistsException
AlreadyExistsException(String) - Constructor for exception class 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 - Enum constant in enum 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 - Enum constant in enum 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,C> - 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 class org.biojava.nbio.genome.io.fastq.IlluminaFastqWriter
append(T, Iterable<Fastq>) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqWriter
append(T, Iterable<Fastq>) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqWriter
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 class org.biojava.nbio.genome.io.fastq.IlluminaFastqWriter
append(T, Fastq...) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqWriter
append(T, Fastq...) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqWriter
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 - Enum constant in enum org.biojava.nbio.structure.Element
Architecture - Enum constant in enum 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> - Class in org.biojava.nbio.core.sequence.loader
ArrayListProxySequenceReader() - Constructor for class org.biojava.nbio.core.sequence.loader.ArrayListProxySequenceReader
ArrayListSequenceReader<C> - 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 - Enum constant in enum org.biojava.nbio.protmod.ModificationOccurrenceType
As - Enum constant in enum 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 - Exception Class in org.biojava.nbio.ontology.utils: An unchecked exception representing an Assertion failure.
AssertionFailure(String) - Constructor for exception class org.biojava.nbio.ontology.utils.AssertionFailure
AssertionFailure(String, Throwable) - Constructor for exception class org.biojava.nbio.ontology.utils.AssertionFailure
AssertionFailure(Throwable) - Constructor for exception class 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 - Enum constant in enum org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass
At - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
AU - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
Ba - Enum constant in enum org.biojava.nbio.structure.Element
BACKGROUND_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
BALL_AND_STICK - Enum constant in enum 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> - 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
batchSize(int) - Method in class org.biojava.nbio.core.sequence.io.FastaStreamer
BCIF - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
bend - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
BETWEEN_12 - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
BETWEEN_13 - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
BETWEEN_22 - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
BETWEEN_23 - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
BETWEEN_33 - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
Bi - Enum constant in enum org.biojava.nbio.structure.Element
BIO - Enum constant in enum 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> - 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> - 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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, Map<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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
BLOSUM50 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
Blosum62 - Static variable in class org.biojava.nbio.ronn.RonnConstraint
BLOSUM62 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
BLOSUM80 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
BLOSUM90 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
BRANCHED - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.survival.cox.CoxMethod
bridge - Enum constant in enum 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<j.
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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
C - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
C - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
CA_AND_SIDE_CHAIN_ANGLE_SCORING - Enum constant in enum 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 - Enum constant in enum 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,C> - 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,C> - 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,C> - 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
CDD_SEARCH - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
claFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
Class - Enum constant in enum org.biojava.nbio.structure.cath.CathCategory
Class - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.core.alignment.template.Profile.StringFormat
CLUSTALW - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
CMD - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
Co - Enum constant in enum 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 - Enum constant in enum 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> - 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
Compound - Interface in org.biojava.nbio.core.sequence.template
COMPOUND - Enum constant in enum org.biojava.nbio.core.alignment.template.AlignedSequence.Step
CompoundNotFoundException - Exception Class in org.biojava.nbio.core.exceptions
CompoundNotFoundException(String) - Constructor for exception class 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> - 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,T> - 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 Class in org.biojava.nbio.structure.align.util
ConfigurationException() - Constructor for exception class org.biojava.nbio.structure.align.util.ConfigurationException
ConfigurationException(String) - Constructor for exception class org.biojava.nbio.structure.align.util.ConfigurationException: Constructs a ConfigurationException object.
ConfigurationException(String, Throwable) - Constructor for exception class org.biojava.nbio.structure.align.util.ConfigurationException
ConfigurationException(Throwable) - Constructor for exception class 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 - Enum constant in enum 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
consumeEm3dReconstruction(Em3dReconstruction) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume Electron Microscopy 3D reconstruction data
consumeEm3dReconstruction(Em3dReconstruction) - 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(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>, 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 - Enum constant in enum 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 - Enum constant in enum 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(ProteinSequence) - Method in class org.biojava.nbio.core.sequence.io.FastaStreamer: Create the sequence with the information from the header.
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
createValidationFiles(URLConnection, File, URL, FileDownloadUtils.Hash) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Creates validation files beside a file to be downloaded.
Whenever possible, for a file.ext file, it creates file.ext.size and file.hash_XXXX in the same folder where file.ext exists (XXXX may be DM5, SHA1, or SHA256).
createValidationFiles(URL, File, URL, FileDownloadUtils.Hash) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Creates validation files beside a file to be downloaded.
Whenever possible, for a file.ext file, it creates file.ext.size and file.hash for in the same folder where file.ext exists.
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 - Enum constant in enum org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_2 - Enum constant in enum org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_3 - Enum constant in enum org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_4 - Enum constant in enum org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_5 - Enum constant in enum org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_6 - Enum constant in enum org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_7 - Enum constant in enum org.biojava.nbio.protmod.ModificationCategory
CROSS_LINK_8_OR_LARGE - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
CS_HSV - Static variable in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace: The HSV color space
Cu - Enum constant in enum org.biojava.nbio.structure.Element
CUBIC - Enum constant in enum org.biojava.nbio.structure.xtal.BravaisLattice
CURATED - Enum constant in enum org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
CURRENT - Enum constant in enum org.biojava.nbio.structure.PDBStatus.Status
CUSTOM - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy: Cycle through the alphabet (e.g., ...xyzABC...)
cyclicPeptide - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
D - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
D - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
DATABASE_PREFIX - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
DATABASE_SORT - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
dBetaPeptideCGammaLinking - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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
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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
DESCRIPTIONS - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.survival.cox.ResidualsCoxph.Type
dfbetas - Enum constant in enum org.biojava.nbio.survival.cox.ResidualsCoxph.Type
dGammaPeptideCDeltaLinking - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
dna5PrimeTerminus - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
dnarna - Enum constant in enum 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
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 - Enum constant in enum org.biojava.nbio.structure.scop.ScopCategory
Domain() - Constructor for class org.biojava.nbio.structure.domain.pdp.Domain
DomainCounter - Enum constant in enum 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 - Enum constant in enum 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: Downloads the SCOP installation file +/- its validation metadata files.
downloadHieFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
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 - Enum constant in enum org.biojava.nbio.structure.chem.PolymerType: polypeptide(D)
dPeptideAminoTerminus - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
dPeptideCarboxyTerminus - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
dPeptideLinking - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
dSaccharide14and14linking - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
dSaccharide14and16linking - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
DYNAMIC - Enum constant in enum org.biojava.nbio.alignment.template.GapPenalty.Type

E

E - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
E - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
E - Static variable in class org.biojava.nbio.aaproperties.Constraints
each() - Method in class org.biojava.nbio.core.sequence.io.FastaStreamer: Enable iteration through the proteins in the file using syntax such as:
ECOD - Enum constant in enum 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> - Interface in org.biojava.nbio.core.sequence.edits: Interface for carrying out edit operations on a Sequence.
Edit.AbstractEdit<C> - 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> - Class in org.biojava.nbio.core.sequence.edits: Implementation which allows for the deletion of bases from a Sequence
Edit.Insert<C> - 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> - 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.ExperimentalTechnique
ELECTRON_MICROSCOPY - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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
Example - Search tag in class org.biojava.nbio.ontology.io.OboParser: Section
Example - Search tag in class org.biojava.nbio.structure.align.StructurePairAligner: Section
Example - Search tag in class org.biojava.nbio.structure.io.PDBFileParser: Section
Example - Search tag in class org.biojava.nbio.structure.io.PDBFileReader: Section
Example: - Search tag in org.biojava.nbio.structure.align.util.AlignmentTools.guessSequentialAlignment(Map<Integer, Integer>, boolean): Section
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 should 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
EXPECT_HIGH - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
EXPECT_LOW - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
ExtinctionCoefficient_True - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
F - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
F - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.scop.ScopCategory
FASTA - Enum constant in enum org.biojava.nbio.core.alignment.template.Profile.StringFormat
FASTA - Enum constant in enum 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,C> - Interface in org.biojava.nbio.core.sequence.io.template
FastaReader<S,C> - 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
FastaStreamer - Class in org.biojava.nbio.core.sequence.io: Read from a FASTA file (or gzipped FASTA file) and create a Java stream of ProteinSequence objects for use in a functional programming paradigm.
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,C> - 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 - Enum constant in enum org.biojava.nbio.genome.io.fastq.FastqVariant: Illumina FASTQ sequence format variant.
FASTQ_SANGER - Enum constant in enum org.biojava.nbio.genome.io.fastq.FastqVariant: Sanger FASTQ sequence format variant.
FASTQ_SOLEXA - Enum constant in enum 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 - Enum constant in enum 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,C> - 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,C> - 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> - 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 - Enum constant in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior: Fetch the most recent version of the PDB entry.
FETCH_FILES - Enum constant in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior: Fetch missing files from the server.
FETCH_IF_OUTDATED - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior: Fetch the obsolete entry from the PDB archives.
FETCH_REMEDIATED - Enum constant in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior: Fetch missing files from the server.
fh2 - Enum constant in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
FIBER_DIFFRACTION - Enum constant in enum 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 - Enum constant in enum 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
FileDownloadUtils.Hash - Enum in org.biojava.nbio.core.util
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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
first_cut - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
FIRST_QUERY_NUM - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
FIRST25 - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
FIRST50 - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
FIRST75 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
FlatQueryAnchoredNoIdentities - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
flemingHarrington - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.scop.ScopCategory
FORCE_DOWNLOAD - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
FORMAT_OBJECT - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.scop.Astral.AstralSet
FORTY_175A - Enum constant in enum org.biojava.nbio.structure.scop.Astral.AstralSet
FORTY_175B - Enum constant in enum org.biojava.nbio.structure.scop.Astral.AstralSet
FORTY_201 - Enum constant in enum org.biojava.nbio.structure.scop.Astral.AstralSet
FORTY_202 - Enum constant in enum org.biojava.nbio.structure.scop.Astral.AstralSet
FORTY_203 - Enum constant in enum org.biojava.nbio.structure.scop.Astral.AstralSet
FOURBAR - Enum constant in enum 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> - 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> - Class in org.biojava.nbio.core.sequence.storage: A four bit per compound implementation of the bit array worker code.
FOURFOLD - Enum constant in enum org.biojava.nbio.structure.xtal.TransformType
FOURFOLDSCREW - Enum constant in enum org.biojava.nbio.structure.xtal.TransformType
Fr - Enum constant in enum 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,C> - 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,C> - 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,C> - 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,C> - 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)
from(File) - Static method in class org.biojava.nbio.core.sequence.io.FastaStreamer
from(Path) - Static method in class org.biojava.nbio.core.sequence.io.FastaStreamer
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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
G - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
G - Static variable in class org.biojava.nbio.aaproperties.Constraints
Ga - Enum constant in enum org.biojava.nbio.structure.Element
GAP - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.core.alignment.template.Profile.StringFormat
GCG - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
Ge - Enum constant in enum org.biojava.nbio.structure.Element
GENBANK - Enum constant in enum 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,C> - Interface in org.biojava.nbio.core.sequence.io.template
GenbankProxySequenceReader<C> - 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,C> - 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,C> - 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,C> - 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 - Enum constant in enum 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,C> - 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,C> - 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,C> - Class in org.biojava.nbio.core.sequence.io
GenericGenbankHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
GenericGenbankHeaderFormat(boolean) - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
GenericGenbankHeaderFormat(String) - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
GenericGenbankHeaderParser<S,C> - Class in org.biojava.nbio.core.sequence.io
GenericGenbankHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
GenericInsdcHeaderFormat<S,C> - 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: Deprecated.
GeneSequence(ChromosomeSequence, AccessionID, 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
GENINFO - Enum constant in enum 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.io.GenericGenbankHeaderParser
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
getAromaticity(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties: An adaptor method to return the aromaticity value of sequence.
getAromaticity(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties: Calculates the aromaticity value of a protein according to Lobry, 1994.
getAromaticity(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
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.
getBatchSize() - Method in class org.biojava.nbio.core.sequence.io.FastaStreamer
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(Map<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.io.GenericGenbankHeaderParser
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 position.
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.io.GenericGenbankHeaderParser
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
getEquivalentResidues(MultipleAlignment, boolean) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools: Convert an MSA into a matrix of equivalent residues.
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.io.FastaStreamer
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() is not unique, keeps the alternative id, e.g.
getIdentifier() - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
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.GenericGenbankHeaderParser
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: The number of aligned residues in the final alignment.
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 class org.biojava.nbio.core.sequence.io.FastaStreamer
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 ProteinSequence 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.io.GenericGenbankHeaderParser
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: Returns the resolution (or effective resolution) of the experiment.
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<S extends Sequence<C>,C extends Compound>.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
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<NucleotideCompound>.
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.
getSequenceCreator() - Method in class org.biojava.nbio.core.sequence.io.FastaStreamer
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
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.core.sequence.io.GenericGenbankHeaderParser
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 - Enum constant in enum org.biojava.nbio.structure.xtal.TransformType
GLOBAL - Enum constant in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
GLOBAL - Enum constant in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
GLOBAL - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
GLOBAL_IDENTITIES - Enum constant in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
GLOBAL_LINEAR_SPACE - Enum constant in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
GLOBAL_LINEAR_SPACE - Enum constant in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
GLOBAL_SIMILARITIES - Enum constant in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
glycine - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
gneg - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.genome.parsers.cytoband.StainType
gpos25 - Enum constant in enum org.biojava.nbio.genome.parsers.cytoband.StainType
gpos50 - Enum constant in enum org.biojava.nbio.genome.parsers.cytoband.StainType
gpos75 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
GRAPH_COMPONENT - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING
group3 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
GROUP3 - Enum constant in enum 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,C> - 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,C> - 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,C> - 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
H - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
H - Enum constant in enum org.biojava.nbio.structure.Element
H - Static variable in class org.biojava.nbio.aaproperties.Constraints
HALOGEN - Enum constant in enum 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
handleResolutionLine(String, Pattern) - Method in class org.biojava.nbio.structure.io.PDBFileParser
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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.secstruc.SecStrucType
helix4 - Enum constant in enum org.biojava.nbio.structure.secstruc.SecStrucType
helix5 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.xtal.BravaisLattice
hexPropertyNames - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo
Hf - Enum constant in enum org.biojava.nbio.structure.Element
Hg - Enum constant in enum 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,C> - 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
Homology - Enum constant in enum org.biojava.nbio.structure.cath.CathCategory
HOMSTRAD - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
Hsp<S,C> - 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum
HYDROPHOBIC - Enum constant in enum org.biojava.nbio.structure.BondType
HYDROPHOBICITY - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.protmod.ModificationOccurrenceType

I

I - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
I - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
I - Enum constant in enum org.biojava.nbio.structure.Element
I - Static variable in class org.biojava.nbio.aaproperties.Constraints
I_THRESH - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
I_THRESH - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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.
initSequenceStorage(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 Class 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 class org.biojava.nbio.ontology.InvalidTermException
InvalidTermException(String) - Constructor for exception class org.biojava.nbio.ontology.InvalidTermException
InvalidTermException(String, Throwable) - Constructor for exception class org.biojava.nbio.ontology.InvalidTermException
InvalidTermException(Throwable) - Constructor for exception class 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 - Enum constant in enum 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(BufferedReader, ReaderProcessor).
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 - Enum constant in enum 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 - Enum constant in enum 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> - 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<Sequence<C extends Compound>>.
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<C extends Compound> 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
K - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
K - Enum constant in enum org.biojava.nbio.structure.Element
K - Static variable in class org.biojava.nbio.aaproperties.Constraints
kaplanMeier - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element

L

L - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
L - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
L - Static variable in class org.biojava.nbio.aaproperties.Constraints
La - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
LCASE_MASK - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
lDNALinking - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
left - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
LEFT - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior: Try to minimize memory consumption, at the price of slower speed when accessing atoms by name
lGammaPeptideCDeltaLinking - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
Li - Enum constant in enum 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,C> - 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.alignment.template.GapPenalty.Type
LINEAR - Enum constant in enum 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
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
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 - Enum constant in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
LOCAL - Enum constant in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
LOCAL - Enum constant in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
LOCAL - Enum constant in enum org.biojava.nbio.core.sequence.DataSource
LOCAL_CONSENSUS - Enum constant in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
LOCAL_IDENTITIES - Enum constant in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
LOCAL_LINEAR_SPACE - Enum constant in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
LOCAL_LINEAR_SPACE - Enum constant in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
LOCAL_ONLY - Enum constant in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior: Never fetch from the server; Throw errors for missing files
LOCAL_SIMILARITIES - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
log_log - Enum constant in enum 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 - Enum constant in enum 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
lp2 - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
lPeptideAminoTerminus - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
lPeptideCarboxyTerminus - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
lPeptideLinking - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
lpolysaccharide - Enum constant in enum org.biojava.nbio.structure.chem.PolymerType: polysaccharide(L)
Lr - Enum constant in enum org.biojava.nbio.structure.Element
lRNALinking - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
lSaccharide - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
lSaccharide14and14linking - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
lSaccharide14and16linking - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
lu() - Method in class org.biojava.nbio.structure.jama.Matrix: LU Decomposition
Lu - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
M - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
M - Static variable in class org.biojava.nbio.aaproperties.Constraints
MACROLIDE - Enum constant in enum 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.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.UncompressFile: Reads a file, uncompresses it, and sends the result to stdout.
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.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.LocIterator: Deprecated.
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
main(String[]) - Static method in class org.biojava.nbio.genome.query.BlastXMLQuery
main(String[]) - Static method in class org.biojava.nbio.genome.query.OutputHitsGFF
main(String[]) - Static method in class org.biojava.nbio.genome.uniprot.UniprotToFasta
main(String[]) - Static method in class org.biojava.nbio.genome.util.SplitFasta
main(String[]) - Static method in class org.biojava.nbio.ontology.App
main(String[]) - Static method in class org.biojava.nbio.phosphosite.Dataset
main(String[]) - Static method in class org.biojava.nbio.ronn.ModelLoader
main(String[]) - Static method in class org.biojava.nbio.ronn.ORonn
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeMain: Example Parameters: -pdbFilePath /tmp -autoFetch -printCE -pdb1 1cnv -pdb2 3cna
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
main(String[]) - Static method in class org.biojava.nbio.structure.align.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
MANUAL - Enum constant in enum org.biojava.nbio.structure.cluster.SubunitClustererMethod: Some other method was used when clustering.
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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
MASK_COLOR - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
MatrixAligner<S,C> - 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
MD5 - Enum constant in enum org.biojava.nbio.core.util.FileDownloadUtils.Hash
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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
MEGABLAST - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
MemoryMonitor - Class in org.biojava.nbio.structure.align.gui: Tracks Memory allocated and 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.ElementType
METHYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
Mg - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
MINIMINAL_SEQUENCES - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.core.sequence.DNASequence.DNAType
ML - Enum constant in enum org.biojava.nbio.phylo.TreeType: Maximum Likelihood Tree
MMCIF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
MMTF - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
Mo - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.core.alignment.template.Profile.StringFormat
MSF - Enum constant in enum 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,C> - 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,C> - Interface in org.biojava.nbio.core.alignment.template: Defines a mutable (editable) data structure for an AlignedSequence.
MutableProfile<S,C> - Interface in org.biojava.nbio.core.alignment.template: Defines a mutable (editable) data structure for a Profile.
MutableProfilePair<S,C> - Interface in org.biojava.nbio.core.alignment.template: Defines a mutable (editable) data structure for a ProfilePair.
MutableSequencePair<S,C> - 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
N - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
N - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.protmod.ModificationOccurrenceType
Nb - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.core.sequence.DataSource
NCBI - Enum constant in enum org.biojava.nbio.core.sequence.DataSource
NCBI_GI - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
Ne - Enum constant in enum org.biojava.nbio.structure.Element
NeedlemanWunsch<S,C> - 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 - Enum constant in enum org.biojava.nbio.core.sequence.Strand
NetCharge_pH_7 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
NEUTRON_DIFFRACTION - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
NINETY_FIVE_175 - Enum constant in enum org.biojava.nbio.structure.scop.Astral.AstralSet
NINETY_FIVE_175A - Enum constant in enum org.biojava.nbio.structure.scop.Astral.AstralSet
NINETY_FIVE_175B - Enum constant in enum org.biojava.nbio.structure.scop.Astral.AstralSet
NINETY_FIVE_201 - Enum constant in enum org.biojava.nbio.structure.scop.Astral.AstralSet
NINETY_FIVE_202 - Enum constant in enum org.biojava.nbio.structure.scop.Astral.AstralSet
NINETY_FIVE_203 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
NO_ROTATION - Enum constant in enum org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod
NOBLE_GAS - Enum constant in enum org.biojava.nbio.structure.ElementType
nodeListFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
NOHEADER - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
NONPOLYMER - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
NUM_OVERVIEW - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.core.sequence.transcription.Frame
ONEBAR - Enum constant in enum 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 Class in org.biojava.nbio.ontology: Thrown to indicate an error in an Ontology object
OntologyException() - Constructor for exception class org.biojava.nbio.ontology.OntologyException
OntologyException(String) - Constructor for exception class org.biojava.nbio.ontology.OntologyException
OntologyException(String, Throwable) - Constructor for exception class org.biojava.nbio.ontology.OntologyException
OntologyException(Throwable) - Constructor for exception class 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 - Enum constant in enum 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: Tools for loading and saving ontologies.
org.biojava.nbio.ontology.obo - package org.biojava.nbio.ontology.obo
org.biojava.nbio.ontology.utils - package org.biojava.nbio.ontology.utils
org.biojava.nbio.phosphosite - package org.biojava.nbio.phosphosite
org.biojava.nbio.phylo - package org.biojava.nbio.phylo
org.biojava.nbio.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: Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.align - package org.biojava.nbio.structure.align: Classes for the alignment of structures.
org.biojava.nbio.structure.align.ce - package org.biojava.nbio.structure.align.ce: Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.client - package org.biojava.nbio.structure.align.client: This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.nbio.structure.align.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: A few convenience classes to view protein structures with Jmol (if it is on the classpath), to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
org.biojava.nbio.structure.gui.events - package org.biojava.nbio.structure.gui.events: Some event classes for the protein structure GUIs.
org.biojava.nbio.structure.gui.util - package org.biojava.nbio.structure.gui.util: Some utility classes for the protein structure GUIs.
org.biojava.nbio.structure.gui.util.color - package org.biojava.nbio.structure.gui.util.color
org.biojava.nbio.structure.io - package org.biojava.nbio.structure.io: Input and Output of Structures
org.biojava.nbio.structure.io.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 - Enum constant in enum org.biojava.nbio.structure.cath.CathCategory
ORTHORHOMBIC - Enum constant in enum org.biojava.nbio.structure.xtal.BravaisLattice
Os - Enum constant in enum org.biojava.nbio.structure.Element
OTHER_ADVANCED - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
OTHER_NONMETAL - Enum constant in enum org.biojava.nbio.structure.ElementType
otherChemComp - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
Other Features - Search tag in package org.biojava.nbio.structure: Section
otherPolymer - Enum constant in enum org.biojava.nbio.structure.chem.PolymerType: other
OUTER - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
P - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
P - Enum constant in enum 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 - Enum constant in enum 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,C> - 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
PAIRWISE_ALIGN - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
PairwiseSequenceAligner<S,C> - Interface in org.biojava.nbio.alignment.template: Defines an Aligner for a pair of Sequences.
PairwiseSequenceScorer<S,C> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes a score for a pair of sequences.
PAM250 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
PAM30 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
PAM70 - Enum constant in enum 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 - Enum constant in enum 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 class org.biojava.nbio.genome.io.fastq.IlluminaFastqReader
parse(Readable, ParseListener) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqReader
parse(Readable, ParseListener) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqReader
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.
Parse mmCif files - Search tag in package org.biojava.nbio.structure: Section
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.
Parse PDB files - Search tag in package org.biojava.nbio.structure: Section
ParserException - Exception Class in org.biojava.nbio.core.exceptions: General abstraction of different parsing errors
ParserException(Exception) - Constructor for exception class org.biojava.nbio.core.exceptions.ParserException
ParserException(String) - Constructor for exception class org.biojava.nbio.core.exceptions.ParserException
ParserException(String, Exception) - Constructor for exception class 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 - Enum constant in enum org.biojava.nbio.phylo.TreeType: Parsimony Tree
Parsing - Search tag in class org.biojava.nbio.structure.io.PDBFileParser: Section
PART_OF - Static variable in class org.biojava.nbio.ontology.OntoTools
PARTIAL_COMPLETE - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.alignment.Alignments.RefinerType
PARTITION_SINGLE_ALL - Enum constant in enum org.biojava.nbio.alignment.Alignments.RefinerType
PARTITION_TREE - Enum constant in enum org.biojava.nbio.alignment.Alignments.RefinerType
PARTITION_TREE_ALL - Enum constant in enum org.biojava.nbio.alignment.Alignments.RefinerType
PartitionRefiner<S,C> - 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
Pd - Enum constant in enum org.biojava.nbio.structure.Element
PDB - Enum constant in enum org.biojava.nbio.structure.align.client.StructureName.Source
PDB - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.core.sequence.DataSource
PDB2 - Enum constant in enum 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 - Enum constant in enum 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 Class in org.biojava.nbio.structure.io: An exception during the parsing of a PDB file.
PDBParseException(String) - Constructor for exception class org.biojava.nbio.structure.io.PDBParseException: Constructs a PDBParseException object.
PDBParseException(String, Throwable) - Constructor for exception class org.biojava.nbio.structure.io.PDBParseException: Constructs a PDBParseException object.
PDBParseException(Throwable) - Constructor for exception class 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 - Enum constant in enum org.biojava.nbio.core.alignment.template.Profile.StringFormat
PDBWEB - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.chem.PolymerType: polypeptide(L)
peptideLike - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
peptideNucleicAcid - Enum constant in enum 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 - Enum constant in enum 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.
peto - Enum constant in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower
PFAM - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
PlainFastaHeaderParser<S,C> - 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 - Enum constant in enum org.biojava.nbio.structure.BondType
PLASMID - Enum constant in enum org.biojava.nbio.core.sequence.DNASequence.DNAType
PLASTID - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
Po - Enum constant in enum 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> - 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: d = -log(1 - D) The gapped positons in the alignment are ignored in the calculation.
POLARITY - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
POLARIZABILITY - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
Polyhedron - Interface in org.biojava.nbio.structure.symmetry.geometry
POLYMER - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.core.sequence.Strand
POST_TRANSITION_METAL - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
PredictDisorder - Class in demo
PredictDisorder() - Constructor for class demo.PredictDisorder
PREDICTED - Enum constant in enum 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 - Enum constant in enum 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,C> - 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,C> - 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,C> - Interface in org.biojava.nbio.alignment.template: Defines an Aligner for a pair of profiles.
ProfileProfileScorer<S,C> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes a score for a pairing of alignment profiles.
ProfileView<S,C> - Interface in org.biojava.nbio.core.alignment.template: Defines a data structure for a view of sequence alignment.
PROGRAM - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
PROLATE - Enum constant in enum 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> - Interface in org.biojava.nbio.core.sequence.template
PSSM - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
Pt - Enum constant in enum org.biojava.nbio.structure.Element
Pu - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.scop.ScopCategory

Q

Q - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
Q - Enum constant in enum 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,C> - 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,C> - 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
QUERY_BELIEVE_DEFLINE - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
QUERY_FROM - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
QUERY_TO - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
QueryAnchored - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
QueryAnchoredNoIdentities - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
QueryIndexComparator() - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator
QUESTIONMARK - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
R - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
R - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
Re - Enum constant in enum 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 class org.biojava.nbio.genome.io.fastq.IlluminaFastqReader
read(File) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqReader
read(File) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqReader
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 class org.biojava.nbio.genome.io.fastq.IlluminaFastqReader
read(InputStream) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqReader
read(InputStream) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqReader
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 class org.biojava.nbio.genome.io.fastq.IlluminaFastqReader
read(URL) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqReader
read(URL) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqReader
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
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 Class in org.biojava.nbio.structure.symmetry.internal: Refinement of the self-alignment failed.
RefinerFailedException() - Constructor for exception class org.biojava.nbio.structure.symmetry.internal.RefinerFailedException
RefinerFailedException(String) - Constructor for exception class org.biojava.nbio.structure.symmetry.internal.RefinerFailedException
RefinerFailedException(String, Throwable) - Constructor for exception class org.biojava.nbio.structure.symmetry.internal.RefinerFailedException
RefinerFailedException(Throwable) - Constructor for exception class 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.alignment.Alignments.RefinerType
RESCORE_SIMILARITIES - Enum constant in enum org.biojava.nbio.alignment.Alignments.RefinerType
RescoreRefiner<S,C> - 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, Map<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 - Enum constant in enum org.biojava.nbio.core.sequence.transcription.Frame
REVERSED_THREE - Enum constant in enum org.biojava.nbio.core.sequence.transcription.Frame
REVERSED_TWO - Enum constant in enum org.biojava.nbio.core.sequence.transcription.Frame
ReversedSequenceView<C> - 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 - Enum constant in enum org.biojava.nbio.structure.Element
RIBBON - Enum constant in enum org.biojava.nbio.structure.gui.RenderStyle
RID - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
right - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
RIGHT - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
rna - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.chem.ResidueType
rna5PrimeTerminus - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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: See http://en.wikipedia.org/wiki/Rotation_group_SO(3)
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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
S - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
S - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
Sc - Enum constant in enum 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 - Enum constant in enum 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 Class in org.biojava.nbio.structure.scop: Indicates that an I/O error occurred with SCOP lazy initialization.
ScopIOException() - Constructor for exception class org.biojava.nbio.structure.scop.ScopIOException
ScopIOException(String) - Constructor for exception class org.biojava.nbio.structure.scop.ScopIOException
ScopIOException(String, Throwable) - Constructor for exception class org.biojava.nbio.structure.scop.ScopIOException
ScopIOException(Throwable) - Constructor for exception class 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 and 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> - Interface in org.biojava.nbio.core.sequence.template: Main interface for defining a collection of Compounds and accessing them using biological indexes
SEQUENCE - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
SEQUENCE_FUNCTION - Enum constant in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
SEQUENCE_FUNCTION - Enum constant in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
SEQUENCE_STRUCTURE - Enum constant in enum 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> - 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 in ascending order of bioBegin property.
SequenceComparator() - Constructor for class org.biojava.nbio.core.sequence.SequenceComparator
SequenceCreatorInterface<C> - 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 - Enum constant in enum org.biojava.nbio.structure.cath.CathCategory
SequenceFileProxyLoader<C> - 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,C> - 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,C> - 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> - 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,C> - 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> - 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> - 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> - 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 class org.biojava.nbio.structure.io.PDBParseException
serialVersionUID - Static variable in exception class 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, List) - 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(List<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 Structure.setPdbId(PdbId)
setPDBCode(String) - Method in class org.biojava.nbio.structure.StructureImpl: Deprecated.
use StructureImpl.setPdbId(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(Map<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(Map<String, Object>) - Method in interface org.biojava.nbio.structure.Group: Properties of this amino acid.
setProperties(Map<String, Object>) - Method in class org.biojava.nbio.structure.HetatomImpl: Properties of this amino acid.
setProperties(Map<String, String>) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
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
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: The last accession passed to this routine will always be the one used.
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
SHA1 - Enum constant in enum org.biojava.nbio.core.util.FileDownloadUtils.Hash
SHA256 - Enum constant in enum org.biojava.nbio.core.util.FileDownloadUtils.Hash
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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
SHORTER - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
SHOW_LINKOUT - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
SHOW_OVERVIEW - Enum constant in enum 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: Deprecated.
Replace with
showMultipleAlignmentPanel(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 Sequence 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 - Enum constant in enum org.biojava.nbio.structure.Element
SIDE_CHAIN_ANGLE_SCORING - Enum constant in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
SIDE_CHAIN_SCORING - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.alignment.Alignments.PairInProfileScorerType
SIMILARITY_COLOR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
SimpleAlignedSequence<S,C> - 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,C> - 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,C> - 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,C> - 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,C> - 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> - 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.
SingleCompoundSequenceReader<C> - 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 - Enum constant in enum org.biojava.nbio.structure.xtal.TransformType
SIXFOLD - Enum constant in enum org.biojava.nbio.structure.xtal.TransformType
SIXFOLDSCREW - Enum constant in enum 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 - Enum constant in enum 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,C> - 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 - Enum constant in enum org.biojava.nbio.structure.Element
SoftHashMap<K,V> - Class in org.biojava.nbio.core.util: An 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 - Enum constant in enum org.biojava.nbio.structure.ExperimentalTechnique
SOLUTION_NMR - Enum constant in enum org.biojava.nbio.structure.ExperimentalTechnique
SOLUTION_SCATTERING - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.scop.ScopCategory
SPHERES - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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,C> - 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 - Enum constant in enum 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() - Method in class org.biojava.nbio.core.sequence.io.FastaStreamer: Create a stream of protein sequences from the contents of the path
stream(Readable, StreamListener) - Method in class org.biojava.nbio.genome.io.fastq.IlluminaFastqReader
stream(Readable, StreamListener) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqReader
stream(Readable, StreamListener) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqReader
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> - 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 - Enum constant in enum 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 Class in org.biojava.nbio.structure: An exception during the parsing of a PDB file.
StructureException(String) - Constructor for exception class org.biojava.nbio.structure.StructureException: Constructs a StructureException object.
StructureException(String, Throwable) - Constructor for exception class org.biojava.nbio.structure.StructureException: Constructs a StructureException object.
StructureException(Throwable) - Constructor for exception class 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.alignment.routines.AlignerHelper.Last
substitutionMatrix - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
SubstitutionMatrix<C> - 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,C> - 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(List<Subunit>, List<List<Integer>>) - Constructor for class org.biojava.nbio.structure.cluster.SubunitCluster: Create the cluster manually by specifying subunits and the equivalent residues
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 - Enum constant in enum 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 - Enum constant in enum 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,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 - Enum constant in enum 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 MultipleAlignment 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
T - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
T - Enum constant in enum org.biojava.nbio.structure.Element: Tritium
T - Static variable in class org.biojava.nbio.aaproperties.Constraints
T0 - Enum constant in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
T1 - Enum constant in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
T2 - Enum constant in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
T3 - Enum constant in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
T4 - Enum constant in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
T5 - Enum constant in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
T6 - Enum constant in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
T7 - Enum constant in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
T8 - Enum constant in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
T9 - Enum constant in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
Ta - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
tblastn - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
tblastx - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
Tc - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
TEMPLATE_TYPE - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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,C> - 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 - Enum constant in enum org.biojava.nbio.structure.Element
The Structure object - Search tag in package org.biojava.nbio.structure: Section
thread - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
THREE - Enum constant in enum org.biojava.nbio.core.sequence.transcription.Frame
THREEBAR - Enum constant in enum org.biojava.nbio.structure.xtal.TransformType
THREEFOLD - Enum constant in enum org.biojava.nbio.structure.xtal.TransformType
THREEFOLDSCREW - Enum constant in enum org.biojava.nbio.structure.xtal.TransformType
Threshold(int) - Constructor for class org.biojava.nbio.ronn.ModelLoader.Threshold
THRESHOLD - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
THROW_EXCEPTION - Enum constant in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior: Throw a StructureException for obsolete entries.
Ti - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
Tm - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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.Compound
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 TranscriptionEngine.
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: Deprecated.
TranscriptSequence(GeneSequence, AccessionID, 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 - Enum constant in enum 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 Class in org.biojava.nbio.core.exceptions: Thrown from AbstractCompundTranslator
TranslationException(Exception) - Constructor for exception class org.biojava.nbio.core.exceptions.TranslationException
TranslationException(String) - Constructor for exception class org.biojava.nbio.core.exceptions.TranslationException
TranslationException(String, Exception) - Constructor for exception class 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error
turn - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.core.sequence.transcription.Frame
TWO_HITS - Enum constant in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
TWOBAR - Enum constant in enum 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> - 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> - Class in org.biojava.nbio.core.sequence.storage: Extension of the BitArrayWorker which provides the 2bit implementation code.
TWOFOLD - Enum constant in enum org.biojava.nbio.structure.xtal.TransformType
TWOFOLDSCREW - Enum constant in enum 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 - Enum constant in enum 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.
UncompressFile - Class in demo: Uncompresses a single tarred or zipped file, writing output to stdandard out
UncompressFile() - Constructor for class demo.UncompressFile
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 - Enum constant in enum org.biojava.nbio.core.sequence.Strand
UNDEFINED - Enum constant in enum org.biojava.nbio.protmod.ModificationCategory
UNDEFINED - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.core.sequence.DataSource
uniProtEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
UniprotProxySequenceReader<C> - 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 - Enum constant in enum org.biojava.nbio.structure.chem.PolymerType: if all else fails...
UNKNOWN - Enum constant in enum org.biojava.nbio.core.sequence.DataSource
UNKNOWN - Enum constant in enum org.biojava.nbio.core.sequence.DNASequence.DNAType
UNKNOWN - Enum constant in enum org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
UNKNOWN - Enum constant in enum org.biojava.nbio.core.util.FileDownloadUtils.Hash
UNKNOWN - Enum constant in enum org.biojava.nbio.structure.ElementType
UNKNOWN - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.phylo.TreeConstructorType: Unweighted Pair-Group Method with Arithmetic mean
UPPER - Enum constant in enum 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 - Enum constant in enum 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)
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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
V - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
V - Enum constant in enum org.biojava.nbio.structure.Element
V - Static variable in class org.biojava.nbio.aaproperties.Constraints
validateFile(File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Validate a local file based on pre-existing metadata files for size and hash.
If the passed in localFile parameter is a file named file.ext, the function searches in the same folder for: file.ext.size: If found, it compares the size stored in it to the length of localFile (in bytes). file.ext.hash_XXXX (where XXXX is DM5, SHA1, or SHA256): If found, it compares the size stored in it to the hash code of localFile. If any of these comparisons fail, the function returns false. otherwise it returns true.
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.core.util.FileDownloadUtils.Hash: 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.core.util.FileDownloadUtils.Hash: 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 - Enum constant in enum org.biojava.nbio.structure.BondType
Variable - Interface in org.biojava.nbio.ontology
VARIABLE_SEQUENCES - Enum constant in enum 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 and 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 - Enum constant in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
vp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

W

W - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
W - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
W - Enum constant in enum 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 - Enum constant in enum 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> - 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 - Enum constant in enum 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.
withHeaderParser(SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.FastaStreamer
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.
withSequenceCreator(SequenceCreatorInterface<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.FastaStreamer
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 - Enum constant in enum 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 class org.biojava.nbio.genome.io.fastq.IlluminaFastqWriter
write(File, Iterable<Fastq>) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqWriter
write(File, Iterable<Fastq>) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqWriter
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 class org.biojava.nbio.genome.io.fastq.IlluminaFastqWriter
write(File, Fastq...) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqWriter
write(File, Fastq...) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqWriter
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 class org.biojava.nbio.genome.io.fastq.IlluminaFastqWriter
write(OutputStream, Iterable<Fastq>) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqWriter
write(OutputStream, Iterable<Fastq>) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqWriter
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, Map<String, ChromosomeSequence>) - Method in class org.biojava.nbio.genome.parsers.gff.GFF3Writer: Output gff3 format for a DNA Sequence
write(OutputStream, Fastq...) - Method in class org.biojava.nbio.genome.io.fastq.IlluminaFastqWriter
write(OutputStream, Fastq...) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqWriter
write(OutputStream, Fastq...) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqWriter
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
writeNucleotideSequenceOriginal(OutputStream, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper: Write a collection of NucleotideSequences to a file using the NucleotideSequences original header as the LOCUS line rather than generating it
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 - Enum constant in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
WWW_BLAST_TYPE - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.ExperimentalTechnique
XREF_ANALOG - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
XTALTRANSL - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
Y - Enum constant in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
Y - Enum constant in enum 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 - Enum constant in enum 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 - Enum constant in enum org.biojava.nbio.structure.Element
Zr - Enum constant in enum 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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