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.