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A

A - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
A - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
A - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
Valid Amino acids
aa2CTerminalPka - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
aa2ExtinctionCoefficient - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
aa2Hydrophathicity - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
aa2MolecularWeight - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
aa2NTerminalPka - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
aa2PKa - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
AAindexFactory - Class in org.biojava.nbio.core.alignment.matrices
Factory class to get Providers for substitution matrices that are provided by the AAINDEX database.
AAindexFactory() - Constructor for class org.biojava.nbio.core.alignment.matrices.AAindexFactory
 
AAIndexFileParser - Class in org.biojava.nbio.core.alignment.matrices
 
AAIndexFileParser() - Constructor for class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser
 
AAIndexProvider - Interface in org.biojava.nbio.core.alignment.matrices
 
aaScore(char, char) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
 
ABITrace - Class in org.biojava.nbio.core.sequence.io
Title: ABITrace
ABITrace(byte[]) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace
The byte[] constructor parses an ABI file represented as a byte array.
ABITrace(File) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace
The File constructor opens a local ABI file and parses the content.
ABITrace(URL) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace
The URL constructor opens an ABI file from any URL.
ABITracerCompoundSet - Class in org.biojava.nbio.core.sequence.compound
 
ABITracerCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet
 
AboutDialog - Class in org.biojava.nbio.structure.align.gui
 
AboutDialog() - Constructor for class org.biojava.nbio.structure.align.gui.AboutDialog
 
abs(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
abs(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
Absorbance_False - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
Absorbance_True - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
AbstractAlignmentJmol - Class in org.biojava.nbio.structure.align.gui.jmol
An Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol.
AbstractAlignmentJmol() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
AbstractAnnotation - Class in org.biojava.nbio.ontology.utils
A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
AbstractAnnotation() - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation
Protected no-args constructor intended for sub-classes.
AbstractAnnotation(Map) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation
Create a new Annotation by copying the key-value pairs from a map.
AbstractAnnotation(Annotation) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation
Copy-constructor.
AbstractCifFileSupplier<S> - Class in org.biojava.nbio.structure.io.cif
Convert a BioJava object to a CifFile.
AbstractCifFileSupplier() - Constructor for class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier
 
AbstractCifFileSupplier.WrappedAtom - Class in org.biojava.nbio.structure.io.cif
Wrapped atoms represent individual atoms enriched with model- and chain-level information.
AbstractCompound - Class in org.biojava.nbio.core.sequence.template
The details of a Compound
AbstractCompound() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound
 
AbstractCompound(String) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound
 
AbstractCompoundSet<C extends Compound> - Class in org.biojava.nbio.core.sequence.template
 
AbstractCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
AbstractCompoundTranslator<F extends Compound,​T extends Compound> - Class in org.biojava.nbio.core.sequence.template
 
AbstractCompoundTranslator(SequenceCreatorInterface<T>, CompoundSet<F>, CompoundSet<T>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
AbstractEdit(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
 
AbstractEdit(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
 
AbstractFeature<S extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.features
A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that feature
AbstractFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.AbstractFeature
A feature has a type and a source
AbstractLocation - Class in org.biojava.nbio.core.sequence.location.template
Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand
AbstractLocation() - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
AbstractLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation
Default constructor
AbstractLocation(Point, Point, Strand, boolean, boolean, AccessionID, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation
Default constructor
AbstractMatrixAligner<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment.template
Implements common code for an Aligner which builds a score matrix during computation.
AbstractMatrixAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner
AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Prepares for an alignment.
AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Prepares for an alignment.
AbstractNucleotideCompoundSet<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.template
 
AbstractNucleotideCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
 
AbstractPairwiseSequenceAligner<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment.template
Implements common code for an Aligner for a pair of Sequences.
AbstractPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
Prepares for a pairwise global sequence alignment.
AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
Prepares for a pairwise sequence alignment.
AbstractProfileProfileAligner<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment.template
Implements common code for an Aligner for a pair of Profiles.
AbstractProfileProfileAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Profile<S, C>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
Prepares for a profile-profile alignment.
AbstractReference - Class in org.biojava.nbio.core.sequence.reference
 
AbstractReference() - Constructor for class org.biojava.nbio.core.sequence.reference.AbstractReference
 
AbstractScorer - Class in org.biojava.nbio.alignment.template
Implements common code for algorithms which compute a score.
AbstractScorer() - Constructor for class org.biojava.nbio.alignment.template.AbstractScorer
 
AbstractScoresCache - Class in org.biojava.nbio.structure.align.multiple
Abstact implementation of the ScoresCache with the shared code used in all objects with a variables cache.
AbstractScoresCache() - Constructor for class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
 
AbstractScoresCache(AbstractScoresCache) - Constructor for class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
 
AbstractSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence.template
The base class for DNA, RNA and Protein sequences.
AbstractSequence() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence
 
AbstractSequence(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence
Create a Sequence from a simple string where the values should be found in compoundSet
AbstractSequence(SequenceReader<C>, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence
A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location of the sequence data.
AbstractSequence.AnnotationType - Enum in org.biojava.nbio.core.sequence.template
 
AbstractStructureAlignment - Class in org.biojava.nbio.structure.align
 
AbstractStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.AbstractStructureAlignment
 
AbstractTerm - Class in org.biojava.nbio.ontology
Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
AbstractTerm() - Constructor for class org.biojava.nbio.ontology.AbstractTerm
 
AbstractUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
Base class for a new structure alignment CLI.
AbstractUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
 
Ac - org.biojava.nbio.structure.Element
 
AccesionedLocation - Interface in org.biojava.nbio.core.sequence.location.template
A location which is bound to an AccessionID.
ACCESSION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
Accessioned - Interface in org.biojava.nbio.core.sequence.template
Indicates an entity is accessioned
AccessionID - Class in org.biojava.nbio.core.sequence
Used in Sequences as the unique 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 - org.biojava.nbio.genome.parsers.cytoband.StainType
 
ACETYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
 
ACTINOID - org.biojava.nbio.structure.ElementType
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.ChooseDirAction
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
The user selected one of the Combo boxes...
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.JPrintPanel
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyAlignmentLoadListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyDistMaxListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyExportListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyOpenPdbFileListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MySaveFileListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.ShowPDBIDListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryListener
 
AD - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
 
adapter - Static variable in class org.biojava.nbio.structure.gui.BiojavaJmol
 
adapter - Static variable in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
add(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
add(int, int, int, int) - Method in class org.biojava.nbio.structure.align.helper.JointFragments
 
add(Collection<FeatureI>) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Add all features in the specified list or collection to this list.
add(FeatureI) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Add specified feature to the end of the list.
add(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
add two atoms ( a + b).
add(AtomContact) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
 
add(GroupContact) - Method in class org.biojava.nbio.structure.contact.GroupContactSet
 
add(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
 
addActiveSite(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addAlgorithm(StructureAlignment) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
Adds a new StructureAlignment algorithm to the list.
addAlignedSequence(S) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
A sequence that has been aligned to other sequences will have inserts.
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
 
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
 
addAligPosListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
addAligPosListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
 
addAll(Collection<AtomContact>) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
 
addAltLoc(Group) - Method in interface org.biojava.nbio.structure.Group
Add a group that is an alternate location for this group.
addAltLoc(Group) - Method in class org.biojava.nbio.structure.HetatomImpl
 
addAnchor(int, int) - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
Adds an additional anchor to the set of anchored compounds
addAnchors(AlignerHelper.Cut[], int[], boolean, int[]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
 
addASPFamPredicted(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addASSwissProt(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addAtom(Atom) - Method in interface org.biojava.nbio.structure.Group
Add an atom to this group.
addAtom(Atom) - Method in class org.biojava.nbio.structure.HetatomImpl
Add an atom to this group.
addAtomAsaC(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
 
addAtomAsaU(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
 
addAtomContact(AtomContact) - Method in class org.biojava.nbio.structure.contact.GroupContact
 
addAtomLinkage(StructureAtomLinkage) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
Add a linkage.
addAtomLinkage(StructureAtomLinkage) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
addAtomLinkages(Collection<StructureAtomLinkage>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
Add a collections of linkages.
addAtomLinkages(Collection<StructureAtomLinkage>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
addAtoms(Atom[]) - Method in class org.biojava.nbio.structure.contact.Grid
Adds a set of atoms, subsequent call to Grid.getIndicesContacts() or Grid.getAtomContacts() will produce the interatomic contacts.
addAtoms(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.contact.Grid
Adds the i and j atoms and fills the grid.
addAtoms(Atom[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid
Adds a set of atoms, subsequent call to Grid.getIndicesContacts() or Grid.getAtomContacts() will produce the interatomic contacts.
addAtoms(Atom[], BoundingBox, Atom[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid
Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
addAxis(Matrix4d, int, CESymmParameters.SymmetryType) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
Adds a new axis of symmetry to the bottom level of the tree
addBond(Bond) - Method in interface org.biojava.nbio.structure.Atom
Add a bond
addBond(Bond) - Method in class org.biojava.nbio.structure.AtomImpl
 
addBridge(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
Adds a Bridge to the residue.
addCDS(AccessionID, int, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
Add a Coding Sequence region with phase to the transcript sequence
addCell(String, String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
Add data to a cell
addChain(Chain) - Method in class org.biojava.nbio.structure.EntityInfo
Add new Chain to this EntityInfo
addChain(Chain) - Method in class org.biojava.nbio.structure.Model
 
addChain(Chain) - Method in interface org.biojava.nbio.structure.Structure
Add a new chain to the first model
addChain(Chain) - Method in class org.biojava.nbio.structure.StructureImpl
Add a new chain to the first model
addChain(Chain, int) - Method in interface org.biojava.nbio.structure.Structure
Add a new chain to the model specified by the given index
addChain(Chain, int) - Method in class org.biojava.nbio.structure.StructureImpl
Add a new chain to the model specified by the given index
addCharges(Structure) - Static method in class org.biojava.nbio.structure.io.ChargeAdder
Function to add the charges to a given structure.
addChemComp(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
Add a new component to the dictionary
addChildElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper
Creates a new element called elementName and adds it to parentElement
addColumn(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
addColumns(ArrayList<String>, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
Add columns to worksheet and set default value
addCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
addCompound(C, C, C...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
addCompound(C, C, Iterable<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
addCompounds(F, T...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
addCompoundsToList(List<T>, List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
addCompoundToLists(List<List<T>>, T) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
addContinuousVariable(String, Double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
addCoords(Point3d[]) - Method in class org.biojava.nbio.structure.contact.Grid
Adds a set of coordinates, subsequent call to Grid.getIndicesContacts() will produce the contacts, i.e. the set of points within distance cutoff.
addCoords(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.contact.Grid
Adds the i and j coordinates and fills the grid.
addCoords(Point3d[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid
Adds a set of coordinates, subsequent call to Grid.getIndicesContacts() will produce the contacts, i.e. the set of points within distance cutoff.
addCoords(Point3d[], BoundingBox, Point3d[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid
Adds the i and j coordinates and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
addDBReference(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
addEntityInfo(EntityInfo) - Method in interface org.biojava.nbio.structure.Structure
Add an EntityInfo to this Structure
addEntityInfo(EntityInfo) - Method in class org.biojava.nbio.structure.StructureImpl
Add an EntityInfo to this Structure
addEquivalent(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
addExon(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence
Add an ExonSequence mainly used to mark as a feature
addExtension(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.
addExtension(String) - Method in interface org.biojava.nbio.structure.io.StructureIOFile
Associates a file extension with this particular StructureIOFile, indicating that files of that type can be parsed.
addFeature(int, int, FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Method to help set the proper details for a feature as it relates to a sequence where the feature needs to have a location on the sequence
addFeature(FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Add a feature to this sequence.
addGene(AccessionID, int, int, Strand) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0.
addGeneIDGFF2GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequences
addGeneMarkGTFGeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
 
addGFBuildMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
addGFFalseDiscoveryRate(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
addGFNewHampshire(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
addGFTreeID(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
addGlimmerGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
 
addGmodGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
Load GFF3 file using mRNA as the gene feature as not all GFF3 files are complete
addGroup(Group) - Method in interface org.biojava.nbio.structure.Chain
Add a group to the list of ATOM record group of this chain.
addGroup(Group) - Method in class org.biojava.nbio.structure.ChainImpl
 
addGroupsToStructure(Structure, Collection<Group>, int, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
Add a list of groups to a new structure.
addGroupToStructure(Structure, Group, int, Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
Adds a particular group to a structure.
addGSAccessionNumber(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addGSdbReference(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addGSDescription(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addGSLook(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addGSOrganismClassification(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addGSOrganismSpecies(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addHelix(Helix) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
 
addIindex(int) - Method in class org.biojava.nbio.structure.contact.GridCell
 
addIndex(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Add an attribute that will be used as index for queries
addIndexes(List<String>) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Add a list of attributes that will be used as indexes for queries
addInteraction(String, String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
To test for interactions use two variables and create a third variable where the two are multiplied together.
addIntron(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addIntron(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence
Add an Intron Currently used to mark an IntronSequence as a feature
addIntronsUsingExons() - Method in class org.biojava.nbio.core.sequence.GeneSequence
Once everything has been added to the gene sequence where you might have added exon sequences only then you can infer the intron sequences and add them.
addJindex(int) - Method in class org.biojava.nbio.structure.contact.GridCell
 
addKeyword(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
Add a keyword associate with the PTM.
addKeywords(Collection<String>) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
 
addLigandBinding(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addMatrixListener(MatrixListener) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
addMatrixListener(MatrixListener) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
addMember(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
 
addMirror(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
addModel(List<Chain>) - Method in interface org.biojava.nbio.structure.Structure
Add a new model.
addModel(List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl
Add a new model.
addMultipleAlignment(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Add a new MultipleAlignment to the end of the ensemble and set its parent ensemble to this.
addMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
addNcsEquivalent(StructureInterface, StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Add an interface to the list, possibly defining it as NCS-equivalent to an interface already in the list.
addNote(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Add notes about this sequence that will get exported for GFF3
addNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
 
addOboFileEventListener(OboFileEventListener) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
 
addOneSystemProperty(String) - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
 
addPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
 
addPoint(Point3d, double) - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
 
addPoint(Point3d, T) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
 
addPosteriorProbability(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
 
addProperty(String, String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
Add a property and type to associate with this DBReferenceInfo
addQualifier(String, Qualifier) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
 
addQualifier(String, Qualifier) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
addQualifier(String, Qualifier) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Add a qualifier
addQuantity(Number) - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature
 
addReference(AbstractReference) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
 
addResidue(SiftsResidue) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
addRotation(Rotation) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
addRow(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
addRows(ArrayList<String>, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
Add rows to the worksheet and fill in default value
addSecondaryStructure(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addSegment(SiftsSegment) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
 
addSeqRes(Chain, String) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Add the missing groups to the SeqResGroups.
addSSBond(Bond) - Method in interface org.biojava.nbio.structure.Structure
Add a single disulfide Bond to this structure
addSSBond(Bond) - Method in class org.biojava.nbio.structure.StructureImpl
Adds a single disulfide Bond to this structure
addStartCodonSequence(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
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 - org.biojava.nbio.alignment.template.GapPenalty.Type
 
AFP - Class in org.biojava.nbio.structure.align.model
A class to represent a FATCAT aligned fragment pair (AFP)
AFP() - Constructor for class org.biojava.nbio.structure.align.model.AFP
 
afp2Res(AFPChain, int, int[], int) - Static method in class org.biojava.nbio.structure.align.AFPTwister
Set the list of equivalent residues in the two proteins given a list of AFPs WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain!
AFPAlignmentDisplay - Class in org.biojava.nbio.structure.align.util
 
AFPAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
 
AFPCalculator - Class in org.biojava.nbio.structure.align.fatcat.calc
A class that performs calculations on AFPChains
AFPCalculator() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
 
AFPChain - Class in org.biojava.nbio.structure.align.model
A bean to contain the core of a structure alignment.
AFPChain(String) - Constructor for class org.biojava.nbio.structure.align.model.AFPChain
Construction of an AFPChain needs the algorithm name, since downstream analysis methods (scores, display, etc) behave differently if the alignment is flexible (created with FatCat).
AFPChain(AFPChain) - Constructor for class org.biojava.nbio.structure.align.model.AFPChain
Copy constructor
AFPChainCoordManager - Class in org.biojava.nbio.structure.align.gui.aligpanel
 
AFPChainCoordManager() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
 
AFPChainer - Class in org.biojava.nbio.structure.align.fatcat.calc
a class to chain AFPs to an alignment
AFPChainer() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
 
AFPChainFlipper - Class in org.biojava.nbio.structure.align.xml
 
AFPChainFlipper() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainFlipper
 
AFPChainScorer - Class in org.biojava.nbio.structure.align.util
 
AFPChainScorer() - Constructor for class org.biojava.nbio.structure.align.util.AFPChainScorer
 
AfpChainWriter - Class in org.biojava.nbio.structure.align.model
A class to convert the data in an AfpChain object to various String outputs.
AfpChainWriter() - Constructor for class org.biojava.nbio.structure.align.model.AfpChainWriter
 
AFPChainXMLConverter - Class in org.biojava.nbio.structure.align.xml
 
AFPChainXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
 
AFPChainXMLParser - Class in org.biojava.nbio.structure.align.xml
 
AFPChainXMLParser() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
 
AFPFromFasta - Class in demo
Demo displaying a structural alignment from a FASTA file using FastaAFPChainConverter.
AFPFromFasta() - Constructor for class demo.AFPFromFasta
 
AFPOptimizer - Class in org.biojava.nbio.structure.align.fatcat.calc
 
AFPOptimizer() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
 
afpPairConn(int, int, FatCatParameters, AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
//Key function: calculate the connectivity of AFP pairs //no compatibility criteria is executed //note: afp1 is previous to afp2 in terms of the position //this module must be optimized
AFPPostProcessor - Class in org.biojava.nbio.structure.align.fatcat.calc
does post processing after alignment chaingin
AFPPostProcessor() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
 
AFPTwister - Class in org.biojava.nbio.structure.align
 
AFPTwister() - Constructor for class org.biojava.nbio.structure.align.AFPTwister
 
Ag - org.biojava.nbio.structure.Element
 
AgScore - Class in org.biojava.nbio.survival.cox.stats
 
AgScore() - Constructor for class org.biojava.nbio.survival.cox.stats.AgScore
 
Al - org.biojava.nbio.structure.Element
 
algorithmName - Static variable in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
 
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeCPMain
 
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeMain
 
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeSideChainMain
 
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
 
algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat
 
algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
 
algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
 
algorithmName - Static variable in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
 
algorithmName - Static variable in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
 
algorithmName - Static variable in class org.biojava.nbio.structure.symmetry.internal.CeSymm
 
ALIGFACTOR - Static variable in class org.biojava.nbio.structure.align.pairwise.Gotoh
 
AligMatEl - Class in org.biojava.nbio.structure.align.helper
 
AligMatEl() - Constructor for class org.biojava.nbio.structure.align.helper.AligMatEl
 
align() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Performs alignment
align(List<Atom[]>) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
 
align(List<Atom[]>) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner
Run an alignment while specifying the atoms to be aligned.
align(List<Atom[]>, Object) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
 
align(List<Atom[]>, Object) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner
Run an alignment and also send a bean containing the parameters.
align(List<Subunit>, List<Subunit>, SubunitClustererParameters, QsAlignParameters) - Static method in class org.biojava.nbio.structure.align.quaternary.QsAlign
 
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
 
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
 
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeMain
 
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
 
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
 
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
 
align(Atom[], Atom[]) - Method in interface org.biojava.nbio.structure.align.StructureAlignment
Run an alignment while specifying the atoms to be aligned.
align(Atom[], Atom[], boolean, FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
 
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
 
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
 
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.CeCPMain
Aligns ca1 and ca2 using a heuristic to check for CPs.
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.CeMain
Align ca2 onto ca1.
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
 
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
 
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
 
align(Atom[], Atom[], Object) - Method in interface org.biojava.nbio.structure.align.StructureAlignment
run an alignment and also send a bean containing the parameters.
align(Atom[], Atom[], FatCatParameters, boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
 
align(Atom[], Atom[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
Calculate the protein structure superimposition, between two sets of atoms.
align(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
 
align(Structure, String, Structure, String) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
Align two chains from the structures.
align(Structure, String, Structure, String, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
Aligns two chains from the structures using user provided parameters.
align(Structure, List<Chain>) - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
 
align(Structure, Structure) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
Calculate the alignment between the two full structures with default parameters
align(Structure, Structure, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
Calculate the alignment between the two full structures with user provided parameters
align(Structure, Structure, SubunitClustererParameters, QsAlignParameters) - Static method in class org.biojava.nbio.structure.align.quaternary.QsAlign
 
align_NPE(Matrix, StrucAligParameters) - Static method in class org.biojava.nbio.structure.align.pairwise.AligNPE
Align without penalizing end-gaps.
Alignable - Interface in org.biojava.nbio.structure.align.pairwise
 
AlignedPosition - Class in org.biojava.nbio.structure.gui.util
 
AlignedPosition() - Constructor for class org.biojava.nbio.structure.gui.util.AlignedPosition
 
AlignedSequence<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.core.alignment.template
Defines a data structure for a Sequence within an alignment.
AlignedSequence.Step - Enum in org.biojava.nbio.core.alignment.template
Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
Aligner<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.alignment.template
Defines an algorithm which computes an alignment Profile from a list of Sequences.
AlignerHelper - Class in org.biojava.nbio.alignment.routines
Static utility to construct alignment routines from a common library of methods.
AlignerHelper() - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper
 
AlignerHelper.Anchor - Class in org.biojava.nbio.alignment.routines
Compounds in query and target sequences that must align
AlignerHelper.Anchor.QueryIndexComparator - Class in org.biojava.nbio.alignment.routines
 
AlignerHelper.Cut - Class in org.biojava.nbio.alignment.routines
Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
AlignerHelper.Last - Enum in org.biojava.nbio.alignment.routines
Define a traceback pointer for the three edit operations: substitution (match/replacement of a query compound with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and insertion (addition of a target compound opening a gap in the query sequence).
AlignerHelper.Subproblem - Class in org.biojava.nbio.alignment.routines
Alignment subproblem.
alignFlexible(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
 
ALIGNMENT_PANEL - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
ALIGNMENT_VIEW - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
alignmentAsMap(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Creates a Map specifying the alignment as a mapping between residue indices of protein 1 and residue indices of protein 2.
AlignmentCalc - Class in org.biojava.nbio.structure.align.gui
A class that obtains two structures via DAS and aligns them This is done in a separate thread.
AlignmentCalc - Class in org.biojava.nbio.structure.gui.util
A class that obtains two structures via DAS and aligns them This is done in a separate thread.
AlignmentCalc(AlignmentGui, Structure, Structure) - Constructor for class org.biojava.nbio.structure.gui.util.AlignmentCalc
requests an alignment of pdb1 vs pdb 2.
AlignmentCalc(AlignmentGui, Structure, Structure, String, String) - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentCalc
requests an alignment of pdb1 vs pdb 2.
AlignmentCalculationRunnable - Interface in org.biojava.nbio.structure.align.gui
 
AlignmentGui - Class in org.biojava.nbio.structure.align.gui
A JFrame that allows to trigger a pairwise structure alignment, either from files in a directory, or after manual upload.
AlignmentGui() - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentGui
 
AlignmentGuiDemo - Class in demo
Get an instance of the two alignment GUIs.
AlignmentGuiDemo() - Constructor for class demo.AlignmentGuiDemo
 
AlignmentPositionListener - Interface in org.biojava.nbio.structure.gui.events
 
AlignmentProgressListener - Class in org.biojava.nbio.structure.align.pairwise
A class to listen to progress of the structure alignment calculations
AlignmentProgressListener() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
 
AlignmentResult - Class in org.biojava.nbio.structure.align.pairwise
A class to track the alignment results in a flat file
AlignmentResult() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
Alignments - Class in org.biojava.nbio.alignment
Static utility to easily run alignment routines.
ALIGNMENTS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
ALIGNMENTS - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
Alignments.PairInProfileScorerType - Enum in org.biojava.nbio.alignment
List of implemented sequence pair in a profile scoring routines.
Alignments.PairwiseSequenceAlignerType - Enum in org.biojava.nbio.alignment
List of implemented pairwise sequence alignment routines.
Alignments.PairwiseSequenceScorerType - Enum in org.biojava.nbio.alignment
List of implemented pairwise sequence scoring routines.
Alignments.ProfileProfileAlignerType - Enum in org.biojava.nbio.alignment
List of implemented profile-profile alignment routines.
Alignments.RefinerType - Enum in org.biojava.nbio.alignment
List of implemented profile refinement routines.
AlignmentTextPanel - Class in org.biojava.nbio.structure.align.gui
 
AlignmentTextPanel() - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentTextPanel
 
AlignmentTools - Class in org.biojava.nbio.structure.align.util
Methods for analyzing and manipulating AFPChains and for other pairwise alignment utilities.
AlignmentTools() - Constructor for class org.biojava.nbio.structure.align.util.AlignmentTools
 
AlignmentTools.IdentityMap<K> - Class in org.biojava.nbio.structure.align.util
A Map can be viewed as a function from K to V.
alignmentToSIF(Writer, AFPChain, Atom[], Atom[], String, String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Creates a simple interaction format (SIF) file for an alignment.
alignOptimal(Atom[], Atom[], Object, AFPChain[]) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
AligNPE - Class in org.biojava.nbio.structure.align.pairwise
 
AligNPE() - Constructor for class org.biojava.nbio.structure.align.pairwise.AligNPE
 
alignPermuted(Atom[], Atom[], Object, int) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
Aligns ca1 with ca2 permuted by cp residues.
alignRigid(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
 
alignRigid(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
 
alignSuperfamily() - Method in class demo.DemoSCOP
 
AlignUtils - Class in org.biojava.nbio.structure.align.helper
Low level helper methods for CE and FATCAT algorithms.
AlignUtils() - Constructor for class org.biojava.nbio.structure.align.helper.AlignUtils
 
AligPanel - Class in org.biojava.nbio.structure.align.gui.aligpanel
A JPanel that can display an AFPChain in a nice way and interact with Jmol.
AligPanel() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
AligPanelMouseMotionListener - Class in org.biojava.nbio.structure.align.gui.aligpanel
 
AligPanelMouseMotionListener(AligPanel) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
AligUIManager - Class in org.biojava.nbio.structure.align.webstart
 
AligUIManager() - Constructor for class org.biojava.nbio.structure.align.webstart.AligUIManager
 
ALKALI_METAL - org.biojava.nbio.structure.ElementType
 
ALKALINE_EARTH_METAL - org.biojava.nbio.structure.ElementType
 
ALL - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
 
ALL_CURRENT_ENDPOINT - Static variable in class org.biojava.nbio.structure.PDBStatus
 
ALL_POLYMER_TYPES - Static variable in enum org.biojava.nbio.structure.chem.PolymerType
Convenience Set of all polymer types.
ALL_SEQUENCES - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
 
AllChemCompProvider - Class in org.biojava.nbio.structure.chem
A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.
AllChemCompProvider() - Constructor for class org.biojava.nbio.structure.chem.AllChemCompProvider
 
allComponents() - Static method in class org.biojava.nbio.protmod.Component
 
allComponents() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
allIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
allKeywords() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
allModifications() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
allPdbccIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
allPsimodIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
allResidIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
ALN - org.biojava.nbio.core.alignment.template.Profile.StringFormat
 
ALN - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
 
AlreadyExistsException - Exception in org.biojava.nbio.ontology
Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
AlreadyExistsException() - Constructor for exception org.biojava.nbio.ontology.AlreadyExistsException
 
AlreadyExistsException(String) - Constructor for exception org.biojava.nbio.ontology.AlreadyExistsException
 
ALT_ID - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
AltAligComparator - Class in org.biojava.nbio.structure.align.pairwise
A comparator to sort AlternativeAlignments based on their number of equivalent residues and RMSD.
AltAligComparator() - Constructor for class org.biojava.nbio.structure.align.pairwise.AltAligComparator
 
AlternativeAlignment - Class in org.biojava.nbio.structure.align.pairwise
Implements a class which handles one possible (alternative) solution.
AlternativeAlignment() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
AlternativeAlignmentFrame - Class in org.biojava.nbio.structure.gui.util
a frame showing the alternative alignments, which are the result of a structure superimposition
AlternativeAlignmentFrame(Structure, Structure) - Constructor for class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
 
Am - org.biojava.nbio.structure.Element
 
AmbiguityDNACompoundSet - Class in org.biojava.nbio.core.sequence.compound
 
AmbiguityDNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet
 
AmbiguityDNARNAHybridCompoundSet - Class in org.biojava.nbio.core.sequence.compound
Ambiguity set for hybrid DNA/RNA sequences.
AmbiguityDNARNAHybridCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet
 
AmbiguityRNACompoundSet - Class in org.biojava.nbio.core.sequence.compound
 
AmbiguityRNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet
 
AMBIGUOUS_AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
Same as AA pattern but with one additional letters - X
AMBIGUOUS_NUCLEOTIDE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
Ambiguous nucleotide
AMINO_ACID_MATCHER - Static variable in class org.biojava.nbio.structure.AtomPositionMap
Matches CA atoms of protein groups
AminoAcid - Interface in org.biojava.nbio.structure
A Group that represents an AminoAcid.
AMINOACID - org.biojava.nbio.structure.GroupType
The type for amino acids (L-peptides)
AminoAcidComposition - Class in org.biojava.nbio.aaproperties.xml
 
AminoAcidComposition() - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
 
AminoAcidComposition(String, String, String, List<Name2Count>, List<Name2Count>) - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
 
AminoAcidCompositionTable - Class in org.biojava.nbio.aaproperties.xml
 
AminoAcidCompositionTable() - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
 
AminoAcidCompositionTable(List<AminoAcidComposition>) - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
 
AminoAcidCompound - Class in org.biojava.nbio.core.sequence.compound
Used to describe an Amino Acid.
AminoAcidCompound(AminoAcidCompoundSet, String, String, String, Float) - Constructor for class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
 
AminoAcidCompoundSet - Class in org.biojava.nbio.core.sequence.compound
Set of proteinogenic amino acids.
AminoAcidCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
 
AminoAcidImpl - Class in org.biojava.nbio.structure
AminoAcid inherits most from Hetatom.
AminoAcidImpl() - Constructor for class org.biojava.nbio.structure.AminoAcidImpl
inherits most from Hetero and has just a few extensions.
AminoAcidProperties - Class in org.biojava.nbio.aaproperties
This class provides the protein properties at the level of individual amino acids.
AminoAcidProperties() - Constructor for class org.biojava.nbio.aaproperties.AminoAcidProperties
 
aminoAcidsCompounds(CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
 
amount(Atom) - Static method in class org.biojava.nbio.structure.Calc
Gets the length of the vector (2-norm)
analyze() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method is the main function call to extract all step parameters, pairing parameters, and sequence information from the Structure object provided to the constructor.
analyze(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
Analyze the symmetries of the input Atom array using the DEFAULT parameters.
analyze(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
Analyze the symmetries of the input Atom array using the provided parameters.
analyzeLevel(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
Analyze a single level of symmetry.
Anchor(int, int) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
 
AnchoredPairwiseSequenceAligner<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment.routines
This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.
AnchoredPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
Prepares for a pairwise global sequence alignment.
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
Prepares for a pairwise global sequence alignment.
anchors - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
angle(Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions
Calculate the rotation angle component of the input unit quaternion.
angle(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
Gets the angle between two vectors
ANGLE - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
 
angleCheckOk(FragmentPair, FragmentPair, float) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
 
AngleOrderDetectorPlus - Class in org.biojava.nbio.structure.symmetry.internal
Guesses an order of rotational symmetry from the angle.
AngleOrderDetectorPlus(double) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
 
AngleOrderDetectorPlus(int) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
 
AngleOrderDetectorPlus(int, double) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
 
AngleOrderDetectorPlus(int, double, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
Determine order by finding the order (up to the maxOrder) which has the closest rotation angle to the observed rotation.
Annotatable - Interface in org.biojava.nbio.ontology.utils
Indicates that an object has an associated annotation.
Annotation - Interface in org.biojava.nbio.ontology.utils
Arbitrary annotation associated with one or more objects.
antiparallel - org.biojava.nbio.structure.secstruc.BridgeType
 
ANY - Static variable in class org.biojava.nbio.ontology.OntoTools
 
ANYTHING_MATCHER - Static variable in class org.biojava.nbio.structure.AtomPositionMap
Matches all atoms
apairs_from_idxlst(JointFragments) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
Set apairs according to a list of (i,j) tuples.
apairs_from_seed(int, int, int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
Set apairs according to a seed position.
ApliphaticIndex - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
App - Class in org.biojava.nbio.genome
Hello world!
App - Class in org.biojava.nbio.ontology
Hello world!
App() - Constructor for class org.biojava.nbio.genome.App
 
App() - Constructor for class org.biojava.nbio.ontology.App
 
append(T, Iterable<Fastq>) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter
Append the specified FASTQ formatted sequences to the specified appendable.
append(T, Fastq...) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter
Append the specified FASTQ formatted sequences to the specified appendable.
appendQuality(String) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.
appendQuality(String) - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
Notify this listener of a quality line.
appendSequence(String) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.
appendSequence(String) - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
Notify this parse listener of an additional sequence line.
appendToSequence(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
appendWorkSheetColumns(WorkSheet) - Method in class org.biojava.nbio.survival.data.WorkSheet
Add columns from a second worksheet to be joined by common row.
appendWorkSheetRows(WorkSheet) - Method in class org.biojava.nbio.survival.data.WorkSheet
Add rows from a second worksheet to be joined by common column.
applyAlignment(Map<S, T>, Map<T, S>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Applies an alignment k times.
applyAlignment(Map<T, T>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Applies an alignment k times.
applyColumnFilter(String, ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
Apply filter to a column to change values from say numberic to nominal based on some range
applyValues() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
 
approach_ap3(Atom[], Atom[], FragmentPair[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
 
Ar - org.biojava.nbio.structure.Element
 
Architecture - org.biojava.nbio.structure.cath.CathCategory
 
areInSameAxis(int, int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
Returns true if both given transform ids belong to the same crystallographic axis (a, b or c) For two non-rotation transformations (i.e. identity operators) it returns true
arrayLeftDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Element-by-element left division, C = A.
arrayLeftDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Element-by-element left division in place, A = A.
ArrayListProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
 
ArrayListProxySequenceReader() - Constructor for class org.biojava.nbio.core.sequence.loader.ArrayListProxySequenceReader
 
ArrayListSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
Stores a Sequence as a collection of compounds in an ArrayList
ArrayListSequenceReader() - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
ArrayListSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
ArrayListSequenceReader(List<C>, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
arrayRightDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Element-by-element right division, C = A.
arrayRightDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Element-by-element right division in place, A = A.
arrayTimes(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Element-by-element multiplication, C = A.
arrayTimesEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Element-by-element multiplication in place, A = A.
ARTIFACTUAL - org.biojava.nbio.protmod.ModificationOccurrenceType
 
As - org.biojava.nbio.structure.Element
 
AsaCalculator - Class in org.biojava.nbio.structure.asa
Class to calculate Accessible Surface Areas based on the rolling ball algorithm by Shrake and Rupley.
AsaCalculator(Point3d[], double, int, int, double) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator
Constructs a new AsaCalculator.
AsaCalculator(Atom[], double, int, int) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator
Constructs a new AsaCalculator.
AsaCalculator(Structure, double, int, int, boolean) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator
Constructs a new AsaCalculator.
asMap() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
 
asMap() - Method in interface org.biojava.nbio.ontology.utils.Annotation
Return a map that contains the same key/values as this Annotation.
AssertionFailure - Error in org.biojava.nbio.ontology.utils
An unchecked exception representing an Assertion failure.
AssertionFailure(String) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
 
AssertionFailure(String, Throwable) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
 
AssertionFailure(Throwable) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
 
assertLocation() - Method in class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
 
assertLocation() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
assignment - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
 
assignSecStruc(Structure, List<SecStrucInfo>) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools
 
Astral - Class in org.biojava.nbio.structure.scop
Provides programmatic access to ASTRAL representative sets.
Astral(String, Reader) - Constructor for class org.biojava.nbio.structure.scop.Astral
Constructs a new Astral object.
Astral(String, URL) - Constructor for class org.biojava.nbio.structure.scop.Astral
Constructs a new Astral object.
Astral(Astral.AstralSet) - Constructor for class org.biojava.nbio.structure.scop.Astral
Constructs a new Astral object.
Astral.AstralSet - Enum in org.biojava.nbio.structure.scop
An ASTRAL sequence-identity cutoff with an identifier such as:
ASYMMETRIC - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass
 
At - org.biojava.nbio.structure.Element
 
Atom - Interface in org.biojava.nbio.structure
A simple interface for an Atom.
ATOM_CA_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.FileParsingParameters
The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
ATOM_PLANE - org.biojava.nbio.structure.BondType
 
AtomCache - Class in org.biojava.nbio.structure.align.util
A utility class that provides easy access to Structure objects.
AtomCache() - Constructor for class org.biojava.nbio.structure.align.util.AtomCache
Default AtomCache constructor.
AtomCache(String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache
Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(String, String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache
Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache
Creates a new AtomCache object based on the provided UserConfiguration.
AtomContact - Class in org.biojava.nbio.structure.contact
A pair of atoms that are in contact
AtomContact(Pair<Atom>, double) - Constructor for class org.biojava.nbio.structure.contact.AtomContact
 
AtomContactSet - Class in org.biojava.nbio.structure.contact
A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations
AtomContactSet(double) - Constructor for class org.biojava.nbio.structure.contact.AtomContactSet
 
AtomIdentifier - Class in org.biojava.nbio.structure.contact
 
AtomIdentifier(int, String) - Constructor for class org.biojava.nbio.structure.contact.AtomIdentifier
 
AtomImpl - Class in org.biojava.nbio.structure
Implementation of an Atom of a PDB file.
AtomImpl() - Constructor for class org.biojava.nbio.structure.AtomImpl
 
AtomInfo - Class in org.biojava.nbio.structure.align.gui.jmol
This class uniquely describes an atom
AtomInfo() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
 
AtomInfoParser - Class in org.biojava.nbio.structure.align.gui.jmol
 
AtomInfoParser() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser
 
AtomIterator - Class in org.biojava.nbio.structure
an iterator over all atoms of a structure / group.
AtomIterator(Group) - Constructor for class org.biojava.nbio.structure.AtomIterator
Constructs an AtomIterator object.
AtomIterator(Structure) - Constructor for class org.biojava.nbio.structure.AtomIterator
Constructs an AtomIterator object over all models
AtomIterator(Structure, int) - Constructor for class org.biojava.nbio.structure.AtomIterator
Constructs an AtomIterator object over a single model
atomn - org.biojava.nbio.structure.chem.ResidueType
 
AtomPositionMap - Class in org.biojava.nbio.structure
A map from ResidueNumbers to ATOM record positions in a PDB file.
AtomPositionMap(Atom[]) - Constructor for class org.biojava.nbio.structure.AtomPositionMap
Creates a new AtomPositionMap containing peptide alpha-carbon atoms
AtomPositionMap(Atom[], AtomPositionMap.GroupMatcher) - Constructor for class org.biojava.nbio.structure.AtomPositionMap
Creates a new AtomPositionMap containing only atoms matched by matcher.
AtomPositionMap(Structure) - Constructor for class org.biojava.nbio.structure.AtomPositionMap
Creates a new AtomPositionMap containing representative atoms from a structure.
AtomPositionMap.GroupMatcher - Interface in org.biojava.nbio.structure
Used as a Predicate to indicate whether a particular Atom should be mapped
ATOMRECORD - Static variable in interface org.biojava.nbio.structure.AminoAcid
Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
atoms - Variable in class org.biojava.nbio.structure.HetatomImpl
 
atomsToPoints(Collection<Atom>) - Static method in class org.biojava.nbio.structure.Calc
Convert an array of atoms into an array of vecmath points
atomsToPoints(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
Convert an array of atoms into an array of vecmath points
ATTACHMENT - org.biojava.nbio.protmod.ModificationCategory
 
attribute(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
attribute(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter
Add an un-qualified attribute to an element.
attribute(String, String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
attribute(String, String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter
Add an attribute to an element.
attributes() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
Get the string of key/value attributes.
attributeValues(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Create a collection of the unique values for the specified key.
Au - org.biojava.nbio.structure.Element
 
AU - org.biojava.nbio.structure.xtal.TransformType
 
AugmentedResidueRange - Class in org.biojava.nbio.structure
Created by douglas on 1/23/15.
AugmentedResidueRange(String, String, String, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
 
AugmentedResidueRange(String, ResidueNumber, ResidueNumber, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
 
Author - Class in org.biojava.nbio.structure
Describes author attributes for author information in a PDB file.
Author() - Constructor for class org.biojava.nbio.structure.Author
 
AUTHORS_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
AUTO - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
 
AutoSuggestProvider - Interface in org.biojava.nbio.structure.align.gui.autosuggest
A class that provides auto-completion suggestions for JAutoSuggest
AV - org.biojava.nbio.phylo.TreeConstructorType
What does this stand for?
available() - Method in class org.biojava.nbio.core.util.UncompressInputStream
 
available() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
AverageHydropathyValue - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
AVGTM_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
 
Axis(Matrix4d, int, CESymmParameters.SymmetryType, int, int) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
 
AxisAligner - Class in org.biojava.nbio.structure.symmetry.axis
 
AxisAligner() - Constructor for class org.biojava.nbio.structure.symmetry.axis.AxisAligner
 
axisStroke - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 

B

B - org.biojava.nbio.structure.Element
 
Ba - org.biojava.nbio.structure.Element
 
BACKGROUND_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
BALL_AND_STICK - org.biojava.nbio.structure.gui.RenderStyle
 
BASE_COUNT_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
BASE_COUNT_TAG_FULL - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
BASE_LIST_DNA - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
BASE_LIST_RNA - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
BASE_MAP - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
BasePairParameters - Class in org.biojava.nbio.structure.basepairs
This module calculates the el Hassan-Calladine Base Pairing and Base-pair Step Parameters for any nucleic acid containing structure that has the information about the core base-pair rings.
BasePairParameters(Structure) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters
This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure for only canonical DNA pairs.
BasePairParameters(Structure, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters
This constructor takes a Structure object, and whether to use the RNA standard bases.
BasePairParameters(Structure, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters
This constructor takes a Structure object, whether to use RNA, and whether to remove duplicate sequences.
BasePairParameters(Structure, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters
This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure.
basePairReferenceFrame(Pair<Group>) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method calculates the central frame (4x4 transformation matrix) of a single base pair.
basicLoad() - Method in class demo.DemoLoadStructure
 
basicLoad(String) - Method in class demo.DemoDomainsplit
 
basicLoad(PDBFileReader, String) - Method in class demo.DemoChangeChemCompProvider
 
BasicSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence
Bare bones version of the Sequence object to be used sparingly.
BasicSequence(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.BasicSequence
 
BasicSequence(ProxySequenceReader<C>) - Constructor for class org.biojava.nbio.core.sequence.BasicSequence
 
BCIF - org.biojava.nbio.structure.io.StructureFiletype
 
BCIF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
 
BcifFileReader - Class in org.biojava.nbio.structure.io
Parse binary Cif files and provide capabilities to store them locally.
BcifFileReader() - Constructor for class org.biojava.nbio.structure.io.BcifFileReader
Constructs a new BcifFileReader, initializing the extensions member variable.
BcifFileReader(String) - Constructor for class org.biojava.nbio.structure.io.BcifFileReader
Constructs a new BcifFileReader, initializing the extensions member variable.
Be - org.biojava.nbio.structure.Element
 
bend - org.biojava.nbio.structure.secstruc.SecStrucType
 
BerkeleyScopInstallation - Class in org.biojava.nbio.structure.scop
SCOPe: The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop.berkeley.edu/).
BerkeleyScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.BerkeleyScopInstallation
 
bestTrace1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
bestTrace1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
bestTrace2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
bestTrace2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
bestTraces1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
bestTraces1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
bestTraces2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
bestTraces2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
bestTraceScore - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
bestTraceScore - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
bestTracesN - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
bestTracesN - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
bestTracesScores - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
bestTracesScores - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
BetaBridge - Class in org.biojava.nbio.structure.secstruc
Container that represents a beta Bridge between two residues.
BetaBridge(int, int, BridgeType) - Constructor for class org.biojava.nbio.structure.secstruc.BetaBridge
 
BETTER_PERFORMANCE_MORE_MEMORY - org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior
use a built-in HashMap for faster access to memory, at the price of more memory consumption
BETWEEN_11 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
 
BETWEEN_12 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
 
BETWEEN_13 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
 
BETWEEN_22 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
 
BETWEEN_23 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
 
BETWEEN_33 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
 
Bi - org.biojava.nbio.structure.Element
 
BIO - org.biojava.nbio.structure.align.client.StructureName.Source
 
BIO_NAME_PATTERN - Static variable in class org.biojava.nbio.structure.BioAssemblyIdentifier
 
BioAssemblyIdentifier - Class in org.biojava.nbio.structure
 
BioAssemblyIdentifier(String) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
 
BioAssemblyIdentifier(String, int) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
 
BioAssemblyIdentifier(PdbId, int) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
 
BioAssemblyInfo - Class in org.biojava.nbio.structure.quaternary
Representation of a Biological Assembly annotation as provided by the PDB.
BioAssemblyInfo() - Constructor for class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
Empty constructor
BioAssemblyTools - Class in org.biojava.nbio.structure.quaternary
 
BioAssemblyTools() - Constructor for class org.biojava.nbio.structure.quaternary.BioAssemblyTools
 
bioEnd() - Method in class org.biojava.nbio.genome.parsers.gff.Location
Get end index, in biocoordinates.
BIOJAVA_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
Secondary strucuture calculated and assigned by DSSP of BioJava
BioJavaAADemo - Class in demo
Created by andreas on 8/9/14.
BioJavaAADemo() - Constructor for class demo.BioJavaAADemo
 
BiojavaJmol - Class in org.biojava.nbio.structure.gui
A class that provides a simple GUI for Jmol
BiojavaJmol() - Constructor for class org.biojava.nbio.structure.gui.BiojavaJmol
 
BioJavaStructureAlignment - Class in org.biojava.nbio.structure.align
Wrapper for the BioJava Structure Alignment Implementation
BioJavaStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.BioJavaStructureAlignment
 
BIOL_ASSEMBLY_IDENTIFIER - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
 
BiologicalAssemblyBuilder - Class in org.biojava.nbio.structure.quaternary
Reconstructs the quaternary structure of a protein from an asymmetric unit
BiologicalAssemblyBuilder() - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
 
BiologicalAssemblyTransformation - Class in org.biojava.nbio.structure.quaternary
The transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file.
BiologicalAssemblyTransformation() - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
Default Constructor
BiologicalAssemblyTransformation(BiologicalAssemblyTransformation) - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
Copy Constructor
bioStart() - Method in class org.biojava.nbio.genome.parsers.gff.Location
Get start index, in biocoordinates.
bioStrand() - Method in class org.biojava.nbio.genome.parsers.gff.Location
Get character representation of strand.
BitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
BitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
BitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
BitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
bitMask() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
This method should return the bit mask to be used to extract the bytes you are interested in working with.
bitMask() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
bitMask() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
 
BitSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
An implementation of the popular bit encodings.
BitSequenceReader(BitSequenceReader.BitArrayWorker<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader
Instance which allows you to supply a different @{BitArrayWorker} object.
BitSequenceReader.BitArrayWorker<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
The logic of working with a bit has been separated out into this class to help developers create the bit data structures without having to put the code into an intermediate format and to also use the format without the need to copy this code.
bitsPerCompound() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
Returns how many bits are used to represent a compound e.g. 2 if using 2bit encoding.
Bk - org.biojava.nbio.structure.Element
 
BLACK_WHITE_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
blankOutBreakFlag(AFPChain, Atom[], int, int, CECalculator, boolean[][], int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
 
blankOutCEOrig(Atom[], int, int, CECalculator, Matrix, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
 
blankOutPreviousAlignment(AFPChain, Atom[], int, int, CECalculator, Matrix, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
 
BLAST_PROGRAM - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
BlastAlignmentParameterEnum - Enum in org.biojava.nbio.ws.alignment.qblast
Alignment request parameters accepted by QBlast service.
Not all are mandatory.
BlastClustReader - Class in org.biojava.nbio.structure.symmetry.utils
 
BlastClustReader(int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
 
BlastHitBuilder - Class in org.biojava.nbio.core.search.io.blast
Designed by Paolo Pavan.
BlastHitBuilder() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
 
BlastHomologyHits - Class in org.biojava.nbio.genome.homology
 
BlastHomologyHits() - Constructor for class org.biojava.nbio.genome.homology.BlastHomologyHits
 
BlastHspBuilder - Class in org.biojava.nbio.core.search.io.blast
Designed by Paolo Pavan.
BlastHspBuilder() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
BlastJob - Class in org.biojava.nbio.ws.alignment.qblast
Information about QBlast search job
BlastJob() - Constructor for class org.biojava.nbio.ws.alignment.qblast.BlastJob
 
BlastMatrixEnum - Enum in org.biojava.nbio.ws.alignment.qblast
Enum representing matrices supported by QBlast
blastn - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
 
BlastOutputAlignmentFormatEnum - Enum in org.biojava.nbio.ws.alignment.qblast
Enum representing available output alignment types.
BlastOutputFormatEnum - Enum in org.biojava.nbio.ws.alignment.qblast
Enum representing available output formats.
BlastOutputParameterEnum - Enum in org.biojava.nbio.ws.alignment.qblast
Output parameters accepted by QBlast service.
blastp - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
 
BlastProgramEnum - Enum in org.biojava.nbio.ws.alignment.qblast
Enum representing available blast programs.
BlastResult - Class in org.biojava.nbio.core.search.io.blast
This class models a Blast/Blast plus result.
BlastResult(String, String, String, String, HashMap<String, String>, int, String, String, int, List<Hit>, Sequence) - Constructor for class org.biojava.nbio.core.search.io.blast.BlastResult
 
BlastResultBuilder - Class in org.biojava.nbio.core.search.io.blast
Designed by Paolo Pavan.
BlastResultBuilder() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
BlastTabularParser - Class in org.biojava.nbio.core.search.io.blast
Designed by Paolo Pavan.
BlastTabularParser() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastTabularParser
 
blastx - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
 
BlastXMLParser - Class in org.biojava.nbio.core.search.io.blast
Re-designed by Paolo Pavan on the footprint of: org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis You may want to find my contacts on Github and LinkedIn for code info or discuss major changes.
BlastXMLParser() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastXMLParser
 
BlastXMLQuery - Class in org.biojava.nbio.genome.query
 
BlastXMLQuery(String) - Constructor for class org.biojava.nbio.genome.query.BlastXMLQuery
 
Block - Interface in org.biojava.nbio.structure.align.multiple
A Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in a sequential order.
BlockImpl - Class in org.biojava.nbio.structure.align.multiple
General implementation of a Block that supports any type of sequential alignment with gaps.
BlockImpl(BlockImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl
Copy constructor.
BlockImpl(BlockSet) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl
Constructor.
blockInfo(AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
get the afp list and residue list for each block
BlockSet - Interface in org.biojava.nbio.structure.align.multiple
A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment.
BlockSetImpl - Class in org.biojava.nbio.structure.align.multiple
A general implementation of a BlockSet to store a flexible part of a multiple alignment.
BlockSetImpl(BlockSetImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl
Copy constructor.
BlockSetImpl(MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl
Constructor.
BLOSUM45 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
 
BLOSUM50 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
 
Blosum62 - Static variable in class org.biojava.nbio.ronn.RonnConstraint
 
BLOSUM62 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
 
BLOSUM80 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
 
BLOSUM90 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
 
Bond - Interface in org.biojava.nbio.structure
A simple bond -- it stores information about two atoms as well as information about its bond order.
BOND_TYPES_TO_PARSE - Static variable in class org.biojava.nbio.structure.io.BondMaker
The types of bonds that are read from struct_conn (type specified in field conn_type_id)
BondImpl - Class in org.biojava.nbio.structure
A simple bond -- it stores information about two atoms as well as information about its bond order.
BondImpl(Atom, Atom, int) - Constructor for class org.biojava.nbio.structure.BondImpl
Constructs a new bond from a pair of atoms and the bond order of the bond between them.
BondImpl(Atom, Atom, int, boolean) - Constructor for class org.biojava.nbio.structure.BondImpl
Constructs a new bond from a pair of atoms and the bond order of the bond between them.
BondLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
 
BondLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
 
BondMaker - Class in org.biojava.nbio.structure.io
Adds polymer bonds for peptides and nucleotides based on distance cutoffs and intra-group (residue) bonds based on data from the Chemical Component Dictionary to the Structure object.
BondMaker(Structure, FileParsingParameters) - Constructor for class org.biojava.nbio.structure.io.BondMaker
 
BONDS_INITIAL_CAPACITY - Static variable in class org.biojava.nbio.structure.AtomImpl
The inital capacity of the bonds list.
BondType - Enum in org.biojava.nbio.structure
Work in progress - NOT final!
bottom - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
 
BoundingBox - Class in org.biojava.nbio.structure.contact
A bounding box for short cutting some geometrical calculations.
BoundingBox(double, double, double, double, double, double) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
 
BoundingBox(Point3d[]) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
Constructs a BoundingBox by calculating maxs and mins of given array of atoms.
BoundingBox(BoundingBox) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
 
BoundingBox(BoundingBox[]) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
Given a set of bounding boxes returns a bounding box that bounds all of them.
bounds() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
The union of all locations of all features in this list, mapped to the positive strand.
Br - org.biojava.nbio.structure.Element
 
BRANCHED - org.biojava.nbio.structure.EntityType
The 'branched' type use mainly to represent carbohydrates.
BravaisLattice - Enum in org.biojava.nbio.structure.xtal
An enum to represent the 7 Bravais lattices
Breslow - org.biojava.nbio.survival.cox.CoxMethod
 
bridge - org.biojava.nbio.structure.secstruc.SecStrucType
 
BridgeType - Enum in org.biojava.nbio.structure.secstruc
A bridge is formed by two non-overlapping stretches of three residues each (i-1,i,i+1) and (j-1,j,j+1), where i
BROAD_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
BROAD_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym
 
BrowserOpener - Class in org.biojava.nbio.structure.align.webstart
 
BrowserOpener() - Constructor for class org.biojava.nbio.structure.align.webstart.BrowserOpener
 
BufferedReaderBytesRead - Class in org.biojava.nbio.core.sequence.io
Need to keep track of actual bytes read and take advantage of buffered reader performance.
BufferedReaderBytesRead(Reader) - Constructor for class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Creates a buffering character-input stream that uses a default-sized input buffer.
BufferedReaderBytesRead(Reader, int) - Constructor for class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Creates a buffering character-input stream that uses an input buffer of the specified size.
build() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
The method to finish any calls to the builder with which returns a transcription engine.
build() - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder
Build and return a new FASTQ formatted sequence configured from the properties of this builder.
build() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
 
build() - Static method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
Builds the mapping by reading SIFTS the tsv file set in SiftsChainToUniprotMapping.DEFAULT_FILE variable.
builder() - Static method in class org.biojava.nbio.genome.io.fastq.Fastq
Create and return a new FastqBuilder.
builder(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.Fastq
Create and return a new FastqBuilder configured from the specified FASTQ formatted sequence.
Builder() - Constructor for class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
 
Builder(String, ModificationCategory, ModificationOccurrenceType, ModificationCondition) - Constructor for class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
 
Builder(ProteinModification) - Constructor for class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
Create a Builder from an existing ProteinModification.
buildFeatureAtrributeIndex(String, FeatureList) - Static method in class org.biojava.nbio.genome.parsers.gff.FeatureHelper
Build a list of individual features to allow easy indexing and to avoid iterating through large genome gff3 files The index for the returned HashMap is the value of the attribute used to build the index
buildSymmetryGraph(List<AFPChain>, Atom[], boolean) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Converts a set of AFP alignments into a Graph of aligned residues, where each vertex is a residue and each edge means the connection between the two residues in one of the alignments.
buildSymmetryGraph(AFPChain) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Converts a self alignment into a directed jGraphT of aligned residues, where each vertex is a residue and each edge means the equivalence between the two residues in the self-alignment.
buildTranslators() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
 
BYTES_PER_INT - Static variable in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
bytesRead - Variable in class org.biojava.nbio.ontology.obo.OboFileParser
 

C

c - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
first allowed c-term
C - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
C - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
C - org.biojava.nbio.structure.Element
 
C - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
C_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name for the backbone carbonyl
C1_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the backbone C1' in RNA
C2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the backbone C2' in RNA
C2_ROTATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod
 
C2RotationSolver - Class in org.biojava.nbio.structure.symmetry.core
 
C2RotationSolver(QuatSymmetrySubunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.C2RotationSolver
 
C3_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the backbone C3' in RNA
C4_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the backbone C4' in RNA
Ca - org.biojava.nbio.structure.Element
 
CA_AND_SIDE_CHAIN_ANGLE_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
 
CA_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the backbone C-alpha atom.
CA_MIN_DIST - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc
min distance of two CA atoms if H-bonds are allowed to form
CA_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
 
cache(K, V) - Method in class org.biojava.nbio.structure.domain.SerializableCache
This will not cache null values.
CACHE_PROPERTY - Static variable in class org.biojava.nbio.core.util.InputStreamProvider
 
cacheFileName - Variable in class org.biojava.nbio.structure.domain.SerializableCache
 
CAConverter - Class in org.biojava.nbio.structure.io
Converts full atom representations to Calpha only ones.
CAConverter() - Constructor for class org.biojava.nbio.structure.io.CAConverter
 
calAfpRmsd(int, int[], int, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
//return the rmsd of the residues from the segments that form the given AFP list //this value can be a measurement (1) for the connectivity of the AFPs
Calc - Class in org.biojava.nbio.structure
Utility operations on Atoms, AminoAcids, Matrices, Point3d, etc.
Calc() - Constructor for class org.biojava.nbio.structure.Calc
 
calc_rmsd(Atom[], Atom[], int, boolean) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
superimpose and get rmsd
calc_rmsd(Atom[], Atom[], int, boolean, boolean) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
superimpose and get rmsd
calcAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together.
calcAsas(int, int, int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together.
calcCenterOfRotation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
calcGlobalSymmetry(List<Subunit>, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
Calculate GLOBAL symmetry results.
calcGlobalSymmetry(Structure, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
Calculate GLOBAL symmetry results.
calcGlobalSymmetry(Stoichiometry, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
Calculate GLOBAL symmetry results.
calcIdSimilarity(char[], char[], int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
 
calcLength(List<ResidueRangeAndLength>) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength
Calculates the combined number of residues of the ResidueRanges in rrs.
calcLocalSymmetries(List<Subunit>, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
Returns a List of LOCAL symmetry results.
calcLocalSymmetries(Structure, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
Returns a List of LOCAL symmetry results.
calcLocalSymmetries(Stoichiometry, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
Returns a List of LOCAL symmetry results.
CalcPoint - Class in org.biojava.nbio.structure.geometry
Utility operations on Point3d.
calcRotationAngleInDegrees(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
Calculates the angle from centerPt to targetPt in degrees.
calcScale(int) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
a value of 100 means that the whole sequence should be displayed in the current visible window a factor of 1 means that one amino acid shoud be drawn as big as possible
calcScores(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
calculates scores for this alignment ( %id )
calcScores(QuatSymmetrySubunits, Matrix4d, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer
Returns minimum, mean, and maximum RMSD and TM-Score for two superimposed sets of subunits TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
calcSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
calculate(Structure, boolean) - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
Predicts the secondary structure of this Structure object, using a DSSP implementation.
calculateAsas() - Method in class org.biojava.nbio.structure.asa.AsaCalculator
Calculates the Accessible Surface Areas for the atoms given in constructor and with parameters given.
calculateBlockGap(int[][][]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Method that calculates the number of gaps in each subunit block of an optimal AFP alignment.
calculatedFragmentPairs(List<FragmentPair>) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
 
calculateDsspSecondaryStructure(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Generate the secondary structure for a Biojava structure object.
calculateIndirectAmbiguities() - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
Loops through all known nucleotides and attempts to find which are equivalent to each other.
calculateInterfaces(Structure) - Static method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Calculates the interfaces for a structure using default parameters
calculateMinCP(int[], int, int, int) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
Finds the alignment index of the residues minCPlength before and after the duplication.
calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
 
calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector
 
calculateOrder(AFPChain, Atom[]) - Method in interface org.biojava.nbio.structure.symmetry.internal.OrderDetector
 
calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector
 
calculateScores(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
Calculates and puts the RMSD and the average TM-Score of the MultipleAlignment.
calculateSuperpositionByIdx(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
calculateTp(Matrix4d) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method calculates pairing and step parameters from 4x4 transformation matrices (used internally) that comes out as a Matrix4d.
calculateWaldTestInfo(CoxInfo) - Static method in class org.biojava.nbio.survival.cox.CoxR
 
calculator - Variable in class org.biojava.nbio.structure.align.ce.CeMain
 
call() - Method in class org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner
 
call() - Method in class org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer
 
call() - Method in class org.biojava.nbio.alignment.template.CallableProfileProfileAligner
 
call() - Method in class org.biojava.nbio.ronn.ORonn
 
call() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
 
call() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer
 
CallablePairwiseSequenceAligner<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment.template
Implements a concurrency wrapper for a PairwiseSequenceAligner.
CallablePairwiseSequenceAligner(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner
Creates a pairwise sequence alignment task for simplified parallel execution.
CallablePairwiseSequenceScorer<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment.template
Implements a concurrency wrapper for a PairwiseSequenceScorer.
CallablePairwiseSequenceScorer(PairwiseSequenceScorer<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer
Creates a pairwise sequence scoring task for simplified parallel execution.
CallableProfileProfileAligner<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment.template
Implements a concurrency wrapper for a ProfileProfileAligner.
CallableProfileProfileAligner(ProfileProfileAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallableProfileProfileAligner
Creates a profile-profile alignment task for simplified parallel execution.
CallableStructureAlignment - Class in org.biojava.nbio.structure.align
Simple Callable Class that calculates a pairwise alignment in a different thread, so that multiple pairwise alignments can be run in parallel (examples: all-to-all alignments, DB search alignments).
CallableStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment
Default constructor.
CallableStructureAlignment(Atom[], Atom[], String, ConfigStrucAligParams) - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment
Constructor for all-to-all alignment calculation.
calNS(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
 
calSigAll(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
 
canComplement(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
Uses the Sequence's CompoundSet to decide if a compound can be assgined to ComplementCompound meaning it can complement
canonical - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
CartesianProduct<T> - Class in org.biojava.nbio.structure.quaternary
A cartesian product between two lists A and B is the set of all ordered pairs of the elements of both sets.
CartesianProduct(List<T>, List<T>) - Constructor for class org.biojava.nbio.structure.quaternary.CartesianProduct
Class constructor specifying the two lists of a cartesian product.
CARTOON - org.biojava.nbio.structure.gui.RenderStyle
 
CaseFreeAminoAcidCompoundSet - Class in org.biojava.nbio.aaproperties.xml
Set of proteinogenic amino acids.
CaseFreeAminoAcidCompoundSet() - Constructor for class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
CaseInsensitiveCompound - Class in org.biojava.nbio.core.sequence.transcription
Attempts to wrap compounds so it is possible to view them in a case insensitive manner
CaseInsensitiveCompound(NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
 
CaseInsensitiveTriplet(NucleotideCompound, NucleotideCompound, NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
CasePreservingProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io
A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.
CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
 
categorizeData(ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
Take a collection of categorical data and convert it to numeric to be used in cox calculations
CATH - org.biojava.nbio.structure.align.client.StructureName.Source
 
CATH_DOWNLOAD_ALL_RELEASES_DIR - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
 
CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
 
CATH_DOWNLOAD_URL - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
 
CathCategory - Enum in org.biojava.nbio.structure.cath
The categories found within CATH.
CathDatabase - Interface in org.biojava.nbio.structure.cath
General API for interacting with CATH.
CathDomain - Class in org.biojava.nbio.structure.cath
A class which represents a single CATH domain.
CathDomain() - Constructor for class org.biojava.nbio.structure.cath.CathDomain
 
CathFactory - Class in org.biojava.nbio.structure.cath
Controls global CathDatabases being used.
CathFragment - Class in org.biojava.nbio.structure.cath
 
CathFragment() - Constructor for class org.biojava.nbio.structure.cath.CathFragment
 
CathInstallation - Class in org.biojava.nbio.structure.cath
 
CathInstallation() - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
 
CathInstallation(String) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
 
CathInstallation(String, boolean, boolean) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
 
CathNode - Class in org.biojava.nbio.structure.cath
Represents a node in the CATH hierarchy.
CathNode() - Constructor for class org.biojava.nbio.structure.cath.CathNode
 
CathSegment - Class in org.biojava.nbio.structure.cath
 
CathSegment() - Constructor for class org.biojava.nbio.structure.cath.CathSegment
 
CB_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the side-chain C-beta atom
Cd - org.biojava.nbio.structure.Element
 
CDD_SEARCH - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
CDS - Static variable in class org.biojava.nbio.genome.util.ChromosomeMappingTools
 
CDSComparator - Class in org.biojava.nbio.core.sequence
 
CDSComparator() - Constructor for class org.biojava.nbio.core.sequence.CDSComparator
 
CDSSequence - Class in org.biojava.nbio.core.sequence
Represents a exon or coding sequence in a gene.
CDSSequence(TranscriptSequence, int, int, int) - Constructor for class org.biojava.nbio.core.sequence.CDSSequence
 
Ce - org.biojava.nbio.structure.Element
 
CE_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
 
CECalculator - Class in org.biojava.nbio.structure.align.ce
This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CECalculator(CeParameters) - Constructor for class org.biojava.nbio.structure.align.ce.CECalculator
 
CeCalculatorEnhanced - Class in org.biojava.nbio.structure.align.ce
This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CeCalculatorEnhanced(CeParameters) - Constructor for class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
CeCPMain - Class in org.biojava.nbio.structure.align.ce
A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.
CeCPMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain
 
CeCPMain.CPRange - Class in org.biojava.nbio.structure.align.ce
Tiny wrapper for the disallowed regions of an alignment.
CECPParameters - Class in org.biojava.nbio.structure.align.ce
Provides parameters to CeCPMain
CECPParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CECPParameters
 
CECPParameters.DuplicationHint - Enum in org.biojava.nbio.structure.align.ce
 
CeCPStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
 
CeCPUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
 
CeCPUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
 
CeCPUserArgumentProcessor.CeCPStartupParams - Class in org.biojava.nbio.structure.align.ce
 
ceil(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
Return the smallest key in the table >= k.
CELLTRANSL - org.biojava.nbio.structure.xtal.TransformType
 
CeMain - Class in org.biojava.nbio.structure.align.ce
The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.
CeMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeMain
 
censored - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
CensorStatus - Class in org.biojava.nbio.survival.kaplanmeier.figure
 
CensorStatus() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
CensorStatus(String, Double, String) - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
CensorStatusSelect - Interface in org.biojava.nbio.survival.kaplanmeier.figure
 
center(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
Center a cloud of points.
centerAtoms(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
Center the atoms at the Centroid.
centerAtoms(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc
Center the atoms at the Centroid, if the centroid is already know.
centered - Variable in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
 
centerOfMass(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
Returns the center of mass of the set of atoms.
centroid(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
Calculate the centroid of the point cloud.
CeParameters - Class in org.biojava.nbio.structure.align.ce
Contains the parameters that can be sent to CE
CeParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CeParameters
 
CeParameters.ScoringStrategy - Enum in org.biojava.nbio.structure.align.ce
 
CeSideChainMain - Class in org.biojava.nbio.structure.align.ce
 
CeSideChainMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainMain
 
CeSideChainUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
 
CeSideChainUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
 
CeStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
CeSymm - Class in org.biojava.nbio.structure.symmetry.internal
Identify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment.
CeSymmIterative - Class in org.biojava.nbio.structure.symmetry.internal
Iterative version of CeSymm that aims at identifying all symmetry axis of a structure.
CeSymmIterative(CESymmParameters) - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative
For the iterative algorithm to work properly the refinement and optimization options should be turned on, because the alignment has to be consistent at every recursive step.
CESymmParameters - Class in org.biojava.nbio.structure.symmetry.internal
Provides parameters to CeSymm.
CESymmParameters() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
CESymmParameters(CESymmParameters) - Constructor for class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
CESymmParameters.OrderDetectorMethod - Enum in org.biojava.nbio.structure.symmetry.internal
 
CESymmParameters.RefineMethod - Enum in org.biojava.nbio.structure.symmetry.internal
 
CESymmParameters.SymmetryType - Enum in org.biojava.nbio.structure.symmetry.internal
The internal symmetry detection can be divided into two types: CLOSE: includes the circular and dihedral symmetries, and OPEN: includes the helical and protein repeats symmetries.
CeSymmResult - Class in org.biojava.nbio.structure.symmetry.internal
This Class stores all the relevant information of an internal symmetry result obtained with CeSymm.
CeSymmResult() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
CeUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
process the arguments from command line
CeUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
 
CeUserArgumentProcessor.CeStartupParams - Class in org.biojava.nbio.structure.align.ce
 
Cf - org.biojava.nbio.structure.Element
 
Chain - Interface in org.biojava.nbio.structure
Defines the interface for a Chain.
CHAIN_NR_SYMBOL - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
 
CHAIN_REGEX - Static variable in class org.biojava.nbio.structure.ResidueRange
 
CHAIN_SPLIT_SYMBOL - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
 
chainEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
 
CHAINID_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier
URL parameter specifying a single chain to include; overridden by residues
ChainImpl - Class in org.biojava.nbio.structure
A Chain in a PDB file.
ChainImpl() - Constructor for class org.biojava.nbio.structure.ChainImpl
Constructs a ChainImpl object.
chainName - Variable in class org.biojava.nbio.structure.align.client.StructureName
 
ChainSignature - Class in org.biojava.nbio.structure.symmetry.misc
 
ChainSignature(String, int, List<String>) - Constructor for class org.biojava.nbio.structure.symmetry.misc.ChainSignature
 
change(String) - Method in interface org.biojava.nbio.survival.data.ChangeValue
 
changeColumnHeader(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
changeColumnHeader(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
changeColumnsHeaders(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
Change the columns in the HashMap Key to the name of the value
changeRowHeader(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
changeRowHeader(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
ChangeValue - Interface in org.biojava.nbio.survival.data
 
charAt(int) - Method in class org.biojava.nbio.survival.data.CompactCharSequence
 
CHARGE - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
 
ChargeAdder - Class in org.biojava.nbio.structure.io
A class to add appropriate charge information to a structure.
ChargeAdder() - Constructor for class org.biojava.nbio.structure.io.ChargeAdder
 
checkDoFirstInstall() - Method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
Checks if the chemical components already have been installed into the PDB directory.
checkFileExists(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
 
checkFileExists(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
 
checkInput(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
Check that the input to the superposition algorithms is valid.
checkPoint() - Method in class org.biojava.nbio.ronn.Timer
 
checkScaleMatrix(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
Given a scale matrix parsed from a PDB entry (SCALE1,2,3 records), compares it to our calculated Mtranspose matrix to see if they coincide and returns true if they do.
checkScaleMatrixConsistency(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
Given a scale matrix parsed from the PDB entry (SCALE1,2,3 records), checks that the matrix is a consistent scale matrix by comparing the cell volume to the inverse of the scale matrix determinant (tolerance of 1/100).
checkSequence(String) - Static method in class org.biojava.nbio.aaproperties.Utils
Checks if the sequence contains invalid characters.
checkSequence(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils
Checks if the sequence contains invalid characters.
checksum(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
Performs a simple CRC64 checksum on any given sequence.
CHEM_COMP_CACHE_DIRECTORY - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
 
chem_comp_type - Variable in enum org.biojava.nbio.structure.chem.ResidueType
String value of the type
chemComp - Variable in class org.biojava.nbio.structure.HetatomImpl
 
ChemComp - Class in org.biojava.nbio.structure.chem
Properties of a chemical component.
ChemComp() - Constructor for class org.biojava.nbio.structure.chem.ChemComp
 
ChemCompAtom - Class in org.biojava.nbio.structure.chem
Properties of an atom of a chemical component.
ChemCompAtom() - Constructor for class org.biojava.nbio.structure.chem.ChemCompAtom
 
ChemCompBond - Class in org.biojava.nbio.structure.chem
Properties of a bond in a chemical component.
ChemCompBond() - Constructor for class org.biojava.nbio.structure.chem.ChemCompBond
 
ChemCompConsumer - Interface in org.biojava.nbio.structure.io.cif
Create the ChemicalComponentDictionary from CIF data.
ChemCompConsumerImpl - Class in org.biojava.nbio.structure.io.cif
Consumes a CCD file to create the ChemicalComponentDictionary.
ChemCompConsumerImpl() - Constructor for class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
 
ChemCompConverter - Class in org.biojava.nbio.structure.io.cif
Convert CifFiles to chem comps.
ChemCompConverter() - Constructor for class org.biojava.nbio.structure.io.cif.ChemCompConverter
 
ChemCompDescriptor - Class in org.biojava.nbio.structure.chem
Properties of the chemical component descriptor.
ChemCompDescriptor() - Constructor for class org.biojava.nbio.structure.chem.ChemCompDescriptor
 
ChemCompDistribution - Class in demo
 
ChemCompDistribution() - Constructor for class demo.ChemCompDistribution
 
ChemCompGroupFactory - Class in org.biojava.nbio.structure.chem
 
ChemCompGroupFactory() - Constructor for class org.biojava.nbio.structure.chem.ChemCompGroupFactory
 
ChemCompProvider - Interface in org.biojava.nbio.structure.chem
Interface that is implemented by all classes that can provide ChemComp definitions.
ChemCompTools - Class in org.biojava.nbio.structure.chem
 
ChemCompTools() - Constructor for class org.biojava.nbio.structure.chem.ChemCompTools
 
CHEMICAL_MODIFICATION - org.biojava.nbio.protmod.ModificationCategory
 
ChemicalComponentDictionary - Class in org.biojava.nbio.structure.chem
A representation of the Chemical Component Dictionary.
ChemicalComponentDictionary() - Constructor for class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
 
children() - Method in class org.biojava.nbio.alignment.GuideTree.Node
 
chiSq(double, int) - Static method in class org.biojava.nbio.survival.cox.stats.ChiSq
 
ChiSq - Class in org.biojava.nbio.survival.cox.stats
 
ChiSq() - Constructor for class org.biojava.nbio.survival.cox.stats.ChiSq
 
chol() - Method in class org.biojava.nbio.structure.jama.Matrix
Cholesky Decomposition
Cholesky2 - Class in org.biojava.nbio.survival.cox.stats
 
Cholesky2() - Constructor for class org.biojava.nbio.survival.cox.stats.Cholesky2
 
CholeskyDecomposition - Class in org.biojava.nbio.structure.jama
Cholesky Decomposition.
CholeskyDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.CholeskyDecomposition
Cholesky algorithm for symmetric and positive definite matrix.
ChooseDirAction - Class in org.biojava.nbio.structure.align.gui
Ask the user to provide a directory containting PDB files.
ChooseDirAction(JTextField, UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.gui.ChooseDirAction
 
CHROMOSOME - org.biojava.nbio.core.sequence.DNASequence.DNAType
 
CHROMOSOME - Static variable in class org.biojava.nbio.genome.util.ChromosomeMappingTools
 
ChromosomeMappingTools - Class in org.biojava.nbio.genome.util
A class that can map chromosomal positions to mRNA (coding sequence) positions.
ChromosomeMappingTools() - Constructor for class org.biojava.nbio.genome.util.ChromosomeMappingTools
 
ChromosomeSequence - Class in org.biojava.nbio.core.sequence
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
ChromosomeSequence() - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
Empty constructor used by tools that need a proper Bean that allows the actual sequence data to be set after construction.
ChromosomeSequence(String) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
String is king and assume DNA
ChromosomeSequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet
ChromosomeSequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
Fairly important constructor given the size of a ChromsomeSequence where the ProxySequenceReader could load from disk via RandomAccessFile so that the sequence doesn't need to be kept in memory.
ChromosomeSequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet
ChromPos - Class in org.biojava.nbio.genome.parsers.genename
Created by ap3 on 27/10/2014.
ChromPos(int, int) - Constructor for class org.biojava.nbio.genome.parsers.genename.ChromPos
 
Chsolve2 - Class in org.biojava.nbio.survival.cox.stats
 
Chsolve2() - Constructor for class org.biojava.nbio.survival.cox.stats.Chsolve2
 
CIF - org.biojava.nbio.structure.io.StructureFiletype
 
CIF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.BcifFileReader
 
CIF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.CifFileReader
 
CIF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.BcifFileReader
 
CIF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.CifFileReader
 
CifBean - Interface in org.biojava.nbio.structure.io.cif
Flag for BioJava beans that resemble categories defined by the mmCIF schema.
CifChainSupplierImpl - Class in org.biojava.nbio.structure.io.cif
Convert a chain to a CifFile.
CifChainSupplierImpl() - Constructor for class org.biojava.nbio.structure.io.cif.CifChainSupplierImpl
 
CifFileConsumer<S> - Interface in org.biojava.nbio.structure.io.cif
Defines a rather generic interface which allows to populate some data structure with data parsed from a CIF file.
CifFileReader - Class in org.biojava.nbio.structure.io
Parse text Cif files and provide capabilities to store them locally.
CifFileReader() - Constructor for class org.biojava.nbio.structure.io.CifFileReader
Constructs a new CifFileReader, initializing the extensions member variable.
CifFileReader(String) - Constructor for class org.biojava.nbio.structure.io.CifFileReader
Constructs a new CifFileReader, initializing the extensions member variable.
CifFileSupplier<S> - Interface in org.biojava.nbio.structure.io.cif
Create a CifFile instance for a given container of structure data.
CifStructureConsumer - Interface in org.biojava.nbio.structure.io.cif
Defines the categories to consume during CIF parsing.
CifStructureConsumerImpl - Class in org.biojava.nbio.structure.io.cif
An implementation of a CifFileConsumer for BioJava.
CifStructureConsumerImpl(FileParsingParameters) - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
CifStructureConverter - Class in org.biojava.nbio.structure.io.cif
Convert BioJava structures to CifFiles and vice versa.
CifStructureConverter() - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureConverter
 
CifStructureSupplierImpl - Class in org.biojava.nbio.structure.io.cif
Convert a structure to a CifFile.
CifStructureSupplierImpl() - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureSupplierImpl
 
CIRCULAR_DNA - Static variable in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
 
circularLocation(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
circularLocation(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
Cl - org.biojava.nbio.structure.Element
 
claFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
 
Class - org.biojava.nbio.structure.cath.CathCategory
 
Class - org.biojava.nbio.structure.scop.ScopCategory
 
classEqual(Object, Object) - Static method in class org.biojava.nbio.core.util.Equals
This method should be called before beginning any equals methods.
ClasspathResource - Class in org.biojava.nbio.core.sequence.io.util
This object represents a classpath resource on the local system.
ClasspathResource(String) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource
Basic constructor only allowing you to specify where to find the file.
ClasspathResource(String, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource
Advanced constructor which allows you to optionally pre-cache the data
ClasspathResource(String, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource
Advanced constructor which lets you set the preCache variable and to force the type of file we are decompressing.
cleanSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
Removes all whitespace chars in the sequence string
cleanSequence(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils
Returns a new sequence with all invalid characters being replaced by '-'.
cleanup() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc
 
cleanup() - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
 
cleanup() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
 
cleanup() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc
 
cleanup() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
 
cleanup(List<Domain>) - Static method in class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
 
cleanUp() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
 
cleanUp() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
 
cleanUp() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
 
cleanUpAltLocs(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
Cleans up the structure's alternate location (altloc) groups.
clear() - Static method in class org.biojava.nbio.core.util.FlatFileCache
Removes all elements from the cache
clear() - Method in class org.biojava.nbio.core.util.SoftHashMap
 
clear() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
reset all suggestions
clear() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
 
clear() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
 
clear() - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
Clear the cached scores.
clear() - Method in interface org.biojava.nbio.structure.align.multiple.Block
Clear scores and other properties which depend on the specific alignment.
clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
clear() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
Clear scores and other properties which depend on the specific alignment.
clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Clear scores and other properties which depend on the specific alignment.
clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Clear scores and other properties which depend on the specific alignment.
clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
clear() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
Clears all domains, requiring the file to be reparsed for subsequent accesses
clear() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
clear() - Method in interface org.biojava.nbio.structure.gui.Selection
 
clear() - Method in class org.biojava.nbio.structure.gui.SelectionImpl
 
clear() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
Clear the current display
clear() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
Clears all finite endpoints
clear() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
 
clear() - Method in class org.biojava.nbio.survival.data.WorkSheet
See if we can free up memory
clearAlgorithms() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
Removes all algorithms from the list
clearAtoms() - Method in interface org.biojava.nbio.structure.Group
Remove all atoms from this group.
clearAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl
 
clearCache() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
clearCache() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
Nullifies cached arrays/objects.
clearCache() - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory
Force the in-memory cache to be reset.
clearExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
clear the supported file extensions
clearListeners() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
 
clearListeners() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
 
clearListeners() - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
 
ClinicalMetaDataOutcome - Class in org.biojava.nbio.survival.kaplanmeier.metadata
 
ClinicalMetaDataOutcome() - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
 
CliTools - Class in org.biojava.nbio.structure.align.util
Utilities for autoconfiguring javabeans based on command line arguments.
clone() - Method in class org.biojava.nbio.structure.align.model.AFPChain
Creates and returns a copy of this object.
clone() - Method in interface org.biojava.nbio.structure.align.multiple.Block
Creates and returns an identical copy of this block.
clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
clone() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
Creates and returns an identical copy of this blockset, including a deep copy of all constituent Blocks.
clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Creates and returns an identical copy of this alignment, including a deep copy of all constituent BlockSets.
clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Creates and returns an identical copy of this ensemble, including a deep clone of all constituent alignments.
clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
clone() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
clone() - Method in class org.biojava.nbio.structure.AminoAcidImpl
returns and identical copy of this Group object .
clone() - Method in class org.biojava.nbio.structure.asa.GroupAsa
 
clone() - Method in interface org.biojava.nbio.structure.Atom
Return an identical copy of this object .
clone() - Method in class org.biojava.nbio.structure.AtomImpl
returns and identical copy of this object .
clone() - Method in interface org.biojava.nbio.structure.Chain
Returns an identical copy of this Chain.
clone() - Method in class org.biojava.nbio.structure.ChainImpl
 
clone() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
clone() - Method in interface org.biojava.nbio.structure.Group
Returns and identical copy of this Group object .
clone() - Method in class org.biojava.nbio.structure.GroupIterator
Creates and returns a copy of this object.
clone() - Method in class org.biojava.nbio.structure.HetatomImpl
returns and identical copy of this Group object .
clone() - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
clone() - Method in class org.biojava.nbio.structure.jama.Matrix
Clone the Matrix object.
clone() - Method in class org.biojava.nbio.structure.NucleotideImpl
 
clone() - Method in class org.biojava.nbio.structure.PdbId
 
clone() - Method in class org.biojava.nbio.structure.scop.ScopDescription
 
clone() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
clone() - Method in class org.biojava.nbio.structure.secstruc.HBond
 
clone() - Method in interface org.biojava.nbio.structure.Structure
Return an identical copy of this Structure object
clone() - Method in class org.biojava.nbio.structure.StructureImpl
Returns an identical copy of this structure .
clone() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
clone(Object) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
Subclasses should override clone and use the copy constructor.
cloneAtomArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
Provides an equivalent copy of Atoms in a new array.
cloneAtomsAndBonds(Group) - Method in class org.biojava.nbio.structure.HetatomImpl
 
cloneDM(BasicSymmetricalDistanceMatrix) - Static method in class org.biojava.nbio.phylo.ForesterWrapper
Helper function to clone a forester symmetrical DistanceMatrix.
cloneGroups(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
Clone a set of representative Atoms, but returns the parent groups
clonePoint() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
clonePoint() - Method in interface org.biojava.nbio.core.sequence.location.template.Point
Returns a copy of this point
clonePoint3dArray(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
Clone an array of points.
close() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
 
close() - Method in class org.biojava.nbio.core.sequence.io.FastaReader
 
close() - Method in class org.biojava.nbio.core.sequence.io.GenbankReader
 
close() - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
close() - Method in interface org.biojava.nbio.core.util.XMLWriter
Close this XMLWriter, and its underlying stream.
close() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitFacade
Closes .2bit file twoBitParser.
close() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
Method closes current sequence and it's necessary to invoke it before setting new current sequence.
close() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
 
close(Closeable) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
Closes any Object which implements the interface Closeable and sending any error to the logger but not forcing any explicit catching of stream errors.
CLOSED - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
 
closeParser() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
Method closes random access file descriptor.
closeTag(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
closeTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter
Closes an un-qualified element.
closeTag(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
closeTag(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter
Closes an element
CLUSTALW - org.biojava.nbio.core.alignment.template.Profile.StringFormat
 
CLUSTALW - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
 
cluster(List<Subunit>, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.cluster.SubunitClusterer
 
cluster(List<Domain>, PDPDistanceMatrix) - Static method in class org.biojava.nbio.structure.domain.pdp.ClusterDomains
 
cluster(AlternativeAlignment[]) - Static method in class org.biojava.nbio.structure.align.ClusterAltAligs
 
cluster(AlternativeAlignment[], int) - Static method in class org.biojava.nbio.structure.align.ClusterAltAligs
 
cluster(Structure, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.cluster.SubunitClusterer
 
ClusterAltAligs - Class in org.biojava.nbio.structure.align
A class that clusters alternative alignments according to their similarity.
ClusterAltAligs() - Constructor for class org.biojava.nbio.structure.align.ClusterAltAligs
 
ClusterDomains - Class in org.biojava.nbio.structure.domain.pdp
 
ClusterDomains() - Constructor for class org.biojava.nbio.structure.domain.pdp.ClusterDomains
 
Cm - org.biojava.nbio.structure.Element
 
CMD - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
Co - org.biojava.nbio.structure.Element
 
Codon(Table.CaseInsensitiveTriplet) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
Codon(Table.CaseInsensitiveTriplet, AminoAcidCompound, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
CodonCompound - Class in org.biojava.nbio.core.sequence.compound
Define a codon
CodonCompound(NucleotideCompound, NucleotideCompound, NucleotideCompound, boolean) - Constructor for class org.biojava.nbio.core.sequence.compound.CodonCompound
 
coil - org.biojava.nbio.structure.secstruc.SecStrucType
 
CollectionTools - Class in org.biojava.nbio.structure.align.util
Utilities for working with collections.
CollectionTools() - Constructor for class org.biojava.nbio.structure.align.util.CollectionTools
 
colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Returns a Jmol script that colors subunits by their sequence cluster ids.
colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
Returns a Jmol script that colors subunits by their sequence cluster ids.
colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Returns a Jmol script that colors the subunits of a structure by different colors
colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
Returns a Jmol script that colors the subunits of a structure by different colors
colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Returns a Jmol script that colors subunits to highlight the symmetry within a structure
colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
Returns a Jmol script that colors subunits to highlight the symmetry within a structure Different subunits should have a consistent color scheme or different shade of the same colors
colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
ColorConverter - Class in org.biojava.nbio.structure.symmetry.jmolScript
 
ColorConverter() - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
 
coloring - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
ColorInterpolator - Interface in org.biojava.nbio.structure.gui.util.color
 
colorPalette - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
ColorUtils - Class in org.biojava.nbio.structure.gui.util.color
 
ColorUtils() - Constructor for class org.biojava.nbio.structure.gui.util.color.ColorUtils
 
colorWheel - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
 
column - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
 
combine(List<Integer>, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
 
combine(BiologicalAssemblyTransformation, BiologicalAssemblyTransformation) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
Returns the combination (product) of two biological assembly transformations.
combineWith(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup
Combine the ResidueGroup with the alignment block.
combineWith(Stoichiometry) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
Make a combined Stoichiometry object of this and the other.
comFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
 
COMMAND_LINE_HELP - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
CommandPrompt - Class in org.biojava.nbio.aaproperties
 
CommandPrompt() - Constructor for class org.biojava.nbio.aaproperties.CommandPrompt
 
CommandPrompt.PropertyName - Enum in org.biojava.nbio.aaproperties
 
COMMENT - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
COMMENT_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
CompactCharSequence - Class in org.biojava.nbio.survival.data
http://www.javamex.com/tutorials/memory/ascii_charsequence.shtml
CompactCharSequence(String) - Constructor for class org.biojava.nbio.survival.data.CompactCharSequence
 
COMPARATOR - Static variable in class org.biojava.nbio.ontology.Synonym
 
compare(int[], int[]) - Method in class org.biojava.nbio.structure.align.helper.IdxComparator
 
compare(AlignerHelper.Anchor, AlignerHelper.Anchor) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator
 
compare(CDSSequence, CDSSequence) - Method in class org.biojava.nbio.core.sequence.CDSComparator
Used to sort two CDSSequences where Negative Strand makes it tough
compare(ExonSequence, ExonSequence) - Method in class org.biojava.nbio.core.sequence.ExonComparator
 
compare(AbstractSequence<?>, AbstractSequence<?>) - Method in class org.biojava.nbio.core.sequence.SequenceComparator
 
compare(AlternativeAlignment, AlternativeAlignment) - Method in class org.biojava.nbio.structure.align.pairwise.AltAligComparator
 
compare(Segment, Segment) - Method in class org.biojava.nbio.structure.domain.pdp.SegmentComparator
 
compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator
 
compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
 
compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.MeanModelComparator
 
compare(SurvivalInfo, SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator
 
compare(SurvivalInfo, SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator
 
compareTo(Point) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
 
compareTo(Point) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
compareTo(FastaSequence) - Method in class org.biojava.nbio.data.sequence.FastaSequence
 
compareTo(Cytoband) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
 
compareTo(GeneChromosomePosition) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
compareTo(GeneName) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
compareTo(Synonym) - Method in class org.biojava.nbio.ontology.Synonym
 
compareTo(ProteinModification) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
compareTo(ModifiedCompound) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
compareTo(StructureGroup) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
compareTo(PdbPair) - Method in class org.biojava.nbio.structure.align.client.PdbPair
 
compareTo(StructureName) - Method in class org.biojava.nbio.structure.align.client.StructureName
Orders identifiers lexicographically by PDB ID and then full Identifier
compareTo(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
compareTo(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
compareTo(Domain) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
 
compareTo(Segment) - Method in class org.biojava.nbio.structure.domain.pdp.Segment
 
compareTo(PdbId) - Method in class org.biojava.nbio.structure.PdbId
 
compareTo(BiologicalAssemblyTransformation) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
 
compareTo(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber
Compare residue numbers by chain, sequence number, and insertion code
compareTo(Site) - Method in class org.biojava.nbio.structure.Site
 
compareTo(ChainSignature) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
 
compareTo(SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
compareTo(SurvivalInfoIndex) - Method in class org.biojava.nbio.survival.cox.SurvivalInfoIndex
 
compareTo(CensorStatus) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
compareTo(HmmerDomain) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
compareTo(HmmerResult) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
compareToPositional(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber
Compare residue numbers by sequence number and insertion code, ignoring the chain
Comparison - Class in org.biojava.nbio.phylo
This class provides static methods for the calculation of the percentage of identity between two aligned sequences.
Comparison() - Constructor for class org.biojava.nbio.phylo.Comparison
 
complementBase(char, boolean) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method returns the complement of a base.
ComplementCompound - Interface in org.biojava.nbio.core.sequence.template
 
ComplementSequenceView<C extends ComplementCompound> - Class in org.biojava.nbio.core.sequence.views
For a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlying base e.g. base A will become base T
ComplementSequenceView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.views.ComplementSequenceView
 
complete() - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
Notify this listener the FASTQ formatted sequence is complete.
complete() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
completeCircularPasses(int, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e. if we have a sequence of length 10 and the location 3..52 we make 4 complete passes through the genome to go from position 3 to position 52.
completeCircularPasses(int, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e. if we have a sequence of length 10 and the location 3..52 we make 4 complete passes through the genome to go from position 3 to position 52.
completeGroup() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
Starts with an incomplete set of group generators in `permutations` and expands it to include all possible combinations.
Component - Class in org.biojava.nbio.protmod
contains information about a certain Component.
COMPONENTS_FILE_LOCATION - Static variable in class org.biojava.nbio.structure.chem.AllChemCompProvider
 
ComponentXMLConverter - Class in org.biojava.nbio.protmod.io
 
ComponentXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.ComponentXMLConverter
 
COMPOSED_OPERATOR_SEPARATOR - Static variable in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
The character separating operator ids that are composed.
COMPOSITION_BASED_STATISTICS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
Compound - Interface in org.biojava.nbio.core.sequence.template
 
COMPOUND - org.biojava.nbio.core.alignment.template.AlignedSequence.Step
 
CompoundNotFoundException - Exception in org.biojava.nbio.core.exceptions
 
CompoundNotFoundException(String) - Constructor for exception org.biojava.nbio.core.exceptions.CompoundNotFoundException
 
compoundsEqual(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
compoundsEquivalent(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
compoundsEquivalent(C, C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
 
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
 
CompoundSet<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
 
compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
Should return the maximum amount of compounds we can encode per int
compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
 
compoundToInt(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
CompoundTranslator<F extends Compound,​T extends Compound> - Interface in org.biojava.nbio.core.sequence.template
 
computeMolecularWeight(ElementTable) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
Computes and store the molecular weight of each amino acid by its symbol in aaSymbol2MolecularWeight.
ConcurrencyTools - Class in org.biojava.nbio.core.util
Static utility to easily share a thread pool for concurrent/parallel/lazy execution.
cond() - Method in class org.biojava.nbio.structure.jama.Matrix
Matrix condition (2 norm)
cond() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
Two norm condition number
ConfigPDBInstallPanel - Class in org.biojava.nbio.structure.align.gui
 
ConfigStrucAligParams - Interface in org.biojava.nbio.structure.align.ce
 
ConfigurationException - Exception in org.biojava.nbio.structure.align.util
 
ConfigurationException() - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
 
ConfigurationException(String) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
Constructs a ConfigurationException object.
ConfigurationException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
 
ConfigurationException(Throwable) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
Constructs a ConfigurationException object.
configureBean(Object, String[]) - Static method in class org.biojava.nbio.structure.align.util.CliTools
Configure a JavaBean based on a set of command line arguments.
configureParameters() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
 
configureParameters() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
 
ConfigXMLHandler - Class in org.biojava.nbio.structure.align.webstart
XML content handler for serialisation of RegistryConfiguration class
ConfigXMLHandler() - Constructor for class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
 
consistentAccessions(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
Scans a list of locations and returns true if all the given locations are linked to the same sequence.
CONSORTIUM_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
CONSTANT - org.biojava.nbio.alignment.template.GapPenalty.Type
 
constrain(double) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Constrain the specified quality score in double precision to the minimum and maximum quality scores in int precision.
Constraints - Class in org.biojava.nbio.aaproperties
This class is used to support the implementation of properties stated in IPeptideProperties.
Constraints() - Constructor for class org.biojava.nbio.aaproperties.Constraints
 
constructWithCopy(double[][]) - Static method in class org.biojava.nbio.structure.jama.Matrix
Construct a matrix from a copy of a 2-D array.
consume(Category) - Method in interface org.biojava.nbio.structure.io.cif.MetalBondConsumer
 
consume(Category) - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl
 
consumeAtomSite(AtomSite) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
Consume a particular Cif category.
consumeAtomSite(AtomSite) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
consumeAtomSites(AtomSites) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
Consume a particular Cif category.
consumeAtomSites(AtomSites) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
consumeAuditAuthor(AuditAuthor) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
Consume a particular Cif category.
consumeAuditAuthor(AuditAuthor) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
consumeCell(Cell) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
Consume a particular Cif category.
consumeCell(Cell) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
consumeChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer
Consume a particular Cif category.
consumeChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
 
consumeChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
Consume a particular Cif category.
consumeChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
consumeChemCompAtom(ChemCompAtom) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer
Consume a particular Cif category.
consumeChemCompAtom(ChemCompAtom) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
 
consumeChemCompBond(ChemCompBond) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer
Consume a particular Cif category.
consumeChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
 
consumeChemCompBond(ChemCompBond) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
Consume a particular Cif category.
consumeChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
consumeDatabasePDBRemark(DatabasePDBRemark) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
Consume a particular Cif category.
consumeDatabasePDBRemark(DatabasePDBRemark) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
consumeDatabasePDBRev(DatabasePDBRev) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
Consume a particular Cif category.
consumeDatabasePDBRev(DatabasePDBRev) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
consumeDatabasePDBRevRecord(DatabasePDBRevRecord) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
Consume a particular Cif category.
consumeDatabasePDBRevRecord(DatabasePDBRevRecord) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
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(File, File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
Copy the content of file src to dst TODO since java 1.7 this is provided in java.nio.file.Files
copy(InputStream, OutputStream) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
Moves the bytes from input to output using a 4KB byte array.
copyEmblReference(EmblReference) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
return copy of EmblReference
copyFile(File, File) - Static method in class org.biojava.nbio.phosphosite.Dataset
 
copyLigandsByProximity(Structure, Structure) - Static method in class org.biojava.nbio.structure.SubstructureIdentifier
Supplements the reduced structure with ligands from the full structure based on a distance cutoff.
copyLigandsByProximity(Structure, Structure, double, int, int) - Static method in class org.biojava.nbio.structure.SubstructureIdentifier
Supplements the reduced structure with ligands from the full structure based on a distance cutoff.
CoreSuperimposer - Class in org.biojava.nbio.structure.align.multiple.util
Superimposes the core aligned residues of every structure in a MultipleAlignment onto a reference structure.
CoreSuperimposer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer
Default Constructor.
CoreSuperimposer(int) - Constructor for class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer
Constructor using a specified structure as reference.
countAT(Sequence<NucleotideCompound>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
Returns the count of AT in the given sequence
countCompounds(C...) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
 
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
Counts the number of times a compound appears in this sequence store
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
 
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
Delegates to SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[])
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
countCompounds(C...) - Method in interface org.biojava.nbio.core.sequence.template.Sequence
Returns the number of times we found a compound in the Sequence
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
countCompounds(Sequence<C>, C...) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
For the given vargs of compounds this method counts the number of times those compounds appear in the given sequence
countGC(Sequence<NucleotideCompound>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
Returns the count of GC in the given sequence
countMatchesInSequence(String, String) - Static method in class org.biojava.nbio.data.sequence.FastaSequence
 
COVALENT - org.biojava.nbio.structure.BondType
 
CoxCC - Class in org.biojava.nbio.survival.cox
 
CoxCC() - Constructor for class org.biojava.nbio.survival.cox.CoxCC
 
CoxCoefficient - Class in org.biojava.nbio.survival.cox
 
CoxCoefficient() - Constructor for class org.biojava.nbio.survival.cox.CoxCoefficient
 
CoxComparatorInterface - Interface in org.biojava.nbio.survival.cox.comparators
 
CoxHelper - Class in org.biojava.nbio.survival.cox
The CoxHelper class is provided to start with a tab delimited file in a similar process in R and return the results as a CoxInfo class.
CoxHelper() - Constructor for class org.biojava.nbio.survival.cox.CoxHelper
 
CoxInfo - Class in org.biojava.nbio.survival.cox
Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R
CoxInfo() - Constructor for class org.biojava.nbio.survival.cox.CoxInfo
 
CoxMart - Class in org.biojava.nbio.survival.cox
 
CoxMart() - Constructor for class org.biojava.nbio.survival.cox.CoxMart
 
CoxMethod - Enum in org.biojava.nbio.survival.cox
 
coxphfitSCleanup(CoxInfo, boolean, boolean, ArrayList<String>) - Method in class org.biojava.nbio.survival.cox.CoxR
 
CoxR - Class in org.biojava.nbio.survival.cox
This is a port of the R survival code used for doing Cox Regression.
CoxR() - Constructor for class org.biojava.nbio.survival.cox.CoxR
 
coxsafe(double) - Method in class org.biojava.nbio.survival.cox.CoxR
 
CoxScore - Class in org.biojava.nbio.survival.cox
 
CoxScore() - Constructor for class org.biojava.nbio.survival.cox.CoxScore
 
CoxVariables - Class in org.biojava.nbio.survival.cox
 
CoxVariables(String, String, String) - Constructor for class org.biojava.nbio.survival.cox.CoxVariables
 
CoxVariablesOverallModelFitComparator - Class in org.biojava.nbio.survival.cox.comparators
 
CoxVariablesOverallModelFitComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator
Variables are stored as a string representation of an ArrayList [META_GENE] or [trtg, META_GENE] add variables used in cox regression to an array and then do toString.
CoxVariablesVariableComparator - Class in org.biojava.nbio.survival.cox.comparators
 
CoxVariablesVariableComparator(String, String) - Constructor for class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
 
cpFastaToAfpChain(File, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
cpFastaToAfpChain(String, String, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
 
cpFastaToAfpChain(ProteinSequence, ProteinSequence, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
cpPoint - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
The CP point, specified as a residue index
CPRange() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
 
Cr - org.biojava.nbio.structure.Element
 
CRC64Checksum - Class in org.biojava.nbio.core.util
Utility class that calculates a CRC64 checksum on a stream of bytes.
CRC64Checksum() - Constructor for class org.biojava.nbio.core.util.CRC64Checksum
 
createAFPChain(Atom[], Atom[], ResidueNumber[], ResidueNumber[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Fundamentally, an alignment is just a list of aligned residues in each protein.
createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.
createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
 
createBlastHit() - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
 
createBlastHsp() - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
createBlastResult() - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
createDNASequence(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
Create and return a new DNASequence from the specified FASTQ formatted sequence.
createDNASequenceWithErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
Create and return a new DNASequence with error probabilities from the specified FASTQ formatted sequence.
createDNASequenceWithQualityScores(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
Create and return a new DNASequence with quality scores from the specified FASTQ formatted sequence.
createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence.
createErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
Create and return a new QuantityFeature from the error probabilities of the specified FASTQ formatted sequence.
createGradients() - Static method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
createImage(String, String, Object, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
createImageIcon(String) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
Returns an ImageIcon, or null if the path was invalid.
createIterator(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
Creates a simple sequence iterator which moves through a sequence going from 1 to the length of the Sequence.
createObjects(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
 
createObjects(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
 
createObjects(double) - Method in interface org.biojava.nbio.core.search.io.ResultFactory
Launch the parsing and get back a list of Result objects representing the search result in the specified file.
createOntology(String, String) - Method in interface org.biojava.nbio.ontology.OntologyFactory
Creates a new Ontology
createOntologyTerm(Ontology) - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
createOutput(String, String) - Method in class org.biojava.nbio.aaproperties.xml.SchemaGenerator
 
createPurelyNonPolyEntities(List<List<Chain>>, List<List<Chain>>, List<EntityInfo>) - Static method in class org.biojava.nbio.structure.io.EntityFinder
Given all chains of all models find entities for the nonpolymers and water chains within them, assigning entity ids, types and descriptions to them.
createQualityScores(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
Create and return a new QualityFeature from the quality scores of the specified FASTQ formatted sequence.
createSequence(Sequence<F>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
createSequence(Sequence<F>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator
 
createSequence(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
 
createSequence(Sequence<NucleotideCompound>, Frame) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
 
createSequences(Sequence<F>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
createSequences(Sequence<F>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator
 
createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
Overloaded local version which delegates to an optional translator when told to (specified during construction).
createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator
Performs the core conversion of RNA to Peptide.
createSubSequence(Sequence<C>, int, int) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
Creates a simple sub sequence view delimited by the given start and end.
createTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
createTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology
Create a new term in this ontology.
createTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
createTerm(String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
createTerm(String, String) - Method in interface org.biojava.nbio.ontology.Ontology
Create a new term in this ontology.
createTerm(String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
createTerm(String, String, Object[]) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
createTerm(String, String, Object[]) - Method in interface org.biojava.nbio.ontology.Ontology
Create a new term in this ontology.
createTerm(String, String, Object[]) - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
createTriple(Term, Term, Term, String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
createTriple(Term, Term, Term, String, String) - Method in interface org.biojava.nbio.ontology.Ontology
Creates a new Triple.
createTriple(Term, Term, Term, String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
createVariable(String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
createVariable(String, String) - Method in interface org.biojava.nbio.ontology.Ontology
Create a new term in this ontology that is used as a variable.
createVariable(String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
createVirtualCBAtom(AminoAcid) - Static method in class org.biojava.nbio.structure.Calc
creates a virtual C-beta atom. this might be needed when working with GLY thanks to Peter Lackner for a python template of this method.
CROSS_LINK_1 - org.biojava.nbio.protmod.ModificationCategory
 
CROSS_LINK_2 - org.biojava.nbio.protmod.ModificationCategory
 
CROSS_LINK_3 - org.biojava.nbio.protmod.ModificationCategory
 
CROSS_LINK_4 - org.biojava.nbio.protmod.ModificationCategory
 
CROSS_LINK_5 - org.biojava.nbio.protmod.ModificationCategory
 
CROSS_LINK_6 - org.biojava.nbio.protmod.ModificationCategory
 
CROSS_LINK_7 - org.biojava.nbio.protmod.ModificationCategory
 
CROSS_LINK_8_OR_LARGE - org.biojava.nbio.protmod.ModificationCategory
 
crossChains() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
 
crossChains() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
CrystalBuilder - Class in org.biojava.nbio.structure.xtal
A class containing methods to find interfaces in a given crystallographic Structure by reconstructing the crystal lattice through application of symmetry operators
CrystalBuilder(Structure) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder
 
CrystalBuilder(Structure, Map<String, String>, Map<String, Matrix4d>) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder
Special constructor for NCS-aware CrystalBuilder.
CrystalCell - Class in org.biojava.nbio.structure.xtal
A crystal cell's parameters.
CrystalCell() - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell
 
CrystalCell(double, double, double, double, double, double) - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell
 
CrystalTransform - Class in org.biojava.nbio.structure.xtal
Representation of a transformation in a crystal: - a transformation id (each of the transformations in a space group, 0 to m) - a crystal translation The transformation matrix in crystal basis is stored, representing the basic transformation together with the crystal translation.
CrystalTransform(CrystalTransform) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform
Copy constructor
CrystalTransform(SpaceGroup) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform
Creates a new CrystalTransform representing the identity transform in cell (0,0,0)
CrystalTransform(SpaceGroup, int) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform
Represents the n-th transform
Cs - org.biojava.nbio.structure.Element
 
CS_HSV - Static variable in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
The HSV color space
Cu - org.biojava.nbio.structure.Element
 
CUBIC - org.biojava.nbio.structure.xtal.BravaisLattice
 
CURATED - org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
 
CURRENT - org.biojava.nbio.structure.PDBStatus.Status
 
CUSTOM - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy
The strategy is defined via an external function, we do not have to do anything.
cut(Atom[], Domain, CutValues, int[][], PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.Cut
 
Cut - Class in org.biojava.nbio.structure.domain.pdp
 
Cut() - Constructor for class org.biojava.nbio.structure.domain.pdp.Cut
 
Cut(int, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
 
CUT_OFF_VALUE - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
CUT_OFF_VALUE1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
CUT_OFF_VALUE1M - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
CUT_OFF_VALUE1S - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
CUT_OFF_VALUE2 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
cutDomain(Domain, CutSites, PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.CutDomain
 
CutDomain - Class in org.biojava.nbio.structure.domain.pdp
 
CutDomain(Atom[], PDPDistanceMatrix) - Constructor for class org.biojava.nbio.structure.domain.pdp.CutDomain
 
CutSites - Class in org.biojava.nbio.structure.domain.pdp
 
CutSites() - Constructor for class org.biojava.nbio.structure.domain.pdp.CutSites
 
cutsPerSection - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
CutValues - Class in org.biojava.nbio.structure.domain.pdp
 
CutValues() - Constructor for class org.biojava.nbio.structure.domain.pdp.CutValues
 
cyan - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
 
CYCLE - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy
Cycle through the alphabet (e.g., ...xyzABC...)
cyclicPeptide - org.biojava.nbio.structure.chem.PolymerType
cyclic peptides
Cytoband - Class in org.biojava.nbio.genome.parsers.cytoband
 
Cytoband() - Constructor for class org.biojava.nbio.genome.parsers.cytoband.Cytoband
 
CytobandParser - Class in org.biojava.nbio.genome.parsers.cytoband
Parses the cytoband (karyotype) file from UCSC.
CytobandParser() - Constructor for class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
 

D

D - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
D - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
D - org.biojava.nbio.structure.Element
Deuterium
D - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
d2 - Static variable in class org.biojava.nbio.structure.io.FileConvert
 
d3 - Static variable in class org.biojava.nbio.structure.io.FileConvert
 
darker(Color, double) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
Make a color darker.
DATABASE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
DATABASE_PREFIX - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
DATABASE_SORT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
DatabasePDBRevRecord - Class in org.biojava.nbio.structure
Represents revision records for use by PDBHeader.
DatabasePDBRevRecord() - Constructor for class org.biojava.nbio.structure.DatabasePDBRevRecord
 
DatabasePDBRevRecord(String, String, String) - Constructor for class org.biojava.nbio.structure.DatabasePDBRevRecord
 
DatabasePDBRevRecord(DatabasePDBRevRecord, int) - Constructor for class org.biojava.nbio.structure.DatabasePDBRevRecord
 
DatabaseReference(String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
DatabaseReference(String, String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
DatabaseReferenceInterface - Interface in org.biojava.nbio.core.sequence.features
If a SequenceProxyReader implements this interface then that external source has a list of cross reference id(s)
Dataset - Class in org.biojava.nbio.phosphosite
Phosphosite is available under the PhosphoSitePlus® is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from http://www.phosphosite.org/staticDownloads.do Please acknowledge PhosphoSitePlus®, www.phosphosite.org" at appropriate locations.
Dataset() - Constructor for class org.biojava.nbio.phosphosite.Dataset
 
DataSource - Enum in org.biojava.nbio.core.sequence
GenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT UNIPROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier
dateFormat - Variable in class org.biojava.nbio.ontology.obo.OboFileParser
 
dateToIsoString(Date) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Covert a Date object to ISO time format.
DB_GENETIC_CODE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
dBetaPeptideCGammaLinking - org.biojava.nbio.structure.chem.ResidueType
 
DBL - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
DBLINK - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
DBRef - Class in org.biojava.nbio.structure
A class to represent database cross references.
DBRef() - Constructor for class org.biojava.nbio.structure.DBRef
 
DBReferenceInfo - Class in org.biojava.nbio.core.sequence.features
If you have a uniprot ID then it is possible to get a collection of other id(s) that the protein is known by.
DBReferenceInfo(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.DBReferenceInfo
The source database and id
DBSOURCE - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
dbxp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
DDBJ - org.biojava.nbio.core.sequence.DataSource
 
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
 
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
 
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
 
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
 
debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
 
debug - Static variable in class org.biojava.nbio.structure.align.util.AlignmentTools
 
debug(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
 
declareNamespace(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
Declare a namespace for current and following elements 'prefixHint' is ignored entirely in this implementation
declareNamespace(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter
Hints that a namespace is going to be used in a sub-tree.
decorateRna(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
Performs an optimisation where RNASequences are not translated into their own objects but are views onto the base DNA sequence.
deepCleanSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
Removes all special characters and digits as well as whitespace chars from the sequence
DEF - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
DEF_NUM_CELLS - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder
 
DEFAULT - Static variable in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
 
DEFAULT - Static variable in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
 
DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
 
DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
 
DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
 
DEFAULT_ALGORITHM_NAME - Static variable in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
 
DEFAULT_ASA_SPHERE_POINTS - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList
Default number of points to use when calculating ASAs
DEFAULT_BCIF_FILE_SERVER - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
The default server to retrieve BinaryCIF files.
DEFAULT_BIOASSEMBLY_STYLE - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
The default output bioassembly style: if true the bioassemblies are multimodel, if false the bioassemblies are flat with renamed chains for symmetry-partners.
DEFAULT_BUFFER_SIZE - Variable in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
DEFAULT_CHAR_SIZE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
size per character
DEFAULT_CHAR_SIZE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
Size per character
DEFAULT_CHEMCOMP_PATHURL_TEMPLATE - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
 
DEFAULT_CLUSTER_CUTOFF - Static variable in class org.biojava.nbio.structure.align.ClusterAltAligs
 
DEFAULT_CONNECTION_TIMEOUT - Static variable in class org.biojava.nbio.structure.align.util.URLConnectionTools
The default connection timeout in ms - 15 seconds
DEFAULT_CONTACT_CUTOFF - Static variable in class org.biojava.nbio.structure.contact.InterfaceFinder
 
DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList
Any 2 interfaces with contact overlap score larger than this value will be considered to be clustered
DEFAULT_DISORDER - Static variable in class org.biojava.nbio.ronn.RonnConstraint
 
DEFAULT_FILE - Static variable in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
 
DEFAULT_FRAGLEN - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
DEFAULT_GAP_EXTENSION - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
DEFAULT_GAP_OPEN - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
DEFAULT_GENENAMES_URL - Static variable in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
 
DEFAULT_HEIGHT - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
DEFAULT_INTERFACE_DISTANCE_CUTOFF - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder
Default maximum distance between two chains to be considered an interface.
DEFAULT_LIGAND_PROXIMITY_CUTOFF - Static variable in class org.biojava.nbio.structure.StructureTools
Threshold for plausible binding of a ligand to the selected substructure
DEFAULT_LIMIT - Static variable in class org.biojava.nbio.core.util.SoftHashMap
 
DEFAULT_LINE_LENGTH - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
number of chars per line
DEFAULT_LINE_LENGTH - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
Number of chars per line
DEFAULT_LINE_SEPARATION - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
separation of line 1 and 2 in alignment
DEFAULT_LINE_SEPARATION - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
Separation between sequences in the alignment
DEFAULT_LOCATION - Static variable in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
 
DEFAULT_MAPPING_URL - Static variable in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
 
DEFAULT_MAX_PROPELLER - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
 
DEFAULT_MAX_PROPELLER - Static variable in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
 
DEFAULT_MAX_SHEAR - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
 
DEFAULT_MAX_STAGGER - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
 
DEFAULT_MAX_STAGGER - Static variable in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
 
DEFAULT_MAX_STRETCH - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
 
DEFAULT_METHOD_NAME - Static variable in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
 
DEFAULT_MIN_COFACTOR_SIZE - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList
Default minimum size of cofactor molecule (non-chain HET atoms) that will be used
DEFAULT_MIN_CP_LENGTH - Static variable in class org.biojava.nbio.structure.align.ce.CECPParameters
 
DEFAULT_MINIMUM_INTERFACE_AREA - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList
Default minimum area for a contact between two chains to be considered a valid interface.
DEFAULT_N_SPHERE_POINTS - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
The default value for number of sphere points to sample.
DEFAULT_NTHREADS - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
 
DEFAULT_ORDER - Static variable in class org.biojava.nbio.ronn.RonnConstraint
 
DEFAULT_oRmsdThr - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
DEFAULT_PDB_FILE_SERVER - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
The default server name, prefixed by the protocol string (http://, https:// or ftp://).
DEFAULT_PROBE_SIZE - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
 
DEFAULT_RANGE_PROBABILITY_THRESHOLD - Static variable in class org.biojava.nbio.ronn.RonnConstraint
 
DEFAULT_RCSB_DATA_API_SERVER - Static variable in class org.biojava.nbio.structure.PDBStatus
 
DEFAULT_RESOLUTION - Static variable in class org.biojava.nbio.structure.PDBHeader
 
DEFAULT_RFREE - Static variable in class org.biojava.nbio.structure.PDBHeader
 
DEFAULT_RIGHT_SPACER - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
Space on the right side between sequence and legend.
DEFAULT_RIGHT_SPACER - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
Space on the right side between sequence and legend.
DEFAULT_SCORING_STRATEGY - Static variable in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
 
DEFAULT_SCRIPT - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
DEFAULT_SERVER_URL - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
 
DEFAULT_SUBSTITUTION_MATRIX - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
DEFAULT_SYMMETRY_THRESHOLD - Static variable in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
DEFAULT_UNIPROT_BASE_URL - Static variable in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
DEFAULT_VARIANT - Static variable in class org.biojava.nbio.genome.io.fastq.FastqBuilder
Default FASTQ sequence format variant, FastqVariant.FASTQ_SANGER.
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathFactory
 
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
 
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.ecod.EcodFactory
 
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
 
DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
 
DEFAULT_WIDTH - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
DEFAULT_X_RIGHT_BORDER - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
DEFAULT_X_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
left boundary
DEFAULT_X_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
Left boundary
DEFAULT_X_START - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
DEFAULT_Y_BOTTOM - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
DEFAULT_Y_HEIGHT - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
DEFAULT_Y_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
top boundary
DEFAULT_Y_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
Top boundary
DEFAULT_Y_START - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
DEFAULT_Y_STEP - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
size of space between rows
DEFAULT_Y_STEP - Variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
Size of space between rows.
DEFAULT_Y_STEP - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
DefaultAAIndexProvider - Class in org.biojava.nbio.core.alignment.matrices
The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directory
DefaultAAIndexProvider() - Constructor for class org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider
 
DefaultAutoSuggestProvider - Class in org.biojava.nbio.structure.align.gui.autosuggest
 
DefaultAutoSuggestProvider() - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
 
DefaultMatrixMapper - Class in org.biojava.nbio.structure.gui.util.color
Color Mapper which mimics the default coloring of JMatrixPanel pixels.
DefaultMatrixMapper(double, float) - Constructor for class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
 
DefaultOps - Class in org.biojava.nbio.ontology
Default implementation of OntologyOps.
DefaultOps() - Constructor for class org.biojava.nbio.ontology.DefaultOps
 
defaultProperties - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo
 
DEFINITION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
delete(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
Delete the key (and paired value) from table.
Delete(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Delete
 
Delete(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Delete
 
deleteColumn(AFPChain, Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Delete an alignment position from the original alignment object.
deleteDirectory(String) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
Recursively delete a folder & contents
deleteDirectory(Path) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
Recursively delete a folder & contents
deleteHighestDistanceColumn(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Find the alignment position with the highest atomic distance between the equivalent atomic positions of the arrays and remove it from the alignment.
deleteStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Attempts to delete all versions of a structure from the local directory.
deleteStructure(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Attempts to delete all versions of a structure from the local directory.
deleteTerm(Term) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
deleteTerm(Term) - Method in interface org.biojava.nbio.ontology.Ontology
Remove a term from an ontology, together with all triples which refer to it.
deleteTerm(Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
DELETION - org.biojava.nbio.alignment.routines.AlignerHelper.Last
 
DELTA - Static variable in class org.biojava.nbio.structure.xtal.SpaceGroup
 
deltaComp(double, double, double) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
demo - package demo
 
DemoAlignmentFromFasta - Class in demo
Demo of how to use the FastaStructureParser class to read protein structures from a FASTA file.
DemoAlignmentFromFasta() - Constructor for class demo.DemoAlignmentFromFasta
 
DemoAlignProteins - Class in demo
 
DemoAlignProteins() - Constructor for class demo.DemoAlignProteins
 
DemoAsa - Class in demo
 
DemoAsa() - Constructor for class demo.DemoAsa
 
DemoAtomCache - Class in demo
Example of how to load PDB files using the AtomCache class.
DemoAtomCache() - Constructor for class demo.DemoAtomCache
 
DemoBerkeleyScop - Class in demo
A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP
DemoBerkeleyScop() - Constructor for class demo.DemoBerkeleyScop
 
DemoBioAssemblies - Class in demo
 
DemoBioAssemblies() - Constructor for class demo.DemoBioAssemblies
 
DemoCATH - Class in demo
An example for how to access CATH data.
DemoCATH() - Constructor for class demo.DemoCATH
 
DemoCE - Class in demo
Example of how to run a structure alignment using the CE algorithm.
DemoCE() - Constructor for class demo.DemoCE
 
DemoCeSymm - Class in demo
Quick demo of how to call CE-Symm programmatically.
DemoCeSymm() - Constructor for class demo.DemoCeSymm
 
DemoChangeChemCompProvider - Class in demo
This demo shows how to use an alternative ChemCompProvider.
DemoChangeChemCompProvider() - Constructor for class demo.DemoChangeChemCompProvider
 
DemoCommandLineStartup - Class in demo
 
DemoCommandLineStartup() - Constructor for class demo.DemoCommandLineStartup
 
DemoContacts - Class in demo
 
DemoContacts() - Constructor for class demo.DemoContacts
 
DemoCrystalInterfaces - Class in demo
 
DemoCrystalInterfaces() - Constructor for class demo.DemoCrystalInterfaces
 
DemoDistanceTree - Class in demo
This demo contains the CookBook example to create a phylogenetic tree from a multiple sequence alignment (MSA).
DemoDistanceTree() - Constructor for class demo.DemoDistanceTree
 
DemoDomainsplit - Class in demo
 
DemoDomainsplit() - Constructor for class demo.DemoDomainsplit
 
DemoFATCAT - Class in demo
 
DemoFATCAT() - Constructor for class demo.DemoFATCAT
 
DemoLoadSecStruc - Class in demo
Demonstration of how to load a Structure with the SS information, either from the PDB file annotation (Author's assignment) or from the DSSP file in the PDB servers (DSSP assignment).
DemoLoadSecStruc() - Constructor for class demo.DemoLoadSecStruc
 
DemoLoadStructure - Class in demo
Example for how to load protein structures (from PDB files).
DemoLoadStructure() - Constructor for class demo.DemoLoadStructure
 
DemoLoadSubstMax - Class in demo
 
DemoLoadSubstMax() - Constructor for class demo.DemoLoadSubstMax
 
DemoMMCIFReader - Class in demo
An example of how to read MMcif files
DemoMMCIFReader() - Constructor for class demo.DemoMMCIFReader
 
DemoMmcifToPdbConverter - Class in demo
An example of how to convert mmCIF file to PDB file
DemoMmcifToPdbConverter() - Constructor for class demo.DemoMmcifToPdbConverter
 
DemoMmtfReader - Class in demo
Class to show how to read a Biojava structure using MMTF
DemoMmtfReader() - Constructor for class demo.DemoMmtfReader
 
DemoMmtfWriter - Class in demo
 
DemoMmtfWriter() - Constructor for class demo.DemoMmtfWriter
 
DemoMultipleMC - Class in demo
Demo for running the MultipleMC Algorithm on a protein family.
DemoMultipleMC() - Constructor for class demo.DemoMultipleMC
 
DemoNWALignment - Class in demo
 
DemoNWALignment() - Constructor for class demo.DemoNWALignment
 
DemoQsAlign - Class in demo
Demo on how to use programatically QsAlign for the alignment of quaternary structures.
DemoQsAlign() - Constructor for class demo.DemoQsAlign
 
DemoQuatSymmetryJmol - Class in demo
This demo shows how to display the QuatSymmetryResults of a structure.
DemoQuatSymmetryJmol() - Constructor for class demo.DemoQuatSymmetryJmol
 
DemoRotationAxis - Class in demo
A demo for how to use RotationAxis to display the rotation for an alignment.
DemoRotationAxis() - Constructor for class demo.DemoRotationAxis
 
DemoSCOP - Class in demo
A class demonstrating the use of the SCOP parsing tools
DemoSCOP() - Constructor for class demo.DemoSCOP
 
DemoSecStrucCalc - Class in demo
Demonstration on how to use the Secondary Structure Prediction (DSSP) implementation in BioJava and obtain different SS representations and outputs.
DemoSecStrucCalc() - Constructor for class demo.DemoSecStrucCalc
 
DemoShowBiolAssembly - Class in demo
 
DemoShowBiolAssembly() - Constructor for class demo.DemoShowBiolAssembly
 
DemoShowCATHDomain - Class in demo
 
DemoShowCATHDomain() - Constructor for class demo.DemoShowCATHDomain
 
DemoShowLargeAssembly - Class in demo
 
DemoShowLargeAssembly() - Constructor for class demo.DemoShowLargeAssembly
 
DemoSixFrameTranslation - Class in demo
Created by andreas on 8/10/15.
DemoSixFrameTranslation() - Constructor for class demo.DemoSixFrameTranslation
 
DemoStructureFromFasta - Class in demo
Demo of how to use the FastaStructureParser class to read protein structures from a FASTA file.
DemoStructureFromFasta() - Constructor for class demo.DemoStructureFromFasta
 
DemoSW3DAligner - Class in demo
 
DemoSW3DAligner() - Constructor for class demo.DemoSW3DAligner
 
DemoSymmetry - Class in demo
A demo on how to use the quaternary symmetry detection algorithms.
DemoSymmetry() - Constructor for class demo.DemoSymmetry
 
description - Variable in class org.biojava.nbio.ontology.AbstractTerm
 
description() - Method in enum org.biojava.nbio.protmod.ModificationCategory
 
description(String) - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
Notify this parse listener of a description line.
DESCRIPTIONS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
DESCRIPTIONS - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
deserialize(File) - Static method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
desFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
 
destroy() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
 
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
 
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
Set all the member variables to null.
destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
Clean up this instance for garbage collection, to avoid memory leaks...
destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
 
destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
 
det() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
Determinant
det() - Method in class org.biojava.nbio.structure.jama.Matrix
Matrix determinant
detectCicular(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
Loops through the given list of locations and returns true if it looks like they represent a circular location.
detectEnd(List<Location>, boolean) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
This will attempt to find what the last point is and returns that position.
detectStart(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
Assumes that the first element is the start & clones it
detectStrand(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
Loops through the given list of locations and returns the consensus Strand class.
dfbeta - org.biojava.nbio.survival.cox.ResidualsCoxph.Type
 
dfbetas - org.biojava.nbio.survival.cox.ResidualsCoxph.Type
 
dGammaPeptideCDeltaLinking - org.biojava.nbio.structure.chem.ResidueType
 
diAA2Instability - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
diag(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
diag(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
dialogAsk(String, String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
DIFFERENT - org.biojava.nbio.structure.align.quaternary.QsRelation
None of the Subunits of one Structure have an equivalent in the other Structure.
DIGIT - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
A digit
disableCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
 
discreteQuantizer - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
 
DiscreteQuantizerInterface - Interface in org.biojava.nbio.survival.kaplanmeier.metadata
 
DISEASE_ASSOC - Static variable in class org.biojava.nbio.phosphosite.Dataset
 
DISJOINT_FROM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
 
display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay
Display an AFPChain alignment
display(AFPChain, Group[], Atom[], Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
display(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
Display a MultipleAlignment with a JmolPanel.
display(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
Displays a single structure in a cartoon representation with each symmetric repeat colored differently.
DISPLAY_SORT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
DisplayAFP - Class in org.biojava.nbio.structure.align.gui
A utility class for visualistion of structure alignments
DisplayAFP() - Constructor for class org.biojava.nbio.structure.align.gui.DisplayAFP
 
displayFull(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
Displays a multiple alignment of the whole structure transformations colored by blocks, corresponding to the symmetric protodomains.
displayRepeats(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
Displays a multiple alignment of the symmetry repeats
dissimilarityScore(MultipleSequenceAlignment<C, D>, SubstitutionMatrix<D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
The dissimilarity score is the additive inverse of the similarity score (sum of scores) between two aligned sequences using a substitution model (Substitution Matrix).
DIST_MATRICES - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
distance(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Return distance between this location and the other location.
DISTANCE - org.biojava.nbio.phylo.TreeType
Distance Tree
DISTANCE_INCREMENT - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
DistanceBox<T> - Class in org.biojava.nbio.structure.symmetry.geometry
 
DistanceBox(double) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
Creates a new instance of DistanceBox
distanceIncrement - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
DistanceMatrixCalculator - Class in org.biojava.nbio.phylo
The DistanceMatrixCalculator methods generate a DistanceMatrix from a MultipleSequenceAlignment or other indirect distance infomation (RMSD).
distanceTree(BasicSymmetricalDistanceMatrix, TreeConstructorType) - Static method in class org.biojava.nbio.phylo.TreeConstructor
 
DistanceTreeEvaluator - Class in org.biojava.nbio.phylo
Check the accuracy of a Distance Tree by least squares error (LSE) of the Tree branch lengths and the original Distance Matrix.
divideInternally(SubunitClustererParameters) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
Analyze the internal symmetry of the SubunitCluster and divide its Subunit into the internal repeats (domains) if they are internally symmetric.
divideStructure(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Method that converts the symmetric units of a structure into different structures, so that they can be individually visualized.
dna - org.biojava.nbio.structure.chem.PolymerType
polydeoxyribonucleotide
DNA_ONLY - Static variable in enum org.biojava.nbio.structure.chem.PolymerType
Convenience Set of polymer types classified as DNA.
dna3PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType
 
dna5PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType
 
dnaCompounds(CompoundSet<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
 
DNACompoundSet - Class in org.biojava.nbio.core.sequence.compound
 
DNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.DNACompoundSet
 
dnaLinking - org.biojava.nbio.structure.chem.ResidueType
 
dnarna - org.biojava.nbio.structure.chem.PolymerType
polydeoxyribonucleotide/polyribonucleotide hybrid
dnaRnaTranslator(DNAToRNATranslator) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
 
DNASequence - Class in org.biojava.nbio.core.sequence
This is class should model the attributes associated with a DNA sequence
DNASequence() - Constructor for class org.biojava.nbio.core.sequence.DNASequence
Shouldn't be used but makes it bean happy
DNASequence(String) - Constructor for class org.biojava.nbio.core.sequence.DNASequence
String is king and create a sequence from DNA with default DNA compound set
DNASequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence
Create a sequence from a string with user defined compound set
DNASequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence
Create a sequence where the actual storage of the sequence data is somewhere else
DNASequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence
Create a sequence from a ProxySequencereader and user defined compound set
DNASequence.DNAType - Enum in org.biojava.nbio.core.sequence
The type of DNA sequence
DNASequenceCreator - Class in org.biojava.nbio.core.sequence.io
A helper class that allows different ways to read a string and create a DNA sequence.
DNASequenceCreator(CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.DNASequenceCreator
 
DNAToRNATranslator - Class in org.biojava.nbio.core.sequence.transcription
Performs the first stage of transcription by going from DNA to RNA.
DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound>, CompoundSet<NucleotideCompound>, CompoundSet<NucleotideCompound>, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
 
doChainAfp(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
// Key function: chain (assembly) the AFPs // a AFP (k) is defined as (i, j, k), with i and j are staring points // AFP extension (eg.
documentEnd() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener
end of parsing a new OBO file
documentEnd() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
 
documentStart() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener
starting to parse a new OBO file
documentStart() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
 
doesSequenceContainInvalidChar(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils
Checks if given sequence contains invalid characters.
doInBackground() - Method in class org.biojava.nbio.structure.align.gui.StructureLoaderThread
 
doIter0(int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
doIter0(int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
Domain - Class in org.biojava.nbio.structure.domain.pdp
 
Domain - org.biojava.nbio.structure.scop.ScopCategory
 
Domain() - Constructor for class org.biojava.nbio.structure.domain.pdp.Domain
 
DomainCounter - org.biojava.nbio.structure.cath.CathCategory
 
domainDescriptionFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
 
domainListFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
 
DomainProvider - Interface in org.biojava.nbio.structure.domain
Decomposes a structure from the PDB into representative domains
DOMAINS_PATH - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
 
domallFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
 
doPOST(URL, String) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
Do a POST to a URL and return the response stream for further processing elsewhere.
doPOST(URL, String, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
Do a POST to a URL and return the response stream for further processing elsewhere.
doPrintConnections() - Method in class org.biojava.nbio.structure.io.FileConvert
Returns if the Connections should be added default is true;
dot(double[], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
dot(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseVector
Calculates the dot product of this vector a with b
DOT_PLOT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
DotPlotListener(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener
 
DotPlotPanel - Class in org.biojava.nbio.structure.align.gui
Displays the dot plot trace for an alignment.
DotPlotPanel(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.DotPlotPanel
 
dotProduct(Quat4d, Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions
Compute the dot (inner) product of two quaternions.
DOUBLE - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy
Represent every cluster with two symbols from the alphabet, this forces us to specify number of subunits for every subunit (e.g., AA1AB1AC1...).
download() - Method in class org.biojava.nbio.phosphosite.Dataset
 
DownloadChemCompProvider - Class in org.biojava.nbio.structure.chem
This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.
DownloadChemCompProvider() - Constructor for class org.biojava.nbio.structure.chem.DownloadChemCompProvider
 
DownloadChemCompProvider(String) - Constructor for class org.biojava.nbio.structure.chem.DownloadChemCompProvider
 
downloadClaFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
downloadComFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
downloadDesFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
downloadDomainDescriptionFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
downloadDomainListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
downloadDomallFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
downloadFile() - Static method in class org.biojava.nbio.structure.chem.AllChemCompProvider
Downloads the components.cif.gz file from the wwPDB site.
downloadFile(URL, File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
Download the content provided at URL url and store the result to a local file, using a temp file to cache the content in case something goes wrong in download.
downloadFile(URL, File) - Method in class org.biojava.nbio.phosphosite.Dataset
 
downloadFileFromRemote(URL, File) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
downloadFileFromRemote(URL, File) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
downloadHieFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
downloadNodeListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
downloadStructure(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Downloads an MMCIF file from the PDB to the local path
downstream(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Return the adjacent location of specified length directly downstream of this location.
dpeptide - org.biojava.nbio.structure.chem.PolymerType
polypeptide(D)
dPeptideAminoTerminus - org.biojava.nbio.structure.chem.ResidueType
 
dPeptideCarboxyTerminus - org.biojava.nbio.structure.chem.ResidueType
 
dPeptideLinking - org.biojava.nbio.structure.chem.ResidueType
 
drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Returns a Jmol script that draws symmetry or inertia axes for a structure.
drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
Returns a Jmol script that draws symmetry or inertia axes for a structure.
drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
drawBoxes(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
draw high scoring fragments that are used for the initial alignment seed selection
drawDistances(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
For each element in matrix, draw it as a colored square or pixel.
drawIdx(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
drawPairs(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
draw alternative alignments
drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Returns a Jmol script that draws an invisible polyhedron around a structure.
drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
Returns a Jmol script that draws an invisible polyhedron around a structure.
drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
drawScale(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
draw the Scale
drawSequence(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
draw the Amino acid sequence
dSaccharide - org.biojava.nbio.structure.chem.ResidueType
 
dSaccharide14and14linking - org.biojava.nbio.structure.chem.ResidueType
 
dSaccharide14and16linking - org.biojava.nbio.structure.chem.ResidueType
 
DSSP_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
Secondary strucuture parsed from a DSSP output file
DSSPParser - Class in org.biojava.nbio.structure.secstruc
Class to parse a DSSP file (output of the DSSP program), that contains the secondary structure assignment of a structure.
DSSPParser() - Constructor for class org.biojava.nbio.structure.secstruc.DSSPParser
 
dump() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
dump(ArrayList<SurvivalInfo>, PrintStream, String) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
For each analysis this allows outputing of the data used in the calculations to a printstream/file.
duplicateCA2(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
Utility method for working with circular permutations.
duplicationHint - Variable in class org.biojava.nbio.structure.align.ce.CECPParameters
 
duplicationHint - Variable in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
 
Dy - org.biojava.nbio.structure.Element
 
DYNAMIC - org.biojava.nbio.alignment.template.GapPenalty.Type
 

E

E - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
E - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
E - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
ECOD - org.biojava.nbio.structure.align.client.StructureName.Source
 
ECOD_RE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
 
ECOD_URL - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
 
EcodDatabase - Interface in org.biojava.nbio.structure.ecod
General API for interacting with ECOD.
EcodDomain - Class in org.biojava.nbio.structure.ecod
An EcodDomain contains all the information of the ECOD database: id, classification groups (from higher to lower in the tree: X,H,T,F), PDB code, chain, residue ranges and status (manual or automatic classification).
EcodDomain() - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
Default constructor with all null properties
EcodDomain(Long, String, Boolean, Integer, Integer, Integer, Integer, String, String, String, String, String, String, String, String, Long, Set<String>) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
 
EcodDomain(Long, String, Boolean, Integer, Integer, Integer, Integer, String, String, String, String, String, String, String, String, String, Long, Set<String>) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
 
EcodDomain(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
 
EcodDomain(EcodDomain) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
 
EcodFactory - Class in org.biojava.nbio.structure.ecod
Controls global EcodDatabases being used.
EcodInstallation - Class in org.biojava.nbio.structure.ecod
Provides access to the Evolutionary Classification of Protein Domains (ECOD).
EcodInstallation() - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation
 
EcodInstallation(String, String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation
Use EcodFactory to create instances.
EcodInstallation.EcodParser - Class in org.biojava.nbio.structure.ecod
 
EcodParser(BufferedReader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
 
EcodParser(File) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
 
EcodParser(Reader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
 
EcodParser(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
 
edit(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
 
edit(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.edits.Edit
 
Edit<C extends Compound> - Interface in org.biojava.nbio.core.sequence.edits
Interface for carrying out edit operations on a Sequence.
Edit.AbstractEdit<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits
Abstract class which defines all edit operations as a call to discover what 5' and 3' ends of an editing Sequence should be joined together with a target Sequence.
Edit.Delete<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits
Implementation which allows for the deletion of bases from a Sequence
Edit.Insert<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits
Edit implementation which allows us to insert a base at any position in a Sequence.
Edit.Substitute<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits
Allows for the substitution of bases into an existing Sequence.
ef - Variable in class org.biojava.nbio.survival.cox.CoxInfo
 
Efron - org.biojava.nbio.survival.cox.CoxMethod
 
eig() - Method in class org.biojava.nbio.structure.jama.Matrix
Eigenvalue Decomposition
EigenvalueDecomposition - Class in org.biojava.nbio.structure.jama
Eigenvalues and eigenvectors of a real matrix.
EigenvalueDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.EigenvalueDecomposition
Check for symmetry, then construct the eigenvalue decomposition Structure to access D and V.
ELECTRON_CRYSTALLOGRAPHY - org.biojava.nbio.structure.ExperimentalTechnique
 
ELECTRON_MICROSCOPY - org.biojava.nbio.structure.ExperimentalTechnique
 
Element - Class in org.biojava.nbio.aaproperties.xml
One way to model the elements
Element - Enum in org.biojava.nbio.structure
Element is an enumeration of the elements of the periodic table.
Element() - Constructor for class org.biojava.nbio.aaproperties.xml.Element
 
Element(String, String, int, List<Isotope>, double) - Constructor for class org.biojava.nbio.aaproperties.xml.Element
 
ElementTable - Class in org.biojava.nbio.aaproperties.xml
 
ElementTable() - Constructor for class org.biojava.nbio.aaproperties.xml.ElementTable
 
ElementTable(List<Element>) - Constructor for class org.biojava.nbio.aaproperties.xml.ElementTable
 
ElementType - Enum in org.biojava.nbio.structure
ElementType is an enumeration of the types of elements found in the periodic table.
EMAIL - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
EmblId - Class in org.biojava.nbio.core.sequence.io.embl
This class contains the processed data of embl file Primary accession number Sequence version number Topology: 'circular' or 'linear' Molecule type Data class Taxonomic division Sequence length
EmblId(String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblId
 
EmblReader - Class in org.biojava.nbio.core.sequence.io.embl
This class should process the data of embl file
EmblReader() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblReader
 
EmblRecord - Class in org.biojava.nbio.core.sequence.io.embl
this class contains the parsed data of embl file
EmblRecord() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
EmblReference - Class in org.biojava.nbio.core.sequence.io.embl
This class contains the processed data of embl file that contains the referenceNumber, referenceComment, referencePosition referenceCrossReference, referenceGroup, referenceAuthor referenceTitle, referenceLocation
EmblReference() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblReference
 
EMPTY - Static variable in interface org.biojava.nbio.core.sequence.location.template.Location
Basic location which is set to the minimum and maximum bounds of Integer.
EMPTY_ANNOTATION - Static variable in interface org.biojava.nbio.ontology.utils.Annotation
A really useful empty and immutable annotation object.
ENA - org.biojava.nbio.core.sequence.DataSource
 
enableCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
 
encodeFileURL(String) - Method in class org.biojava.nbio.survival.cox.CoxVariables
 
end() - Method in class org.biojava.nbio.genome.parsers.gff.Location
Get the ending index.
END_SEQUENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
endIndex - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair
 
ENDOFFILE - Static variable in class org.biojava.nbio.core.exceptions.Messages
 
ENDS - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
endsAfter(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Check if this location ends after other location ends.
endsBefore(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Check if this location ends before other location ends.
ENDSEND - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
ensureClaInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
ensureComInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
ensureDesInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
ensureDomainDescriptionInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
ensureDomainListInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
ensureDomainsFileInstalled() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
Blocks until ECOD domains file has been downloaded and parsed.
ensureDomallInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
ensureHieInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
ensureNodeListInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
entity_poly_type - Variable in enum org.biojava.nbio.structure.chem.PolymerType
 
EntityFinder - Class in org.biojava.nbio.structure.io
Heuristical finding of Entities (called Compounds in legacy PDB format) in a given Structure.
EntityFinder() - Constructor for class org.biojava.nbio.structure.io.EntityFinder
 
EntityInfo - Class in org.biojava.nbio.structure
An object to contain the info from the PDB header for a Molecule.
EntityInfo() - Constructor for class org.biojava.nbio.structure.EntityInfo
 
EntityInfo(EntityInfo) - Constructor for class org.biojava.nbio.structure.EntityInfo
Constructs a new EntityInfo copying all data from the given one but not setting the Chains
EntityType - Enum in org.biojava.nbio.structure
The type of entity (polymer, non-polymer, water, macrolide) as defined in the mmCIF dictionary:
entityTypeFromString(String) - Static method in enum org.biojava.nbio.structure.EntityType
Creates a new EntityType from a String value.
ENTREZ_QUERY - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
entrySet() - Method in class org.biojava.nbio.core.util.SoftHashMap
 
entrySet() - Method in class org.biojava.nbio.ontology.utils.SmallMap
 
entrySet() - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
 
entrySet() - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
Always returns the empty set
entrySet() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
EQR_COLOR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
equal(boolean, boolean) - Static method in class org.biojava.nbio.core.util.Equals
 
equal(int, int) - Static method in class org.biojava.nbio.core.util.Equals
 
equal(long, long) - Static method in class org.biojava.nbio.core.util.Equals
 
equal(Object, Object) - Static method in class org.biojava.nbio.core.util.Equals
Does not compare class types.
equalLengthSequences(ProteinSequence[]) - Static method in class org.biojava.nbio.core.util.SequenceTools
A method to check whether an array of sequences contains at least two sequences having an equal length.
equals(Object) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
equals(Object) - Method in class org.biojava.nbio.core.search.io.Hit
Implements conceptual comparisons of search results.
equals(Object) - Method in class org.biojava.nbio.core.search.io.Hsp
Experimental.
equals(Object) - Method in class org.biojava.nbio.core.search.io.Result
Experimental.
equals(Object) - Method in class org.biojava.nbio.core.sequence.AccessionID
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
equals(Object) - Method in class org.biojava.nbio.data.sequence.FastaSequence
 
equals(Object) - Method in class org.biojava.nbio.genome.parsers.gff.Location
 
equals(Object) - Method in class org.biojava.nbio.ontology.Term.Impl
 
equals(Object) - Method in interface org.biojava.nbio.ontology.Triple
Check to see if an object is an equivalent Triple.
equals(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl
Two triples are equal if all their fields are identical.
equals(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
 
equals(Object) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
equals(Object) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureAtom
 
equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
 
equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
equals(Object) - Method in class org.biojava.nbio.ronn.Jronn.Range
 
equals(Object) - Method in class org.biojava.nbio.ronn.ModelLoader.Model
 
equals(Object) - Method in class org.biojava.nbio.structure.align.client.PdbPair
 
equals(Object) - Method in class org.biojava.nbio.structure.align.client.StructureName
 
equals(Object) - Method in class org.biojava.nbio.structure.align.model.AFPChain
A week equality metric.
equals(Object) - Method in class org.biojava.nbio.structure.Author
 
equals(Object) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
equals(Object) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
 
equals(Object) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
 
equals(Object) - Method in class org.biojava.nbio.structure.contact.Pair
 
equals(Object) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
 
equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
equals(Object) - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
equals(Object) - Method in class org.biojava.nbio.structure.PdbId
 
equals(Object) - Method in class org.biojava.nbio.structure.ResidueNumber
 
equals(Object) - Method in class org.biojava.nbio.structure.ResidueRange
 
equals(Object) - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
 
equals(Object) - Method in class org.biojava.nbio.structure.scop.ScopDescription
Compares the fields sunID, category, classificationId, and name for equality
equals(Object) - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
 
equals(Object) - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
 
equals(Object) - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
 
equals(Object) - Method in class org.biojava.nbio.structure.Site
 
equals(Object) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
 
equals(Object) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
 
equals(Object) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
equals(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
 
equals(GeneName) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
equals(PDBHeader) - Method in class org.biojava.nbio.structure.PDBHeader
Compare two PDBHeader objects
Equals - Class in org.biojava.nbio.core.util
A set of helper methods which return true if the two parameters are equal to each other.
Equals() - Constructor for class org.biojava.nbio.core.util.Equals
 
equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
 
equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
 
equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
 
equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
 
equalsIgnoreCase(Compound) - Method in interface org.biojava.nbio.core.sequence.template.Compound
 
equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
 
equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
equalsPositional(Object) - Method in class org.biojava.nbio.structure.ResidueNumber
Check if the seqNum and insertion code are equivalent, ignoring the chain
equalsToIgnoreEndline(String, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
Compares two strings in a case-sensitive manner for equality, line by line, ignoring any difference of end line delimiters contained within the 2 Strings.
equalsToXml(String, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
This method is not implemented or used, never returns true and should probably be removed.
EQUIVALENCE - Static variable in class org.biojava.nbio.ontology.OntoTools
 
EQUIVALENT - org.biojava.nbio.structure.align.quaternary.QsRelation
All the Subunits of one Structure have an equivalent in the other Structure.
EQUIVALENT - Static variable in class org.biojava.nbio.structure.gui.util.AlignedPosition
flag if this position is equivalent
EQUIVALENT_VERSIONS - Static variable in class org.biojava.nbio.structure.scop.BerkeleyScopInstallation
A map from SCOP version names which the Berkeley server offers as a download to an array of equivalent deprecated SCOP version names.
Er - org.biojava.nbio.structure.Element
 
error(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
 
errorEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
 
errorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
Return the error probabilities from the specified FASTQ formatted sequence.
errorProbabilities(Fastq, double[]) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.
errorProbability(char) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Convert the specified quality in ASCII format to an error probability.
errorProbability(int) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Calculate the error probability given the specified quality score.
Es - org.biojava.nbio.structure.Element
 
escape(String, boolean) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
 
escapeChars - Static variable in class org.biojava.nbio.ontology.obo.OboFileParser
 
Eu - org.biojava.nbio.structure.Element
 
eval(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
evalString(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
Execute a command String in the current Jmol panel.
evalString(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
 
evalString(String) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
 
evaluate(Phylogeny, DistanceMatrix) - Static method in class org.biojava.nbio.phylo.DistanceTreeEvaluator
Evaluate the goodness of fit of a given tree to the original distance matrix.
EXACT_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
EXACT_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym
 
execute(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative
This method uses iteratively CeSymm to calculate all symmetries in the input array of atoms and organize them in a multiple alignment of the repeats.
executeCmd(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
 
ExonComparator - Class in org.biojava.nbio.core.sequence
Sort Exon where it is a little confusing if exons 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 - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
EXPECT_HIGH - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
EXPECT_LOW - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
ExperimentalTechnique - Enum in org.biojava.nbio.structure
An enum to represent the experimental technique of a PDB structure
EXPERT - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
ExpressionFigure - Class in org.biojava.nbio.survival.kaplanmeier.figure
 
ExpressionFigure() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
 
extended - org.biojava.nbio.structure.secstruc.SecStrucType
 
extendFragments(Atom[], Atom[], JointFragments[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
 
extendFragments(Atom[], Atom[], JointFragments, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
 
extendHelix(int) - Method in class org.biojava.nbio.structure.symmetry.core.HelixExtender
 
ExtinctionCoefficient_False - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
ExtinctionCoefficient_True - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
extractAFPChains(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
 
extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
extractSubunits(Structure, int, double, int) - Static method in class org.biojava.nbio.structure.cluster.SubunitExtractor
Extract the information of each protein Chain in a Structure and converts them into a List of Subunit.

F

f(Double) - Method in class org.biojava.nbio.survival.cox.StrataInfo
 
F - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
F - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
F - org.biojava.nbio.structure.Element
 
F - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
F_UNCLASSIFIED - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
String for unclassified F-groups
f1Dot2(float) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
 
Family - org.biojava.nbio.structure.scop.ScopCategory
 
FASTA - org.biojava.nbio.core.alignment.template.Profile.StringFormat
 
FASTA - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
 
FASTA_FORMAT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
FastaAFPChainConverter - Class in org.biojava.nbio.structure.io
A collection of static utilities to convert between AFPChains and FastaSequences.
FastaAFPChainConverter() - Constructor for class org.biojava.nbio.structure.io.FastaAFPChainConverter
 
fastaFileToAfpChain(File, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
Reads the file fastaFile, expecting exactly two sequences which give a pairwise alignment.
FastaGeneWriter - Class in org.biojava.nbio.core.sequence.io
A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.
FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.FastaGeneWriter
 
FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean, int) - Constructor for class org.biojava.nbio.core.sequence.io.FastaGeneWriter
 
FastaHeaderFormatInterface<S extends Sequence<?>,​C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
 
FastaReader<S extends Sequence<?>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.io
Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta files
FastaReader(File, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaReader
If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
FastaReader(InputStream, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaReader
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.
FastaReaderHelper - Class in org.biojava.nbio.core.sequence.io
 
FastaReaderHelper() - Constructor for class org.biojava.nbio.core.sequence.io.FastaReaderHelper
 
FastaSequence - Class in org.biojava.nbio.data.sequence
A FASTA formatted sequence.
FastaSequence(String, String) - Constructor for class org.biojava.nbio.data.sequence.FastaSequence
Upon construction the any whitespace characters are removed from the sequence
FastaSequenceParser - Class in org.biojava.nbio.core.sequence.io
Used to parse a stream of a fasta file to get the sequence
FastaSequenceParser() - Constructor for class org.biojava.nbio.core.sequence.io.FastaSequenceParser
 
fastaStringToAfpChain(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
FastaStructureParser - Class in org.biojava.nbio.structure.io
Reads a protein sequence from a fasta file and attempts to match it to a 3D structure.
FastaStructureParser(File, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
 
FastaStructureParser(InputStream, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
 
FastaStructureParser(FastaReader<ProteinSequence, AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
 
fastaToAfpChain(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
TODO Write comment
fastaToAfpChain(Map<String, ProteinSequence>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment.
fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>, AminoAcidCompound>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
Provided only for convenience.
fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
FastaWriter<S extends Sequence<?>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.io
The FastaWriter writes a collection of sequences to an outputStream.
FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriter
Use default line length of 60
FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriter
Set custom lineLength
FastaWriterHelper - Class in org.biojava.nbio.core.sequence.io
The class that should be used to write out fasta file of a sequence collection
FastaWriterHelper() - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriterHelper
 
fastq(Fastq) - Method in interface org.biojava.nbio.genome.io.fastq.StreamListener
Notify this listener of a FASTQ formatted sequence.
Fastq - Class in org.biojava.nbio.genome.io.fastq
FASTQ formatted sequence.
FASTQ_ILLUMINA - org.biojava.nbio.genome.io.fastq.FastqVariant
Illumina FASTQ sequence format variant.
FASTQ_SANGER - org.biojava.nbio.genome.io.fastq.FastqVariant
Sanger FASTQ sequence format variant.
FASTQ_SOLEXA - org.biojava.nbio.genome.io.fastq.FastqVariant
Solexa FASTQ sequence format variant.
FastqBuilder - Class in org.biojava.nbio.genome.io.fastq
Fluent builder API for creating FASTQ formatted sequences.
FastqBuilder() - Constructor for class org.biojava.nbio.genome.io.fastq.FastqBuilder
Create a new FASTQ formatted sequence builder.
FastqBuilder(Fastq) - Constructor for class org.biojava.nbio.genome.io.fastq.FastqBuilder
Create a new FASTQ formatted sequence builder configured from the specified FASTQ formatted sequence.
FastqReader - Interface in org.biojava.nbio.genome.io.fastq
Reader for FASTQ formatted sequences.
FastqTools - Class in org.biojava.nbio.genome.io.fastq
Utility methods for FASTQ formatted sequences.
FastqVariant - Enum in org.biojava.nbio.genome.io.fastq
FASTQ sequence format variant.
FastqWriter - Interface in org.biojava.nbio.genome.io.fastq
Writer for FASTQ formatted sequences.
fatal(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
 
fatalEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
 
FatCat - Class in org.biojava.nbio.structure.align.fatcat
 
FatCat() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCat
 
FATCAT_BLOCK - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
FATCAT_TEXT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
FatCatAligner - Class in org.biojava.nbio.structure.align.fatcat.calc
A class that does calculations on an AFPChain
FatCatAligner() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
 
FatCatFlexible - Class in org.biojava.nbio.structure.align.fatcat
 
FatCatFlexible() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
 
FatCatParameters - Class in org.biojava.nbio.structure.align.fatcat.calc
 
FatCatParameters() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
FatCatRigid - Class in org.biojava.nbio.structure.align.fatcat
 
FatCatRigid() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatRigid
 
FatCatStartupParams() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
 
FatCatUserArgumentProcessor - Class in org.biojava.nbio.structure.align.fatcat
 
FatCatUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
 
FatCatUserArgumentProcessor.FatCatStartupParams - Class in org.biojava.nbio.structure.align.fatcat
 
FCAlignHelper - Class in org.biojava.nbio.structure.align.fatcat.calc
 
FCAlignHelper(double[][], int, int, double, double) - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper
do an alignment given the provided matrix sij0
fDot2(double) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
 
Fe - org.biojava.nbio.structure.Element
 
Feature - Class in org.biojava.nbio.genome.parsers.gff
A Feature corresponds to a single row in a GFF file.
Feature(String, String, String, Location, Double, int, String) - Constructor for class org.biojava.nbio.genome.parsers.gff.Feature
Construct a new Feature from raw data (usually a GFF row).
Feature(Feature) - Constructor for class org.biojava.nbio.genome.parsers.gff.Feature
Make a copy of the specified feature.
FEATURE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
FeatureDbReferenceInfo<S extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.features
It is DBReferenceInfo which implements FeatureInterface.
FeatureDbReferenceInfo(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
featureGlobalEnd - Variable in class org.biojava.nbio.core.sequence.location.InsdcParser
these variables are used to compute the global start and end of complex features
featureGlobalStart - Variable in class org.biojava.nbio.core.sequence.location.InsdcParser
these variables are used to compute the global start and end of complex features
FeatureHelper - Class in org.biojava.nbio.genome.parsers.gff
 
FeatureHelper() - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureHelper
 
FeatureI - Interface in org.biojava.nbio.genome.parsers.gff
A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.
FeatureInterface<S extends AbstractSequence<C>,​C extends Compound> - Interface in org.biojava.nbio.core.sequence.features
Interface class to handle describing arbitrary features.
FeatureList - Class in org.biojava.nbio.genome.parsers.gff
A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.
FeatureList() - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureList
Construct an empty list.
FeatureList(Collection<FeatureI>) - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureList
Construct a new list containing the same features as the specified list.
FeatureRetriever<C extends Compound> - Interface in org.biojava.nbio.core.sequence.features
If a SequenceProxyReader implements this interface then that external source has a list features
FeaturesKeyWordInterface - Interface in org.biojava.nbio.core.sequence.features
Models the keywords that are annotated for a protein sequence at Uniprot.
FETCH_CURRENT - org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
Fetch the most recent version of the PDB entry.
FETCH_FILES - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
Fetch missing files from the server.
FETCH_IF_OUTDATED - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
Fetch missing files from the server, also fetch if file present but older than the server file.
FETCH_OBSOLETE - org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
Fetch the obsolete entry from the PDB archives.
FETCH_REMEDIATED - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
Fetch missing files from the server.
fh2 - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
 
FIBER_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique
 
figureLineInfoLowerPercentX - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
figureLineInfoLowerPercentY - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
FILE - org.biojava.nbio.structure.align.client.StructureName.Source
 
FileConvert - Class in org.biojava.nbio.structure.io
Methods to convert a structure object into different file formats.
FileConvert(Structure) - Constructor for class org.biojava.nbio.structure.io.FileConvert
Constructs a FileConvert object.
FileDownloadUtils - Class in org.biojava.nbio.core.util
 
FileDownloadUtils() - Constructor for class org.biojava.nbio.core.util.FileDownloadUtils
 
FileParsingParameters - Class in org.biojava.nbio.structure.io
A class that configures parameters that can be sent to the PDB file parsers FileParsingParameters.setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms FileParsingParameters.setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.
FileParsingParameters() - Constructor for class org.biojava.nbio.structure.io.FileParsingParameters
 
FileProxyDNASequenceCreator - Class in org.biojava.nbio.core.sequence.io
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
FileProxyDNASequenceCreator(File, CompoundSet<NucleotideCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
FileProxyProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
FileProxyProteinSequenceCreator(File, CompoundSet<AminoAcidCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
FileProxyRNASequenceCreator - Class in org.biojava.nbio.core.sequence.io
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
FileProxyRNASequenceCreator(File, CompoundSet<NucleotideCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
FILESPLIT - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
 
FILESPLIT - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
 
fillAlignedAtomArrays(AFPChain, Atom[], Atom[], Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Fill the aligned Atom arrays with the equivalent residues in the afpChain.
FILTER - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
filterByCathCode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
Return list of CATH descriptions whose CATH codes (e.g. 1.4.6.10) start with the query.
filterByCathCode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
filterByClassificationId(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
Get all scop descriptions that start with a classification ID, e.g. b.1.18
filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
filterByDescription(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
Return list of CATH descriptions whose descriptions (name field) starts with the query.
filterByDescription(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
filterByDescription(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
Get all scop descriptions that start with a certain name. e.g.
filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
filterByDomainName(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
search through SCOP and filter based on domain name
filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
filterByHierarchy(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase
Get a list of domains within a particular level of the hierarchy
filterByHierarchy(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
Get a list of domains within a particular level of the hierarchy
filterByNodeName(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
Return list of CATH domains whose node name (e.g.
filterByNodeName(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
Takes as input an AFPChain where ca2 has been artificially duplicated.
filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[], CECPParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
 
filterLigands(List<Group>) - Static method in class org.biojava.nbio.structure.StructureTools
Removes all polymeric and solvent groups from a list of groups
finalizeStructure() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
 
findAtomLinkages(Group, Group, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
Find linkages between two groups within tolerance of bond length, from potential atoms.
findAtomLinkages(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
Find linkages between two groups within tolerance of bond length, from potential atoms.
findGroup(String, String) - Method in interface org.biojava.nbio.structure.Structure
Request a particular group from a structure.
findGroup(String, String) - Method in class org.biojava.nbio.structure.StructureImpl
Request a particular group from a structure.
findGroup(String, String, int) - Method in interface org.biojava.nbio.structure.Structure
Request a particular group from a structure.
findGroup(String, String, int) - Method in class org.biojava.nbio.structure.StructureImpl
Request a particular group from a structure.
findLinkage(Group, Group, String, String, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
Find a linkage between two groups within tolerance of bond length.
findNearestAtomLinkage(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
Find a linkage between two groups within tolerance of bond length, from potential atoms.
findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method performs a search for base pairs in the structure.
findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
This is an implementation for finding non-canonical base pairs when there may be missing or overhanging bases.
findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
This is an alternative implementation of findPair() that looks for anything that would fit the criteria for a base-pair, useful for the context of tertiary structure of RNA.
findPolyEntities(List<List<Chain>>) - Static method in class org.biojava.nbio.structure.io.EntityFinder
Utility method that employs some heuristics to find the EntityInfos for the polymeric chains given in constructor.
findUnescaped(String, char) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
 
findUnescaped(String, char, int, int) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
 
findUnescaped(String, char, int, int, boolean) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
 
finish() - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
 
finish() - Method in interface org.biojava.nbio.structure.io.cif.CifFileConsumer
Ultimate setup which can include steps which require several categories to be available and integrate them into the final container.
finish() - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
finish() - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl
 
finish(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
FIRST - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
 
first_cut - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
 
FIRST_QUERY_NUM - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
FIRST25 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
 
FIRST50 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
 
FIRST75 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
 
fixMicroheterogenity(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
This sets all microheterogeneous groups (previously alternate location groups) as separate groups.
flagLoading(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
flagLoadingFinished(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
FlatFileCache - Class in org.biojava.nbio.core.util
Provides a cache for storing multiple small files in memory.
FlatQueryAnchored - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
 
FlatQueryAnchoredNoIdentities - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
 
flemingHarrington - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
 
flipAlignment(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
Takes an XML representation of the alignment and flips the positions of name1 and name2
flipChain(AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainFlipper
Flip the position of name1 and name2 (as well as all underlying data) in an AFPChain.
floor(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
Return the largest key in the table <= k.
FLUORESCENCE_TRANSFER - org.biojava.nbio.structure.ExperimentalTechnique
 
flush() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
 
flushCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
 
Fm - org.biojava.nbio.structure.Element
 
fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxInfo
 
fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxVariables
 
fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
fmtpl(String, int) - Method in class org.biojava.nbio.survival.cox.CoxInfo
Pad left a string with spaces
fmtpr(String, int) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
Fold - org.biojava.nbio.structure.scop.ScopCategory
 
FORCE_DOWNLOAD - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
For every file, force downloading from the server
ForesterWrapper - Class in org.biojava.nbio.phylo
This class contains wrapper methods for communication between BioJava and forester (e.g, Data Structure conversion).
FORMAT_ENTREZ_QUERY - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
FORMAT_OBJECT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
FORMAT_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier
URL parameter specifying the file format (PDB or CIF)
FORMAT_TYPE - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
formatExonStructure(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Pretty print the details of a GeneChromosomePosition to a String
formBondsFromStructConn(StructConn) - Method in class org.biojava.nbio.structure.io.BondMaker
 
formDisulfideBonds(List<SSBondImpl>) - Method in class org.biojava.nbio.structure.io.BondMaker
Creates disulfide bond objects and references in the corresponding Atoms objects, given a list of SSBondImpls parsed from a PDB file.
formLinkRecordBond(PDBTemporaryStorageUtils.LinkRecord) - Method in class org.biojava.nbio.structure.io.BondMaker
Creates bond objects from a LinkRecord as parsed from a PDB file
formMatrix(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
 
FORTY_175 - org.biojava.nbio.structure.scop.Astral.AstralSet
 
FORTY_175A - org.biojava.nbio.structure.scop.Astral.AstralSet
 
FORTY_175B - org.biojava.nbio.structure.scop.Astral.AstralSet
 
FORTY_201 - org.biojava.nbio.structure.scop.Astral.AstralSet
 
FORTY_202 - org.biojava.nbio.structure.scop.Astral.AstralSet
 
FORTY_203 - org.biojava.nbio.structure.scop.Astral.AstralSet
 
FOURBAR - org.biojava.nbio.structure.xtal.TransformType
 
FourBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
FourBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
FourBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
FourBitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
FourBitSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
Four bit encoding of the bit formats.
FourBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader.FourBitArrayWorker<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
A four bit per compound implementation of the bit array worker code.
FOURFOLD - org.biojava.nbio.structure.xtal.TransformType
 
FOURFOLDSCREW - org.biojava.nbio.structure.xtal.TransformType
 
Fr - org.biojava.nbio.structure.Element
 
fractionalDissimilarity(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
The fractional dissimilarity (D) is defined as the percentage of sites that differ between two aligned sequences.
fractionalDissimilarityScore(MultipleSequenceAlignment<C, D>, SubstitutionMatrix<D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
The fractional dissimilarity score (Ds) is a relative measure of the dissimilarity between two aligned sequences.
FractionalIdentityInProfileScorer<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
FractionalIdentityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityInProfileScorer
Creates a fractional identity scorer for an aligned pair of sequences in the given alignment profile.
FractionalIdentityScorer<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment
Implements an algorithm which computes a score for a sequence alignment pair.
FractionalIdentityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityScorer
Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
FractionalIdentityScorer(SequencePair<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityScorer
Creates a fractional identity scorer for an aligned pair of sequences.
FractionalSimilarityInProfileScorer<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
FractionalSimilarityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer
Creates a fractional similarity scorer for an aligned pair of sequences in the given alignment profile.
FractionalSimilarityScorer<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment
Implements an algorithm which computes a score for a sequence alignment pair.
FractionalSimilarityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityScorer
Creates a fractional similarity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
FractionalSimilarityScorer(SequencePair<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityScorer
Creates a fractional similarity scorer for an aligned pair of sequences.
frag_pairwise_compat(FragmentPair[], int, float, int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
Calculate the pairwise compatibility of fpairs.
FragmentJoiner - Class in org.biojava.nbio.structure.align.pairwise
Joins the initial Fragments together to larger Fragments
FragmentJoiner() - Constructor for class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
 
FragmentPair - Class in org.biojava.nbio.structure.align.pairwise
a pair of fragments of two protein structures
FragmentPair(int, int, int) - Constructor for class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
frame - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
frame() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
Get frame (aka phase).
Frame - Enum in org.biojava.nbio.core.sequence.transcription
Indicates a way of translating a sequence.
from - Variable in class org.biojava.nbio.ronn.Jronn.Range
Range starting position counts from 1 (the first position on the sequence is 1)
fromAFP(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Converts a refined symmetry AFPChain alignment into the standard representation of symmetry in a MultipleAlignment, that contains the entire Atom array of the strcuture and the symmetric repeats are orgaized in different rows in a single Block.
fromBio(int, int, char) - Static method in class org.biojava.nbio.genome.parsers.gff.Location
Create location from "biocoordinates", as in GFF file.
fromBioExt(int, int, char, int) - Static method in class org.biojava.nbio.genome.parsers.gff.Location
Create a location from MAF file coordinates, which represent negative strand locations as the distance from the end of the sequence.
fromCathCode(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory
 
fromCharacter(Character) - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType
 
fromCharacter(Character) - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType
Converts a Character representing a Secondary Structure type into the corresponding enum object.
fromCIEXYZ(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
 
fromCifFile(CifFile) - Static method in class org.biojava.nbio.structure.io.cif.ChemCompConverter
Convert CifFile to chem comp dictionary.
fromCifFile(CifFile) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Convert CifFile to Structure without any FileParsingParameters.
fromCifFile(CifFile, FileParsingParameters) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Convert CifFile to Structure.
fromConciseAlignmentString(String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
 
fromInputStream(InputStream) - Static method in class org.biojava.nbio.structure.io.cif.ChemCompConverter
Convert InputStream to chem comp dictionary.
fromInputStream(InputStream) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Convert InputStream to Structure without any FileParsingParameters.
fromInputStream(InputStream, FileParsingParameters) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Convert InputStream to Structure.
fromMultiXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
 
fromPath(Path) - Static method in class org.biojava.nbio.structure.io.cif.ChemCompConverter
Read data from a file and convert to chem comp dictionary.
fromPath(Path) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Read data from a file and convert to Structure without any FileParsingParameters.
fromPath(Path, FileParsingParameters) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Read data from a file and convert to Structure.
fromRGB(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
 
fromStartupParams(StartupParameters) - Static method in class org.biojava.nbio.structure.align.util.UserConfiguration
 
fromString(String) - Static method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
 
fromString(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory
 
fromString(String) - Static method in enum org.biojava.nbio.structure.PDBStatus.Status
 
fromString(String) - Static method in class org.biojava.nbio.structure.ResidueNumber
Convert a string representation of a residue number to a residue number object.
fromString(String) - Static method in enum org.biojava.nbio.structure.scop.ScopCategory
 
fromURL(URL) - Static method in class org.biojava.nbio.structure.io.cif.ChemCompConverter
Get data from a URL and convert to chem comp dictionary.
fromURL(URL) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Get data from a URL and convert to Structure without any FileParsingParameters.
fromURL(URL, FileParsingParameters) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Get data from a URL and convert to Structure.
fromXML(String) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter
 
fromXML(String) - Static method in class org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter
 
fromXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
 
fromXML(String) - Static method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
 
fromXML(String) - Static method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
 
fromXML(String, String, String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed
fromXML(String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
 
fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter
 
fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.StructureAtomXMLConverter
 
fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.StructureGroupXMLConverter
 
FULL_SEQUENCE_DATA - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
 
functionXY(String, int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
functionXYZ(String, int, int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
FuzzyPoint - Class in org.biojava.nbio.core.sequence.location
Implementation for resolving fuzzy locations.
FuzzyPoint(int, int) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint
 
FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint
 
FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint
 

G

G - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
G - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
G - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
Ga - org.biojava.nbio.structure.Element
 
GAP - org.biojava.nbio.core.alignment.template.AlignedSequence.Step
 
GAP_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
GAP_COVERAGE_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.EntityFinder
Gap coverage value (num gaps over length of sequence) for each chain of the match: 2 chains with more gap coverage than this value will not be considered part of the same entity
GapArray - Class in org.biojava.nbio.structure.align.helper
 
GapArray() - Constructor for class org.biojava.nbio.structure.align.helper.GapArray
 
GAPCOSTS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
gapPenalty - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
GapPenalty - Interface in org.biojava.nbio.alignment.template
Defines a data structure for the gap penalties used during a sequence alignment routine.
GapPenalty.Type - Enum in org.biojava.nbio.alignment.template
Defines the possible types of gap penalties.
GCG - org.biojava.nbio.core.alignment.template.Profile.StringFormat
 
GCG - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
 
GCStats - Class in org.biojava.nbio.genome.parsers.gff
 
GCStats() - Constructor for class org.biojava.nbio.genome.parsers.gff.GCStats
 
Gd - org.biojava.nbio.structure.Element
 
Ge - org.biojava.nbio.structure.Element
 
GENBANK - org.biojava.nbio.core.sequence.DataSource
 
GENBANK_FORMAT - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
The name of this format
GenbankHeaderFormatInterface<S extends Sequence<?>,​C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
 
GenbankProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
 
GenbankProxySequenceReader(String, String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
 
GenbankReader<S extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.io
Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank files
GenbankReader(File, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReader
If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
GenbankReader(InputStream, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReader
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.
GenbankReaderHelper - Class in org.biojava.nbio.core.sequence.io
 
GenbankReaderHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
 
GenbankReference - Class in org.biojava.nbio.core.sequence.reference
For Genbank format file only.
GenbankReference() - Constructor for class org.biojava.nbio.core.sequence.reference.GenbankReference
 
GenbankSequenceParser<S extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.io
 
GenbankSequenceParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
genbankSplitPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser
Decodes a split pattern.
GenbankWriter<S extends Sequence<?>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.io
 
GenbankWriter(OutputStream, Collection<S>, GenbankHeaderFormatInterface<S, C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriter
Use default line length of 60
GenbankWriter(OutputStream, Collection<S>, GenbankHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriter
Set custom lineLength
GenbankWriterHelper - Class in org.biojava.nbio.core.sequence.io
The class that should be used to write out genbank file of a sequence collection
GenbankWriterHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
 
GeneChromosomePosition - Class in org.biojava.nbio.genome.parsers.genename
 
GeneChromosomePosition() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
GeneChromosomePositionParser - Class in org.biojava.nbio.genome.parsers.genename
A parser that parses a file from the UCSC genome browser that contains mapping of gene name to chromosome positions
GeneChromosomePositionParser() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
 
GeneFeatureHelper - Class in org.biojava.nbio.genome
 
GeneFeatureHelper() - Constructor for class org.biojava.nbio.genome.GeneFeatureHelper
 
GeneIDGFF2Reader - Class in org.biojava.nbio.genome.parsers.gff
http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneIDGFF2Reader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
 
GeneIDXMLReader - Class in org.biojava.nbio.genome.parsers.geneid
 
GeneIDXMLReader(String) - Constructor for class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
 
GeneMarkGTFReader - Class in org.biojava.nbio.genome.parsers.gff
http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneMarkGTFReader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
 
GeneName - Class in org.biojava.nbio.genome.parsers.genename
A simple bean that contains gene name information as available from www.genenames.org
GeneName() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneName
 
GeneNamesParser - Class in org.biojava.nbio.genome.parsers.genename
Parses a file from the www.genenames.org website that contains a mapping of human gene names to other databases
GeneNamesParser() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
 
GENERAL - org.biojava.nbio.core.sequence.DataSource
 
generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
Returns what the value of a compound is in the backing bit storage i.e.
generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
Returns a Map which encodes the contents of CompoundSet.
generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
Returns a Map which encodes TCAG into positions 0,1,2,3.
generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
Should return the inverse information that BitSequenceReader.BitArrayWorker.generateCompoundsToIndex() returns i.e. if the Compound C returns 1 from compoundsToIndex then we should find that compound here in position 1
generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
Returns a List which reverse encodes the Compound, Integer map
generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
Returns a List which encodes TCAG into positions 0,1,2,3.
GenericFastaHeaderFormat<S extends AbstractSequence<?>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.io
We store the original header if the sequence is parsed from a fasta file and will use that exact sequence if we write out the sequences to a fasta file.
GenericFastaHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat
 
GenericFastaHeaderParser<S extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.io
The default fasta header parser where some headers are well defined based on the source database which allows us to set the source of the protein sequence and the identifier that can be used in future implementations to load features from external sources If the user has a custom header with local data then they can create their own implementation of a FastaHeaderParserInterface
GenericFastaHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser
 
GenericGenbankHeaderFormat<S extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.io
 
GenericGenbankHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
 
GenericGenbankHeaderFormat(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 extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.io
 
GenericGenbankHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
 
GenericInsdcHeaderFormat<S extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.io
 
GenericInsdcHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat
 
GeneSequence - Class in org.biojava.nbio.core.sequence
 
GeneSequence(ChromosomeSequence, int, int, Strand) - Constructor for class org.biojava.nbio.core.sequence.GeneSequence
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 - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
GENINFO - org.biojava.nbio.core.sequence.DataSource
 
get(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
Returns the window specified at the given index in offsets i.e. asking for position 2 in a moving window sequence of size 3 will get you the window starting at position 4.
get(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Gets the interface corresponding to given id.
get(int) - Method in class org.biojava.nbio.structure.math.SparseVector
get a value
get(int, int) - Method in class org.biojava.nbio.structure.jama.Matrix
Get a single element.
get(int, int) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix
access a value at i,j
get(Object) - Method in class org.biojava.nbio.core.util.SoftHashMap
 
get(Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap
 
get(Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
 
get(Object) - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
 
get(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
get(K) - Method in class org.biojava.nbio.structure.domain.SerializableCache
 
get(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
Return the value paired with given key; null if key is not in table.
get(Chain) - Method in class org.biojava.nbio.structure.io.cif.CifChainSupplierImpl
 
get(Structure) - Method in class org.biojava.nbio.structure.io.cif.CifStructureSupplierImpl
 
get(S) - Method in interface org.biojava.nbio.structure.io.cif.CifFileSupplier
Convert some model instance describing structure information to a CifFile instance.
get1LetterCode(String) - Static method in class org.biojava.nbio.structure.StructureTools
Convert a three letter amino acid or nucleotide code into a single character code.
get1LetterCodeAmino(String) - Static method in class org.biojava.nbio.structure.StructureTools
Convert three character amino acid codes into single character e.g.
getA() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
 
getA() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
getAAComposition(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAAComposition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
Returns the composition of the 20 standard amino acid in the sequence.
getAAComposition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
 
getAACompositionChar(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAACompositionString(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAAIndexProvider() - Static method in class org.biojava.nbio.core.alignment.matrices.AAindexFactory
Gets singleton instance of an AAIndexProvider, always non-null
getABITracerCompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet
 
getAboutMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
getAbsoluteMinimumSequenceLength() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
getAbsorbance(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
An adaptor method to returns the absorbance (optical density) of sequence.
getAbsorbance(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
Returns the absorbance (optical density) of sequence.
getAbsorbance(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
 
getAcc() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
getAccept1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
getAccept2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
getAcceptedAtomNames() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
By default the parser will read in all atoms (unless using the CAonly switch).
getAccession() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
getAccession() - Method in class org.biojava.nbio.core.sequence.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
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
getAsList() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getAsList() - Method in interface org.biojava.nbio.core.sequence.template.Sequence
Returns the Sequence as a List of compounds
getAsList() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
getAssemblyHeader() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
The AH (Assembly Header) line provides column headings for the assembly information.
getAssemblyId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
getAssemblyInformation() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
The AS (Assembly Information) lines provide information on the composition of a TPA or TSA sequence.
getAssignment() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
 
getAsymmetryParameter(double) - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
 
getAtcc() - Method in class org.biojava.nbio.structure.EntityInfo
 
getAtom() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom
 
getAtom(int) - Method in interface org.biojava.nbio.structure.Group
Get at atom by position.
getAtom(int) - Method in class org.biojava.nbio.structure.HetatomImpl
Get at atom by position.
getAtom(String) - Method in interface org.biojava.nbio.structure.Group
Get an atom given its PDB name.
getAtom(String) - Method in class org.biojava.nbio.structure.HetatomImpl
Get an atom given its PDB name.
getAtom1() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
 
getAtom2() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
 
getAtomA() - Method in interface org.biojava.nbio.structure.Bond
Gets atom 'A' of this bond.
getAtomA() - Method in class org.biojava.nbio.structure.BondImpl
Gets atom 'A' of this bond.
getAtomArray(Atom[], List<Group>) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
Returns the first atom for each group
getAtomArray(Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
 
getAtomArray(Chain, String[]) - Static method in class org.biojava.nbio.structure.StructureTools
Returns an array of the requested Atoms from the Chain object.
getAtomArray(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools
Returns an array of the requested Atoms from the Structure object.
getAtomArrayAllModels(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools
Returns an array of the requested Atoms from the Structure object.
getAtomArrays() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
getAtomArrays() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Returns the array of Atoms for each structure from its parent Ensemble.
getAtomArrays() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Get an array of representative atoms for each structure (CA atoms for proteins).
getAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
getAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
getAtomAsaCs() - Method in class org.biojava.nbio.structure.asa.GroupAsa
 
getAtomAsaUs() - Method in class org.biojava.nbio.structure.asa.GroupAsa
 
getAtomB() - Method in interface org.biojava.nbio.structure.Bond
Gets atom 'B' of this bond.
getAtomB() - Method in class org.biojava.nbio.structure.BondImpl
Gets atom 'B' of this bond.
getAtomCAArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools
Returns an Atom array of the C-alpha atoms.
getAtomCAArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
Return an Atom array of the C-alpha atoms.
getAtomCache() - Static method in class org.biojava.nbio.structure.StructureIO
 
getAtomCaThreshold() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
getAtomContacts() - Method in class org.biojava.nbio.structure.contact.Grid
Returns all contacts, i.e. all atoms that are within the cutoff distance.
getAtomContacts() - Method in class org.biojava.nbio.structure.contact.GroupContact
 
getAtomCoordinateBounds(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
 
getAtomDistance(Atom, Atom) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
 
getAtomForAligPos(AFPChain, int, int, Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
Return the atom at alignment position aligPos. at the present only works with block 0
getAtomForSequencePosition(MultipleAlignment, List<Integer>, int, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Returns the Atom of the specified structure that is aligned in the sequence alignment position specified.
getAtomGroup(int) - Method in interface org.biojava.nbio.structure.Chain
Return the Group at given position, from within Groups with observed density in the chain, i.e.
getAtomGroup(int) - Method in class org.biojava.nbio.structure.ChainImpl
 
getAtomGroups() - Method in interface org.biojava.nbio.structure.Chain
Return all Groups with observed density in the chain, i.e.
getAtomGroups() - Method in class org.biojava.nbio.structure.ChainImpl
 
getAtomGroups(GroupType) - Method in interface org.biojava.nbio.structure.Chain
Return a List of all (observed) Groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
getAtomGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl
 
getAtomicMass() - Method in enum org.biojava.nbio.structure.Element
Returns the atomic mass for this Element.
getAtomicNumber() - Method in enum org.biojava.nbio.structure.Element
Returns the atomic number of this Element.
getAtomId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getAtomId() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom
 
getAtomId1() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
getAtomId2() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
getAtomLength() - Method in interface org.biojava.nbio.structure.Chain
Returns the number of Groups with observed density in the chain, i.e.
getAtomLength() - Method in class org.biojava.nbio.structure.ChainImpl
 
getAtomLinkages() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
 
getAtomLinkages() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
getAtomName() - Method in class org.biojava.nbio.protmod.structure.StructureAtom
 
getAtomName() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
 
getAtomNames(Group) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
 
getAtoms() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getAtoms() - Method in interface org.biojava.nbio.structure.Group
Get list of atoms.
getAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl
Get list of atoms.
getAtoms() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
getAtoms(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns the CA atoms for the provided name.
getAtoms(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
getAtomsCAInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools
Returns the set of intra-chain contacts for the given chain for C-alpha atoms (including non-standard aminoacids appearing as HETATM groups), i.e. the contact map.
getAtomSequence() - Method in interface org.biojava.nbio.structure.Chain
Returns the sequence of amino acids as it has been provided in the ATOM records.
getAtomSequence() - Method in class org.biojava.nbio.structure.ChainImpl
 
getAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
getAtomsForGroup(Group) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Get a list of atoms for a group.
getAtomsInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools
Returns the set of intra-chain contacts for the given chain for all non-H atoms of non-hetatoms, i.e. the contact map.
getAtomsInContact(Chain, String[], double) - Static method in class org.biojava.nbio.structure.StructureTools
Returns the set of intra-chain contacts for the given chain for given atom names, i.e. the contact map.
getAtomsInContact(Chain, Chain, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
Returns the set of inter-chain contacts between the two given chains for all non-H atoms.
getAtomsInContact(Chain, Chain, String[], double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
Returns the set of inter-chain contacts between the two given chains for the given atom names.
getAtomType1() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
 
getAtomType2() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
 
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
 
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
 
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
 
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
 
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
 
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
 
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
 
getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
Return the attribute of the grouping
getAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
Get value of specified attribute key.
getAttribute(String) - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
Get the attribute value for this key.
getAttributeOld(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
 
getAttributes() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
 
getAttributes() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
 
getAuBoundingBox(int) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox
Get the AU BoundingBox for the given cell index (cellIdx=0 would be original AU) The AU BoundingBox is the BoundingBox that bounds all chains belonging to the AU
getAuthorList() - Method in class org.biojava.nbio.structure.JournalArticle
Get the list of Authors of the JournalArticle
getAuthors() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getAuthors() - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference
The authors are a list of Inventors that retrieved from the Reference section.
getAuthors() - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
 
getAuthors() - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface
Get the authors that retrieved from Reference section.
getAuthors() - Method in class org.biojava.nbio.structure.PDBHeader
Return the names of the authors as listed in the AUTHORS section of a PDB file.
getAutoSuggestProvider() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
 
getAverageResidueDistances(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.
getAverageResidueDistances(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.
getAverageScore() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
Returns the average similarity score between all pairs of members in the cluster
getAvgHydropathy(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
An adaptor method to return the average hydropathy value of sequence.
getAvgHydropathy(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
Returns the average hydropathy value of sequence.
getAvgHydropathy(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
 
getAvgTMScore(List<Atom[]>, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
Calculates the average TMScore all the possible pairwise structure comparisons of the given a set of superimposed Atoms and the original structure lengths.
getAvgTMScore(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
Calculates the average TMScore of all the possible pairwise structure comparisons of the given alignment.
getAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
getAxisAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
Returns the AxisAngle of the helix transformation
getAxisAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
getAxisAngle(int, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
 
getAxisAngle(int, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
 
getAxisAngle(int, AxisAngle4f) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
 
getAxisAngle4d() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
Returns the rotation axis and angle in a single javax.vecmath.AxisAngle4d object
getAxisEnds(Atom[]) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
Find a segment of the axis that covers the specified set of atoms.
getAxisFoldType(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
Given a transformId returns the type of axis of rotation: 1 (no rotation), 2, 3, 4 or 6 -fold and for improper rotations: -1, -2, -3, -4 and -6
getAxisTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
getAxisTypes() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getB() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
 
getB() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
getBackboneAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
Return an Atom array of the main chain atoms: CA, C, N, O Any group that contains those atoms will be included, be it a standard aminoacid or not
getBackingSequence() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
Access the sequence which backs this window
getBadRmsd() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getBase() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
 
getBasecalls() - Method in class org.biojava.nbio.core.sequence.io.ABITrace
Returns an int[] array that represents the basecalls - each int in the array corresponds to an x-coordinate point in the graph that is a peak (a base location).
getBaseIdentifier() - Method in class org.biojava.nbio.structure.align.client.StructureName
StructureName wraps another StructureIdentifier.
getBegin() - Method in class org.biojava.nbio.genome.parsers.gff.Location
 
getBeta() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
 
getBeta() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
getBinaryOperators() - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver
Returns a list of operators for this assembly.
getBioAssemblies() - Method in class org.biojava.nbio.structure.PDBHeader
Return the map of biological assemblies.
getBioBegin() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getBioEnd() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getBioEnd() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
getBioEnd() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView
1-indexed, inclusive.
getBiologicalAssemblies(String) - Static method in class org.biojava.nbio.structure.StructureIO
Returns all biological assemblies for the given PDB id, using multiModel=false
getBiologicalAssemblies(String, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns all biological assemblies for given PDB id.
getBiologicalAssemblies(String, boolean) - Static method in class org.biojava.nbio.structure.StructureIO
Returns all biological assemblies for the given PDB id.
getBiologicalAssembly(String) - Static method in class org.biojava.nbio.structure.StructureIO
Returns the first biological assembly that is available for the given PDB id, using multiModel=false
getBiologicalAssembly(String, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns the default biological unit (bioassemblyId=1, known in PDB as pdb1.gz).
getBiologicalAssembly(String, boolean) - Static method in class org.biojava.nbio.structure.StructureIO
Returns the first biological assembly that is available for the given PDB id.
getBiologicalAssembly(String, int) - Static method in class org.biojava.nbio.structure.StructureIO
Returns the biological assembly for the given PDB id and bioassembly identifier, using multiModel=false
getBiologicalAssembly(String, int, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()
getBiologicalAssembly(String, int, boolean) - Static method in class org.biojava.nbio.structure.StructureIO
Returns the biological assembly for the given PDB id and bioassembly identifier.
getBiologicalAssembly(PdbId, int, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()
getBiologicalMoleculeBounds(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
 
getBiologicalMoleculeCentroid(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
Returns the centroid of the biological molecule.
getBiologicalMoleculeMaximumExtend(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
Returns the maximum extend of the biological molecule in the x, y, or z direction.
getBiologicalUnit() - Method in class org.biojava.nbio.structure.EntityInfo
 
getBioSequences() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
used to retrieve sequences from the structure
getBioSequences(boolean) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
Because some database files have incorrectly small letters (e.g.
getBioSequences(boolean, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
This function tolerates mixed case letters, and allows for forcing the output biosequence type (PFAM/RFAM).
getBioStart() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
getBioStart() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView
1-indexed, inclusive.
getBioUnitTransformationList(PdbxStructAssembly, int, PdbxStructAssemblyGen, PdbxStructOperList) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
Returns a list of transformation matrices for the generation of a macromolecular assembly for the specified assembly Id.
getBJSequence() - Method in interface org.biojava.nbio.structure.Chain
Converts the SEQRES groups of a Chain to a Biojava Sequence object.
getBJSequence() - Method in class org.biojava.nbio.structure.ChainImpl
 
getBlastAdvancedOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
getBlastDatabase() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
getBlastExpect() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
getBlastFromPosition() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
getBlastGapCosts() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Returns the actual string for the GAPCOSTS parameter which is used to build the URL
getBlastGapCreation() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Returns the value for the GAP_CREATION parameter (first half of GAPCOSTS parameter)
getBlastGapExtension() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Returns the value for the gap extension parameter (second half of GAPCOSTS parameter)
getBlastMatrix() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Returns the value of the specified substitution matrix
getBlastProgram() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
getBlastToPosition() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
getBlastWordSize() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Returns the value of the WORD_SIZE parameter used for this blast run
getBlock(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Returns the Block with the specified index of the MultipleAlignment.
getBlock(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
getBlock2Afp() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getBlockForSequencePosition(MultipleAlignment, List<Integer>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Returns the block number of a specified position in the sequence alignment, given the mapping from structure to function.
getBlockGap() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getBlockNrForAlignPos(AFPChain, int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
get the block number for an aligned position
getBlockNum() - Method in class org.biojava.nbio.structure.align.model.AFPChain
The number of blocks in the alignment
getBlockNumClu() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getBlockNumIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getBlockNumSpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getBlockResList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
tracks the residues of the initial blocks (before optimization)
getBlockResSize() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getBlockRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getBlockRotationMatrix() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getBlocks() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
Returns the List of alignment Blocks of the BlockSet.
getBlocks() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
getBlocks() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Convenience method to get a List of all Blocks from all BlockSets.
getBlocks() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
getBlockScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getBlockSequenceAlignment(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
getBlockSequenceAlignment(MultipleAlignment, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
getBlockSet() - Method in interface org.biojava.nbio.structure.align.multiple.Block
Returns the parent BlockSet of the Block.
getBlockSet() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
getBlockSet(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Returns the BlockSet with the specified index of the MultipleAlignment.
getBlockSet(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
getBlockSets() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Returns the BlockSet List of the multiple structure alignment.
getBlockSets() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
getBlockShiftVector() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getBlockSize() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getBlosum100() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 100 matrix by Henikoff & Henikoff
getBlosum30() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 30 matrix by Henikoff & Henikoff
getBlosum35() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 35 matrix by Henikoff & Henikoff
getBlosum40() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 40 matrix by Henikoff & Henikoff
getBlosum45() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 45 matrix by Henikoff & Henikoff
getBlosum50() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 50 matrix by Henikoff & Henikoff
getBlosum55() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 55 matrix by Henikoff & Henikoff
getBlosum60() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 60 matrix by Henikoff & Henikoff
getBlosum62() - Static method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
 
getBlosum62() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 62 matrix by Henikoff & Henikoff
getBlosum65() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 65 matrix by Henikoff & Henikoff
getBlosum70() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 70 matrix by Henikoff & Henikoff
getBlosum75() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 75 matrix by Henikoff & Henikoff
getBlosum80() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 80 matrix by Henikoff & Henikoff
getBlosum85() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 85 matrix by Henikoff & Henikoff
getBlosum90() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns Blosum 90 matrix by Henikoff & Henikoff
getBondOrder() - Method in interface org.biojava.nbio.structure.Bond
Gets the bond order of this bond.
getBondOrder() - Method in class org.biojava.nbio.structure.BondImpl
Gets the bond order of this bond.
getBonds() - Method in interface org.biojava.nbio.structure.Atom
Get all Bonds this atom is part of.
getBonds() - Method in class org.biojava.nbio.structure.AtomImpl
Get all Bonds this atom is part of.
getBonds() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getBottom() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
getBravLattice() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getBridge1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
getBridge2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
getBsa() - Method in class org.biojava.nbio.structure.asa.GroupAsa
Returns the BSA value for this group, i.e. the difference between ASA uncomplexed and ASA complexed
getBsaToAsaRatio() - Method in class org.biojava.nbio.structure.asa.GroupAsa
Returns the bsa/asa(uncomplexed) ratio, i.e. the ratio of burial of a residue upon complexation
getBtype() - Method in class org.biojava.nbio.structure.secstruc.Ladder
 
getBuckle(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method returns the buckle in degrees for the given base pair
getBufferedReader() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource
Returns the reader representation of this classpath resource
getBuildMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getByCategory(ModificationCategory) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
getByCategory(CathCategory) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
Return list of CATH descriptions for node representatives at a CATH category (e.g.
getByCategory(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
getByCategory(ScopCategory) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
Get all records of a particular classification.
getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
getByChainId(String, String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
 
getByComponent(Component, Component...) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
Get ProteinModifications that involves one or more components.
getById(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
getByKeyword(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
getByLabel(String) - Static method in enum org.biojava.nbio.protmod.ModificationCategory
 
getByLabel(String) - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType
 
getByLargestContacts() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
 
getByLargestContactsNotLowestAngle() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
 
getByLowestAngle() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
 
getByName(String) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique
Returns the ExpTechnique given an experimental technique name as used in the PDB, e.g.
getByName(String) - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice
 
getByOccurrenceType(ModificationOccurrenceType) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
getByPdbccId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
getByPsimodId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
getByResidId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
 
getBytesRead() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Keep track of bytesread via ReadLine to account for CR-LF in the stream.
getByUniProtId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
 
getC() - Method in interface org.biojava.nbio.structure.AminoAcid
Get C atom.
getC() - Method in class org.biojava.nbio.structure.AminoAcidImpl
Get C atom.
getC() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
 
getC() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
getC2Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
 
getC3Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
 
getC4Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
 
getCA() - Method in interface org.biojava.nbio.structure.AminoAcid
Get CA atom.
getCA() - Method in class org.biojava.nbio.structure.AminoAcidImpl
Get CA atom.
getCa1() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
 
getCa1() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
getCa1() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
getCa1Length() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getCa2() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
getCa2() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
getCa2Length() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getCache() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
 
getCacheFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
getCacheFilePath() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
 
getCacheLocation() - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
getCacheLocation() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
Get the location of the cache directory (usually set to the PDB_CACHE_DIR property).
getCacheLocation() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
getCachePath() - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns the path that contains the caching file for utility data, such as domain definitions.
getCalculationTime() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getCalculationTime() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Returns the running time of the structure alignment calculation, in milliseconds.
getCalculationTime() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
getCalculationTime() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
getCalphaCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
 
getCategories() - Method in class demo.DemoSCOP
Get various categories
getCategory() - Method in class org.biojava.nbio.ontology.Synonym
 
getCategory() - Method in interface org.biojava.nbio.protmod.ProteinModification
 
getCategory() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
getCategory() - Method in class org.biojava.nbio.structure.cath.CathNode
 
getCategory() - Method in class org.biojava.nbio.structure.scop.ScopDescription
 
getCATH() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getCathDatabase() - Static method in class org.biojava.nbio.structure.cath.CathFactory
Returns the default (singleton) CathDatabase.
getCathDatabase(String) - Static method in class org.biojava.nbio.structure.cath.CathFactory
Returns a CATH database of the specified version.
getCathDownloadUrl() - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
getCathNode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
Return the CathNode for a node ID.
getCathNode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
getCathVersion() - Method in interface org.biojava.nbio.structure.cath.CathDatabase
Return the CATH release version.
getCathVersion() - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
getCB() - Method in interface org.biojava.nbio.structure.AminoAcid
Get CB atom.
getCB() - Method in class org.biojava.nbio.structure.AminoAcidImpl
Get CB atom.
getCdsEnd() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
getCDSExonRanges(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Extracts the exon boundaries in CDS coordinates.
getCDSLength(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Get the length of the CDS in nucleotides.
getCDSLengthForward(List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Get the length of the coding sequence
getCDSLengthReverse(List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Get the length of the coding sequence
getCDSPosForChromosomeCoordinate(int, GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
I have a genomic coordinate, where is it on the mRNA
getCDSPosForward(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene living on the forward DNA strand.
getCDSPosReverse(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene living on the reverse DNA strand.
getCDSRegions(List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Extracts the exons boundaries in CDS coordinates corresponding to the forward DNA strand.
getCDSSequences() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
Get the CDS sequences that have been added to the TranscriptSequences
getCdsStart() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
getCECalculator() - Method in class org.biojava.nbio.structure.align.ce.CeMain
 
getCell() - Method in class org.biojava.nbio.structure.EntityInfo
 
getCell(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
Get cell value
getCellColor() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
 
getCellColor() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
getCellDouble(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
getCellIndices(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
Get the index of a unit cell to which the query point belongs.
getCellLine() - Method in class org.biojava.nbio.structure.EntityInfo
 
getCellTranslation(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getCellTranslations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getCellularLocation() - Method in class org.biojava.nbio.structure.EntityInfo
 
getCenter(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils
Get the centroid for the set of atoms starting from position pos, length fragmentLenght
getCenter1() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
getCenter2() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
getCenterOfMass() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
 
getCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
 
getCenterVector(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
Returns the Vector that needs to be applied to shift a set of atoms to the Centroid.
getCenterVector(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc
Returns the Vector that needs to be applied to shift a set of atoms to the Centroid, if the centroid is already known
getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
 
getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
 
getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
 
getCentroid(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
Returns the centroid of the set of atoms.
getChain() - Method in interface org.biojava.nbio.structure.Group
Returns the parent Chain of the Group.
getChain() - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
getChain() - Method in class org.biojava.nbio.structure.HetatomImpl
Returns the parent Chain of the Group.
getChain(String) - Method in interface org.biojava.nbio.structure.Structure
Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first model
getChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first model
getChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the given model index
getChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the given model index
getChain1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
getChain1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
 
getChain2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
getChainBoundingBox(int, int) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox
Get the chain BoundingBox for the given cell index (cellIdx=0 would be original AU) and chain index
getChainByIndex(int) - Method in interface org.biojava.nbio.structure.Structure
Retrieve a chain by its index within the Structure .
getChainByIndex(int) - Method in class org.biojava.nbio.structure.StructureImpl
Retrieve a chain by its index within the Structure .
getChainByIndex(int, int) - Method in interface org.biojava.nbio.structure.Structure
Retrieve a chain by its indices within the Structure and model.
getChainByIndex(int, int) - Method in class org.biojava.nbio.structure.StructureImpl
Retrieve a chain by its indices within the Structure and model.
getChainId() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
getChainId() - Method in class org.biojava.nbio.structure.align.client.StructureName
Gets the chain ID, for structures where it is unique and well-defined.
getChainId() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
 
getChainId() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
 
getChainId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
getChainId() - Method in interface org.biojava.nbio.structure.Group
Utility method for returning the chainId of the Group or null if no Chain has been set.
getChainId() - Method in class org.biojava.nbio.structure.HetatomImpl
Utility method for returning the chainId of the Group or null if no Chain has been set.
getChainId() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom
 
getChainId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
getChainId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
getChainId() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
Returns the chain identifier (asym id) that this transformation should be applied to.
getChainId1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
 
getChainID1() - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
getChainID1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
 
getChainId2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
 
getChainID2() - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
getChainID2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
 
getChainIds() - Method in class org.biojava.nbio.structure.EntityInfo
Return the list of member chain ids (asym ids) that are described by this EntityInfo, only unique chain IDs are contained in the list.
getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
This method is provisional and should only be used for coloring Subunits.
getChainIds() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
 
getChainIdsInEntry(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
 
getChainIdToIndexMap() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
 
getChainLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getChainName() - Method in class org.biojava.nbio.structure.DBRef
The name of the corresponding chain.
getChainName() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom
 
getChainName() - Method in class org.biojava.nbio.structure.ResidueNumber
 
getChainName() - Method in class org.biojava.nbio.structure.ResidueRange
 
getChainRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getChains() - Method in class org.biojava.nbio.structure.cath.CathDomain
Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
getChains() - Method in class org.biojava.nbio.structure.EntityInfo
Get the list of chains that are part of this EntityInfo.
getChains() - Method in class org.biojava.nbio.structure.Model
Get all chains: polymeric, non-polymeric and water
getChains() - Method in class org.biojava.nbio.structure.scop.ScopDomain
Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
getChains() - Method in interface org.biojava.nbio.structure.Structure
Retrieve all chains for the first model.
getChains() - Method in class org.biojava.nbio.structure.StructureImpl
Retrieve all chains for the first model.
getChains(int) - Method in interface org.biojava.nbio.structure.Structure
Retrieve all chains of a model.
getChains(int) - Method in class org.biojava.nbio.structure.StructureImpl
Retrieve all chains of a model.
getCharge() - Method in interface org.biojava.nbio.structure.Atom
Get the charge of this atom
getCharge() - Method in class org.biojava.nbio.structure.AtomImpl
 
getCharge() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getChargeOfAminoAcid(char) - Static method in class org.biojava.nbio.aaproperties.AminoAcidProperties
Returns the charge of amino acid.
getChargesOfAminoAcids(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
Returns the array of charges of each amino acid in a protein.
getChemComp() - Method in interface org.biojava.nbio.structure.Group
Get the chemical component that closer describes this group.
getChemComp() - Method in class org.biojava.nbio.structure.HetatomImpl
 
getChemComp(String) - Method in class org.biojava.nbio.structure.chem.AllChemCompProvider
Returns a new instance of a chemical component definition.
getChemComp(String) - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory
 
getChemComp(String) - Method in interface org.biojava.nbio.structure.chem.ChemCompProvider
Returns a new instance of a chemical component definition.
getChemComp(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
 
getChemComp(String) - Method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
Loads the definitions for this ChemComp from a local file and instantiates a new object.
getChemComp(String) - Method in class org.biojava.nbio.structure.chem.ReducedChemCompProvider
 
getChemComp(String) - Method in class org.biojava.nbio.structure.chem.ZipChemCompProvider
(non-Javadoc)
getChemCompProvider() - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory
 
getChild1() - Method in class org.biojava.nbio.alignment.GuideTree.Node
 
getChild1() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
Returns the first child node of this node.
getChild2() - Method in class org.biojava.nbio.alignment.GuideTree.Node
 
getChild2() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
Returns the second child node of this node.
getChildAt(int) - Method in class org.biojava.nbio.alignment.GuideTree.Node
 
getChildCount() - Method in class org.biojava.nbio.alignment.GuideTree.Node
 
getChildren() - Method in class org.biojava.nbio.structure.scop.ScopNode
 
getChildrenFeatures() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
Get the children features
getChildrenFeatures() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
getChildrenFeatures() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Get the features contained by this feature
getChiSquare() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getChrLoc() - Method in class org.biojava.nbio.phosphosite.Site
 
getChromosomalRangesForCDS(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Extracts the boundaries of the coding regions in chromosomal coordinates
getChromosome() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
 
getChromosome() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
getChromosome() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
getChromosomeMappings() - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
 
getChromosomeMappings(InputStream) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
 
getChromosomeNumber() - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
 
getChromosomePosForCDScoordinate(int, GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Maps the position of a CDS nucleotide back to the genome
getChromosomeSequenceFromDNASequence(LinkedHashMap<String, DNASequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
 
getChromPosForward(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Get the CDS position mapped onto the chromosome position
getChromPosReverse(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Get the CDS position mapped on the chromosome position
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
Returns the radius of a circumscribed sphere, that goes through all vertices
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
Returns the radius of a circumscribed sphere, that goes through all vertices
getCirumscribedRadius() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
 
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
Returns the radius of a circumscribed sphere, that goes through all vertices
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
Returns the radius of a circumscribed sphere (length of diagonal of rectangular prism/2, that goes through at least four vertices
getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
Returns the radius of a circumscribed sphere, that goes through all vertices
getClaFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
getClan() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getClassId() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getClassId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
getClassification() - Method in class org.biojava.nbio.structure.PDBHeader
 
getClassificationId() - Method in class org.biojava.nbio.structure.scop.ScopDescription
 
getClassificationId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
getClassificationId(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getClassificationId(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopDescription
Return a portion of the classificationID corresponding to the specified category (class, fold, superfamily, family).
getClaURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
 
getCloseMenuItem(JFrame) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
getCluster() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
get the number of the cluster this alignment belongs to
getCluster() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
getCluster() - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
getClustererMethod() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
 
getClustererMethod() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Method to cluster subunits.
getClusterIds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
 
getClusters() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Calculate the interface clusters for this StructureInterfaceList using a contact overlap score to measure the similarity of interfaces.
getClusters() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
 
getClusters(double) - Method in class org.biojava.nbio.core.util.SingleLinkageClusterer
Get the clusters by cutting the dendrogram at given cutoff
getClusters(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Calculate the interface clusters for this StructureInterfaceList using Jaccard contact set scores to measure the similarity of interfaces.
getClustersNcs() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Get the interface clusters for this StructureInterfaceList grouped by NCS-equivalence.
getClusterValue() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getCodingSequence() - Method in class org.biojava.nbio.core.sequence.CDSSequence
A CDS sequence if negative stranded needs to be reverse complement to represent the actual coding sequence.
getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
Returns the compound set of codons
getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava.nbio.core.sequence.transcription.Table
 
getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
Returns a list of codons where the source and target compounds are the same as those given by the parameters.
getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava.nbio.core.sequence.transcription.Table
 
getCoeff() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
getCoefficient(String) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getCoefficientsList() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getCoefficientText(boolean, String, String, String, String) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getCohortName() - Method in class org.biojava.nbio.survival.cox.CoxVariables
 
getCol() - Method in class org.biojava.nbio.structure.align.helper.IndexPair
 
getColor() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
getColor() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
 
getColor(double) - Method in interface org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper
 
getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform
Return the color corresponding to submapper.getColor(transform(value)).
getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
 
getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
getColor(int) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
getColorPalette() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
Return the color pattelete of the AlignmentJmol instance.
getCols() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
getCols() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
getCols() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
getColumn(C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
 
getColumn(C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
 
getColumn(AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
getColumnDimension() - Method in class org.biojava.nbio.structure.jama.Matrix
Get column dimension.
getColumnIndex(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
getColumnLookup() - Method in class org.biojava.nbio.survival.data.WorkSheet
 
getColumnPackedCopy() - Method in class org.biojava.nbio.structure.jama.Matrix
Make a one-dimensional column packed copy of the internal array.
getColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
Get the list of column names.
getComFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
getComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getComment() - Static method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
getComment() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getComments() - Method in class org.biojava.nbio.core.sequence.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
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.
getContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
getContacts() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
getContactsToOtherCell(GridCell) - Method in class org.biojava.nbio.structure.contact.GridCell
Calculates all distances of atoms between this cell and the given cell returning those that are within the given cutoff as a list of Contacts containing the indices of the pair and the calculated distance.
getContactsWithinCell() - Method in class org.biojava.nbio.structure.contact.GridCell
Calculates all distances of atoms within this cell returning those that are within the given cutoff as a list of Contacts containing the indices of the pair and the calculated distance.
getContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
Returns the list of contacts from this set that are within the given distance.
getContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.GroupContact
Returns the list of atom contacts in this GroupContact that are within the given distance.
getContainer() - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
 
getContainer() - Method in interface org.biojava.nbio.structure.io.cif.CifFileConsumer
Retrieve the created container representing a CIF file.
getContainer() - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
getContainer() - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl
 
getContig() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
 
getContinuousVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getConvergenceSteps() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
getCoordManager() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
getCoordManager() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
getCoordpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getCoords() - Method in interface org.biojava.nbio.structure.Atom
Get the coordinates.
getCoords() - Method in class org.biojava.nbio.structure.AtomImpl
Get the coordinates.
getCoordsAsPoint3d() - Method in interface org.biojava.nbio.structure.Atom
Get the coordinates.
getCoordsAsPoint3d() - Method in class org.biojava.nbio.structure.AtomImpl
Get the coordinates.
getCopy() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
getCopyWorkSheet(WorkSheet) - Static method in class org.biojava.nbio.survival.data.WorkSheet
Create a copy of a worksheet.
getCopyWorkSheetSelectedRows(WorkSheet, ArrayList<String>) - Static method in class org.biojava.nbio.survival.data.WorkSheet
Create a copy of a worksheet.
getCoreElectronCount() - Method in enum org.biojava.nbio.structure.Element
Returns the number of core electrons for this Element.
getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.Block
Returns the number of aligned positions (columns) without gaps in the Block.
getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all Block core lengths.
getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all BlockSet core lengths.
getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
getCoreOntology() - Static method in class org.biojava.nbio.ontology.OntoTools
Get the Ontology that defines our core "central dogma".
getCorePositions(Block) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Calculate a List of alignment indicies that correspond to the core of a Block, which means that all structures have a residue in that positon.
getCoreResidues(double, double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
Returns the residues belonging to the interface core, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is above the given bsaToAsaCutoff
getCount() - Method in class org.biojava.nbio.aaproperties.xml.Name2Count
 
getCovalentRadius() - Method in enum org.biojava.nbio.structure.Element
Returns the covalent radius of this Element.
getCoverage() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
getCoverage() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
Returns the coverage, as a fraction between 0 and 1, of this AlignedSequence with respect to the original sequence.
getCoverage1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
Get the coverage of protein 1 with the alignment
getCoverage2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
Get the coverage of protein 2 with the alignment
getCoverages() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Returns the coverage of the alignment for each structure in the alignment as a fraction between 0.0 and 1.0.
getCoverages() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
getCovered() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
getCoxInfo(String) - Method in class org.biojava.nbio.survival.cox.CoxVariables
 
getCoxInfoHashMap() - Method in class org.biojava.nbio.survival.cox.CoxVariables
 
getCPPoint() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
 
getCreate_co() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getCreatedDate() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
The DT line shows when an entry first appeared in the database
getCreator() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
getCrystalCell() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
Return the crystal cell
getCrystalIds() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Returns a pair of identifiers for each of the 2 member molecules that identify them uniquely in the crystal: <molecule id (asym unit id)>+<operator id>+<crystal translation>
getCrystallographicInfo() - Method in class org.biojava.nbio.structure.PDBHeader
 
getCrystallographicInfo() - Method in interface org.biojava.nbio.structure.Structure
Get crystallographic information for this structure
getCrystallographicInfo() - Method in class org.biojava.nbio.structure.StructureImpl
Gets crystallographic information for this structure
getCrystalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
 
getCurrent(String) - Static method in class org.biojava.nbio.structure.PDBStatus
Gets the current version of a PDB ID.
getCurrentChain() - Method in class org.biojava.nbio.structure.AtomIterator
Get the chain that contains the current atom.
getCurrentChain() - Method in class org.biojava.nbio.structure.GroupIterator
Get the current Chain.
getCurrentModel() - Method in class org.biojava.nbio.structure.AtomIterator
Get the model number of the model containing the current atom.
getCurrentModel() - Method in class org.biojava.nbio.structure.GroupIterator
Get the model number of the current model.
getCurrentPDBIds() - Static method in class org.biojava.nbio.structure.PDBStatus
Returns all current PDB IDs
getCurrentSequencePosition() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
getCut_sites() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
 
getCutoff() - Method in class org.biojava.nbio.structure.contact.Grid
 
getCuts(int, AlignerHelper.Subproblem, int[], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
 
getCutsPerSection() - Method in class org.biojava.nbio.alignment.routines.GuanUberbacher
Returns the number of cuts added to each section during each pass.
getD() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition
Return the block diagonal eigenvalue matrix
getData() - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
 
getDatabase() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
getDatabase() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
 
getDatabase() - Method in class org.biojava.nbio.structure.DBRef
The database of the db-ref.
getDatabaseCrossReference() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
The DR (Database Cross-reference) line cross-references other databases which contain information related to the entry in which the DR line appears.
getDatabaseReferences() - Method in interface org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface
 
getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
 
getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
The Uniprot mappings to other database identifiers for this sequence
getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getDataClass() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
 
getDataColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
 
getDataRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
Get the list of row names
getDataSource() - Method in class org.biojava.nbio.core.sequence.AccessionID
 
getDataSource() - Method in class org.biojava.nbio.core.sequence.location.InsdcParser
 
getDataSource() - Method in class org.biojava.nbio.core.sequence.TaxonomyID
 
getDataVariables() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getDate() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getDbAccession() - Method in class org.biojava.nbio.structure.DBRef
Sequence database accession code.
getDbComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getDbFile() - Method in class org.biojava.nbio.core.search.io.Result
 
getDbIdCode() - Method in class org.biojava.nbio.structure.DBRef
Sequence database identification code.
getDbReferences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getDBRefs() - Method in interface org.biojava.nbio.structure.Structure
Get the list of database references
getDBRefs() - Method in class org.biojava.nbio.structure.StructureImpl
Get the list of database references
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
 
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
 
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
 
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
 
getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
 
getDBSearchParameters() - Static method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getDbSearchResult(AFPChain) - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
 
getDbSeqBegin() - Method in class org.biojava.nbio.structure.DBRef
Initial sequence number of the database seqment.
getDbSeqEnd() - Method in class org.biojava.nbio.structure.DBRef
Ending sequence position of the database segment.
getDbxrefList(String, int, int) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
 
getDcl() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
getdCutoff() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
The maximum allowed distance between the centroids of two equivalent Subunits, in A.
getDefault() - Static method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
Default instance to use when Transcribing from DNA -> RNA -> Protein.
getDefaultConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
 
getDefaultFactory() - Static method in class org.biojava.nbio.ontology.OntoTools
 
getDefaultFrame() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
 
getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Returns a Jmol script to set the default orientation for a structure
getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
Returns a Jmol script to set the default orientation for a structure
getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
getDefaultParameters() - Static method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getDefaultText() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
 
getDefinition() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getDegreeFreedom() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getDelta() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getDendrogram() - Method in class org.biojava.nbio.core.util.SingleLinkageClusterer
Get the full dendrogram (size n-1) result of the hierarchical clustering
getDensityCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getDepDate() - Method in class org.biojava.nbio.structure.PDBHeader
Return the deposition date of the structure in the PDB.
getDesc() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
getDescription() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
getDescription() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
 
getDescription() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
Returns the description of this matrix.
getDescription() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
 
getDescription() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
 
getDescription() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
getDescription() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Get the description that can be used to describe the feature
getDescription() - Method in class org.biojava.nbio.core.sequence.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
 
getEvalCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getEvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
getEvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
getEvalueThreshold() - Method in class org.biojava.nbio.core.search.io.SearchIO
 
getEvCode() - Method in class org.biojava.nbio.structure.Site
gets the REMARK 800 EVIDENCE CODE for the site.
getExampleUnitCell() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
 
getExitMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
getExonCount() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
getExonEnds() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
getExonSequences() - Method in class org.biojava.nbio.core.sequence.GeneSequence
Get the exons as an ArrayList.
getExonStarts() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
getExpectedExecutionTime() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
 
getExperimentalTechniques() - Method in class org.biojava.nbio.structure.PDBHeader
Return the Set of ExperimentalTechniques, usually the set is of size 1 except for hybrid experimental techniques when the Set will contain 2 or more values
getExportPDBMenuItem(AbstractAlignmentJmol) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
getExpressionSystem() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemAtccNumber() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemCell() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemCellLine() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemCellularLocation() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemGene() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemOrgan() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemOrganelle() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemOtherDetails() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemPlasmid() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemStrain() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemTaxId() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemTissue() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemVariant() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemVector() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExpressionSystemVectorType() - Method in class org.biojava.nbio.structure.EntityInfo
 
getExtensionPenalty() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
Returns the negative of the extension penalty passed to the constructor.
getExtensionPenalty() - Method in interface org.biojava.nbio.alignment.template.GapPenalty
Returns penalty given when an already open gap elongates by a single element
getExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
 
getExtensions() - Method in enum org.biojava.nbio.structure.io.StructureFiletype
 
getExtensions() - Method in interface org.biojava.nbio.structure.io.StructureIOFile
Returns a list of extensions supported by this class
getExtinctionCoefficient(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
An adaptor method to return the extinction coefficient of sequence.
getExtinctionCoefficient(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
Returns the extinction coefficient of sequence.
getExtinctionCoefficient(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
 
getFailedLines() - Method in class org.biojava.nbio.structure.scop.Astral
Gets a map describing lines read in the file that weren't understood.
getFalseDiscoveryRate() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getFamilyId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
getFatCatAligner() - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
 
getFeatureHeader() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
The FH (Feature Header) lines are present only to improve readability of an entry when it is printed or displayed on a terminal screen.
getFeatureRetriever() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getFeatures() - Method in interface org.biojava.nbio.core.sequence.features.FeatureRetriever
 
getFeatures() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
getFeatures() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
 
getFeatures() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getFeatures(int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Return features at a sequence position
getFeatures(String) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
getFeatures(String, int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Return features at a sequence position by type
getFeaturesByType(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getFeaturesKeyWord() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getFeatureTable() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
The FT (Feature Table) lines provide a mechanism for the annotation of the sequence data.
getFetchBehavior() - Method in class org.biojava.nbio.structure.align.util.AtomCache
Get the behavior for fetching files from the server
getFetchBehavior() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
 
getFetchBehavior() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Get the behavior for fetching files from the server
getFGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
getFGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
getFile() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
getFile1() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
getFile2() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
getFileAnnotation() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
getFileExtension(File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
Gets the file extension of a file, excluding '.'.
getFileExtensions() - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
 
getFileExtensions() - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
 
getFileExtensions() - Method in interface org.biojava.nbio.core.search.io.ResultFactory
returns a list of file extensions associated to this ResultFactory
getFileFormat() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
 
getFileFormatSelect() - Static method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
 
getFilename(String) - Method in class org.biojava.nbio.structure.io.BcifFileReader
 
getFilename(String) - Method in class org.biojava.nbio.structure.io.CifFileReader
 
getFilename(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Converts a PDB ID into a filename with the proper extension
getFilename(String) - Method in class org.biojava.nbio.structure.io.MMTFFileReader
 
getFilename(String) - Method in class org.biojava.nbio.structure.io.PDBFileReader
 
getFileName() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
 
getFileName() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
 
getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.PDBFileParser
 
getFileParsingParameters() - Method in interface org.biojava.nbio.structure.io.StructureProvider
Get the parameters that should be used for file parsing
getFileParsingParams() - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
getFilePath1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
 
getFilePrefix(File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
Gets the file name up to and excluding the first '.' character.
getFiletype() - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns the currently active file type that will be parsed.
getFinalIndex(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block
Calculates and returns the last position of the specified structure in the alignment that is not null.
getFinalIndex(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
getFinalResidue(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block
Calculates and returns the last residue of the specified structure in the alignment that is not null.
getFinalResidue(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
getFirst() - Method in class org.biojava.nbio.structure.AtomPositionMap
 
getFirst() - Method in class org.biojava.nbio.structure.contact.Pair
 
getFirst(String) - Method in class org.biojava.nbio.structure.AtomPositionMap
 
getFirstAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
getFirstGroupAsa(ResidueNumber) - Method in class org.biojava.nbio.structure.contact.StructureInterface
Gets the GroupAsa for the corresponding residue number of first chain
getFirstGroupAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Gets a map of ResidueNumbers to GroupAsas for all groups of first chain.
getFirstRepeat() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
Get the index of the first repeat used by this axis
getFirstRepeats(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
Get the first repeat index of each axis of a specified level.
getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
Should return the 5-prime end of the given Sequence according to the edit.
getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
 
getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Insert
 
getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute
 
getFocusAfpList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getFocusAfpn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getFocusRes1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getFocusRes2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getFocusResn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getFold() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
getFold() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
getFoldId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
getFolds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
 
getFoldType() - Method in enum org.biojava.nbio.structure.xtal.TransformType
 
getFormat() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getFormat() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getFormatedSequence(int) - Method in class org.biojava.nbio.data.sequence.FastaSequence
Format sequence per width letter in one string.
getFormattedFasta() - Method in class org.biojava.nbio.data.sequence.FastaSequence
 
getFormula() - Method in interface org.biojava.nbio.protmod.ProteinModification
 
getFormula() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
getFormula() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getFormulaWeight() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getForwardFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
Returns all frames in the forward orientation
getFragCompat() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getFragLen() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getFragLen() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
 
getFragLen() - Method in class org.biojava.nbio.structure.align.model.AFP
 
getFragLenSq() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getFragment() - Method in class org.biojava.nbio.structure.EntityInfo
 
getFragment(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils
Get a continue subset of Atoms based by the starting position and the length
getFragmentFromIdxList(Atom[], int[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils
Get a subset of Atoms based by their positions
getFragmentId() - Method in class org.biojava.nbio.structure.cath.CathFragment
 
getFragmentLength() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getFragmentMiniDistance() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getFragmentNoClone(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils
Get a continue subset of Atoms based by the starting position and the length does not clone the original atoms.
getFragmentPairs() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
get the results of step 1 - the FragmentPairs used for seeding the alignment
getFragmentPairs() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
 
getFragmentPairs() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
getFragmentsByPdbId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
 
getFragmentsByPdbId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
getFragScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getFrame() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
 
getFrame() - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
 
getFrom() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
 
getFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
 
getFromCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
getFromFtp() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
 
getFullAtomSequence(List<Group>, Map<Integer, Integer>, boolean) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
Returns the full sequence of the Atom records of a parent with X instead of HETATMSs.
getFullMatrix() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
Returns a matrix that describes both rotation and translation.
getGamma() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
 
getGamma() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
getGapCreate() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getGapExtCol() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
getGapExtCol() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
getGapExtend() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getGapExtend() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
 
getGapExtend() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
 
getGapExtension() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
getGapExtension() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
getGapExtension() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
getGapExtension() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getGapExtRow() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
getGapExtRow() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
getGapLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getGapOpen() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
getGapOpen() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
getGapOpen() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
getGapOpen() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
 
getGapOpen() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
 
getGapOpen() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getGapOpenCol() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
getGapOpenCol() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
getGapOpenRow() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
getGapOpenRow() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
getGapPenalty() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Returns the gap penalties.
getGaps() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
return the number of gaps in this alignment
getGatheringThreshs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
Not always 2.
It may undergo further change.
getGC() - Method in class org.biojava.nbio.core.sequence.RNASequence
 
getGCCount() - Method in class org.biojava.nbio.core.sequence.DNASequence
Get the GC count in the DNA Sequence
getGCGChecksum(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
Calculates GCG checksum for entire list of sequences
getGCGChecksum(S) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
Calculates GCG checksum for a given sequence
getGCGHeader(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
Assembles a GCG file header
getGCGType(CompoundSet<C>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
Determines GCG type
getGCStats(Collection<DNASequence>) - Static method in class org.biojava.nbio.genome.parsers.gff.GCStats
 
getGCStatsString(Collection<String>) - Static method in class org.biojava.nbio.genome.parsers.gff.GCStats
 
getGenbankDirectoryCache() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
Local directory cache of Genbank that can be downloaded
getGene() - Method in class org.biojava.nbio.structure.EntityInfo
 
getGene(String) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
Get the gene based on accession.
getGeneAliases() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
Pull uniprot gene aliases associated with this sequence
getGenebankId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
getGeneName() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
Get the gene name associated with this sequence.
getGeneName() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
getGeneNames() - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
 
getGeneNames(InputStream) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
Get a list of GeneNames from an input stream.
getGenes() - Method in class org.biojava.nbio.survival.cox.CoxVariables
 
getGeneSequences() - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key.
getGeneSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
 
getGeneSet() - Method in class org.biojava.nbio.survival.cox.CoxVariables
 
getGeneSymb() - Method in class org.biojava.nbio.phosphosite.Site
 
getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
Returns a transformation matrix transform polyhedra for Cn structures.
getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
Returns a transformation matrix transform polyhedra for Cn structures.
getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
Returns the geometric center of polyhedron.
getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
Returns the geometric center of polyhedron.
getGonnet250() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns PAM 250 matrix by Gonnet, Cohen & Benner
getGradientMapper(int, double, double) - Static method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
Constructs a gradientMapper to draw one of the pre-defined gradients For example, GradientMapper.getGradientMapper(GradientMapper.RAINBOW_GRADIENT, 0, 10)
getGroup() - Method in class org.biojava.nbio.phosphosite.Site
 
getGroup() - Method in class org.biojava.nbio.protmod.structure.StructureAtom
 
getGroup() - Method in class org.biojava.nbio.structure.asa.GroupAsa
 
getGroup() - Method in interface org.biojava.nbio.structure.Atom
Return the parent Group of the Atom.
getGroup() - Method in class org.biojava.nbio.structure.AtomImpl
Return the parent Group of the Atom.
getGroup() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
 
getGroupAsas() - Method in class org.biojava.nbio.structure.asa.AsaCalculator
Calculates ASA for all atoms and return them as a GroupAsa array (one element per residue in structure) containing ASAs per residue and per atom.
getGroupByPDB(ResidueNumber) - Method in interface org.biojava.nbio.structure.Chain
Get a group by its PDB residue numbering.
getGroupByPDB(ResidueNumber) - Method in class org.biojava.nbio.structure.ChainImpl
 
getGroupByPDBResidueNumber(Structure, ResidueNumber) - Static method in class org.biojava.nbio.structure.StructureTools
Get a group represented by a ResidueNumber.
getGroupCategories(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getGroupCategories(String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
 
getGroupContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
getGroupDistancesWithinShell(Structure, Atom, Set<ResidueNumber>, double, boolean, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
Finds Groups in structure that contain at least one Atom that is within radius Angstroms of centroid.
getGroupFromChemCompDictionary(String) - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory
 
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
 
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
 
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
 
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
 
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
 
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
 
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
 
getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
Returns the groupings of the attribute
getGroups() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
 
getGroups() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
getGroups() - Method in class org.biojava.nbio.structure.Site
 
getGroups() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
Get the name of the groups that are being plotted in the figure
getGroups(boolean) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
 
getGroups(boolean) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
getGroups(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Returns the List of Groups of the corresponding representative Atom array.
getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in interface org.biojava.nbio.structure.Chain
Get all groups that are located between two PDB residue numbers.
getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.ChainImpl
 
getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in interface org.biojava.nbio.structure.Chain
Get all groups that are located between two PDB residue numbers.
getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in class org.biojava.nbio.structure.ChainImpl
 
getGroupsWithinShell(Structure, Atom, Set<ResidueNumber>, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
 
getGroupsWithinShell(Structure, Group, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
Returns a Set of Groups in a structure within the distance specified of a given group.
getGroupTable() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
 
getH() - Method in class org.biojava.nbio.structure.jama.QRDecomposition
Return the Householder vectors
getHazardRatio() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
getHazardRatioHiCI() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
getHazardRatioLoCI() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
getHeader() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
getHeader() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
 
getHeader(S) - Method in class org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat
 
getHeader(S) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
 
getHeader(S) - Method in interface org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface
 
getHeader(S) - Method in interface org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface
 
getHeaderParser() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
 
getHeaderVars() - Method in class org.biojava.nbio.structure.EntityInfo
 
getHeight() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
 
getHeight() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
Returns the radius of a sphere, that is tangent to each of the octahedron's edges
getHelix(int) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
 
getHelixLayers() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getHelixLayers() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
 
getHelixRmsdThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
getHelixRmsdToRiseRatio() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
getHelpMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
getHgncId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
getHGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
getHGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
getHieFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
getHieURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
 
getHigherOrderRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
getHillOrder() - Method in enum org.biojava.nbio.structure.Element
Returns the Hill Order of this Element.
getHitAccession() - Method in class org.biojava.nbio.core.search.io.Hit
 
getHitCounter() - Method in class org.biojava.nbio.core.search.io.Result
 
getHitDef() - Method in class org.biojava.nbio.core.search.io.Hit
 
getHitId() - Method in class org.biojava.nbio.core.search.io.Hit
 
getHitLen() - Method in class org.biojava.nbio.core.search.io.Hit
 
getHitNum() - Method in class org.biojava.nbio.core.search.io.Hit
 
getHitSequence() - Method in class org.biojava.nbio.core.search.io.Hit
returns the reference to the original and whole sequence hit in the database.
getHitsQueryDef(double) - Method in class org.biojava.nbio.genome.query.BlastXMLQuery
 
getHmmAcc() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
getHmmDesc() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
getHmmFrom() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
getHmmName() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
getHmmTo() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
getHomologyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getHRText() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
getHSDMTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Calculate a phylogenetic tree of the MultipleAlignment using dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for distantly related proteins, structure-derived) and the Neighbor Joining algorithm from forester.
getHspAlignLen() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspBitScore() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspEvalue() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspGaps() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspHitFrame() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspHitFrom() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspHitTo() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspHseq() - Method in class org.biojava.nbio.core.search.io.Hsp
HSP aligned hit sequence string
getHspIdentity() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspIdentityString() - Method in class org.biojava.nbio.core.search.io.Hsp
Identity string representing correspondence between aligned residues
getHspNum() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspPositive() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspQseq() - Method in class org.biojava.nbio.core.search.io.Hsp
HSP aligned query sequence string
getHspQueryFrame() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspQueryFrom() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspQueryTo() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHspScore() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getHSVColorSpace() - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
 
getI() - Method in class org.biojava.nbio.structure.contact.Contact
 
getIAtoms() - Method in class org.biojava.nbio.structure.contact.Grid
 
getIclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
 
getiCode1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
 
getiCode2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
 
getIcon(ActionListener, String) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
getId() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
 
getId() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
 
getId() - Method in class org.biojava.nbio.data.sequence.FastaSequence
Gets the value of id
getId() - Method in interface org.biojava.nbio.protmod.ProteinModification
 
getId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
getId() - Method in class org.biojava.nbio.structure.align.model.AFP
 
getId() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getId() - Method in interface org.biojava.nbio.structure.Chain
Get the 'private' asymId (internal chain IDs in mmCif) for this chain.
getId() - Method in class org.biojava.nbio.structure.ChainImpl
 
getId() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getId() - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
getId() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
 
getId() - Method in class org.biojava.nbio.structure.DBRef
Get the ID used by Hibernate.
getId() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
 
getId() - Method in class org.biojava.nbio.structure.EntityInfo
get the ID used by Hibernate
getId() - Method in class org.biojava.nbio.structure.HetatomImpl
the Hibernate database ID
getId() - Method in class org.biojava.nbio.structure.PDBHeader
Get the ID used by Hibernate.
getId() - Method in class org.biojava.nbio.structure.PdbId
Get a String representation of this PdbId instance.
By default this function will try to get the PdbId in the short (4 letters) format.
getId() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
The identifier for this Biological Assembly, from 1 to n
getId() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
Returns the identifier for this biological assembly transformation.
getId() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
 
getId() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement
Returns the ID of this element.
getId() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
 
getId() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
Gets the standard numeric identifier for the space group.
getId() - Method in enum org.biojava.nbio.structure.xtal.TransformType
 
getId() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getId() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
Request id (RID) as received from QBlast server
getId(boolean) - Method in class org.biojava.nbio.structure.PdbId
Get a String representation of this PdbId instance, using the passed in behavior.
getID() - Method in class org.biojava.nbio.core.sequence.AccessionID
 
getID() - Method in class org.biojava.nbio.core.sequence.TaxonomyID
 
getIdbnsBegin() - Method in class org.biojava.nbio.structure.DBRef
Insertion code of initial residue of the segment, if PDB is the reference.
getIdbnsEnd() - Method in class org.biojava.nbio.structure.DBRef
Insertion code of the ending residue of the segment, if PDB is the reference.
getIdCode() - Method in class org.biojava.nbio.structure.DBRef
get the idCode for this entry
getIdCode() - Method in class org.biojava.nbio.structure.PDBHeader
Deprecated.
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
 
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
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 Ã…).
getPairInProfileScorer() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
 
getPairInProfileScorer() - Method in interface org.biojava.nbio.alignment.template.RescoreRefiner
Returns class type of pairwise scoring subroutine.
getPairs() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
 
getPairSequence() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method returns the primary strand's sequence where parameters were found.
getPairwiseAligner(S, S, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
Factory method which constructs a pairwise sequence aligner.
getPairwiseAlignment(S, S, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
Factory method which computes a sequence alignment for the given Sequence pair.
getPairwiseAlignmentMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
getPairwiseStructureAligner() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
 
getPAM250() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
Returns PAM 250 matrix by Dayhoff
getPanelPos(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
 
getPanelPos(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
get the position of the sequence position on the Panel
getPanelPos(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
Get the X position on the Panel of a particular sequence position.
getPara(int, int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
 
getParameters() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
 
getParameters() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
 
getParameters() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
 
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
 
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeMain
 
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
 
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
 
getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
 
getParameters() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
 
getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
 
getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
 
getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
 
getParameters() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
 
getParameters() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner
Return the parameters of this algorithm instance.
getParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
 
getParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
 
getParameters() - Method in interface org.biojava.nbio.structure.align.StructureAlignment
Return the paramers for this algorithm.
getParameters() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
 
getParams() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
get the parameters.
getParams() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
getParent() - Method in class org.biojava.nbio.alignment.GuideTree.Node
 
getParent() - Method in class org.biojava.nbio.structure.DBRef
Get the structure object that this DBRef relates to.
getParent(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
Get the parent of a component.
getParentChains() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Finds the parent chains by looking up the references of first atom of each side of this interface
getParentChromosomeSequence() - Method in class org.biojava.nbio.core.sequence.GeneSequence
The parent ChromosomeSequence which contains the actual DNA sequence data
getParentCompounds() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Finds the parent entities by looking up the references of first atom of each side of this interface
getParentFeature() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
Get the parent Feature
getParentFeature() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
getParentFeature() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Get the parent feature
getParentId() - Method in class org.biojava.nbio.structure.cath.CathNode
 
getParentSequence() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getParentSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode
 
getPartner() - Method in class org.biojava.nbio.structure.secstruc.HBond
 
getPartner1() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
 
getPartner2() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
 
getPath() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
getPath() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
getPath() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
getPath() - Method in class org.biojava.nbio.structure.align.util.AtomCache
Get the path that is used to cache PDB files.
getPath() - Static method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
Get this provider's cache path
getPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Returns the path value.
getPathSize() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
getPathSize() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
getPaulingElectronegativity() - Method in enum org.biojava.nbio.structure.Element
Returns the Pauling electronegativity for this Element.
getPdb1() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
getPdb1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
getPdb2() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
getPdb2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
getPdbAln() - Method in class org.biojava.nbio.structure.align.model.AFPChain
used temporarily during XML serialization to track the PDB positions of the alignmnet
getPdbccId() - Method in interface org.biojava.nbio.protmod.ProteinModification
 
getPdbccId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
getPdbccIds() - Method in class org.biojava.nbio.protmod.Component
 
getPdbccName() - Method in interface org.biojava.nbio.protmod.ProteinModification
 
getPdbccName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
getPdbChainIdClusters() - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
 
getPdbChainIdClusters(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
 
getPDBCharacter(boolean, char, char, boolean, char) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
Creates formatted String for a single character of PDB output
getPDBCode() - Method in interface org.biojava.nbio.structure.Structure
Deprecated.
use Structure.getPdbId() to get a PdbId object or getPdbId().getId() to get a String
getPDBCode() - Method in class org.biojava.nbio.structure.StructureImpl
Deprecated.
use StructureImpl.getPdbId() to get a PdbId object or getPdbId().getId() to get a String
getPDBCode1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
Deprecated.
getPDBCode2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
Deprecated.
getPDBConservation(boolean, char, char, boolean) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
Creates formatted String for displaying conservation in PDB output
getPDBDirField() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
 
getPdbEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
getPdbFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
getPdbFilePath() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
 
getPdbGroup() - Method in interface org.biojava.nbio.structure.SeqMisMatch
 
getPdbGroup() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
 
getPDBHeader() - Method in interface org.biojava.nbio.structure.Structure
Return the header information for this PDB file.
getPDBHeader() - Method in class org.biojava.nbio.structure.StructureImpl
Return the header information for this PDB file.
getPdbId() - Method in class org.biojava.nbio.structure.align.client.StructureName
Get the PDB ID for this name, if any.
getPdbId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
Gets the PdbId object.
Before 6.0.0, this method used to return a String.
getPdbId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
getPdbId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
getPdbId() - Method in class org.biojava.nbio.structure.PDBHeader
Gets the PDB identifier for this protein structure.
getPdbId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
Gets the PDB identifier for this protein structure.
getPdbId() - Method in interface org.biojava.nbio.structure.Structure
Returns the PDB identifier associated with this StructureIdentifier.
getPdbId() - Method in class org.biojava.nbio.structure.StructureImpl
Returns the PDB identifier associated with this StructureIdentifier.
getPdbId() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
Get the PDB identifier part of the SubstructureIdentifier
getPdbId1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
 
getPdbId2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
 
getPdbIdAndChain() - Method in class org.biojava.nbio.structure.cath.CathDomain
Returns a string of the form PDBID.CHAIN.
getPdbInfo(Atom) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools
get jmol style info: jmol style: [MET]508:A.CA/1 #3918 insertion code: [ASP]1^A:A.CA/1 #2
getPdbInfo(Atom, boolean) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools
 
getPDBLegend() - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
Creates formatted String for displaying conservation legend in PDB output
getPDBName() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
getPDBName() - Method in interface org.biojava.nbio.structure.Group
Get the PDB 3-letter name for this group.
getPDBName() - Method in class org.biojava.nbio.structure.HetatomImpl
 
getPDBNameOfPotentialAtomsOnComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
 
getPDBNameOfPotentialAtomsOnComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
 
getPDBResidueNumber() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
getPdbResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
getPdbResNum() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
getPdbResNum() - Method in interface org.biojava.nbio.structure.SeqMisMatch
 
getPdbResNum() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
 
getPDBresnum(int, AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
Return a list of pdb Strings corresponding to the aligned positions of the molecule.
getPDBresnum(int, MultipleAlignment, Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
Utility method used in the MultipleAlignmentJmol Frame, when the aligned residues of a structure in the alignment have to be selected for formatting them (coloring and style).
getPDBresnum1() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
getPDBresnum2() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
getPdbSerial() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
 
getPDBserial() - Method in interface org.biojava.nbio.structure.Atom
Get PDB atom number.
getPDBserial() - Method in class org.biojava.nbio.structure.AtomImpl
Get PDB atom number.
getPdbStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
getPdbxAlign() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxAmbiguousFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxAromaticFlag() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxAromaticFlag() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
getPdbxComponentAtomId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxComponentCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxComponentId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxFormalCharge() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxIdealCoordinatesDetails() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxIdealCoordinatesMissingFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxInitialDate() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxLeavingAtomFlag() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxModelCartnXIdeal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxModelCartnYIdeal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxModelCartnZIdeal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxModelCoordinatesDbCode() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxModelCoordinatesDetails() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxModelCoordinatesMissingFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxModifiedDate() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxOrdinal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxOrdinal() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
getPdbxPolymerType() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxProcessingSite() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxRefId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxReleaseStatus() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxReplacedBy() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxReplaces() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxResidueNumbering() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxStereoConfig() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getPdbxStereoConfig() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
getPdbxSubcomponentList() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxSynonyms() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPdbxType() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPercentage() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
getPercentageIdentity() - Method in class org.biojava.nbio.core.search.io.Hsp
 
getPercentageOfIdentity(boolean) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.
getPercentageOfIdentity(boolean) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.
getPercId() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
getPeriod() - Method in enum org.biojava.nbio.structure.Element
Returns the period in the periodic table of this Element.
getPermutation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
getPermutation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
getPermutation(int) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
 
getPermutationSize() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getPfamAccession() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getPhase() - Method in class org.biojava.nbio.core.sequence.CDSSequence
 
getPhase() - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos
 
getPhi() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
getPhi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc
Calculate the phi angle.
getPivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
Return pivot permutation vector
getPmid() - Method in class org.biojava.nbio.structure.JournalArticle
Get the value of PMID field.
getPointGroup() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
getPolarityOfAminoAcid(char) - Static method in class org.biojava.nbio.aaproperties.AminoAcidProperties
There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
getPolarityOfAminoAcids(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
Returns the array of polarity values of each amino acid in a protein sequence.
getPolyChain(String) - Method in interface org.biojava.nbio.structure.Structure
Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the first model
getPolyChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
 
getPolyChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the given model index
getPolyChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
 
getPolyChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure
Retrieve a polymeric Chain based on the 'public' chain name (authId) for the first model
getPolyChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl
 
getPolyChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure
Retrieve a polymeric Chain based on the 'public' chain name (authId) for the given model index.
getPolyChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
 
getPolyChains() - Method in class org.biojava.nbio.structure.Model
 
getPolyChains() - Method in interface org.biojava.nbio.structure.Structure
Return all polymeric chains for the first model
getPolyChains() - Method in class org.biojava.nbio.structure.StructureImpl
 
getPolyChains(int) - Method in interface org.biojava.nbio.structure.Structure
Return all polymeric chains for the given model index.
getPolyChains(int) - Method in class org.biojava.nbio.structure.StructureImpl
 
getPolygonVertices(int, double, Point3d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.Prism
Returns the vertices of an n-fold polygon of given radius and center
getPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
getPolymerType() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getPolymerType() - Method in enum org.biojava.nbio.structure.chem.ResidueType
Gets the associated PolymerType, which are less specific
getPolymerType(ResidueType) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools
 
getPos() - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos
 
getPos(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
 
getPos1() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
getPos1() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
 
getPos2() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
getPos2() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
 
getPosition() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
 
getPosition() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
getPosition() - Method in interface org.biojava.nbio.core.sequence.location.template.Point
Returns the position held by this object
getPosition(ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap
Gets the 0-based index of residueNumber to the matched atoms
getPredicate() - Method in interface org.biojava.nbio.ontology.Triple
Return a Term which defines the type of relationship between the subject and object terms.
getPredicate() - Method in class org.biojava.nbio.ontology.Triple.Impl
 
getPredominantGroupType() - Method in interface org.biojava.nbio.structure.Chain
Get the predominant GroupType for a given Chain, following these rules: if the ratio of number of residues of a certain GroupType to total non-water residues is above the threshold 0.95, then that GroupType is returned if there is no GroupType that is above the threshold then the GroupType with most members is chosen, logging it
getPredominantGroupType() - Method in class org.biojava.nbio.structure.ChainImpl
 
getPreferredHeight() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
Y coordinate size
getPreferredHeight() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
Y coordinate size
getPreferredSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
 
getPreferredWidth() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
X coordinate size
getPreferredWidth() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
X coordinate size
getPreviousIDs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getPreviousNames() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
getPreviousSymbols() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
getPrimaryAccession() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
 
getPrimitiveMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getPrincipalAxes() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
The principal axes of intertia
getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
 
getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
 
getPrincipalAxisIndex() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
getPrincipalMomentsOfInertia() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
 
getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
 
getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
 
getPrintMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
getProbability() - Method in class org.biojava.nbio.structure.align.model.AFPChain
The probability (FATCAT) or Z-score (CE) of the alignment.
getProfile() - Method in class org.biojava.nbio.alignment.FractionalIdentityInProfileScorer
 
getProfile() - Method in class org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer
 
getProfile() - Method in class org.biojava.nbio.alignment.GuideTree.Node
 
getProfile() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
 
getProfile() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
getProfile() - Method in interface org.biojava.nbio.alignment.template.Aligner
Returns the alignment Profile produced by this alignment algorithm.
getProfile() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
Returns the profile stored at this node.
getProfile() - Method in interface org.biojava.nbio.alignment.template.PairInProfileScorer
Returns the Profile from which the aligned pair originated.
getProfileFuture() - Method in class org.biojava.nbio.alignment.GuideTree.Node
 
getProfileFuture() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
Returns the profile future stored at this node, but does not force the calculation, yet.
getProfileProfileAligner() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
 
getProfileProfileAligner() - Method in interface org.biojava.nbio.alignment.template.PartitionRefiner
Returns class type of profile-profile alignment subroutine.
getProfileProfileAligner() - Method in interface org.biojava.nbio.alignment.template.RescoreRefiner
Returns class type of profile-profile alignment subroutine.
getProgram() - Method in class org.biojava.nbio.core.search.io.Result
 
getProgram() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
 
getProgramSpecificParameter(String) - Method in class org.biojava.nbio.core.search.io.Result
 
getProgramSpecificParametersList() - Method in class org.biojava.nbio.core.search.io.Result
 
getProgramVersion() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
 
getProgressiveAlignment(GuideTree<S, C>, Alignments.ProfileProfileAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
Factory method to run the profile-profile alignments of a progressive multiple sequence alignment concurrently.
getProjectedDistance(Atom) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
Get the distance from a point to the axis of rotation
getProjectedPoint(Atom) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
Projects a given point onto the axis of rotation
getProjectIdentifier() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
getPropeller(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method returns the propeller ("propeller-twist") in degrees for the given base pair
getProperties() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
Get the properties
getProperties() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
Implement this to return the Map delegate.
getProperties() - Method in class org.biojava.nbio.ontology.utils.SmallAnnotation
 
getProperties() - Method in interface org.biojava.nbio.structure.Group
Return properties.
getProperties() - Method in class org.biojava.nbio.structure.HetatomImpl
 
getProperty(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
 
getProperty(Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation
Retrieve the value of a property by key.
getProperty(String) - Method in interface org.biojava.nbio.structure.Group
Get a single property .
getProperty(String) - Method in class org.biojava.nbio.structure.HetatomImpl
 
getProtein() - Method in class org.biojava.nbio.phosphosite.Site
 
getProteinAliases() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
Pull uniprot protein aliases associated with this sequence
getProteinCDSSequences() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
Return a list of protein sequences based on each CDS sequence where the phase shift between two CDS sequences is assigned to the CDS sequence that starts the triplet.
getProteinSequence() - Method in class org.biojava.nbio.core.sequence.RNASequence
Get the ProteinSequence from the RNA sequence
getProteinSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
Get the protein sequence
getProteinSequence() - Method in class org.biojava.nbio.structure.cluster.Subunit
Get the protein sequence of the Subunit.
getProteinSequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.RNASequence
Get the ProteinSequence from the RNA sequence with user-defined transcription engine
getProteinSequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
Get the protein sequence with user defined TranscriptEngine
getProteinSequenceCreator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
 
getProteinSequenceForStructure(Structure, Map<Integer, Group>) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher
Generates a ProteinSequence corresponding to the sequence of struct, and maintains a mapping from the sequence back to the original groups.
getProteinSequences() - Method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
 
getProteinSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
 
getProteinSequenceString() - Method in class org.biojava.nbio.structure.cluster.Subunit
Get the protein sequence of the Subunit as String.
getProxySequenceReader() - Method in interface org.biojava.nbio.core.sequence.location.template.AccesionedLocation
Return the proxy reader used to get sequence for this location.
getProxySequenceReader() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getPsi() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
getPsi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc
Calculate the psi angle.
getPsimodId() - Method in interface org.biojava.nbio.protmod.ProteinModification
 
getPsimodId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
getPsimodName() - Method in interface org.biojava.nbio.protmod.ProteinModification
 
getPsimodName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
getPublicationDate() - Method in class org.biojava.nbio.structure.JournalArticle
 
getPublisher() - Method in class org.biojava.nbio.structure.JournalArticle
 
getPvalue() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
getPvalue() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
 
getPvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
getPx() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
getQ() - Method in class org.biojava.nbio.structure.jama.QRDecomposition
Generate and return the (economy-sized) orthogonal factor
getQcalls() - Method in class org.biojava.nbio.core.sequence.io.ABITrace
Returns an int[] array that represents the quality - each int in the array corresponds to an quality value 90-255) in the graph at a base location).
getQualifiers() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
 
getQualifiers() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
getQualifiers() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Get the qualifiers for this feature
getQualities() - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
 
getQualities(int, int) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
 
getQuality() - Method in class org.biojava.nbio.genome.io.fastq.Fastq
Return the quality scores for this FASTQ formatted sequence.
getQualityAt(int) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
 
getQuantities() - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature
 
getQuat4d(int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
 
getQuat4d(int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
 
getQuaternarySymmetry(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Given a symmetry result, it calculates the overall global symmetry, factoring out the alignment and detection steps of QuatSymmetryDetector algorithm.
getQuery() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
 
getQuery() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
 
getQuery() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
 
getQuery() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
 
getQuery() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
 
getQuery() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceScorer
Returns the first sequence of the pair.
getQuery() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileScorer
Returns the first profile of the pair.
getQuery() - Method in class org.biojava.nbio.core.alignment.SimpleProfilePair
 
getQuery() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
 
getQuery() - Method in interface org.biojava.nbio.core.alignment.template.ProfilePair
Returns the first Profile of the pair.
getQuery() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
Returns the first AlignedSequence of the pair.
getQueryDef() - Method in class org.biojava.nbio.core.search.io.Result
 
getQueryEndIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
 
getQueryID() - Method in class org.biojava.nbio.core.search.io.Result
 
getQueryIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
 
getQueryIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
 
getQueryLength() - Method in class org.biojava.nbio.core.search.io.Result
 
getQuerySequence() - Method in class org.biojava.nbio.core.search.io.Result
returns the reference to the original and whole sequence used to query the database.
getQueryStartIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
 
getR() - Method in class org.biojava.nbio.structure.jama.QRDecomposition
Return the upper triangular factor
getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
Returns the radius for drawing polyhedra
getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
Returns the radius for drawing the minor rotation axis in the xy-plane
getRadius(Atom) - Static method in class org.biojava.nbio.structure.asa.AsaCalculator
Gets the van der Waals radius of the given atom following the values defined by Chothia (1976) J.Mol.Biol.105,1-14 NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates" slightly the heavy atoms to account for Hydrogens.
getRadiusOfGyration() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
 
getRandomDataColumns(int) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
getRandomDataColumns(int, ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
getRandomSeed() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
getRange() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
Get the range of this domain, in PDB residue numbers (mmCif's _pdbx_poly_seq_scheme.pdb_seq_num and pdb_ins_code).
getRange() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement
Returns the residue range of this SSE.
getRanges() - Method in class org.biojava.nbio.structure.AtomPositionMap
Returns a list of ResidueRanges corresponding to this entire AtomPositionMap.
getRanges() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
getRealEigenvalues() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition
Return the real parts of the eigenvalues
getRealEnd() - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
 
getRealStart() - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
 
getReason() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
Return a String describing the reasons for the CE-Symm final decision in this particular result.
getRecordAdditionalAttachments() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
 
getRecordType() - Method in interface org.biojava.nbio.structure.AminoAcid
Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
getRecordType() - Method in class org.biojava.nbio.structure.AminoAcidImpl
Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
getRecordUnidentifiableCompounds() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
 
getReducedStructure(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
Reduce a structure to a single-atom representation (e.g.
getRef() - Method in class org.biojava.nbio.structure.JournalArticle
Get the value of REF field.
getRefAuthor() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
 
getRefChainId() - Method in class org.biojava.nbio.structure.EntityInfo
Return the ref chain id value.
getRefComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getReference() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
getReference() - Method in class org.biojava.nbio.core.search.io.Result
 
getReferenceAuthor() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
The RA (Reference Author) lines list the authors of the paper (or other work) cited.
getReferenceComment() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
The RC (Reference Comment) linetype is an optional linetype which appears if The reference has a comment.
getReferenceCrossReference() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
The RX (reference cross-reference) linetype is an optional linetype which appears if one or more contiguous base spans of the presented sequence can be attributed to the reference in question.
getReferenceFrames() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
getReferenceGroup() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
The RG (Reference Group) lines list the working groups/consortia that produced the record.
getReferenceLocation() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
The RL (Reference Location) line contains the conventional citation information for the reference.
getReferenceNumber() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
The RN (Reference Number) line gives a unique number to each reference Citation within an entry.
getReferencePosition() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
The RP (Reference Position) linetype is an optional linetype which appears if one or more contiguous base spans of the presented sequence can be attributed to the reference in question.
getReferences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getReferences() - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
 
getReferences() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getReferenceTitle() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
The RT (Reference Title) lines give the title of the paper (or other work) as exactly as is possible given the limitations of computer character sets.
getRefinedScoreThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
getRefineMethod() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
getRefLocation() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
 
getRefMedline() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
 
getRefn() - Method in class org.biojava.nbio.structure.JournalArticle
Get the value of REFN field.
getRefRMSD(List<Atom[]>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.
getRefRMSD(MultipleAlignment, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
/** Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.
getRefseqIds() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
getRefTitle() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
 
getRefTMScore(List<Atom[]>, List<Integer>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.
getRefTMScore(MultipleAlignment, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.
getRegistryInfo() - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
getRelation() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
The quaternary structure relation QsRelation between the two groups of Subunits.
getRelativeAsaC() - Method in class org.biojava.nbio.structure.asa.GroupAsa
Returns the relative (complexed) ASA, i.e. the ASA of the residue with respect to its ASA in an extended tri-peptide conformation (GLY-x-GLY)
getRelativeAsaU() - Method in class org.biojava.nbio.structure.asa.GroupAsa
Returns the relative (uncomplexed) ASA, i.e. the ASA of the residue with respect to its ASA in an extended tri-peptide conformation (GLY-x-GLY)
getRelDate() - Method in class org.biojava.nbio.structure.PDBHeader
Return the release date of the structure in the PDB.
getRelevantSubLocations() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
Returns the normalised list of sub locations i.e. only those locations which do not have a sub location.
getRelevantSubLocations() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
An extension to Location.getSubLocations() which returns sub-locations of sub-locations; this will continue until it runs out of those locations.
getRelevantSubSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
getRelevantSubSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.location.template.Location
Will return a SequenceReader object which offers a view of all resolved locations i.e. those locations which are not complex and define the true Sequence represented
getRemoteBlastInfo() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
A simple method to check the availability of the QBlast service.
getRemoteTerm() - Method in interface org.biojava.nbio.ontology.RemoteTerm
Return the imported term
getRemoteTerm() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
 
getRemoteTerms() - Method in interface org.biojava.nbio.ontology.OntologyOps
Get the set of all remote terms.
getRepeatRelation(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
Get the indices of participating repeats in Cauchy two-line form.
getRepeatRelation(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
 
getRepeatRelation(SymmetryAxes.Axis) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
 
getRepeatsCyclicForm(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
 
getRepeatsCyclicForm(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
Get the indices of participating repeats in cyclic form.
getRepeatsCyclicForm(List<List<Integer>>, List<?>) - Static method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
 
getRepeatsCyclicForm(SymmetryAxes.Axis) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
 
getRepeatsCyclicForm(SymmetryAxes.Axis, List<?>) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
 
getRepeatsID() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
Return the symmetric repeats as structure identifiers, if the result is symmetric and it was refined, return null otherwise.
getRepeatTransform(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
Return the transformation that needs to be applied to a repeat in order to superimpose onto repeat 0.
getRepeatTransform(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
Return the transformation that needs to be applied to repeat x in order to superimpose onto repeat y.
getRepeatUnitCenters() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
 
getRepeatUnitIndices() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
 
getRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
 
getRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
getReplaced(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
 
getReplaced(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
If ChemComp is replacing another one, get the old version otherwise return the same ChemComp again.
getReplacer(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
 
getReplacer(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
If ChemComp is replaced by another one, get the newer version otherwise return the same ChemComp again.
getRepresentative() - Method in class org.biojava.nbio.structure.cath.CathNode
 
getRepresentative() - Method in class org.biojava.nbio.structure.EntityInfo
Get the representative Chain for this EntityInfo.
getRepresentative() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
 
getRepresentativeAtomArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools
Gets a representative atom for each group that is part of the chain backbone.
getRepresentativeAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
Gets a representative atom for each group that is part of the chain backbone.
getRepresentativeAtoms() - Method in class org.biojava.nbio.structure.cluster.Subunit
Get all the representative Atoms of the Subunit.
getRepresentativeAtoms(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns the representative atoms for the provided name.
getRepresentativeAtoms(Structure) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Returns the representative Atom Array of the first model, if the structure is NMR, or the Array for each model, if it is a biological assembly with multiple models.
getRepresentativeAtoms(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
getRepresentativeAtomsInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools
Returns the set of intra-chain contacts for the given chain for C-alpha or C3' atoms (including non-standard aminoacids appearing as HETATM groups), i.e. the contact map.
getRepresentativeAtomsOnly(List<Chain>) - Static method in class org.biojava.nbio.structure.io.CAConverter
Convert a List of chain objects to another List of chains, containing Representative atoms only.
getRepresentativeAtomsOnly(Chain) - Static method in class org.biojava.nbio.structure.io.CAConverter
Convert a Chain to a new Chain containing C-alpha atoms only.
getRepresentativeChain(String, String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
 
getRepresentativeDomains() - Method in interface org.biojava.nbio.structure.domain.DomainProvider
Get the full list of representative domains for the PDB.
getRepresentatives(String) - Static method in class org.biojava.nbio.structure.scop.Astral
Get a list of representatives' names for the specified ASTRAL cutoff.
getRepresentatives(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
 
getRepresentatives(Astral.AstralSet) - Static method in class org.biojava.nbio.structure.scop.Astral
Get a list of representatives' names for the specified ASTRAL cutoff.
getResidId() - Method in interface org.biojava.nbio.protmod.ProteinModification
 
getResidId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
getResidName() - Method in interface org.biojava.nbio.protmod.ProteinModification
 
getResidName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
getResidual() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getResidualVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getResidue() - Method in class org.biojava.nbio.phosphosite.Site
 
getResidue(int) - Method in class org.biojava.nbio.structure.AugmentedResidueRange
Returns the ResidueNumber that is at position positionInRange in this ResidueRange.
getResidue(int, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange
Returns the ResidueNumber that is at position positionInRange in this ResidueRange.
getResidueName() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
 
getResidueNumber() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
getResidueNumber() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
 
getResidueNumber() - Method in interface org.biojava.nbio.structure.Group
Returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.
getResidueNumber() - Method in class org.biojava.nbio.structure.HetatomImpl
Returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.
getResidueRanges() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
getResidueRanges() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
getResidueRanges() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
 
getResidues() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
For each residue in the fasta file, return the ResidueNumber in the corresponding structure.
getResidues() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
getResidueType() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getResidueTypeFromString(String) - Static method in enum org.biojava.nbio.structure.chem.ResidueType
Get ResidueType by chem_comp_type
getResidueTypes() - Method in enum org.biojava.nbio.structure.GroupType
Get a set of ResidueTypes loosely equivalent to this GroupType.
getResName1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
 
getResName2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
 
getResNames() - Method in class org.biojava.nbio.structure.EntityInfo
 
getResnum1() - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
getResnum2() - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
getResolution() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getResolution() - Method in class org.biojava.nbio.structure.PDBHeader
Returns the resolution (or effective resolution) of the experiment.
getResolver() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
 
getResourceManager(String) - Static method in class org.biojava.nbio.structure.align.util.ResourceManager
 
getResScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getResSeq1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
 
getResSeq2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
 
getReverse() - Method in class org.biojava.nbio.core.sequence.DNASequence
Returns a Sequence which runs in the current reverse order
getReverse() - Method in enum org.biojava.nbio.core.sequence.Strand
 
getReverse() - Method in class org.biojava.nbio.structure.align.client.PdbPair
 
getReverseComplement() - Method in class org.biojava.nbio.core.sequence.DNASequence
Delegates to AbstractSequence.getInverse() for the reverse complement
getReverseComplement() - Method in class org.biojava.nbio.core.sequence.RNASequence
Get reverse complement view of the sequence
getReverseFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
Returns all frames which are in the reverse orientation
getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
 
getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
 
getRevisionRecords() - Method in class org.biojava.nbio.structure.PDBHeader
 
getRevNum() - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord
 
getRfree() - Method in class org.biojava.nbio.structure.PDBHeader
 
getRight() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
getRimResidues(double, double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
Returns the residues belonging to the interface rim, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is below the given bsaToAsaCutoff
getRise() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
getRise(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method returns the rise for the given base pair, relative to the one before it.
getRms() - Method in class org.biojava.nbio.structure.align.helper.JointFragments
 
getRms() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
getRMS(Atom[], Atom[], JointFragments) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
Get the RMS of the JointFragments pair frag
getRmsd() - Method in class org.biojava.nbio.structure.align.model.AFP
 
getRmsd() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
getRmsd() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
The RMSD between the equivalent residues of the equivalent Subunits after superposition of the Subunit groups.
getRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
getRmsd(Point3d[], Point3d[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition
Calculate the RMSD between two arrays of equivalent points that are not superposed.
getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP
 
getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQuat
 
getRmsd(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
Use the SuperPosition.getRmsd(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.
getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionSVD
 
getRMSD(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
Calculates the RMSD of all-to-all structure comparisons (distances), given a set of superimposed atoms.
getRMSD(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
Calculates the RMSD of all-to-all structure comparisons (distances) of the given MultipleAlignment.
getRmsdAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
Use the SuperPosition.getRmsd(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.
getRmsdCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
getRmsdCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
The cutoff to be used during AFP detection
getRmsdCut() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
 
getRmsdIntra() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
getRMSDMatrix(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Calculate the RMSD matrix of a MultipleAlignment, that is, entry (i,j) of the matrix contains the RMSD between structures i and j.
getRmsdThr() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
RMSD Threshold
getRmsdThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
getRMSDThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.
getRmsdThrJoin() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
RMSD threshold for joining of AFPs
getRnaAminoAcidTranslator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
 
getRnaCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
 
getRNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet
 
getRNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.RNACompoundSet
 
getRNASequence() - Method in class org.biojava.nbio.core.sequence.DNASequence
Return the RNASequence equivalent of the DNASequence using default Transcription Engine.
getRNASequence(Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence
Allows the user to pass in the Frame shift.
getRNASequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.DNASequence
Allow a user to pass in a rules engine to do the DNA to RNA translation
getRNASequence(TranscriptionEngine, Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence
 
getRnaSequenceCreator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
 
getRnaToDna() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
 
getRndSeed() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
getRobustStdError() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
getRoll(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method returns the roll for the given base pair, relative to the one before it.
getRoot() - Method in class org.biojava.nbio.alignment.GuideTree
Returns the root GuideTree.Node which corresponds to the full multiple sequence alignment.
getRoot() - Method in interface org.biojava.nbio.alignment.template.HierarchicalClusterer
Returns the root node of the tree resulting from this clustering algorithm.
getRootURL() - Method in class org.biojava.nbio.structure.scop.ScopMirror
Get the URL for the root download directory, or null if none is set.
getRot() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
getRotatedAtoms(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay
New structures are downloaded if they were not cached in the alignment and they are entirely transformed here with the superposition information in the Multiple Alignment.
getRotation(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
getRotationAxis() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
Get a unit vector along the rotation axis
getRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
Get the transformation operator as a rotation axis.
getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
 
getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
 
getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
getRotationJAMA(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices
Convert a transformation matrix into a JAMA rotation matrix.
getRotationMatrix() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
Gets the rotation matrix from the last call to calc_rmsd.
getRotationMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
Gets the rotation matrix from the last call to calc_rmsd.
getRotationMatrix() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1
getRotationMatrix() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
Get the rotation matrix corresponding to this axis
getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
 
getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
 
getRotationMatrix(double) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
Get the rotation matrix corresponding to a rotation about this axis
getRotationMatrix(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices
Convert a transformation matrix into a rotation matrix.
getRotationPos() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
Get a position on the rotation axis.
getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
 
getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
 
getRotAxisAndAngle(Matrix3d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
Given a rotation matrix calculates the rotation axis and angle for it.
getRotAxisAngle(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getRotAxisType(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
Given a transformation matrix containing a rotation returns the type of rotation: 1 for identity, 2 for 2-fold rotation, 3 for 3-fold rotation, 4 for 4-fold rotation, 6 for 6-fold rotation, -1 for inversions, -2 for mirror planes, -3 for 3-fold improper rotation, -4 for 4-fold improper rotation and -6 for 6-fold improper rotation
getRotMax(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
 
getRow() - Method in class org.biojava.nbio.structure.align.helper.IndexPair
 
getRow(C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
 
getRow(C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
 
getRow(AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
getRowDimension() - Method in class org.biojava.nbio.structure.jama.Matrix
Get row dimension.
getRowHeader() - Method in class org.biojava.nbio.survival.data.WorkSheet
 
getRowIndex(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
getRowLookup() - Method in class org.biojava.nbio.survival.data.WorkSheet
 
getRowPackedCopy() - Method in class org.biojava.nbio.structure.jama.Matrix
Make a one-dimensional row packed copy of the internal array.
getRows() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
getRows() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
getRows() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
getRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
Get the list of row names.
getRscore() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getRscoreLogrankTestpvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getRwork() - Method in class org.biojava.nbio.structure.PDBHeader
 
getS() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
Return the diagonal matrix of singular values
getSaturation() - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
 
getSaveAlignmentMenuItem(AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
getSaveOutputDir() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
getScale() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
getScale() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
 
getScale() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
 
getScale() - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
getScaleableMatrixPanel(Matrix) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
 
getScalevalue() - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
 
getSCOP() - Method in class org.biojava.nbio.structure.gui.util.ScopInstallationInstance
 
getSCOP() - Static method in class org.biojava.nbio.structure.scop.ScopFactory
Get the current default instance for the default version
getSCOP(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
Gets an instance of the specified scop version.
getScopDescriptionBySunid(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
Return the SCOP description for a node in the hierarchy by its "sunid" id.
getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
getScopDomainsBySunid(Integer) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
Get a SCOP domain by its sunid
getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
getScope() - Method in class org.biojava.nbio.ontology.Synonym
 
getScopId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
getScopNode(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
Access a particular ScopNode.
getScopNode(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
getScopVersion() - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
Returns the SCOP version
getScopVersion() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
getScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
 
getScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
 
getScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
 
getScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
 
getScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
getScore() - Method in interface org.biojava.nbio.alignment.template.Scorer
Returns score resulting from algorithm.
getScore() - Method in class org.biojava.nbio.structure.align.model.AFP
 
getScore() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
getScore() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
the alignment score
getScore() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
getScore() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
 
getScore() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
 
getScore() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getScore() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
getScore(String) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
 
getScore(String) - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache
Get the value for a particular score.
getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
getScoreLogrankTest() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getScoreLogrankTestpvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getScoreMatrix() - Method in class org.biojava.nbio.alignment.GuideTree
Returns the similarity matrix used to construct this guide tree.
getScoreMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
getScoreMatrix() - Method in interface org.biojava.nbio.alignment.template.MatrixAligner
Returns the entire score matrix built during alignment.
getScoreMatrixAsString() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
getScoreMatrixAsString() - Method in interface org.biojava.nbio.alignment.template.MatrixAligner
Returns a depiction of the score matrix as a String.
getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
 
getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
 
getScores() - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
 
getScores() - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache
Get a collection of all scores that have been set.
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
Returns QuatSymmetryScores averaged over all rotations (except the first rotation, which is the unit operation E)
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
 
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
getScores() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
Returns QuatSymmetryScores averaged over all rotations (except the first rotation, which is the unit operation E)
getScores(File) - Method in class org.biojava.nbio.ronn.ORonnModel
 
getScoringStrategy() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
getScoringStrategy() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
getScrewTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
Get the component of translation parallel to the axis of rotation
getSearchFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
An input file to be used for the DB search
getSearchMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getSecond() - Method in class org.biojava.nbio.structure.contact.Pair
 
getSecondAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
getSecondGroupAsa(ResidueNumber) - Method in class org.biojava.nbio.structure.contact.StructureInterface
Gets the GroupAsa for the corresponding residue number of second chain
getSecondGroupAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Gets a map of ResidueNumbers to GroupAsas for all groups of second chain.
getSecretion() - Method in class org.biojava.nbio.structure.EntityInfo
 
getSecStrucElements(List<Group>) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools
Obtain the List of secondary structure elements (SecStrucElement) of a List of Groups (assumed to be sequential, this is, connected in the original Structure).
getSecStrucElements(Structure) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools
Obtain the List of secondary structure elements (SecStrucElement) of a Structure.
getSecStrucInfo(Structure) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools
Obtain the List of secondary structure information (SecStrucInfo) of a Structure.
getSecStructType(Group) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Get the secondary structure as defined by DSSP.
getSecStructTypeFromDsspIndex(int) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Set the DSSP type based on a numerical index.
getSeedFragmentLength() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getSeedRmsdCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getSegId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
getSegmentAtPos(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
 
getSegmentId() - Method in class org.biojava.nbio.structure.cath.CathSegment
 
getSegments() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getSegments() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
 
getSegments() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
 
getSelectedAlignmentPos() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
 
getSelectedAlignmentPos() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
getSelection() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
getSelection() - Method in interface org.biojava.nbio.structure.gui.Selection
 
getSelection() - Method in class org.biojava.nbio.structure.gui.SelectionImpl
 
getSelection() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
 
getSelfAlignment() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
getSeparatorSequence() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
 
getSeqBegin() - Method in class org.biojava.nbio.structure.DBRef
Initial sequence number of the PDB sequence segment.
getSeqEnd() - Method in class org.biojava.nbio.structure.DBRef
Ending sequence number of the PDB sequence segment.
getSeqIdRange() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
Get the range of this domain, in 1-based residue indices (mmCif's _pdbx_poly_seq_scheme.seq_id) Note that EcodDomain.getRange() is used when constructing the domain.
getSeqMisMatches() - Method in interface org.biojava.nbio.structure.Chain
Gets annotated sequence mismatches for this chain.
getSeqMisMatches() - Method in class org.biojava.nbio.structure.ChainImpl
 
getSeqNum() - Method in class org.biojava.nbio.structure.ResidueNumber
 
getSeqNum() - Method in interface org.biojava.nbio.structure.SeqMisMatch
 
getSeqNum() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
 
getSeqPos(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
start counting at 0...
getSeqPos(int, Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
Convert from a X position in the JPanel to alignment position
getSeqPos(int, Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
Convert from an X position in the JPanel to the position in the sequence alignment.
getSeqresEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
getSeqResGroup(int) - Method in interface org.biojava.nbio.structure.Chain
Return the Group at given position, from within groups in the SEQRES records of the chain, i.e.
getSeqResGroup(int) - Method in class org.biojava.nbio.structure.ChainImpl
 
getSeqResGroups() - Method in interface org.biojava.nbio.structure.Chain
Returns a list of all groups in SEQRES records of the chain, i.e.
getSeqResGroups() - Method in class org.biojava.nbio.structure.ChainImpl
 
getSeqResGroups(GroupType) - Method in interface org.biojava.nbio.structure.Chain
Returns a List of all SEQRES groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
getSeqResGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl
 
getSeqResLength() - Method in interface org.biojava.nbio.structure.Chain
Returns the number of groups in the SEQRES records of the chain, i.e.
getSeqResLength() - Method in class org.biojava.nbio.structure.ChainImpl
 
getSeqResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
getSeqResOneLetterSeq() - Method in class org.biojava.nbio.structure.ChainImpl
Get the one letter sequence so that Sequence is guaranteed to be the same length as seqResGroups.
getSeqResSequence() - Method in interface org.biojava.nbio.structure.Chain
Returns the PDB SEQRES sequence as a one-letter sequence string.
getSeqResSequence() - Method in class org.biojava.nbio.structure.ChainImpl
 
getSeqresStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
getSequence() - Method in class org.biojava.nbio.core.sequence.io.ABITrace
Returns the original programmatically determined (unedited) sequence as a AbstractSequence.
getSequence() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
The Sequence Data Line
getSequence() - Method in class org.biojava.nbio.core.sequence.location.SequenceLocation
 
getSequence() - Method in class org.biojava.nbio.data.sequence.FastaSequence
Gets the value of sequence
getSequence() - Method in class org.biojava.nbio.genome.io.fastq.Fastq
Return the sequence for this FASTQ formatted sequence.
getSequence() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getSequence() - Method in class org.biojava.nbio.structure.cath.CathSegment
 
getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.FastaSequenceParser
 
getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
getSequence(BufferedReader, int) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceParserInterface
 
getSequence(String, int, int) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitFacade
Extract a sequence from a chromosome, using chromosomal coordinates
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
 
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
 
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator
Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator
Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator
Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
 
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
 
getSequence(String, long) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
 
getSequence(List<C>) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
 
getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
Assumes all compounds were uppercase
getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator
Not sure of use case and currently not supported
getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
 
getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
 
getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator
Not sure of use case and currently not supported
getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator
Not sure of use case and currently not supported
getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
 
getSequence(ProxySequenceReader<C>, long) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
 
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
 
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator
Should be able to extend the same concept to a remote URL call or database connection.
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
 
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
 
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator
Should be able to extend the same concept to a remote URL call or database connection.
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator
Should be able to extend the same concept to a remote URL call or database connection.
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
 
getSequence5PrimeTo3Prime() - Method in class org.biojava.nbio.core.sequence.GeneSequence
Try to give method clarity where you want a DNASequence coding in the 5' to 3' direction Returns the DNASequence representative of the 5' and 3' reading based on strand
getSequenceAlignment(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Calculate the sequence alignment Strings for the whole alignment.
getSequenceAlignment(MultipleAlignment, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Calculate the sequence alignment Strings for the whole alignment.
getSequenceAsString() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
 
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
Returns the sequence as a String
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
 
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
getSequenceAsString() - Method in interface org.biojava.nbio.core.sequence.template.Sequence
Returns the String representation of the Sequence
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
 
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.ReversedSequenceView
 
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
 
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
 
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getSequenceAsString(List<C>, CompoundSet<C>, Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper
 
getSequenceCollection() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
 
getSequenceCoverageThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
The minimum coverage of the sequence alignment between two subunits to be clustered together.
getSequenceDescription() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
The DE (Description) lines contain general descriptive information about the sequence stored.
getSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getSequenceFromAlignment() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
getSequenceFromAlignment() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
Returns the sequence positions at each alignment index
getSequenceFromString(String) - Method in class org.biojava.nbio.core.util.SequenceTools
Attempts to parse String as a DNA sequence first.
If this fails it tries to parse as a ProteinSequence.
getSequenceHeader() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
The SQ (SeQuence header) line marks the beginning of the sequence data and Gives a summary of its content.
getSequenceHeader() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getSequenceHeader() - Method in class org.biojava.nbio.structure.cath.CathSegment
 
getSequenceHeaderParser() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
getSequenceIdentityThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Sequence identity threshold to consider for the subunits clustering.
getSequenceIndexAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
getSequenceIndexAt(int) - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
Returns the index in the original Sequence corresponding to the given index within an alignment.
getSequenceLength() - Method in class org.biojava.nbio.core.sequence.io.ABITrace
Returns the length of the sequence (number of bases) in this trace.
getSequenceLength() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
Sequence length The last item on the ID line is the length of the sequence (the total number of bases in the sequence).
getSequenceNames() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
getSequences() - Method in class org.biojava.nbio.alignment.GuideTree
Returns the Sequences which make up the leaves of this tree.
getSequences() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
getSequences() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
Gets the protein sequences read from the Fasta file.
getSequenceScore() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Provide place holder for a metric that indicate a score associated with the sequence
getSequenceUsage() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
 
getSequenceVersion() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
return the sequence version
getSeqWeight() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
Should sequence conservation be considered as part of the alignment?
getSerialversionuid() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getSerNum() - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
getServerName() - Static method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Return the String with the PDB server name, including the leading protocol String (http:// or ftp://).
getShear(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method returns the shear in Ã… for the given base pair
getShift() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
Gets the shift from the last call to calc_rmsd.
getShift() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
Gets the shift from the last call to calc_rmsd.
getShift() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
returns the shift vector that has to be applied on structure to to shift on structure one
getShift(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
Return the shift for the given base pair, relative to the one before it.
getShorName() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
 
getShortDescription() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
 
getShortDescription() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
getShortDescription() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Get the short description that can be used to describe the feature
getShortId() - Method in class org.biojava.nbio.structure.PdbId
Get the PDB Id in the short format.
getShortName() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
 
getShortName() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
 
getShortName() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
 
getShortName() - Method in interface org.biojava.nbio.core.sequence.template.Compound
 
getShortName() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
 
getShortName() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
getShortName() - Method in enum org.biojava.nbio.structure.xtal.TransformType
 
getShortSymbol() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
Gets the international short name (as used in PDB), e.g.
getShowDBresult() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
getShowPDBMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
getSiftsMapping(String) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
Return the SIFTS mappings by getting the info from individual SIFTS xml files at URL "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/%s.xml.gz"
getSimCount() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
getSimilarity() - Method in class org.biojava.nbio.alignment.template.AbstractScorer
 
getSimilarity() - Method in interface org.biojava.nbio.alignment.template.Scorer
Returns score as a similarity between 0.0 and 1.0.
getSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain
Returns the similarity score for the alignment.
getSimilarity(double) - Method in class org.biojava.nbio.alignment.template.AbstractScorer
 
getSimilarity(double) - Method in interface org.biojava.nbio.alignment.template.Scorer
Returns score as a similarity between 0.0 and scale.
getSingularValues() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
Return the one-dimensional array of singular values
getSiteID() - Method in class org.biojava.nbio.structure.Site
 
getSites() - Method in interface org.biojava.nbio.structure.Structure
 
getSites() - Method in class org.biojava.nbio.structure.StructureImpl
 
getSize() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
 
getSize() - Method in interface org.biojava.nbio.core.alignment.template.Profile
Returns the number of rows in this profile.
getSize() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
Get the number of sequences in the MSA
getSize() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
Returns the number of rows in this profile.
getSize() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
 
getSlide(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method returns the slide for the given base pair, relative to the one before it.
getSOILD() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getSortVariable() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
 
getSortVariable() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
 
getSource() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
The feature source
getSource() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
getSource() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
The source of the feature.
getSource() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Added support for the source of this sequence for GFF3 export If a sub sequence doesn't have source then check for parent source
getSource() - Method in class org.biojava.nbio.structure.align.client.StructureName
 
getSource() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getSourceSeed() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getSourceStructure() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getSpaceGroup() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
Get the SpaceGroup
getSpaceGroup(int) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser
Gets the space group for the given standard identifier.
getSpaceGroup(String) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser
Get the space group for the given international short name, using the PDB format, e.g.
getSpaceGroupAsString(SpaceGroup) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Get the string representation of a space group.
getSparse() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getSpeciesId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
getSphereCount() - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
 
getSphereCount() - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
 
getSplitDirPath() - Method in class org.biojava.nbio.structure.io.BcifFileReader
 
getSplitDirPath() - Method in class org.biojava.nbio.structure.io.CifFileReader
 
getSplitDirPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Location of split files within the directory, as an array of paths.
getSplitDirPath() - Method in class org.biojava.nbio.structure.io.MMTFFileReader
 
getSplitDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader
 
getSplitpat1() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getSplitpat2() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getSqFrom() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
getSqTo() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
getSsBondListFromBondList(List<Bond>) - Static method in class org.biojava.nbio.structure.io.SSBondImpl
 
getSSBonds() - Method in interface org.biojava.nbio.structure.Structure
Get the list of disulfide Bonds as they have been defined in the PDB files
getSSBonds() - Method in class org.biojava.nbio.structure.StructureImpl
Get the list of disulfide Bonds as they have been defined in the PDB files
getSSEThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
getStagger(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method returns the stagger in Ã… for the given base pair
getStainTypeFromString(String) - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType
 
getStandardDeviation() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
getStart() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
getStart() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
Returns the Point within an alignment of the first element of the original Sequence.
getStart() - Method in interface org.biojava.nbio.core.alignment.template.ProfileView
Returns the column index of the viewed Profile corresponding to the first element in this view
getStart() - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
 
getStart() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
getStart() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
Start of the location
getStart() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
 
getStart() - Method in class org.biojava.nbio.structure.cath.CathFragment
 
getStart() - Method in class org.biojava.nbio.structure.cath.CathSegment
 
getStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
getStart() - Method in class org.biojava.nbio.structure.ResidueRange
 
getStartCodonSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
 
getStartIndex(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block
Calculates and returns the first position of the specified structure in the alignment that is not null.
getStartIndex(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
getStartPage() - Method in class org.biojava.nbio.structure.JournalArticle
 
getStartResidue(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block
Calculates and returns the first residue of the specified structure in the alignment that is not null.
getStartResidue(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
getStartTimestamp() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
 
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
StartupParameters is a bean to store all the possible command line parameters.
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
 
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
 
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
 
getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
 
getStatus() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
getStatus() - Method in class org.biojava.nbio.survival.cox.StrataInfo
 
getStatus() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getStatus(String) - Static method in class org.biojava.nbio.structure.PDBStatus
Get the status of a PDB id.
getStatus(String[]) - Static method in class org.biojava.nbio.structure.PDBStatus
Get the status of a collection of PDB ids (in a single API query).
getStatusListener() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
 
getStderr() - Method in class org.biojava.nbio.survival.cox.StrataInfo
 
getStdError() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
getStdlow() - Method in class org.biojava.nbio.survival.cox.StrataInfo
 
getStepParameters() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method reports all the base-pair step parameters, in the order of: tilt, roll, twist (in degrees), shift, slide, rise (in Ã…).
getStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
 
getStop() - Method in class org.biojava.nbio.structure.cath.CathFragment
 
getStop() - Method in class org.biojava.nbio.structure.cath.CathSegment
 
getStopCodonSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
 
getStrain() - Method in class org.biojava.nbio.structure.EntityInfo
 
getStrand() - Method in class org.biojava.nbio.core.sequence.CDSSequence
 
getStrand() - Method in class org.biojava.nbio.core.sequence.GeneSequence
A gene should have Strand
getStrand() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
getStrand() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
Strand which the location is located on
getStrand() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
 
getStrata() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getStrataInfoHashMap() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
 
getStrategy() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
 
getStretch(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method returns the stretch in Ã… for the given base pair
getString(String) - Method in class org.biojava.nbio.structure.align.util.ResourceManager
 
getStringForCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
getStringForCompound(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
 
getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
 
getStringRepresentation() - Method in enum org.biojava.nbio.core.sequence.Strand
 
getStructuralTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Calculate a phylogenetic tree of the MultipleAlignment using RMSD distances and the Neighbor Joining algorithm from forester.
getStructure() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
Return the current Structure in the AlignmentJmol instance.
getStructure() - Method in interface org.biojava.nbio.structure.Chain
Returns the parent Structure of this chain.
getStructure() - Method in class org.biojava.nbio.structure.ChainImpl
 
getStructure() - Method in class org.biojava.nbio.structure.cluster.Subunit
The parent Structure from which the Subunit atoms were obtained.
getStructure() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
Gets the structure.
getStructure() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
 
getStructure(File) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
 
getStructure(File) - Method in interface org.biojava.nbio.structure.io.StructureIOFile
Read file from File and returns a Structure object.
getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.BcifFileReader
 
getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.CifFileReader
 
getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Handles the actual parsing of the file into a Structure object.
getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.MMTFFileReader
 
getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.PDBFileReader
 
getStructure(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Request a Structure based on a name.
getStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
 
getStructure(String) - Method in interface org.biojava.nbio.structure.io.StructureIOFile
Open filename and return a Structure object.
getStructure(String) - Static method in class org.biojava.nbio.structure.StructureIO
Loads a structure based on a name.
getStructure(String) - Static method in class org.biojava.nbio.structure.StructureTools
Short version of StructureTools.getStructure(String, PDBFileParser, AtomCache) which creates new parsers when needed
getStructure(String, PDBFileParser, AtomCache) - Static method in class org.biojava.nbio.structure.StructureTools
Flexibly get a structure from an input String.
getStructure(URL) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
 
getStructure(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Get the structure corresponding to the given StructureIdentifier.
getStructure1() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
 
getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBDirPanel
 
getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBServerPanel
 
getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
 
getStructure1() - Method in class org.biojava.nbio.structure.gui.util.ScopSelectPanel
 
getStructure1() - Method in interface org.biojava.nbio.structure.gui.util.StructurePairSelector
 
getStructure2() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
 
getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBDirPanel
 
getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBServerPanel
 
getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
 
getStructure2() - Method in class org.biojava.nbio.structure.gui.util.ScopSelectPanel
 
getStructure2() - Method in interface org.biojava.nbio.structure.gui.util.StructurePairSelector
 
getStructureAlignment() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
 
getStructureAtom(Atom, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
 
getStructureAtomLinkage(Atom, boolean, Atom, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
 
getStructureById(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Get the structure for a PDB ID
getStructureById(String) - Method in interface org.biojava.nbio.structure.io.StructureProvider
Get the structure for a PDB ID
getStructureById(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Get the structure for a PDB ID
getStructureById(PdbId) - Method in interface org.biojava.nbio.structure.io.StructureProvider
Get the structure for a PDB ID
getStructureCoverageThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
The minimum coverage of the structure alignment between two subunits to be clustered together.
getStructureFiletype() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
 
getStructureForCathDomain(StructureName) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns a Structure corresponding to the CATH identifier supplied in structureName, using the the CathDatabase at CathFactory.getCathDatabase().
getStructureForCathDomain(StructureName, CathDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns a Structure corresponding to the CATH identifier supplied in structureName, using the specified CathDatabase.
getStructureForDomain(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForDomain(String, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForDomain(ScopDomain) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForDomain(ScopDomain, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForDomain(ScopDomain, ScopDatabase, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Returns the representation of a ScopDomain as a BioJava Structure object.
getStructureForPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Loads a structure directly by PDB ID
getStructureForPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Loads a structure directly by PDB ID
getStructureFromFasta() - Static method in class demo.DemoStructureFromFasta
 
getStructureGroup(Group, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
 
getStructureId() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
getStructureIdentifier() - Method in interface org.biojava.nbio.structure.Structure
Get an identifier corresponding to this structure
getStructureIdentifier() - Method in class org.biojava.nbio.structure.StructureImpl
 
getStructureIdentifier(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Returns the StructureIdentifier associated with the structure index from its parent Ensemble.
getStructureIdentifier(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
getStructureIdentifiers() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
getStructureIdentifiers() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
getStructureInfo(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Get summary information for the structure.
getStructurePairAligner() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
 
getStructures() - Method in class org.biojava.nbio.structure.gui.util.SelectMultiplePanel
 
getStructures() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
Gets the protein structures mapped from the Fasta file.
getSubject() - Method in interface org.biojava.nbio.ontology.Triple
Return the subject term of this triple
getSubject() - Method in class org.biojava.nbio.ontology.Triple.Impl
 
getSubLocations() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
getSubLocations() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
Gives access to the sub locations for this location.
getSubproblems(List<AlignerHelper.Anchor>, int, int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
Convert a list of anchors into a subproblem list.
getSubProfile(Location) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
 
getSubProfile(Location) - Method in interface org.biojava.nbio.core.alignment.template.Profile
Returns a ProfileView windowed to contain only the given Location.
getSubSequence(int, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
Returns a sub sequence view
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
 
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
 
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
 
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
Creates a SequenceProxyView for the given coordinates
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getSubSequence(Integer, Integer) - Method in interface org.biojava.nbio.core.sequence.template.Sequence
Returns a portion of the sequence from the different positions.
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
getSubSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
If circular this will return the sequence represented by the sub locations joined.
getSubSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.location.template.Location
Will return a SequenceReader object which represents the outer bounds of this Location
getSubstitutionMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Returns the substitution matrix.
getSubstitutionMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
 
getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
 
getSubstitutionScoreVector(int) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Returns score for the alignment of the query column to all target columns
getSubstitutionScoreVector(int, AlignerHelper.Subproblem) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Returns score for the alignment of the query column to all target columns
getSubstructureMatchingProteinSequence(ProteinSequence, Structure) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher
Get a substructure of wholeStructure containing only the Groups that are included in sequence.
getSubunitClusters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
Returns the List of SubunitCluster used to calculate symmetry.
getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
Return the number of Subunits involved in the symmetry.
getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
 
getSubunitMap() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
Map of Subunit equivalencies from the first to the second group.
getSubunitRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
getSubunits() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
Subunits contained in the SubunitCluster.
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
 
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
 
getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
Returns the List of Subunits used to calculate symmetry.
getSubunits1() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
Original Subunits of the first group.
getSubunits2() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
Original Subunits of the second group.
getSubunitTypeCount() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
 
getSuggestion(String) - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
get a list of suggestions for a userInput
getSuggestion(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
 
getSuggestion(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
 
getSummaryPos() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
 
getSummaryPos() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
 
getSunid() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
getSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode
 
getSunID() - Method in class org.biojava.nbio.structure.scop.ScopDescription
 
getSuperfamilyId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
getSuperpositionAlgorithm() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Method to superpose subunits (i.e., structural aligner).
getSurfaceResidues(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
Returns the residues belonging to the surface
getSurname() - Method in class org.biojava.nbio.structure.Author
 
getSurv() - Method in class org.biojava.nbio.survival.cox.StrataInfo
 
getSurvivalFitInfo() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
getSurvivalInfoList() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getSurvivalInfoList() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
The data used to draw the graph
getSurvivalTimePercentile(String, double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
To get the median percentile for a particular group pass the value of .50.
getSym1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
 
getSym2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
 
getSymbol() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
 
getSymbolSet() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
 
getSymDeviation() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
 
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
 
getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
 
getSymmetryAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
Return all symmetry axes of of the structure: the set of axes that describe all parts of the structure.
getSymmetryClass(double) - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
 
getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.C2RotationSolver
 
getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.HelixSolver
 
getSymmetryOperations() - Method in interface org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver
 
getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.RotationSolver
 
getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.SystematicSolver
 
getSymmetryOrder(Map<Integer, Integer>, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Helper for AlignmentTools.getSymmetryOrder(Map, Map, int, float) with a true identity function (X->X).
getSymmetryOrder(Map<Integer, Integer>, Map<Integer, Integer>, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Tries to detect symmetry in an alignment.
getSymmetryOrder(AFPChain, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Guesses the order of symmetry in an alignment
getSymmGroup() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
getSymmLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
getSymmLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
getSymmTitle(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
Create a symmetry title for a display frame (Jmol, alignment, etc).
getSymmType() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
getSymmType() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
 
getSynonyms() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
getSynonyms() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
 
getSynonyms() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
 
getSynonyms() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
 
getSynonyms() - Method in interface org.biojava.nbio.ontology.Term
Return the synonyms for this term.
getSynonyms() - Method in class org.biojava.nbio.ontology.Term.Impl
 
getSynonyms() - Method in class org.biojava.nbio.ontology.Triple.Impl
 
getSynonyms() - Method in class org.biojava.nbio.structure.EntityInfo
 
getSynthetic() - Method in class org.biojava.nbio.structure.EntityInfo
 
getSystematicName() - Method in interface org.biojava.nbio.protmod.ProteinModification
 
getSystematicName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
getT() - Method in class org.biojava.nbio.structure.align.model.AFP
 
getTable() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
 
getTable(Integer) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser
Returns a table by its identifier i.e. 1 means universal codon tables
getTable(String) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser
Returns a table by its name
getTables() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser
Returns a list of all available IUPAC tables
getTarget() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
 
getTarget() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
 
getTarget() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
 
getTarget() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
 
getTarget() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
 
getTarget() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceScorer
Returns the second sequence of the pair.
getTarget() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileScorer
Returns the second profile of the pair.
getTarget() - Method in class org.biojava.nbio.core.alignment.SimpleProfilePair
 
getTarget() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
 
getTarget() - Method in interface org.biojava.nbio.core.alignment.template.ProfilePair
Returns the second Profile of the pair.
getTarget() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
Returns the second AlignedSequence of the pair.
getTargetEndIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
 
getTargetIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
 
getTargetIndex(int) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
 
getTargetOntology() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
 
getTargetSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
Returns the Sequence which is our edit.
getTargetStartIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
 
getTaxonomicDivision() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
 
getTaxonomy() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getTempBuffer() - Method in class org.biojava.nbio.ontology.obo.OboFileParser
 
getTempFactor() - Method in interface org.biojava.nbio.structure.Atom
Get temp factor.
getTempFactor() - Method in class org.biojava.nbio.structure.AtomImpl
 
getTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
getTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology
Fetch the term with the specified name.
getTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
getTerms() - Method in class org.biojava.nbio.ontology.IntegerOntology
 
getTerms() - Method in interface org.biojava.nbio.ontology.Ontology
Return all the terms in this ontology
getTerms() - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
getTest() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
 
getText(Group) - Method in class org.biojava.nbio.structure.io.GroupToSDF
 
getTGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
getTGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
getThePdbId() - Method in class org.biojava.nbio.structure.cath.CathDomain
Returns the PDB ID.
getThreadPool() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
Returns current shared thread pool.
getThree() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
 
getThree() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
getThree() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
getThreeLetterCode() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
Should return the 3-prime end of the given Sequence according to the edit.
getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
 
getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Insert
 
getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute
 
getTilt(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method returns the tilt for the given base pair, relative to the one before it.
getTime() - Method in class org.biojava.nbio.survival.cox.StrataInfo
 
getTime() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getTimeAxisIncrementPercentage() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
Get the percentage increment for the time axis
getTissue() - Method in class org.biojava.nbio.structure.EntityInfo
 
getTitle() - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference
The title that retrieved from the Reference section.
getTitle() - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
 
getTitle() - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface
Get the title that retrieved from Reference section.
getTitle() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
Return the title of the AlignmentJmol window.
getTitle() - Method in class org.biojava.nbio.structure.EntityInfo
 
getTitle() - Method in class org.biojava.nbio.structure.JournalArticle
Get the value of title
getTitle() - Method in class org.biojava.nbio.structure.PDBHeader
 
getTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
getTmIntra() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
getTMScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
Returns the tmScore of the alignment.
getTMScore(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPChainScorer
 
getTMScore(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.util.AFPChainScorer
 
getTMScore(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.Calc
Calculate the TM-Score for the superposition.
getTMScore(Atom[], Atom[], int, int, boolean) - Static method in class org.biojava.nbio.structure.Calc
Calculate the TM-Score for the superposition.
getTMThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.
getTo() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
 
getTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder
 
getToCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
getTool() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
Get the tool identifier for QBlast.
getTop() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
getTopology() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
 
getTopologyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getTorsionPenalty() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getTotal() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
 
getTotalArea() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Returns the total area buried upon formation of this interface, defined as: 1/2[ (ASA1u-ASA1c) + (ASA2u-ASA2u) ] , with:
getTotalArea() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
Return the average buried surface area for this interface cluster
getTotalLenIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getTotalLenOpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getTotalRmsdIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
this is the init-RMSD, not the final RMSD after refinement.
getTotalRmsdOpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
The RMSD of the final alignment.
getTrace(String) - Method in class org.biojava.nbio.core.sequence.io.ABITrace
Returns one of the four traces - all of the y-coordinate values, each of which correspond to a single x-coordinate relative to the position in the array, so that if element 4 in the array is 972, then x is 4 and y is 972 for that point.
getTraceLength() - Method in class org.biojava.nbio.core.sequence.io.ABITrace
Returns the length of the trace (number of x-coordinate points in the graph).
getTraceRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
getTraces() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
 
getTraceTmScoreMin() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
getTrans() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
getTranscoefpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getTranscript(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence
Get the transcript sequence by accession
getTranscriptDNASequence(TwoBitFacade, String, List<Integer>, List<Integer>, int, int, Character) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Extracts the DNA sequence transcribed from the input genetic coordinates.
getTranscriptDNASequence(TwoBitFacade, GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Extracts the DNA sequence transcribed from the input genetic coordinates.
getTranscriptionEnd() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
getTranscriptionStart() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
getTranscripts() - Method in class org.biojava.nbio.core.sequence.GeneSequence
Get the collection of transcription sequences assigned to this gene
getTransfAlgebraic() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
getTransfAlgebraic(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
Gets a transformation algebraic string given its index.
getTransform() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
The transformation 4D matrix that needs to be applied to the second group of Subunits to superimpose them onto the first group of Subunits, given the equivalent residues in the SubunitCluster and the Subunit equivalencies.
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
 
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
 
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Returns transformation matrix to orient structure
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
 
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
getTransformation(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
Gets a transformation by index expressed in crystal axes basis.
getTransformation(Matrix, Atom) - Static method in class org.biojava.nbio.structure.Calc
Convert JAMA rotation and translation to a Vecmath transformation matrix.
getTransformation(Matrix, Matrix) - Static method in class org.biojava.nbio.structure.geometry.Matrices
Convert JAMA rotation and translation to a Vecmath transformation matrix.
getTransformationMap() - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser
Returns a map of bioassembly transformations
getTransformationMatrix() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
Return the transformation (both rotational and translational component) as a 4x4 transformation matrix.
getTransformations() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
Returns a transformation matrix for each structure giving the 3D superimposition information of the multiple structure alignment.
getTransformations() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
getTransformations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
Gets all transformations except for the identity in crystal axes basis.
getTransformationsOrthonormal() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
Gets all symmetry transformation operators corresponding to this structure's space group (including the identity, at index 0) expressed in the orthonormal basis.
getTransformId() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
 
getTransformMap(BioAssemblyInfo, Map<String, Integer>) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Convert a bioassembly information into a map of transform, chainindices it relates to.
getTransforms() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Return the 2 crystal transform operations performed on each of the molecules of this interface.
getTransforms() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
Return the list of BiologicalAssemblyTransformations needed to generate the biological assembly.
getTransformType() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
Returns the TransformType of this transformation: AU, crystal translation, fractional translation , 2 3 4 6-fold rotations, 2 3 4 6-fold screw rotations, -1 -3 -2 -4 -6 inversions/rotoinversions.
getTransition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
 
getTransition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
 
getTransition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
 
getTransition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
 
getTransition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
 
getTransition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
 
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
 
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
 
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
 
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
An adaptor method which returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
 
getTranslatedBbs(Vector3d) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox
Returns a new BoundingBoxes object containing the same bounds as this BoundingBoxes object translated by the given translation
getTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
 
getTranslation(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
 
getTranslationVector(Matrix4d) - Static method in class org.biojava.nbio.structure.Calc
Extract the translational vector as an Atom of a transformation matrix.
getTranslationVector(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices
Extract the translational vector of a transformation matrix.
getTranslScrewComponent() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
 
getTranslScrewComponent(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.CrystalTransform
Given a transformation matrix containing a rotation and translation returns the screw component of the rotation.
getTree(CathDomain) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
Return the CATH sub-tree for a particular domain.
getTree(CathDomain) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
getTree(ScopDomain) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
get the SCOP sub-tree for a particular domain.
getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
getTreshold(int) - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
 
getTriples(Term, Term, Term) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
getTriples(Term, Term, Term) - Method in interface org.biojava.nbio.ontology.Ontology
Return all triples from this ontology which match the supplied pattern.
getTriples(Term, Term, Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
getTriplet() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
getTrustedCutoffs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
Not always 2.
It may undergo further change.
getTurn() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
getTwi() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getTwist(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This method returns the twist for the given base pair, relative to the one before it.
getTwistedGroups() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
 
getTwo() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
 
getTwo() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
getTwo() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
getTwoFoldsPerpendicular() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
getType() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
 
getType() - Method in interface org.biojava.nbio.alignment.template.GapPenalty
Returns GapPenalty.Type stored.
getType() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
The feature type
getType() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
getType() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
The type of the feature.
getType() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
 
getType() - Method in class org.biojava.nbio.structure.AminoAcidImpl
 
getType() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
getType() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
 
getType() - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord
 
getType() - Method in class org.biojava.nbio.structure.EntityInfo
Get the type of entity this EntityInfo describes.
getType() - Method in interface org.biojava.nbio.structure.Group
getType() - Method in class org.biojava.nbio.structure.HetatomImpl
getType() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
 
getType() - Method in class org.biojava.nbio.structure.NucleotideImpl
 
getType() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
 
getType() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement
Returns the SecStrucType of this element.
getType() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
 
getTypeField() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getTypeSymbol() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
getU() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
Return upper triangular factor
getU() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
Return the left singular vectors
getUid() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
getUnalignedGroups(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
List of groups from the structure not included in ca (e.g. ligands).
getUnaryOperators() - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver
Returns a list of operators for this assembly.
getUnderlyingCompound() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
 
getUnidentifiableAtomLinkages() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
 
getUnidentifiableModifiedResidues() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
 
getUniprot() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
getUniprot() - Method in class org.biojava.nbio.phosphosite.Site
 
getUniProtAccessionId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
getUniprotbaseURL() - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
The current UniProt URL to deal with caching issues. www.uniprot.org is load balanced but you can access pir.uniprot.org directly.
getUniprotDirectoryCache() - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
Local directory cache of XML that can be downloaded
getUniprotEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
getUniProtId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
getUniProtId() - Method in interface org.biojava.nbio.structure.SeqMisMatch
 
getUniProtId() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
 
getUniProtPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
getUniProtResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
getUniprotStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
getUniqueID() - Method in class org.biojava.nbio.survival.cox.CoxVariables
Need a unique id from String
getUniqueInterfaces() - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder
Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.
getUniqueInterfaces(double) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder
Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.
getUnitCellAsArray(PDBCrystallographicInfo) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Get the length six array of the unit cell information.
getUnitv() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
getUnitVectors() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
 
getUnknownDataTypeVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getUnrefinedScoreThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
getUnweightedStrataInfoHashMap() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
 
getUpdateFrequency() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
The expected ECOD update frequency determines whether the version "latest" should be re-downloaded
getUpper() - Method in class org.biojava.nbio.survival.cox.StrataInfo
 
getUpperBound() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
 
getUpperedBase() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
 
getUpperLimit() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
 
getUrl() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
Get the top-level ECOD server URL.
getUrl() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
 
getURL() - Method in class org.biojava.nbio.structure.URLIdentifier
 
getUsed() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
getUsedAtomNames() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
getUserCollection() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Provided for convince if the developer needs to associate data with a sequence
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
 
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
getUserConfigHelp() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
The help text for each of these parameters.
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
 
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
 
getUserConfigHelp() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
 
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
getUserConfigParameterNames() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
The labels to be displayed to the user for each parameter
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
 
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
 
getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
 
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
getUserConfigParameters() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
get the list of parameters that the user can change through the user interface.
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
 
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
 
getUserConfigParameters() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
 
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
getUserConfigTypes() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
Get the data types of the parameters
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
 
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
 
getUserConfigTypes() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
getUserObject() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
 
getUserObject() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
getUserObject() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
 
getUserOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
getV() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition
Return the eigenvector matrix
getV() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
Return the right singular vectors
getValenceElectronCount() - Method in enum org.biojava.nbio.structure.Element
Returns the number of valence electrons for this Element.
getValidFolds(List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Find valid symmetry orders for a given stoichiometry.
getValue() - Method in class org.biojava.nbio.core.sequence.features.Qualifier
 
getValue() - Method in class org.biojava.nbio.core.util.CRC64Checksum
 
getValue() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
 
getValue() - Method in class org.biojava.nbio.structure.align.helper.GapArray
 
getValue(C, C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
 
getValue(C, C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
Returns value in matrix for conversion from first Compound to the second.
getValue(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
getValueOrder() - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
getValues() - Method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
 
getVarhaz() - Method in class org.biojava.nbio.survival.cox.StrataInfo
 
getVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getVariableResiduals() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getVariance() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getVariant() - Method in class org.biojava.nbio.genome.io.fastq.Fastq
Return the FASTQ sequence format variant for this FASTQ formatted sequence.
getVariant() - Method in class org.biojava.nbio.genome.io.fastq.IlluminaFastqReader
 
getVariant() - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqReader
 
getVariant() - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqReader
 
getVariant() - Method in class org.biojava.nbio.structure.EntityInfo
 
getVDWRadius() - Method in enum org.biojava.nbio.structure.Element
Returns the van der Waals radius of this Element.
getVector3dScrewTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
 
getVersion() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getVersion() - Method in class org.biojava.nbio.core.search.io.Result
 
getVersion() - Method in class org.biojava.nbio.core.sequence.AccessionID
In case if the AccessionID.getID() is not unique keeps the id version.
getVersion() - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
 
getVersion() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
 
getVersion() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
 
getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeCPMain
 
getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeMain
 
getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
 
getVersion() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
 
getVersion() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
 
getVersion() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
 
getVersion() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
getVersion() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
 
getVersion() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Returns the version of the algorithm used to generate the MultipleAlignment objects.
getVersion() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
getVersion() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner
Get the Version information for this Algorithm.
getVersion() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
 
getVersion() - Method in interface org.biojava.nbio.structure.align.StructureAlignment
Get the Version information for this Algorithm.
getVersion() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
getVersion() - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase
Return the release version.
getVersion() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
 
getVersion() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
Return the ECOD version, as parsed from the file.
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
 
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
Returns the vertices of an n-fold polygon of given radius and center
getVertices() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
 
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
Returns the vertices of an n-fold polygon of given radius and center
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
Returns the vertices of an n-fold polygon of given radius and center
getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
Returns the vertices of an n-fold polygon of given radius and center
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
 
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
 
getViewCount() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
 
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
 
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
 
getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
 
getViewedProfile() - Method in interface org.biojava.nbio.core.alignment.template.ProfileView
Returns the entire Profile being viewed
getViewedSequence() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
getViewedSequence() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView
 
getViewer() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
 
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
 
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
 
getViewMatrix(int) - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
 
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
 
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
 
getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
 
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
 
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
 
getViewName(int) - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
 
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
 
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
 
getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
 
getVolume() - Method in class org.biojava.nbio.structure.JournalArticle
 
getVolume() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
Returns the volume of this unit cell.
getWaldTestInfo() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getWaterChain(String) - Method in interface org.biojava.nbio.structure.Structure
Retrieve a water Chain based on the 'internal' chain id (asymId) for the first model
getWaterChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
 
getWaterChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
Retrieve a water chain based on the 'internal' chain id (asymId) for the given model index
getWaterChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
 
getWaterChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure
Retrieve a water Chain based on the 'public' chain name (authId) for the first model
getWaterChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl
 
getWaterChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure
Retrieve a water Chain based on the 'public' chain name (authId) for the given model index
getWaterChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
 
getWaterChains() - Method in class org.biojava.nbio.structure.Model
 
getWaterChains() - Method in interface org.biojava.nbio.structure.Structure
Return all water chains for the first model
getWaterChains() - Method in class org.biojava.nbio.structure.StructureImpl
 
getWaterChains(int) - Method in interface org.biojava.nbio.structure.Structure
Return all water chains for the given model index
getWaterChains(int) - Method in class org.biojava.nbio.structure.StructureImpl
 
getWebStartConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
 
getWeight() - Method in class org.biojava.nbio.survival.cox.StrataInfo
 
getWeight() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
getWeighted() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
getWeightedRmsd(Point3d[], Point3d[], double[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP
 
getWidth() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
Returns the radius of an inscribed sphere, that is tangent to each of the octahedron's faces
getWikipediaLink() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getWindowSize() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
Access the current window size
getWinSize() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
The window size to look at
getWinSize() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
getX() - Method in interface org.biojava.nbio.structure.Atom
Get coordinate X.
getX() - Method in class org.biojava.nbio.structure.AtomImpl
Get coordinate X.
getxAxisTimeCoordinates() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
getxAxisTimeValues() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
getXGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
getXGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
getXYZEuler(Matrix) - Static method in class org.biojava.nbio.structure.Calc
Convert a rotation Matrix to Euler angles.
getY() - Method in interface org.biojava.nbio.structure.Atom
Get coordinate Y.
getY() - Method in class org.biojava.nbio.structure.AtomImpl
Get coordinate Y.
getZ() - Method in interface org.biojava.nbio.structure.Atom
Get coordinate Z.
getZ() - Method in class org.biojava.nbio.structure.AtomImpl
Get coordinate Z.
getZ() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Returns the Jmol zoom to fit polyhedron and symmetry axes.
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
 
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
 
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
 
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
 
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorI
 
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorO
 
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorT
 
getZYZEuler(Matrix) - Static method in class org.biojava.nbio.structure.Calc
Gets euler angles for a matrix given in ZYZ convention.
GFF3FromUniprotBlastHits - Class in org.biojava.nbio.genome.homology
 
GFF3FromUniprotBlastHits() - Constructor for class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
 
GFF3Reader - Class in org.biojava.nbio.genome.parsers.gff
http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GFF3Reader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GFF3Reader
 
GFF3Writer - Class in org.biojava.nbio.genome.parsers.gff
 
GFF3Writer() - Constructor for class org.biojava.nbio.genome.parsers.gff.GFF3Writer
 
GLIDE - org.biojava.nbio.structure.xtal.TransformType
 
GLOBAL - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
 
GLOBAL - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
 
GLOBAL - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
 
GLOBAL_ALIGN1 - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
GLOBAL_ALIGN2 - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
GLOBAL_CONSENSUS - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
 
GLOBAL_IDENTITIES - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
 
GLOBAL_LINEAR_SPACE - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
 
GLOBAL_LINEAR_SPACE - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
 
GLOBAL_SIMILARITIES - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
 
glycine - org.biojava.nbio.structure.chem.ResidueType
 
gneg - org.biojava.nbio.genome.parsers.cytoband.StainType
 
gold - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
 
GOParser - Class in org.biojava.nbio.ontology.io
Simple parser for the Gene Ontology (GO) flatfile format.
GOParser() - Constructor for class org.biojava.nbio.ontology.io.GOParser
 
Gotoh - Class in org.biojava.nbio.structure.align.pairwise
a class to perform Gotoh algorithm
Gotoh(Alignable) - Constructor for class org.biojava.nbio.structure.align.pairwise.Gotoh
 
gpos100 - org.biojava.nbio.genome.parsers.cytoband.StainType
 
gpos25 - org.biojava.nbio.genome.parsers.cytoband.StainType
 
gpos50 - org.biojava.nbio.genome.parsers.cytoband.StainType
 
gpos75 - org.biojava.nbio.genome.parsers.cytoband.StainType
 
GradientMapper - Class in org.biojava.nbio.structure.gui.util.color
Maps a set of real values onto a gradient.
GradientMapper() - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
GradientMapper(Color, Color) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
GradientMapper(Color, Color, ColorSpace) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
GradientPanel - Class in org.biojava.nbio.structure.gui.util.color
 
GradientPanel(ContinuousColorMapper, double, double) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientPanel
 
GradientRenderer() - Constructor for class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer
 
gradients - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
GRAPH_COMPONENT - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
 
GRAPH_COMPONENT - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
 
GraphComponentOrderDetector - Class in org.biojava.nbio.structure.symmetry.internal
The GraphOrderDetector transforms the self-alignment into a Graph and extracts its maximally connected Components.
GraphComponentOrderDetector() - Constructor for class org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector
 
GraphComponentRefiner - Class in org.biojava.nbio.structure.symmetry.internal
The GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components.
GraphComponentRefiner() - Constructor for class org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner
 
grayOutCEOrig(Atom[], int, int, CECalculator, Matrix, int, double[], double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Grays out the main diagonal of a duplicated distance matrix.
grayOutPreviousAlignment(AFPChain, Atom[], int, int, CECalculator, Matrix, int, double[], double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
 
greenwood - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error
 
Grid - Class in org.biojava.nbio.structure.contact
A grid to be used for calculating atom contacts through a spatial hashing algorithm.
Grid(double) - Constructor for class org.biojava.nbio.structure.contact.Grid
Creates a Grid, the cutoff is in the same units as the coordinates (Angstroms if they are atom coordinates) and can be specified to a precision of 0.01.
GridCell - Class in org.biojava.nbio.structure.contact
A grid cell to be used in contact calculation via spatial hashing algorithm.
GridCell(Grid) - Constructor for class org.biojava.nbio.structure.contact.GridCell
 
group - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
group() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
Get the first item (everything before first semicolon, if it has one) in the attribute field, which is assumed to be a group identifer.
group() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
Get the group id of the feature.
Group - Interface in org.biojava.nbio.structure
This is the data structure for a single Group of atoms.
group1 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf
An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.
The seven different attributes are
group1 - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
 
GROUP1 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING
 
group1WorseOutcome - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
 
group2 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
 
group2 - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
 
GROUP2 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING
 
group3 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
 
GROUP3 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING
 
GroupAsa - Class in org.biojava.nbio.structure.asa
A class to store the results of ASA calculations, it can hold ASA values per atom present in Group
GroupAsa(Group) - Constructor for class org.biojava.nbio.structure.asa.GroupAsa
 
groupByRange(double[], String, String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
Need to allow a range of values similar to cut in R and a continuous c
GroupContact - Class in org.biojava.nbio.structure.contact
A pair of residues that are in contact
GroupContact() - Constructor for class org.biojava.nbio.structure.contact.GroupContact
 
GroupContactSet - Class in org.biojava.nbio.structure.contact
A set of residue-residue contacts.
GroupContactSet() - Constructor for class org.biojava.nbio.structure.contact.GroupContactSet
 
GroupContactSet(AtomContactSet) - Constructor for class org.biojava.nbio.structure.contact.GroupContactSet
Constructs a GroupContactSet by collapsing the given AtomContactSet into residue-residue (group-group) contacts.
GroupIterator - Class in org.biojava.nbio.structure
An iterator over all groups of a structure.
GroupIterator(Structure) - Constructor for class org.biojava.nbio.structure.GroupIterator
Constructs a GroupIterator object over all models
GroupIterator(Structure, int) - Constructor for class org.biojava.nbio.structure.GroupIterator
Constructs a GroupIterator object over a specific model
GroupLocation(boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
 
GroupLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
 
GroupLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
 
GroupLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
 
GroupLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
 
GroupLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
 
GroupLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
 
GroupLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
 
GroupLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
 
GroupResults - Class in org.biojava.nbio.survival.kaplanmeier.figure
 
GroupResults() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
 
GroupToSDF - Class in org.biojava.nbio.structure.io
 
GroupToSDF() - Constructor for class org.biojava.nbio.structure.io.GroupToSDF
 
GroupType - Enum in org.biojava.nbio.structure
This contains basic categories for Group types.
groupValues() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Create a collection of all unique group ids in the list, as defined by the group() method of the features.
GTSlikeScore(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
 
GuanUberbacher<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment.routines
Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
GuanUberbacher() - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher
GuanUberbacher(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher
Prepares for a pairwise global sequence alignment.
GuanUberbacher(S, S, GapPenalty, SubstitutionMatrix<C>, int) - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher
Prepares for a pairwise global sequence alignment.
guessFiletype(String) - Static method in class org.biojava.nbio.structure.StructureIO
Attempts to guess the type of a structure file based on the extension
guessOrderFromAngle(double, int) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
Returns the rotation order o that gives the lowest value of |2PI / o - theta, given that the value is strictly lower than threshold, for orders o=1,...,maxOrder.
guessPDBID(String) - Static method in class org.biojava.nbio.structure.URLIdentifier
Recognizes PDB IDs that occur at the beginning of name followed by some delimiter.
guessScopDomain(String, ScopDatabase) - Static method in class org.biojava.nbio.structure.align.client.StructureName
Guess a scop domain.
guessSequentialAlignment(Map<Integer, Integer>, boolean) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Takes a potentially non-sequential alignment and guesses a sequential version of it.
GuideTree<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment
Implements a data structure for a guide tree used during progressive multiple sequence alignment.
GuideTree(List<S>, List<PairwiseSequenceScorer<S, C>>) - Constructor for class org.biojava.nbio.alignment.GuideTree
Creates a guide tree for use during progressive multiple sequence alignment.
GuideTree.Node - Class in org.biojava.nbio.alignment
Implements a data structure for the node in a guide tree used during progressive multiple sequence alignment.
GuideTreeNode<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.alignment.template
Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
GuiWrapper - Class in org.biojava.nbio.structure.align.ce
A class to wrap some of the strucutre.gui classes using Reflection
GuiWrapper() - Constructor for class org.biojava.nbio.structure.align.ce.GuiWrapper
 
gvar - org.biojava.nbio.genome.parsers.cytoband.StainType
 
GZIP_MAGIC - Static variable in class org.biojava.nbio.core.util.InputStreamProvider
The magic number found at the start of a GZIP stream.

H

H - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
H - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
H - org.biojava.nbio.structure.Element
 
H - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
HALOGEN - org.biojava.nbio.structure.ElementType
 
handleChain(Chain, int, List<AbstractCifFileSupplier.WrappedAtom>) - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier
 
handleEvent(ValidationEvent) - Method in class org.biojava.nbio.aaproperties.xml.MyValidationEventHandler
 
handlePopupMenu(int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
handleResolutionLine(String, Pattern) - Method in class org.biojava.nbio.structure.io.PDBFileParser
 
has3D() - Method in interface org.biojava.nbio.structure.Group
Return true or false, depending if this group has 3D coordinates or not.
has3D() - Method in class org.biojava.nbio.structure.HetatomImpl
 
hasAltLoc() - Method in interface org.biojava.nbio.structure.Group
Check if this group has alternate location groups.
hasAltLoc() - Method in class org.biojava.nbio.structure.HetatomImpl
 
hasAminoAtoms() - Method in interface org.biojava.nbio.structure.Group
Calculate if this group has all atoms required for an amino acid backbone.
hasAminoAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl
Calculate if this group has all atoms required for an amino acid backbone.
hasAnyContact(Collection<Point3d>) - Method in class org.biojava.nbio.structure.contact.Grid
 
hasAnyContact(Point3d[]) - Method in class org.biojava.nbio.structure.contact.Grid
Fast determination of whether any atoms from a given set fall within the cutoff of iAtoms.
hasAtom(String) - Method in interface org.biojava.nbio.structure.Group
Tell whether a particular atom exists within this group.
hasAtom(String) - Method in class org.biojava.nbio.structure.HetatomImpl
Tell whether a particular atom exists within this group.
hasAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
 
hasAttribute(String) - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
Check if the feature has a value defined for the specified key.
hasAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Check if any feature in list has the specified attribute key.
hasAttribute(String, String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
 
hasAttribute(String, String) - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
Check if the feature attributes include the specified key/value pair.
hasAttribute(String, String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Check if any feature in list has the specified attribute key/value pair.
hasBond(Atom) - Method in interface org.biojava.nbio.structure.Atom
Test if another atom has a bond to this atom
hasBond(Atom) - Method in class org.biojava.nbio.structure.AtomImpl
Test if another atom has a bond to this atom
hasChain(String) - Method in interface org.biojava.nbio.structure.Structure
Check if a chain with the chainId aymId is contained in this structure.
hasChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
Check if a chain with the chainId aymId is contained in this structure.
hasCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
hasCompound(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
 
hasCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
hasCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
hasCompound(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
 
hasContact(Atom, Atom) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
 
hasContact(AtomIdentifier, AtomIdentifier) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
 
hasContact(ResidueIdentifier, ResidueIdentifier) - Method in class org.biojava.nbio.structure.contact.GroupContactSet
Tell whether the given pair is a contact in this GroupContactSet, in a chain-identifier independent way: contacts happening between different copies of the same Compound(Entity) will be considered equal as long as they have the same residue numbers.
hasContact(Group, Group) - Method in class org.biojava.nbio.structure.contact.GroupContactSet
Tell whether the given group pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers
hasContact(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.contact.GroupContactSet
Tell whether the given pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers
hasContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
Returns true if at least 1 contact from this set is within the given distance.
hasContactToAtom(Point3d[], Point3d[], Point3d, double) - Method in class org.biojava.nbio.structure.contact.GridCell
Tests whether any atom in this cell has a contact with the specified query atom
hasDeuteratedEquiv(Atom, Group) - Static method in class org.biojava.nbio.structure.StructureTools
Check to see if a Hydrogen has a Deuterated brother in the group.
hasGap(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
 
hasGap(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile
Returns true if any AlignedSequence has a gap at the given index.
hasGaps(int) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Check size of gaps between successive features in list.
hash(int, boolean) - Static method in class org.biojava.nbio.core.util.Hashcoder
 
hash(int, char) - Static method in class org.biojava.nbio.core.util.Hashcoder
 
hash(int, double) - Static method in class org.biojava.nbio.core.util.Hashcoder
double support which is done using the same techinque as float hashing except we convert to a long not to an int.
hash(int, float) - Static method in class org.biojava.nbio.core.util.Hashcoder
float support done via Float.floatToIntBits(float) which allows the encoding of a float as an int.
hash(int, int) - Static method in class org.biojava.nbio.core.util.Hashcoder
Used for ints, bytes and shorts
hash(int, long) - Static method in class org.biojava.nbio.core.util.Hashcoder
long support done by shifting by 32 (using unsigned shift)
hash(int, Object) - Static method in class org.biojava.nbio.core.util.Hashcoder
o is a possibly-null object field, and possibly an array.
hashCode() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
hashCode() - Method in class org.biojava.nbio.core.search.io.Hit
 
hashCode() - Method in class org.biojava.nbio.core.search.io.Hsp
 
hashCode() - Method in class org.biojava.nbio.core.search.io.Result
 
hashCode() - Method in class org.biojava.nbio.core.sequence.AccessionID
 
hashCode() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
 
hashCode() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
 
hashCode() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
 
hashCode() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
 
hashCode() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
hashCode() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
hashCode() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
 
hashCode() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
hashCode() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
hashCode() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
hashCode() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
hashCode() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
 
hashCode() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
 
hashCode() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
 
hashCode() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
 
hashCode() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
hashCode() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
hashCode() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
hashCode() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
 
hashCode() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
hashCode() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
hashCode() - Method in class org.biojava.nbio.data.sequence.FastaSequence
 
hashCode() - Method in class org.biojava.nbio.genome.parsers.gff.Location
 
hashCode() - Method in class org.biojava.nbio.ontology.Term.Impl
 
hashCode() - Method in interface org.biojava.nbio.ontology.Triple
The hashcode for a Triple.
hashCode() - Method in class org.biojava.nbio.ontology.Triple.Impl
 
hashCode() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
 
hashCode() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
hashCode() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
hashCode() - Method in class org.biojava.nbio.protmod.structure.StructureAtom
 
hashCode() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
 
hashCode() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
hashCode() - Method in class org.biojava.nbio.ronn.Jronn.Range
 
hashCode() - Method in class org.biojava.nbio.ronn.ModelLoader.Model
 
hashCode() - Method in class org.biojava.nbio.structure.align.client.PdbPair
 
hashCode() - Method in class org.biojava.nbio.structure.align.client.StructureName
 
hashCode() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
hashCode() - Method in class org.biojava.nbio.structure.Author
 
hashCode() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
hashCode() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
 
hashCode() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
 
hashCode() - Method in class org.biojava.nbio.structure.contact.Pair
 
hashCode() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
 
hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
hashCode() - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
hashCode() - Method in class org.biojava.nbio.structure.PdbId
 
hashCode() - Method in class org.biojava.nbio.structure.ResidueNumber
 
hashCode() - Method in class org.biojava.nbio.structure.ResidueRange
 
hashCode() - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
 
hashCode() - Method in class org.biojava.nbio.structure.scop.ScopDescription
 
hashCode() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
 
hashCode() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
 
hashCode() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
 
hashCode() - Method in class org.biojava.nbio.structure.Site
 
hashCode() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
 
hashCode() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
 
hashCode() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
Hashcoder - Class in org.biojava.nbio.core.util
Contains helper methods for generating a HashCode without having to resort to the commons lang hashcode builders.
Hashcoder() - Constructor for class org.biojava.nbio.core.util.Hashcoder
 
hasJournalArticle() - Method in class org.biojava.nbio.structure.PDBHeader
Return whether or not the entry has an associated journal article or publication.
hasJournalArticle() - Method in interface org.biojava.nbio.structure.Structure
Return whether or not the entry has an associated journal article or ation.
hasJournalArticle() - Method in class org.biojava.nbio.structure.StructureImpl
Return whether or not the entry has an associated journal article or publication.
hasMore() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
 
hasNcsOps() - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder
 
hasNext() - Method in class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator
 
hasNext() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator
Check if next window of default size is available.
hasNext() - Method in class org.biojava.nbio.structure.AtomIterator
Is there a next atom ?
hasNext() - Method in class org.biojava.nbio.structure.GroupIterator
is there a group after the current one in the structure?
hasNext(int, int) - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator
Check if next window of specified size is available.
hasNonDeuteratedEquiv(Atom, Group) - Static method in class org.biojava.nbio.structure.StructureTools
Check to see if an Deuterated atom has a non deuterated brother in the group.
hasNonPolyChain(String) - Method in interface org.biojava.nbio.structure.Structure
Check if a non polymeric chain with chainId asymId is contained in the structure.
hasNonPolyChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
Check if a non polymeric chain with chainId asymId is contained in the structure.
hasParent() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
hasPdbChain(String) - Method in interface org.biojava.nbio.structure.Structure
Check if a chain with chain name authId is contained in the structure
hasPdbChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
Check if a chain with chain name authId is contained in the structure
HBond - Class in org.biojava.nbio.structure.secstruc
Container that represents a hidrogen bond.
HBond() - Constructor for class org.biojava.nbio.structure.secstruc.HBond
 
HBond(HBond) - Constructor for class org.biojava.nbio.structure.secstruc.HBond
 
HBOND - org.biojava.nbio.structure.BondType
 
HBONDHIGHENERGY - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc
higher limit for H-bond energy
HBONDLOWENERGY - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc
Minimal H-bond energy in cal/mol
He - org.biojava.nbio.structure.Element
 
HeaderInfo - Class in org.biojava.nbio.survival.data
 
HeaderInfo(Integer) - Constructor for class org.biojava.nbio.survival.data.HeaderInfo
 
headerLine - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
height - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
HelicalRepeatUnit - Class in org.biojava.nbio.structure.symmetry.core
 
HelicalRepeatUnit(QuatSymmetrySubunits) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
 
Helix - Class in org.biojava.nbio.structure.symmetry.core
 
Helix() - Constructor for class org.biojava.nbio.structure.symmetry.core.Helix
 
helix3 - org.biojava.nbio.structure.secstruc.SecStrucType
 
helix4 - org.biojava.nbio.structure.secstruc.SecStrucType
 
helix5 - org.biojava.nbio.structure.secstruc.SecStrucType
 
HelixAxisAligner - Class in org.biojava.nbio.structure.symmetry.axis
 
HelixAxisAligner(QuatSymmetryResults) - Constructor for class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
 
HelixExtender - Class in org.biojava.nbio.structure.symmetry.core
 
HelixExtender(QuatSymmetrySubunits, Helix) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixExtender
 
HelixLayers - Class in org.biojava.nbio.structure.symmetry.core
 
HelixLayers() - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixLayers
 
HelixSolver - Class in org.biojava.nbio.structure.symmetry.core
 
HelixSolver(QuatSymmetrySubunits, int, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixSolver
 
HelloWorld - Class in org.biojava.nbio.proteincomparisontool
A dummy class that does nothing.
HelloWorld() - Constructor for class org.biojava.nbio.proteincomparisontool.HelloWorld
 
HelpDialog - Class in org.biojava.nbio.structure.align.gui
 
HelpDialog() - Constructor for class org.biojava.nbio.structure.align.gui.HelpDialog
 
HETATM - org.biojava.nbio.structure.GroupType
The type for hetero groups (everything else)
HetatomImpl - Class in org.biojava.nbio.structure
Generic Implementation of a Group interface.
HetatomImpl() - Constructor for class org.biojava.nbio.structure.HetatomImpl
Construct a Hetatom instance.
HetatomImpl.PerformanceBehavior - Enum in org.biojava.nbio.structure
Behaviors for how to balance memory vs. performance.
HEXAGONAL - org.biojava.nbio.structure.xtal.BravaisLattice
 
hexPropertyNames - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo
 
Hf - org.biojava.nbio.structure.Element
 
Hg - org.biojava.nbio.structure.Element
 
hideAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Returns a Jmol script to hide axes
hideAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
Returns a Jmol script to hide axes
hideAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
hideColumn(String, boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
hideEmptyColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
 
hideEmptyRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
 
hideMetaDataColumns(boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
hideMetaDataRows(boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
hidePolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
 
hidePolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
 
hidePolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
hideRow(String, boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
hideSuggest() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
Force the suggestions to be hidden (Useful for buttons, e.g. to use JSuggestionField like a ComboBox)
hieFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
 
HierarchicalClusterer<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.alignment.template
Defines a clustering algorithm that converts a distance matrix into a tree.
Hit - Class in org.biojava.nbio.core.search.io
This class models a search Hit.
Hit(int, String, String, String, int, List<Hsp>, Sequence) - Constructor for class org.biojava.nbio.core.search.io.Hit
 
HITLIST_SIZE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
HMMER_SERVICE - Static variable in class org.biojava.nbio.ws.hmmer.RemoteHmmerScan
 
HmmerDemo - Class in demo
The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service
HmmerDemo() - Constructor for class demo.HmmerDemo
 
HmmerDomain - Class in org.biojava.nbio.ws.hmmer
Provides the details of a domain hit
HmmerDomain() - Constructor for class org.biojava.nbio.ws.hmmer.HmmerDomain
 
HmmerResult - Class in org.biojava.nbio.ws.hmmer
The results of a Hmmer search for a single sequence
HmmerResult() - Constructor for class org.biojava.nbio.ws.hmmer.HmmerResult
 
HmmerScan - Interface in org.biojava.nbio.ws.hmmer
Interface for performing Hmmscans on sequences.
Ho - org.biojava.nbio.structure.Element
 
Homology - org.biojava.nbio.structure.cath.CathCategory
 
HOMSTRAD - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
Hsp<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.search.io
This class models a search Hsp.
Hsp(int, double, int, double, int, int, int, int, int, int, int, int, int, int, String, String, String, Double, Integer) - Constructor for class org.biojava.nbio.core.search.io.Hsp
 
HSP_SORT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
HSVColorSpace - Class in org.biojava.nbio.structure.gui.util.color
 
HSVColorSpace() - Constructor for class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
 
HTML - org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum
 
HYDROPHOBIC - org.biojava.nbio.structure.BondType
 
HYDROPHOBICITY - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
 
hypot(double, double) - Static method in class org.biojava.nbio.structure.jama.Maths
sqrt(a^2 + b^2) without under/overflow.
HYPOTHETICAL - org.biojava.nbio.protmod.ModificationOccurrenceType
 

I

I - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
I - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
I - org.biojava.nbio.structure.Element
 
I - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
I_THRESH - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
I_THRESH - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
IcosahedralSampler - Class in org.biojava.nbio.structure.symmetry.geometry
Represents an even coverage of quaternion space by 60 points.
Icosahedron - Class in org.biojava.nbio.structure.symmetry.geometry
 
Icosahedron() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
 
ID_KEY - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
IdenticalSequenceFamily - org.biojava.nbio.structure.cath.CathCategory
 
identify(List<Chain>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
Identify all registered modifications in chains.
identify(List<Chain>, Set<ProteinModification>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
Identify a set of modifications in a a list of chains.
identify(Chain) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
Identify all registered modifications in a chain.
identify(Chain, Set<ProteinModification>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
Identify a set of modifications in a a chains.
identify(Structure) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
Identify all registered modifications in a structure.
identify(Structure, Set<ProteinModification>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
Identify a set of modifications in a structure.
IDENTITIES - org.biojava.nbio.alignment.Alignments.PairInProfileScorerType
 
identity(int) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
identity(int, int) - Static method in class org.biojava.nbio.structure.jama.Matrix
Generate identity matrix
IDENTITY - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder
 
IDENTITY - Static variable in class org.biojava.nbio.structure.xtal.CrystalTransform
 
IDENTITY_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.EntityFinder
Identity value for 2 chains to be considered part of same entity
IdentityMap() - Constructor for class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
 
IDX_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
IdxComparator - Class in org.biojava.nbio.structure.align.helper
 
IdxComparator() - Constructor for class org.biojava.nbio.structure.align.helper.IdxComparator
 
IlluminaFastqReader - Class in org.biojava.nbio.genome.io.fastq
Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.
IlluminaFastqReader() - Constructor for class org.biojava.nbio.genome.io.fastq.IlluminaFastqReader
 
IlluminaFastqWriter - Class in org.biojava.nbio.genome.io.fastq
Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences.
IlluminaFastqWriter() - Constructor for class org.biojava.nbio.genome.io.fastq.IlluminaFastqWriter
 
Impl(String, String) - Constructor for class org.biojava.nbio.ontology.Ontology.Impl
 
Impl(Ontology, String) - Constructor for class org.biojava.nbio.ontology.Term.Impl
 
Impl(Ontology, String, String) - Constructor for class org.biojava.nbio.ontology.Term.Impl
 
Impl(Ontology, String, String) - Constructor for class org.biojava.nbio.ontology.Variable.Impl
 
Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.nbio.ontology.Term.Impl
 
Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.nbio.ontology.Variable.Impl
 
Impl(Ontology, Ontology) - Constructor for class org.biojava.nbio.ontology.OntologyTerm.Impl
 
Impl(Ontology, Ontology, Object[]) - Constructor for class org.biojava.nbio.ontology.OntologyTerm.Impl
 
Impl(Ontology, Term, String) - Constructor for class org.biojava.nbio.ontology.RemoteTerm.Impl
 
Impl(Ontology, Term, String, Object[]) - Constructor for class org.biojava.nbio.ontology.RemoteTerm.Impl
 
Impl(Term, Term, Term) - Constructor for class org.biojava.nbio.ontology.Triple.Impl
 
Impl(Term, Term, Term, Object[]) - Constructor for class org.biojava.nbio.ontology.Triple.Impl
 
Impl(Term, Term, Term, String, String) - Constructor for class org.biojava.nbio.ontology.Triple.Impl
 
Impl(Term, Term, Term, String, String, Object[]) - Constructor for class org.biojava.nbio.ontology.Triple.Impl
 
importTerm(Term, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
importTerm(Term, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
importTerm(Term, String) - Method in interface org.biojava.nbio.ontology.Ontology
Create a view of a term from another ontology.
In - org.biojava.nbio.structure.Element
 
index - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair
 
index - Variable in class org.biojava.nbio.structure.align.helper.GapArray
 
INDEX - Static variable in class org.biojava.nbio.ronn.RonnConstraint
 
indexOf(String, String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
 
indexOf(Sequence<C>, C) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
Performs a linear search of the given Sequence for the given compound.
IndexPair - Class in org.biojava.nbio.structure.align.helper
 
IndexPair() - Constructor for class org.biojava.nbio.structure.align.helper.IndexPair
 
IndexPair(short, short) - Constructor for class org.biojava.nbio.structure.align.helper.IndexPair
 
INFINITY - Static variable in class org.biojava.nbio.alignment.io.StockholmFileParser
indicates reading as much as possible, without limits
info(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
 
INFRARED_SPECTROSCOPY - org.biojava.nbio.structure.ExperimentalTechnique
 
init() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
Initialization the static variables and register common modifications.
init(InputStream) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
Initialization the static variables and register common modifications.
init(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
initAlignmentGUIMenu(JFrame) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
initCoords() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
Display the structures after the variable initialization in the constructor.
initCoords() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
 
initCoords() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
 
initExtinctionCoefficient() - Static method in class org.biojava.nbio.aaproperties.Constraints
Does the initialization of extinction coefficient based on http://au.expasy.org/tools/protparam-doc.html
initializeBreakFlag(boolean[][]) - Method in interface org.biojava.nbio.structure.align.ce.MatrixListener
 
initializeCellTranslations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
initJmolMenu(JFrame, AbstractAlignmentJmol, AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
Provide a JMenuBar that can be added to a JFrame containing a JmolPanel.
initMenu() - Static method in class org.biojava.nbio.structure.gui.util.MenuCreator
provide a JMenuBar that can be added to a JFrame
initMet(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
 
initMolecularWeight() - Static method in class org.biojava.nbio.aaproperties.Constraints
Does the initialization of molecular weights based on http://au.expasy.org/tools/findmod/findmod_masses.html#AA
initPaths() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Should be called whenever any of the path variables change.
initSequenceStorage(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
initStructure(int, int, int, int, int, String) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
 
initSumOfDistances(int, int, int, int, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
initSumOfDistances(int, int, int, int, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
INNER - org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
 
InputStreamProvider - Class in org.biojava.nbio.core.util
A class that provides an InputStream from a File.
InputStreamProvider() - Constructor for class org.biojava.nbio.core.util.InputStreamProvider
 
inputStreamToDocument(InputStream) - Static method in class org.biojava.nbio.core.util.XMLHelper
Creates an org.w3c.dom.Document from the content of the inputStream
InsdcLocations - Class in org.biojava.nbio.core.sequence.location
A collection of locations which are used whenever we work with INSDC; some of which could be deprecated (from INSDC's point of view) yet appear in records.
InsdcLocations() - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations
 
InsdcLocations.BondLocation - Class in org.biojava.nbio.core.sequence.location
Used to represent bond locations equivalent to bond(7,8) or bond(7).
InsdcLocations.GroupLocation - Class in org.biojava.nbio.core.sequence.location
Deprecated in INSDC yet still appears; equivalent to the order() directive except no 5' to 3' ordering is defined.
InsdcLocations.OneOfLocation - Class in org.biojava.nbio.core.sequence.location
Deprecated in INSDC; refers to a set of locations of which one location could be valid e.g. one-of(location, location, location).
InsdcLocations.OrderLocation - Class in org.biojava.nbio.core.sequence.location
Used to describe a 5' to 3' ordering but no firm assurance it is correct
InsdcParser - Class in org.biojava.nbio.core.sequence.location
Parser for working with INSDC style locations.
InsdcParser() - Constructor for class org.biojava.nbio.core.sequence.location.InsdcParser
 
InsdcParser(DataSource) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcParser
 
Insert(String, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert
 
Insert(String, int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert
 
Insert(Sequence<C>, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert
 
Insert(Sequence<C>, int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert
 
INSERTION - org.biojava.nbio.alignment.routines.AlignerHelper.Last
 
insertSeqResGroup(Chain, Group, int) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Insert the group in the given position in the sequence.
InstabilityIndex - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
IntegerOntology - Class in org.biojava.nbio.ontology
 
IntegerOntology.IntTerm - Class in org.biojava.nbio.ontology
 
InterfaceFinder - Class in org.biojava.nbio.structure.contact
A class containing methods to find interfaces in a given structure.
InterfaceFinder(Structure) - Constructor for class org.biojava.nbio.structure.contact.InterfaceFinder
 
interpolate(Color, Color, float) - Method in interface org.biojava.nbio.structure.gui.util.color.ColorInterpolator
Interpolates to a color between a and b
interpolate(Color, Color, float) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
Interpolates to a color between a and b
INTERPRO - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
interrupt() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc
stops what is currently happening and does not continue
interrupt() - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
 
interrupt() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
 
interrupt() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc
stops what is currently happening and does not continue
interrupt() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
 
intersection(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Return the intersection, or null if no overlap.
INTERSECTION_OF - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
IntronSequence - Class in org.biojava.nbio.core.sequence
 
IntronSequence(GeneSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.IntronSequence
Place holder for Intron sequence features
IntTerm(int) - Constructor for class org.biojava.nbio.ontology.IntegerOntology.IntTerm
 
IntTerm(int, Object[]) - Constructor for class org.biojava.nbio.ontology.IntegerOntology.IntTerm
 
intValue() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
Attempts to provide an int version of this codon which multiplies each position by
intValue() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
 
InvalidTermException - Exception in org.biojava.nbio.ontology
Thrown to indicate that an ontology term is not acceptable or appropriate in a given context
InvalidTermException() - Constructor for exception org.biojava.nbio.ontology.InvalidTermException
 
InvalidTermException(String) - Constructor for exception org.biojava.nbio.ontology.InvalidTermException
 
InvalidTermException(String, Throwable) - Constructor for exception org.biojava.nbio.ontology.InvalidTermException
 
InvalidTermException(Throwable) - Constructor for exception org.biojava.nbio.ontology.InvalidTermException
 
inverse() - Method in class org.biojava.nbio.structure.jama.Matrix
Matrix inverse or pseudoinverse
inverse(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
A method which attempts to do the right thing when is comes to a reverse/reverse complement
invert(Atom) - Static method in class org.biojava.nbio.structure.Calc
 
invertAlignment(AFPChain) - Method in class org.biojava.nbio.structure.align.ce.CeCPMain
Swaps the order of structures in an AFPChain
IONIC - org.biojava.nbio.structure.BondType
 
IOUtils - Class in org.biojava.nbio.core.sequence.io.util
 
IOUtils() - Constructor for class org.biojava.nbio.core.sequence.io.util.IOUtils
 
IOUtils.ReaderProcessor - Interface in org.biojava.nbio.core.sequence.io.util
Closure interface used when working with IOUtils#processReader(String).
IPeptideProperties - Interface in org.biojava.nbio.aaproperties
An interface to generate some basic physico-chemical properties of protein sequences.
The following properties could be generated:
IProfeatProperties - Interface in org.biojava.nbio.aaproperties.profeat
 
IProfeatProperties.ATTRIBUTE - Enum in org.biojava.nbio.aaproperties.profeat
Enumeration of the seven different attributes
IProfeatProperties.DISTRIBUTION - Enum in org.biojava.nbio.aaproperties.profeat
Enumeration of the distribution for the first, first 25%, first 50%, first 75% and 100% of the grouping
IProfeatProperties.GROUPING - Enum in org.biojava.nbio.aaproperties.profeat
Enumeration of the three different groupings for each attributes
IProfeatProperties.TRANSITION - Enum in org.biojava.nbio.aaproperties.profeat
Enumeration of the transition between groupA and groupB
Ir - org.biojava.nbio.structure.Element
 
IS_A - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
IS_A - Static variable in class org.biojava.nbio.ontology.OntoTools
 
IS_DOMAIN_ASSEMBLY - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
Deprecated way of indicating there is an assembly. replaced by the assembly id
IS_OBSOLETE - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
IS_REPRESENTATIVE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
Indicates a manual representative
isAfter(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Check if this location is entirely after the other location (no overlap).
isAlignSeqRes() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.
isAmbiguosProtein(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
Check whether the sequence confirms to amboguous protein sequence
isAmbiguous() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
 
isAminoAcid() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
isAminoAcid() - Method in interface org.biojava.nbio.structure.Group
Check if this group is an aminoacid group, from the definition in Chemical Component Dictionary
isAminoAcid() - Method in class org.biojava.nbio.structure.HetatomImpl
 
isAutoFetch() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
isBefore(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Check if this location is entirely before other location (no overlap).
isBend() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
isBetaStrand() - Method in enum org.biojava.nbio.structure.secstruc.SecStrucType
A Beta-Strand is an extended set of sequential Bridges that, together with other Beta-Strands, is part of a Beta-Sheet.
isBetweenCompounds() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
isBetweenCompounds() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
Returns true if the position is meant to represent a point between two points such as 78^79.
isBioAssembly() - Method in class org.biojava.nbio.structure.align.client.StructureName
 
isBiologicalAssembly() - Method in interface org.biojava.nbio.structure.Structure
Get flag that indicates if this structure is a biological assembly
isBiologicalAssembly() - Method in class org.biojava.nbio.structure.StructureImpl
Gets flag that indicates if this structure is a biological assembly
isCacheEnabled() - Method in class org.biojava.nbio.structure.domain.SerializableCache
 
isCathID() - Method in class org.biojava.nbio.structure.align.client.StructureName
 
isCellReasonable() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
Checks whether the dimensions of this crystal cell are reasonable for protein crystallography: if all 3 dimensions are below 10.0 the cell is considered unrealistic and false returned
isChalcogen() - Method in enum org.biojava.nbio.structure.Element
Returns true if Element is a chalcogen (O, S, Se, Te, Po).
isCharged(char) - Static method in class org.biojava.nbio.aaproperties.AminoAcidProperties
At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains), and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
isCircular() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
isCircular() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
 
isCircular() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
Returns true if this Sequence wraps around from the last alignment column back to the first.
isCircular() - Method in interface org.biojava.nbio.core.alignment.template.Profile
Returns true if any AlignedSequence is circular.
isCircular() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
isCircular() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
Indicates if this location is circular.
isClosed() - Method in class org.biojava.nbio.core.sequence.io.GenbankReader
 
isCompatible(ResidueGroup) - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup
Determine if two Residuegroups (maximally connected components of the alignment Graph) are compatible, based in the following criterion:
isComplementable() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
isComplementable() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
isComplementable() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
 
isComplementable() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
isComplementable() - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
NucleotideCompounds can always complement
isComplementable() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
 
isComplete() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
isComplex() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
isComplex() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.
isCompoundStringLengthEqual() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
isCompoundStringLengthEqual() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
isCompoundStringLengthEqual() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
 
isCompoundStringLengthEqual() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
isCompoundStringLengthEqual() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
Returns true if all String representations of Compounds are of the same length.
isConnected(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc
Test if two amino acids are connected, i.e. if the distance from C to N < 2.5 Angstrom.
isCrossLink() - Method in enum org.biojava.nbio.protmod.ModificationCategory
 
isCrystallographic() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique
 
isCrystallographic() - Method in interface org.biojava.nbio.structure.Structure
Test if this structure is a crystallographic structure, i.e. it is an asymmetric unit from which it is possible to reconstruct the crystal lattice given cell parameters and space group.
isCrystallographic() - Method in class org.biojava.nbio.structure.StructureImpl
Whether this Structure is a crystallographic structure or not.
isCrystallographic(Set<ExperimentalTechnique>) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique
Given a Set of ExperimentalTechniques returns true if at least one is crystallographic
isCTerminal() - Method in class org.biojava.nbio.protmod.Component
 
isDefined() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
 
isDoAngleCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
isDoDensityCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
isDoDistanceCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
isDomainSplit() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
isDoRMSCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
isDownloadAll() - Method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
By default this provider will download only some of the ChemComp files.
isEcodDomain() - Method in class org.biojava.nbio.structure.align.client.StructureName
 
isEmpty() - Method in class org.biojava.nbio.structure.chem.ChemComp
Indicates whether this compound was created with
isEmpty() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
isEnantiomorphic() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
isEquivalent(CrystalTransform) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
Returns true if the given CrystalTransform is equivalent to this one.
isErrorXML(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
returns true if the alignment XML contains an error message
isEscapeStarter(char) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
 
isFile() - Method in class org.biojava.nbio.structure.align.client.StructureName
Indicates that the identifier was determined to correspond to a file.
isFlexible() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
 
isFractionalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
Tells whether this transformation contains a fractional translational component (whatever its rotational component).
isFullRank() - Method in class org.biojava.nbio.structure.jama.QRDecomposition
Is the matrix full rank?
isGap(char) - Static method in class org.biojava.nbio.phylo.Comparison
Method that determines if a character means a gap in the alignment.
isGap(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
isGap(int) - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
Returns true if this Sequence has a gap at a particular alignment column.
isGaps() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
isGuiModuleInstalled() - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
 
isHalogen() - Method in enum org.biojava.nbio.structure.Element
Returns true if Element is a halogen (F, Cl, Br, I, At).
isHeaderOnly() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
Parse only the PDB file header out of the files
isHeavyAtom() - Method in enum org.biojava.nbio.structure.Element
Returns true is the Element is an not Hydrogen (or an isotope of Hydrogen).
isHelixType() - Method in enum org.biojava.nbio.structure.secstruc.SecStrucType
Helix type can be 3-10 helix, pi-helix or alpha-helix.
isHetAtomInFile() - Method in interface org.biojava.nbio.structure.Group
Tells whether the group is annotated as HETATM in the file.
isHetAtomInFile() - Method in class org.biojava.nbio.structure.HetatomImpl
 
isHeteroAtom() - Method in enum org.biojava.nbio.structure.Element
Returns true if Element is not Hydrogen and not Carbon.
isHexProperty(String) - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
 
isHide() - Method in class org.biojava.nbio.survival.data.HeaderInfo
 
isHighConfidenceScores(double, double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Whether the subunits can be considered "identical" by sequence alignment.
isHigher(Point) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
isHigher(Point) - Method in interface org.biojava.nbio.core.sequence.location.template.Point
Returns true if the point is higher in value to the current point
isHomomeric() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Returns true if the 2 molecules of this interface are the same entity (i.e. homomeric interface), false otherwise (i.e. heteromeric interface)
isHydrogen() - Method in enum org.biojava.nbio.structure.Element
Returns true if this Element is Hydrogen.
isIdenticalByEntityIdTo(SubunitCluster) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
Tells whether the other SubunitCluster contains exactly the same Subunit.
isIdenticalTo(SubunitCluster) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
Tells whether the other SubunitCluster contains exactly the same Subunit.
isIdentity() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
Tells whether this transformation is in identity.
isIdentity() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
Tells whether this transformation is the identity: no rotation and no translation
isIllumina() - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_ILLUMINA.
isInfinite() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Returns true if the transformation applied to the second molecule of this interface has an infinite character (pure translation or screw rotation) and both molecules of the interface have the same asymmetric unit identifier (chain id): in such cases the interface would lead to infinite fiber-like (linear or helical) assemblies
isInfinite() - Method in enum org.biojava.nbio.structure.xtal.TransformType
Tells whether the transform type produces infinite assemblies if interface happens between identical chains
isInternalSymmetry() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
The internal symmetry option divides each Subunit of each SubunitCluster into its internally symmetric repeats.
isIsologous() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Tell whether the interface is isologous, i.e. it is formed by the same patches of same entity on both sides.
isJoinFast() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
isJoinPlo() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
isLeaf() - Method in class org.biojava.nbio.alignment.GuideTree.Node
 
isLocal() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Returns whether alignment finds a region of similarity rather than aligning every compound.
isLocal() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
A local result means that only a subset of the original Subunits was used for symmetry determination.
isLocalLimitsExceeded() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
isLocalLimitsExceeded(Set<?>) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
isLower(Point) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
isLower(Point) - Method in interface org.biojava.nbio.core.sequence.location.template.Point
Returns true if the current point is at a lower position than the point given.
isMetaDataColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
isMetaDataRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
isMetal() - Method in enum org.biojava.nbio.structure.Element
Returns true if ElementType is a metal.
isMetal() - Method in enum org.biojava.nbio.structure.ElementType
Returns true if ElementType is a metal.
isMetalloid() - Method in enum org.biojava.nbio.structure.Element
Returns true if ElementType is a metalloid.
isMetalloid() - Method in enum org.biojava.nbio.structure.ElementType
Returns true if ElementType is a metalloid.
isNegative() - Method in class org.biojava.nbio.genome.parsers.gff.Location
Check if location is on negative strand.
isNmr() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique
 
isNmr() - Method in interface org.biojava.nbio.structure.Structure
Test if this structure is an NMR structure.
isNmr() - Method in class org.biojava.nbio.structure.StructureImpl
Whether this Structure is a NMR structure or not.
isNmr(Set<ExperimentalTechnique>) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique
Given a Set of ExperimentalTechniques returns true if at least one is NMR
isNonAmbNucleotideSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!)
isNonMetal() - Method in enum org.biojava.nbio.structure.Element
Returns true if ElementType is a non-metal.
isNonMetal() - Method in enum org.biojava.nbio.structure.ElementType
Returns true if ElementType is a non-metal.
isNonsingular() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
Is the matrix nonsingular?
isNonStandardCoordFrameConvention() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
Whether this structure is non-standard coordinate frame convention, for which our scale matrix calculation and thus the crystal reconstruction will be incorrect.
isNonStandardSg() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
Whether this structure has a non-standard space group not supported by Biojava.
isNoOverlap() - Method in class org.biojava.nbio.structure.contact.Grid
Tells whether (after having added atoms to grid) the i and j grids are not overlapping.
isNTerminal() - Method in class org.biojava.nbio.protmod.Component
 
isNucleicAcid() - Method in interface org.biojava.nbio.structure.Chain
Tell whether given chain is DNA or RNA
isNucleicAcid() - Method in class org.biojava.nbio.structure.ChainImpl
 
isNucleotide() - Method in interface org.biojava.nbio.structure.Group
Check if this group is a nucleotide group, from the definition in Chemical Component Dictionary
isNucleotide() - Method in class org.biojava.nbio.structure.HetatomImpl
 
isNucleotide(String) - Static method in class org.biojava.nbio.structure.StructureTools
Test if the three-letter code of an ATOM entry corresponds to a nucleotide or to an aminoacid.
isNucleotideSequence(String) - Static method in class org.biojava.nbio.core.util.SequenceTools
 
isNucleotideSequence(FastaSequence) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
 
IsoelectricPoint - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
isOnTheFly() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
On-the-fly Jmol bioassembly generation.
isOptimizeAlignment() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level.
isOptimizeAlignment() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.
isOptimizeAlignment() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.
Isotope - Class in org.biojava.nbio.aaproperties.xml
 
Isotope() - Constructor for class org.biojava.nbio.aaproperties.xml.Isotope
 
Isotope(String, int, double) - Constructor for class org.biojava.nbio.aaproperties.xml.Isotope
 
isOutputPDB() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
When writing the results to a file, don;t write as XML but write aligned PDB file
isParseBioAssembly() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
Should the biological assembly info (REMARK 350) be parsed from the PDB file?
isParseCAOnly() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
The flag if only the C-alpha atoms of the structure should be parsed.
isParseSecStruc() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
Is secondary structure assignment being parsed from the file?
isPartial() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
isPartialOn3prime() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
isPartialOn5prime() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
isPdbId() - Method in class org.biojava.nbio.structure.align.client.StructureName
 
isPFam() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
isPolar(char) - Static method in class org.biojava.nbio.aaproperties.AminoAcidProperties
There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
isPolymeric() - Method in interface org.biojava.nbio.structure.Group
Check if this group is a polymeric group, from the definition in Chemical Component Dictionary
isPolymeric() - Method in class org.biojava.nbio.structure.HetatomImpl
 
isPrint - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
isPrint - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
isPrintCE() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
Display the output string in CE style
isPrintFatCat() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
isPrintXML() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
isProtein() - Method in interface org.biojava.nbio.structure.Chain
Tell whether given chain is a protein chain
isProtein() - Method in class org.biojava.nbio.structure.ChainImpl
 
isProteinSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
 
isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
 
isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
 
isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
A pseudostoichiometric SubunitCluster was obtained using the SubunitClustererMethod.STRUCTURE similarity, or SubunitClustererMethod.SEQUENCE similarity with low scores.
isPublished() - Method in class org.biojava.nbio.structure.JournalArticle
 
isPureCrystalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
Tells whether this transformation is a pure crystal lattice translation, i.e. no rotational component and an integer translation vector.
isPureNonPolymer() - Method in interface org.biojava.nbio.structure.Chain
Returns true if the given chain is composed of non-polymeric (including water) groups only.
isPureNonPolymer() - Method in class org.biojava.nbio.structure.ChainImpl
 
isPureTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
Tells whether this transformation is a pure translation: either a pure crystal (lattice) translation or a fractional (within unit cell) translation: space groups Ixxx, Cxxx, Fxxx have operators with fractional translations within the unit cell.
isQuote(char) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
 
isReachable() - Method in class org.biojava.nbio.structure.scop.ScopMirror
 
isReady() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
isReady() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
 
isReady() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
 
isReady(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
Wrapper method for NCBIQBlastService.isReady(String, long), omitting unnecessary present property.
isReady(String, long) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
Checks for completion of request.
isReady(String, long) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService
Simple method to check if the specified request has been completed by the service used.
isRefined() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
isReplaced(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
 
isReplaced(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
 
isReplacer(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
 
isReplacer(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
 
isRFam() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
isRotation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
Tells whether this transformation is a rotation disregarding the translational component, i.e. either pure rotation or screw rotation, but not improper rotation.
isSameStrand(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Check if this location is on same strand as other location.
isSanger() - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_SANGER.
isScopName() - Method in class org.biojava.nbio.structure.align.client.StructureName
 
isScrew() - Method in enum org.biojava.nbio.structure.xtal.TransformType
Tells whether the transform type is a screw or glide plane
isSequentialAlignment() - Method in class org.biojava.nbio.structure.align.model.AFPChain
Get whether this alignment has the normal topology, ie the residues aligned in each block increase sequentially over the original protein.
isSequentialAlignment(AFPChain, boolean) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Checks that the alignment given by afpChain is sequential.
isShortAlign() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
isShortCompatible(String) - Static method in class org.biojava.nbio.structure.PdbId
Checks whether an Extended PDB ID is shortable, assuming it is a valid extended PDB ID.
isShow3d() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
isShowAFPRanges() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
isShowAFPRanges() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
isShowMenu() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
isSignificant() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
Conditions checked are: score above the threshold, number of repeats higher than 1 and refinement succeeded.
isSignificantResult() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
isSolexa() - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_SOLEXA.
isSPD() - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition
Is the matrix symmetric and positive definite?
isStandard() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
isStandardChemComp(ChemComp) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools
 
isStart() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
 
isStart() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
isStart(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
Returns true if the given compound was a start codon in this codon table.
isStart(AminoAcidCompound) - Method in interface org.biojava.nbio.core.sequence.transcription.Table
Returns true if the given compound could have been a start amino acid; this does not assert if the codon that actually coded for the amino acid was a start codon.
isStartAnchored() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
Indicates whether the start query and start target index compounds are anchored to each other
isStop() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
isStoringScoreMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Returns choice to cache the score matrix or to save memory by deleting score matrix after alignment.
isSuggestVisible() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
 
isSupersededBy(QuatSymmetryResults) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
Determine if this symmetry result is a subset of the other Symmetry result.
isSymRelated() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Tells whether the interface corresponds to one mediated by crystallographic symmetry, i.e. it is between symmetry-related molecules (with same chain identifier)
isTryAllCPs() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
 
isUnaryExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
Checks if the passed in expression is a unary operator expression Example: (1,2,3) or (1-60) are unary operator expressions (1-60)(61-88) is a binary operator expression, representing a cartesian product of the two parenthesised lists
isUncertain() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
isUncertain() - Method in interface org.biojava.nbio.core.sequence.location.template.Point
Returns a true if the exact point is unknown.
isUnknown() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
isUnknown() - Method in interface org.biojava.nbio.core.sequence.location.template.Point
Returns true if the current position is unknown but is beyond the position encoded for.
isURL() - Method in class org.biojava.nbio.structure.align.client.StructureName
 
isURLProperty(String) - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
 
isUseEntityIdForSeqIdentityDetermination() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Whether to use the entity id of subunits to infer that sequences are identical.
isUseGlobalMetrics() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only
isUseRMSD() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Use RMSD for evaluating structure similarity
isUseSequenceCoverage() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Use sequence coverage for evaluating sequence similarity
isUseStructureCoverage() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Use structure coverage for evaluating sequence similarity
isUseTMScore() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Use TMScore for evaluating structure similarity
isValidColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
isValidExtendedPdbId(String) - Static method in class org.biojava.nbio.structure.PdbId
Check whether id represents a valid PDB ID in the extended format.
isValidRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
isValidSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
isValidSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
 
isValidSequence(Sequence<AminoAcidCompound>) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
isValidSequence(Sequence<AminoAcidCompound>) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
isValidSequence(Sequence<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
 
isValidShortPdbId(String) - Static method in class org.biojava.nbio.structure.PdbId
Check whether id represents a valid PDB ID in the short format.
isWater() - Method in interface org.biojava.nbio.structure.Group
Determines if this group is water.
isWater() - Method in class org.biojava.nbio.structure.HetatomImpl
 
isWaterOnly() - Method in interface org.biojava.nbio.structure.Chain
Tests if a chain is consisting of water molecules only
isWaterOnly() - Method in class org.biojava.nbio.structure.ChainImpl
 
isWeighted() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
 
iterator() - Method in class org.biojava.nbio.alignment.GuideTree
Returns a post-order Iterator that traverses the tree from leaves to root.
iterator() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
iterator() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
 
iterator() - Method in class org.biojava.nbio.core.search.io.Hit
 
iterator() - Method in class org.biojava.nbio.core.search.io.Result
 
iterator() - Method in class org.biojava.nbio.core.search.io.SearchIO
 
iterator() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
 
iterator() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
iterator() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
iterator() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
Iterates through all known sub-locations for this location but does not descend
iterator() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
iterator() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
Provides basic iterable access to this class
iterator() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
Iterator implementation which attempts to move through the 2D structure attempting to skip onto the next sequence as & when it is asked to
iterator() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
Returns an instance of SequenceMixin.SequenceIterator
iterator() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
iterator() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
iterator() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
Returns an iterator which will return the windows in a sequence in sequential order.
iterator() - Method in class org.biojava.nbio.genome.parsers.gff.Location
Create a location iterator over this location with a window size of 1 and an increment of +1 (successive symbols from start to end).
iterator() - Method in class org.biojava.nbio.structure.AugmentedResidueRange
Returns a new Iterator over every ResidueNumber in this ResidueRange.
iterator() - Method in class org.biojava.nbio.structure.contact.AtomContactSet
 
iterator() - Method in class org.biojava.nbio.structure.contact.GroupContactSet
 
iterator() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
 
iterator() - Method in interface org.biojava.nbio.structure.Group
Get an Atom Iterator.
iterator() - Method in class org.biojava.nbio.structure.HetatomImpl
 
iterator() - Method in class org.biojava.nbio.structure.math.SymbolTable
Return an Iterator for the keys in the table.
iterator() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
 
iterator() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
iterator(int, int) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Create a location iterator over this location, using specified window size and increment.
iterator(AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange
Returns a new Iterator over every ResidueNumber in this ResidueRange.
iterator(AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
Returns a new Iterator over every ResidueNumber in this ResidueRange.
IUPAC_LOCATION - Static variable in class org.biojava.nbio.core.sequence.io.IUPACParser
 
IUPACParser - Class in org.biojava.nbio.core.sequence.io
Available translations 1 - UNIVERSAL 2 - VERTEBRATE_MITOCHONDRIAL 3 - YEAST_MITOCHONDRIAL 4 - MOLD_MITOCHONDRIAL 5 - INVERTEBRATE_MITOCHONDRIAL 6 - CILIATE_NUCLEAR 9 - ECHINODERM_MITOCHONDRIAL 10 - EUPLOTID_NUCLEAR 11 - BACTERIAL 12 - ALTERNATIVE_YEAST_NUCLEAR 13 - ASCIDIAN_MITOCHONDRIAL 14 - FLATWORM_MITOCHONDRIAL 15 - BLEPHARISMA_MACRONUCLEAR 16 - 2CHLOROPHYCEAN_MITOCHONDRIAL 21 - TREMATODE_MITOCHONDRIAL 23 - SCENEDESMUS_MITOCHONDRIAL Taken from NCBI with slight modification and put into the classpath resource.
IUPACParser() - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser
Default version and uses the classpath based IUPAC table
IUPACParser(InputStream) - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser
Allows you to specify a different IUPAC table.
IUPACParser.IUPACTable - Class in org.biojava.nbio.core.sequence.io
Holds the concept of a codon table from the IUPAC format
IUPACTable(String, int, String, String, String, String, String) - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
 
IUPACTable(String, Integer, String, String) - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
Constructor which uses the basic IUPAC codon table format.

J

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

K

K - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
K - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
K - org.biojava.nbio.structure.Element
 
K - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
kaplanMeier - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
 
KaplanMeierFigure - Class in org.biojava.nbio.survival.kaplanmeier.figure
 
KaplanMeierFigure() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
key - Variable in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements
 
KeyedWeakReference - Class in org.biojava.nbio.ontology.utils
Subclass of WeakReference which includes and extra field (the key) which can be used to help cleanup once this reference has been enqueued.
KeyedWeakReference(Object, Object) - Constructor for class org.biojava.nbio.ontology.utils.KeyedWeakReference
 
KeyedWeakReference(Object, Object, ReferenceQueue) - Constructor for class org.biojava.nbio.ontology.utils.KeyedWeakReference
 
keyMask - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
keyReleased(KeyEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
takes care of the cursor up/down keys. triggers copying of stored commands into the current textfield
keys() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
 
keys() - Method in interface org.biojava.nbio.ontology.utils.Annotation
Get a set of key objects.
keys() - Method in class org.biojava.nbio.structure.math.SymbolTable
Return an Iterable for the keys in the table.
keySet() - Method in class org.biojava.nbio.ontology.utils.SmallMap
 
keySet() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
keySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
 
KEYWORDS_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
kimuraDistance(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
The Kimura evolutionary distance (d) is a correction of the fractional dissimilarity (D) specially needed for large evolutionary distances.
KMERS - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
 
kmf - Variable in class org.biojava.nbio.survival.cox.CoxInfo
 
KMFigureInfo - Class in org.biojava.nbio.survival.kaplanmeier.figure
 
KMFigureInfo() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
kmStroke - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
Kr - org.biojava.nbio.structure.Element
 

L

L - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
L - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
L - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
La - org.biojava.nbio.structure.Element
 
label() - Method in enum org.biojava.nbio.protmod.ModificationCategory
 
label() - Method in enum org.biojava.nbio.protmod.ModificationOccurrenceType
 
Ladder - Class in org.biojava.nbio.structure.secstruc
A Ladder is a set of one or more consecutive bridges of identical type.
Ladder() - Constructor for class org.biojava.nbio.structure.secstruc.Ladder
 
LANTHANOID - org.biojava.nbio.structure.ElementType
 
LAST_REMEDIATION_DATE - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
Date of the latest PDB file remediation
lastIndexOf(Sequence<C>, C) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
Performs a reversed linear search of the given Sequence by wrapping it in a ReversedSequenceView and passing it into SequenceMixin.indexOf(Sequence, Compound).
LATEST_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathFactory
 
LATEST_VERSION - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
lBetaPeptideCGammaLinking - org.biojava.nbio.structure.chem.ResidueType
 
LCASE_MASK - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
lDNALinking - org.biojava.nbio.structure.chem.ResidueType
 
left - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
 
LEFT - org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint
 
legendColor - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
legendUpperPercentX - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
legendUpperPercentY - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
length() - Method in class org.biojava.nbio.genome.parsers.gff.Location
Get length of range.
length() - Method in interface org.biojava.nbio.structure.align.multiple.Block
Returns the total number of aligned positions (columns) in the Block.
length() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
length() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
Returns the total number of aligned residues (columns) in the alignment: the sum of all Block lengths.
length() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
length() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Returns the total number of aligned residues (columns) in the multiple alignment: the sum of all BlockSet lengths.
length() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
length() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
The length of the alignment is the number of Subunit equivalencies it contains.
length() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
 
length() - Method in class org.biojava.nbio.survival.data.CompactCharSequence
 
LENGTH - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature
Sort features by length.
LESS_MEMORY_SLOWER_PERFORMANCE - org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior
Try to minimize memory consumption, at the price of slower speed when accessing atoms by name
lGammaPeptideCDeltaLinking - org.biojava.nbio.structure.chem.ResidueType
 
Li - org.biojava.nbio.structure.Element
 
lighter(Color, double) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
Make a color lighter.
LightweightProfile<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
Defines a minimal data structure for reading and writing a sequence alignment.
LightweightProfile.StringFormat - Enum in org.biojava.nbio.core.sequence.template
List of output formats.
LikeSequenceFamily - org.biojava.nbio.structure.cath.CathCategory
 
line - Variable in class org.biojava.nbio.ontology.obo.OboFileParser
 
LINE_HEIGHT - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
LINEAR - org.biojava.nbio.alignment.template.GapPenalty.Type
 
LINEAR - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass
 
LINEAR_DNA - Static variable in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
 
LinearColorInterpolator - Class in org.biojava.nbio.structure.gui.util.color
 
LinearColorInterpolator() - Constructor for class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
 
LinearColorInterpolator(ColorSpace) - Constructor for class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
 
LinearColorInterpolator.InterpolationDirection - Enum in org.biojava.nbio.structure.gui.util.color
 
linenum - Variable in class org.biojava.nbio.ontology.obo.OboFileParser
 
lineSplit - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
 
lineSplit - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
 
LinkRecord(String, String, String, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
 
load() - Static method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
Loads the SIFTS mapping.
load(boolean) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
Loads the SIFTS mapping.
LOAD - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
LOAD_ALIGNMENT_XML - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
LOAD_DB_RESULTS - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
loadFastaAddGeneFeaturesFromGeneIDGFF2(File, File) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
Loads Fasta file and GFF2 feature file generated from the geneid prediction algorithm
loadFastaAddGeneFeaturesFromGeneMarkGTF(File, File) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
 
loadFastaAddGeneFeaturesFromGlimmerGFF3(File, File) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
 
loadFastaAddGeneFeaturesFromGmodGFF3(File, File, boolean) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
Lots of variations in the ontology or descriptors that can be used in GFF3 which requires writing a custom parser to handle a GFF3 generated or used by a specific application.
loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(File, File, boolean) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
 
loadFragment(long, int) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
loadFromDirectAccess() - Method in class demo.DemoMMCIFReader
An example demonstrating how to directly use the mmCif file parsing classes.
loadSimple() - Method in class demo.DemoMMCIFReader
A basic example how to load an mmCif file and get a Structure object
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.align.client.StructureName
 
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier
 
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.PassthroughIdentifier
Passthrough identifiers don't know how to load a structure
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
loadStructure(AtomCache) - Method in interface org.biojava.nbio.structure.StructureIdentifier
Loads a structure encompassing the structure identified.
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.SubstructureIdentifier
Loads the complete structure based on SubstructureIdentifier.getPdbId().
loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.URLIdentifier
Load the structure from the URL
loadStructureFromBcifByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
loadStructureFromBcifByPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
loadStructureFromCache() - Method in class demo.DemoLoadStructure
 
loadStructureFromCifByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
loadStructureFromCifByPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
loadStructureFromMmtfByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
loadStructureFromMmtfByPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Load a Structure from MMTF either from the local file system.
loadStructureFromPdbByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
loadStructureFromPdbByPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
loadStructureIO() - Method in class demo.DemoLoadStructure
 
loadXML(String) - Static method in class org.biojava.nbio.core.util.XMLHelper
Given a path to an XML file, parses into an org.w3c.dom.Document
LOCAL - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
 
LOCAL - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
 
LOCAL - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
 
LOCAL - org.biojava.nbio.core.sequence.DataSource
 
LOCAL_CONSENSUS - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
 
LOCAL_IDENTITIES - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
 
LOCAL_LINEAR_SPACE - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
 
LOCAL_LINEAR_SPACE - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
 
LOCAL_ONLY - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
Never fetch from the server; Throw errors for missing files
LOCAL_SIMILARITIES - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
 
LocalPDBDirectory - Class in org.biojava.nbio.structure.io
Superclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and CifFileReader.
LocalPDBDirectory() - Constructor for class org.biojava.nbio.structure.io.LocalPDBDirectory
 
LocalPDBDirectory(String) - Constructor for class org.biojava.nbio.structure.io.LocalPDBDirectory
Subclasses should provide default and single-string constructors.
LocalPDBDirectory.FetchBehavior - Enum in org.biojava.nbio.structure.io
Controls when the class should fetch files from the ftp server
LocalPDBDirectory.ObsoleteBehavior - Enum in org.biojava.nbio.structure.io
Behaviors for when an obsolete structure is requested.
LocalProteinDomainParser - Class in org.biojava.nbio.structure.domain
Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures.
LocalScopDatabase - Interface in org.biojava.nbio.structure.scop
Classes which implement ScopDatabase in a way which allows them to serve queries without accessing the internet should implement this interface instead.
location() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
Get location of feature.
location() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
Get the location of the feature.
location(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.
location(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.
location(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
Used as a thin wrapper to the LocationHelper.location(java.util.List, java.lang.String) method to bring the given location list together as a join (the default type)
location(List<Location>, Integer, String) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
Used for building a location from a series of sub-locations
location(List<Location>, String) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
Builds a location from a List of locations; this can be circular or linear joins.
Location - Class in org.biojava.nbio.genome.parsers.gff
A location on a sequence.
Location - Interface in org.biojava.nbio.core.sequence.location.template
Sets of integers used to represent the location of features on sequence.
Location(int, int) - Constructor for class org.biojava.nbio.genome.parsers.gff.Location
Construct new location from coordinates.
Location(Location) - Constructor for class org.biojava.nbio.genome.parsers.gff.Location
Clone other location.
LOCATION_LENGTH - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature
Sort features by start position and then longest length.
Location.Tools - Class in org.biojava.nbio.core.sequence.location.template
Helper methods for use with the Location classes.
LocationHelper - Class in org.biojava.nbio.core.sequence.location
Helper methods for use with the Location classes.
LocationHelper() - Constructor for class org.biojava.nbio.core.sequence.location.LocationHelper
 
locationParser - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
locationSplitPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser
designed to recursively split a location string in tokens.
LocIterator - Class in org.biojava.nbio.genome.parsers.gff
Move a sliding window over a Location.
LocIterator(Location, int, int) - Constructor for class org.biojava.nbio.genome.parsers.gff.LocIterator
Construct an iterator that slides a window over a Location.
LOCUS_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
log - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
 
log_log - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
 
LogColorMapper - Class in org.biojava.nbio.structure.gui.util.color
Performs a log10 transform on input before passing the values off to another colorMapper.
LogColorMapper(ContinuousColorMapper) - Constructor for class org.biojava.nbio.structure.gui.util.color.LogColorMapper
Creates a new LogColorMapper with base 10.
LogColorMapper(ContinuousColorMapper, int) - Constructor for class org.biojava.nbio.structure.gui.util.color.LogColorMapper
If logspaceMapper maps values x1 to x2, this creates a mapper for values base^x1 to base^x2
logger - Static variable in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
logger - Static variable in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
 
LOWER - org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
 
lowercaseName() - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Return the name of this FASTQ sequence format variant in lowercase-with-dashes style.
lp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
lp2 - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
lPeptideAminoTerminus - org.biojava.nbio.structure.chem.ResidueType
 
lPeptideCarboxyTerminus - org.biojava.nbio.structure.chem.ResidueType
 
lPeptideLinking - org.biojava.nbio.structure.chem.ResidueType
 
lpolysaccharide - org.biojava.nbio.structure.chem.PolymerType
polysaccharide(L)
Lr - org.biojava.nbio.structure.Element
 
lRNALinking - org.biojava.nbio.structure.chem.ResidueType
 
lSaccharide - org.biojava.nbio.structure.chem.ResidueType
 
lSaccharide14and14linking - org.biojava.nbio.structure.chem.ResidueType
 
lSaccharide14and16linking - org.biojava.nbio.structure.chem.ResidueType
 
lu() - Method in class org.biojava.nbio.structure.jama.Matrix
LU Decomposition
Lu - org.biojava.nbio.structure.Element
 
LUDecomposition - Class in org.biojava.nbio.structure.jama
LU Decomposition.
LUDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.LUDecomposition
LU Decomposition provides a data structure to access L, U and piv.

M

M - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
M - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
M - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
MACROLIDE - org.biojava.nbio.structure.EntityType
Macrolide.
main(String[]) - Static method in class demo.AFPFromFasta
 
main(String[]) - Static method in class demo.AlignmentGuiDemo
 
main(String[]) - Static method in class demo.BioJavaAADemo
 
main(String[]) - Static method in class demo.ChemCompDistribution
 
main(String[]) - Static method in class demo.CookBook
 
main(String[]) - Static method in class demo.CookbookMSA
 
main(String[]) - Static method in class demo.DemoAlignmentFromFasta
 
main(String[]) - Static method in class demo.DemoAlignProteins
 
main(String[]) - Static method in class demo.DemoAsa
 
main(String[]) - Static method in class demo.DemoAtomCache
 
main(String[]) - Static method in class demo.DemoBerkeleyScop
 
main(String[]) - Static method in class demo.DemoBioAssemblies
 
main(String[]) - Static method in class demo.DemoCATH
 
main(String[]) - Static method in class demo.DemoCE
 
main(String[]) - Static method in class demo.DemoCeSymm
 
main(String[]) - Static method in class demo.DemoChangeChemCompProvider
 
main(String[]) - Static method in class demo.DemoCommandLineStartup
 
main(String[]) - Static method in class demo.DemoContacts
 
main(String[]) - Static method in class demo.DemoCrystalInterfaces
 
main(String[]) - Static method in class demo.DemoDistanceTree
 
main(String[]) - Static method in class demo.DemoDomainsplit
 
main(String[]) - Static method in class demo.DemoFATCAT
 
main(String[]) - Static method in class demo.DemoLoadSecStruc
 
main(String[]) - Static method in class demo.DemoLoadStructure
 
main(String[]) - Static method in class demo.DemoLoadSubstMax
 
main(String[]) - Static method in class demo.DemoMMCIFReader
 
main(String[]) - Static method in class demo.DemoMmcifToPdbConverter
 
main(String[]) - Static method in class demo.DemoMmtfReader
Main function to run the demo
main(String[]) - Static method in class demo.DemoMmtfWriter
 
main(String[]) - Static method in class demo.DemoMultipleMC
 
main(String[]) - Static method in class demo.DemoQsAlign
 
main(String[]) - Static method in class demo.DemoQuatSymmetryJmol
 
main(String[]) - Static method in class demo.DemoRotationAxis
 
main(String[]) - Static method in class demo.DemoSCOP
 
main(String[]) - Static method in class demo.DemoSecStrucCalc
 
main(String[]) - Static method in class demo.DemoShowBiolAssembly
 
main(String[]) - Static method in class demo.DemoShowCATHDomain
 
main(String[]) - Static method in class demo.DemoShowLargeAssembly
 
main(String[]) - Static method in class demo.DemoSixFrameTranslation
 
main(String[]) - Static method in class demo.DemoStructureFromFasta
 
main(String[]) - Static method in class demo.DemoSW3DAligner
 
main(String[]) - Static method in class demo.DemoSymmetry
 
main(String[]) - Static method in class demo.HmmerDemo
 
main(String[]) - Static method in class demo.NCBIQBlastServiceDemo
 
main(String[]) - Static method in class demo.ParseFastaFileDemo
e.g. download ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz and pass in path to local location of file
main(String[]) - Static method in class demo.ParseGO
Parses Biosapiens OBO file and logs name/description at INFO level
main(String[]) - Static method in class demo.PredictDisorder
 
main(String[]) - Static method in class demo.ShowStructureInJmol
 
main(String[]) - Static method in class demo.TestDNANeedlemanWunsch
 
main(String[]) - Static method in class demo.UncompressFile
Reads a file, uncompresses it, and sends the result to stdout.
main(String[]) - Static method in class demo.WebStartClientDemo
 
main(String[]) - Static method in class org.biojava.nbio.aaproperties.CommandPrompt
The main method
main(String[]) - Static method in class org.biojava.nbio.genome.App
 
main(String[]) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
 
main(String[]) - Static method in class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
 
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
 
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
 
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
 
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
parses a file from the genenames website
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
 
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
 
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Reader
 
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Writer
 
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.LocIterator
Deprecated. 
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
main(String[]) - Static method in class org.biojava.nbio.genome.query.BlastXMLQuery
 
main(String[]) - Static method in class org.biojava.nbio.genome.query.OutputHitsGFF
 
main(String[]) - Static method in class org.biojava.nbio.genome.uniprot.UniprotToFasta
 
main(String[]) - Static method in class org.biojava.nbio.genome.util.SplitFasta
 
main(String[]) - Static method in class org.biojava.nbio.ontology.App
 
main(String[]) - Static method in class org.biojava.nbio.phosphosite.Dataset
 
main(String[]) - Static method in class org.biojava.nbio.ronn.ModelLoader
 
main(String[]) - Static method in class org.biojava.nbio.ronn.ORonn
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeMain
Example Parameters: -pdbFilePath /tmp -autoFetch -printCE -pdb1 1cnv -pdb2 3cna
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.fatcat.FatCat
See demo/FatCatDemo.java for an example how to run.
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.AlignmentGui
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.DotPlotPanel
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.MemoryMonitor
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.StructurePairAligner
example usage of this class
main(String[]) - Static method in class org.biojava.nbio.structure.align.webstart.JNLPProxy
 
main(String[]) - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
If no arguments, shows AlignmentGui for pairwise alignments.
main(String[]) - Static method in class org.biojava.nbio.structure.Calc
 
main(String[]) - Static method in class org.biojava.nbio.structure.ecod.EcodInstallation
 
main(String[]) - Static method in class org.biojava.nbio.structure.gui.BiojavaJmol
 
main(String[]) - Static method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
main(String[]) - Static method in class org.biojava.nbio.structure.gui.SequenceDisplay
 
main(String[]) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
 
main(String[]) - Static method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
main(String[]) - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
 
main(String[]) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
Prints out the XML representation of an AFPChain from a file containing exactly two FASTA sequences.
main(String[]) - Static method in class org.biojava.nbio.structure.io.MMTFFileReader
 
main(String[]) - Static method in class org.biojava.nbio.structure.PDBStatus
 
main(String[]) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
 
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxCC
 
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxHelper
 
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxMart
 
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxR
 
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxScore
 
main(String[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
main(String[]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO
Test client.
main(String[]) - Static method in class org.biojava.nbio.survival.cox.ResidualsCoxph
 
main(String[]) - Static method in class org.biojava.nbio.survival.cox.stats.AgScore
 
main(String[]) - Static method in class org.biojava.nbio.survival.cox.stats.ChiSq
 
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
 
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
 
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
 
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
 
makeBonds() - Method in class org.biojava.nbio.structure.io.BondMaker
Creates bond objects and corresponding references in Atom objects: peptide bonds: inferred from sequence and distances nucleotide bonds: inferred from sequence and distances intra-group (residue) bonds: read from the chemical component dictionary, via ChemCompProvider
mandatoryArgs - Static variable in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
 
mapper - Variable in class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform
 
mapSeqresRecords(Chain, Chain) - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
Map the seqRes groups to the atomRes chain.
MapToStringTransformer - Class in org.biojava.nbio.ws.alignment.qblast
Transforms Map to String.
MapToStringTransformer() - Constructor for class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
Creates MapToStringTransformer with defaults:
MapToStringTransformer(String, String, String) - Constructor for class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
Creates MapToStringTransformer with given values
mark(int) - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Marks the present position in the stream.
markMetaDataColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
markMetaDataColumns(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
marks columns as containing meta data
markMetaDataRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
markSupported() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Tells whether this stream supports the mark() operation, which it does.
markSupported() - Method in class org.biojava.nbio.core.util.UncompressInputStream
This stream does not support mark/reset on the stream.
marshal(List<String>) - Method in class org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter
 
MASK_CHAR - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
MASK_COLOR - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
mat - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
mat - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
match(char, char, boolean) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters
This returns true if a is the complement of b, false otherwise.
MATCH_SCORES - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
matches(Group) - Method in interface org.biojava.nbio.structure.AtomPositionMap.GroupMatcher
 
matchSequenceToStructure(ProteinSequence, Structure) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher
Given a sequence and the corresponding Structure, get the ResidueNumber for each residue in the sequence.
Maths - Class in org.biojava.nbio.structure.jama
 
Maths() - Constructor for class org.biojava.nbio.structure.jama.Maths
 
Matrices - Class in org.biojava.nbio.structure.geometry
Matrices contains static methods to operate and transform matrices used in 3D geometry (transformation matrices and rotation matrices).
matrix - Static variable in class org.biojava.nbio.core.alignment.SimpleProfile
 
Matrix - Class in org.biojava.nbio.structure.jama
Jama = Java Matrix class.
Matrix - Class in org.biojava.nbio.survival.cox.matrix
*********************************************************************** Compilation: javac Matrix.java Execution: java Matrix A bare-bones collection of static methods for manipulating matrices.
Matrix() - Constructor for class org.biojava.nbio.survival.cox.matrix.Matrix
 
Matrix(double[][]) - Constructor for class org.biojava.nbio.structure.jama.Matrix
Construct a matrix from a 2-D array.
Matrix(double[][], int, int) - Constructor for class org.biojava.nbio.structure.jama.Matrix
Construct a matrix quickly without checking arguments.
Matrix(double[], int) - Constructor for class org.biojava.nbio.structure.jama.Matrix
Construct a matrix from a one-dimensional packed array
Matrix(int, int) - Constructor for class org.biojava.nbio.structure.jama.Matrix
Construct an m-by-n matrix of zeros.
Matrix(int, int, double) - Constructor for class org.biojava.nbio.structure.jama.Matrix
Construct an m-by-n constant matrix.
MATRIX_NAME - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
MatrixAligner<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.alignment.template
Defines an Aligner which builds a score matrix during computation.
matrixFromEuler(double, double, double) - Static method in class org.biojava.nbio.structure.Calc
This conversion uses NASA standard aeroplane conventions as described on page: http://www.euclideanspace.com/maths/geometry/rotations/euler/index.htm Coordinate System: right hand Positive angle: right hand Order of euler angles: heading first, then attitude, then bank. matrix row column ordering: [m00 m01 m02] [m10 m11 m12] [m20 m21 m22]
matrixInOptimizer(double[][]) - Method in interface org.biojava.nbio.structure.align.ce.MatrixListener
 
MatrixListener - Interface in org.biojava.nbio.structure.align.ce
 
max - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
max() - Method in class org.biojava.nbio.structure.math.SymbolTable
Return the largest key in the table.
MAX_ATOMS - Static variable in class org.biojava.nbio.structure.io.FileParsingParameters
The maximum number of atoms we will add to a structure, this protects from memory overflows in the few really big protein structures.
MAX_CUTS - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
MAX_NUM_SEQ - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
MAX_PEPTIDE_BOND_LENGTH - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc
max distance CA atoms in peptide bond (backbone discontinuity)
MAX_RESOLVER - Static variable in class org.biojava.nbio.core.sequence.location.FuzzyPoint
Always uses the max point to resolve a location
MAX_SCALE - Static variable in class org.biojava.nbio.structure.gui.SequenceDisplay
the maximum value that the scale can get
MAX_WIDTH - Static variable in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat
 
MAXCONT - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
MAXDOM - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
maxGapSize - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
maxGapSize - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
maximumQualityScore() - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Return the maximum quality score for this FASTQ sequence format variant.
MAXLEN - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
maxNrIterationsForOptimization - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
maxOptRMSD - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
maxOptRMSD - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
MAXSIZE - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
MC_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
 
Md - org.biojava.nbio.structure.Element
 
MEAN_RESOLVER - Static variable in class org.biojava.nbio.core.sequence.location.FuzzyPoint
Combines min and max and then gets the mean of it
MeanModelComparator - Class in org.biojava.nbio.survival.cox.comparators
 
MeanModelComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.MeanModelComparator
 
MeanQuantizer - Class in org.biojava.nbio.survival.kaplanmeier.metadata
 
MeanQuantizer() - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MeanQuantizer
 
MEDLINE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
megablast - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
 
MEGABLAST - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
MemoryMonitor - Class in org.biojava.nbio.structure.align.gui
Tracks Memory allocated & used, displayed in graph form.
MemoryMonitor() - Constructor for class org.biojava.nbio.structure.align.gui.MemoryMonitor
 
MemoryMonitor.Surface - Class in org.biojava.nbio.structure.align.gui
 
MenuCreator - Class in org.biojava.nbio.structure.align.gui
Create the menus for structure alignment GUI windows (JFrames).
MenuCreator - Class in org.biojava.nbio.structure.gui.util
Create the menu for BiojavaJmol
MenuCreator() - Constructor for class org.biojava.nbio.structure.align.gui.MenuCreator
 
MenuCreator() - Constructor for class org.biojava.nbio.structure.gui.util.MenuCreator
 
MenuCreator.DotPlotListener - Class in org.biojava.nbio.structure.align.gui
Creates a frame to display a DotPlotPanel.
mergeIdentical(SubunitCluster) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
Merges the other SubunitCluster into this one if it contains exactly the same Subunit.
mergeIdenticalByEntityId(SubunitCluster) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
Merges the other SubunitCluster into this one if it contains exactly the same Subunit.
mergeSequence(SubunitCluster, SubunitClustererParameters) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).
mergeSequence(SubunitCluster, SubunitClustererParameters, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<AminoAcidCompound>) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).
mergeStructure(SubunitCluster, SubunitClustererParameters) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (according to the criteria in params).
MESH - org.biojava.nbio.structure.gui.RenderStyle
 
Messages - Class in org.biojava.nbio.core.exceptions
 
Messages() - Constructor for class org.biojava.nbio.core.exceptions.Messages
 
MetaDataInfo - Class in org.biojava.nbio.survival.kaplanmeier.metadata
 
MetaDataInfo(String) - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
 
MetaDataInfo(String, boolean, DiscreteQuantizerInterface) - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
 
METAL - org.biojava.nbio.structure.BondType
 
MetalBondConsumer - Interface in org.biojava.nbio.structure.io.cif
Consume metal bond data.
MetalBondConsumerImpl - Class in org.biojava.nbio.structure.io.cif
Created by andreas on 6/9/16.
MetalBondConsumerImpl() - Constructor for class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl
 
MetalBondConverter - Class in org.biojava.nbio.structure.io.cif
Created by andreas on 6/6/16.
MetalBondConverter() - Constructor for class org.biojava.nbio.structure.io.cif.MetalBondConverter
 
MetalBondDistance - Class in org.biojava.nbio.structure.chem
A bean that contains cutoffs for correctly detecting metal bonds.
MetalBondDistance() - Constructor for class org.biojava.nbio.structure.chem.MetalBondDistance
 
METALLOID - org.biojava.nbio.structure.ElementType
 
METHYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
 
Mg - org.biojava.nbio.structure.Element
 
mid - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
midpoint of the alignment
MIM - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
min - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
min() - Method in class org.biojava.nbio.structure.math.SymbolTable
Return the smallest key in the table.
MIN_DOMAIN_LENGTH - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
MIN_PDB_FILE_SIZE - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
Minimum size for a valid structure file (CIF or PDB), in bytes
MIN_RESOLVER - Static variable in class org.biojava.nbio.core.sequence.location.FuzzyPoint
Always uses the min point to resolve a location
MIN_VALID_CELL_SIZE - Static variable in class org.biojava.nbio.structure.xtal.CrystalCell
 
minCPLength - Variable in class org.biojava.nbio.structure.align.ce.CECPParameters
 
minCPLength - Variable in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
 
MINDIST - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc
min distance between two residues
MINIMAL_SEQUENCE_DATA - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
 
MINIMINAL_SEQUENCES - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
 
MINIMUM_HEIGHT - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
minimumLayoutSize(Container) - Method in class org.biojava.nbio.structure.gui.WrapLayout
Returns the minimum dimensions needed to layout the visible components contained in the specified target container.
minimumQualityScore() - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Return the minimum quality score for this FASTQ sequence format variant.
minus() - Method in class org.biojava.nbio.genome.parsers.gff.Location
Return location that is in same position on negative strand.
minus(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
C = A - B
minusEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
A = A - B
MismatchedBasePairParameters - Class in org.biojava.nbio.structure.basepairs
This class allows for finding inter-strand base pairs that are not necessarily canonical Watson-Crick pairs.
MismatchedBasePairParameters(Structure, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
This constructor is used to create the TertiaryBasePairParameters object.
MITOCHONDRIAL - org.biojava.nbio.core.sequence.DNASequence.DNAType
 
ML - org.biojava.nbio.phylo.TreeType
Maximum Likelihood Tree
MMCIF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
 
MMTF - org.biojava.nbio.structure.io.StructureFiletype
 
MMTF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
 
MMTF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.MMTFFileReader
 
MMTF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.MMTFFileReader
 
MmtfActions - Class in org.biojava.nbio.structure.io.mmtf
A class of functions for reading and writing Biojava structures using MMTF
MmtfActions() - Constructor for class org.biojava.nbio.structure.io.mmtf.MmtfActions
 
MMTFFileReader - Class in org.biojava.nbio.structure.io
A class to read MMTF files and cache them locally.
MMTFFileReader() - Constructor for class org.biojava.nbio.structure.io.MMTFFileReader
Constructs a new MMTFFileReader, initializing the extensions member variable.
MMTFFileReader(String) - Constructor for class org.biojava.nbio.structure.io.MMTFFileReader
Constructs a new MMTFFileReader, initializing the extensions member variable.
MmtfStructureReader - Class in org.biojava.nbio.structure.io.mmtf
A biojava specific structure inflator for MMTF.
MmtfStructureReader() - Constructor for class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
Instantiates a new bio java structure decoder.
MmtfStructureWriter - Class in org.biojava.nbio.structure.io.mmtf
Class to take Biojava structure data and covert to the DataApi for encoding.
MmtfStructureWriter(Structure, StructureAdapterInterface) - Constructor for class org.biojava.nbio.structure.io.mmtf.MmtfStructureWriter
Pass data from Biojava structure to another generic output type.
MmtfSummaryDataBean - Class in org.biojava.nbio.structure.io.mmtf
Class to store the summary data for a given structure.
MmtfSummaryDataBean() - Constructor for class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
 
MmtfUtils - Class in org.biojava.nbio.structure.io.mmtf
A utils class of functions needed for Biojava to read and write to mmtf.
MmtfUtils() - Constructor for class org.biojava.nbio.structure.io.mmtf.MmtfUtils
 
Mn - org.biojava.nbio.structure.Element
 
Mo - org.biojava.nbio.structure.Element
 
Model - Class in org.biojava.nbio.structure
An internal utility class for StructureImpl to make it easier to manage poly and nonpoly chains.
Model() - Constructor for class org.biojava.nbio.structure.Model
 
Model(int, int) - Constructor for class org.biojava.nbio.ronn.ModelLoader.Model
 
ModelLoader - Class in org.biojava.nbio.ronn
Class that loads data from the model files into ModelLoader.Model objects
ModelLoader() - Constructor for class org.biojava.nbio.ronn.ModelLoader
 
ModelLoader.Model - Class in org.biojava.nbio.ronn
Represent a RONN model
ModelLoader.Threshold - Class in org.biojava.nbio.ronn
Represents a Threshold
ModificationCategory - Enum in org.biojava.nbio.protmod
define modification categories.
ModificationCondition - Interface in org.biojava.nbio.protmod
Conditions of a protein modification, e.g. components and atoms.
ModificationConditionImpl - Class in org.biojava.nbio.protmod
 
ModificationConditionImpl(List<Component>, List<ModificationLinkage>) - Constructor for class org.biojava.nbio.protmod.ModificationConditionImpl
 
ModificationLinkage - Class in org.biojava.nbio.protmod
 
ModificationLinkage(List<Component>, int, int) - Constructor for class org.biojava.nbio.protmod.ModificationLinkage
 
ModificationLinkage(List<Component>, int, String, int, String) - Constructor for class org.biojava.nbio.protmod.ModificationLinkage
 
ModificationLinkage(List<Component>, int, List<String>, int, List<String>) - Constructor for class org.biojava.nbio.protmod.ModificationLinkage
 
ModificationLinkage(List<Component>, int, List<String>, String, int, List<String>, String) - Constructor for class org.biojava.nbio.protmod.ModificationLinkage
 
ModificationOccurrenceType - Enum in org.biojava.nbio.protmod
 
modified - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower
 
ModifiedAminoAcidCompoundSet - Class in org.biojava.nbio.aaproperties.xml
 
ModifiedAminoAcidCompoundSet(List<AminoAcidComposition>, Map<Character, Double>) - Constructor for class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
ModifiedCompound - Interface in org.biojava.nbio.protmod.structure
Root interface for all modifications in structure.
ModifiedCompoundImpl - Class in org.biojava.nbio.protmod.structure
 
ModifiedCompoundImpl() - Constructor for class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
ModifiedCompoundImpl(ProteinModification, Collection<StructureAtomLinkage>) - Constructor for class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
ModifiedCompoundImpl(ProteinModification, StructureGroup) - Constructor for class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
Create a ModifiedCompoundImpl that has only one involved component.
ModifiedCompoundXMLConverter - Class in org.biojava.nbio.protmod.io
 
ModifiedCompoundXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter
 
modulateCircularIndex(int, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base.
modulateCircularIndex(int, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base.
MolecularWeight - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
MomentsOfInertia - Class in org.biojava.nbio.structure.geometry
The moment of inertia, otherwise known as the angular mass or rotational inertia, of a rigid body determines the torque needed for a desired angular acceleration about a rotational axis.
MomentsOfInertia() - Constructor for class org.biojava.nbio.structure.geometry.MomentsOfInertia
Creates a new empty instance of MomentsOfInertia
MomentsOfInertia.SymmetryClass - Enum in org.biojava.nbio.structure.geometry
 
MONOCLINIC - org.biojava.nbio.structure.xtal.BravaisLattice
 
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
 
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
 
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
 
mouseDragged(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mouseDragged(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
 
mouseDragged(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
mouseDragged(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
 
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
 
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
 
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
 
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
 
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
 
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
 
mouseMoved(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mouseMoved(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
 
mouseMoved(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
mouseMoved(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
 
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
mouseOverPosition(AlignedPosition) - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
 
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
 
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
 
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
 
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
 
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
 
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
 
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
 
mPanel - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
MSF - org.biojava.nbio.core.alignment.template.Profile.StringFormat
 
MSF - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
 
multiIterator(AtomPositionMap, List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange
Returns a new Iterator over every ResidueNumber in the list of ResidueRanges.
multiIterator(AtomPositionMap, ResidueRange...) - Static method in class org.biojava.nbio.structure.ResidueRange
Returns a new Iterator over every ResidueNumber in the list of ResidueRanges.
MULTIPLE_ALIGN - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
MultipleAlignment - Interface in org.biojava.nbio.structure.align.multiple
A MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type.
MultipleAlignmentCalc - Class in org.biojava.nbio.structure.align.gui
A class that obtains structures via DAS and aligns them.
MultipleAlignmentCalc(MultipleAlignmentGUI, List<Structure>, List<StructureIdentifier>) - Constructor for class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
Requests an alignment of the pdbs.
MultipleAlignmentCoordManager - Class in org.biojava.nbio.structure.align.gui.aligpanel
Generalization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization.
MultipleAlignmentCoordManager(int, int) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
Constructor.
MultipleAlignmentDisplay - Class in org.biojava.nbio.structure.align.multiple.util
Utility functions to generalize the visualization of MultipleAlignments in molecular viewers.
MultipleAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay
 
MultipleAlignmentEnsemble - Interface in org.biojava.nbio.structure.align.multiple
A MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm, version, creation time, etc.).
MultipleAlignmentEnsembleImpl - Class in org.biojava.nbio.structure.align.multiple
A general implementation of a MultipleAlignmentEnsemble.
MultipleAlignmentEnsembleImpl() - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
Default Constructor.
MultipleAlignmentEnsembleImpl(List<StructureIdentifier>) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
Constructor using structure identifiers.
MultipleAlignmentEnsembleImpl(AFPChain, Atom[], Atom[], boolean) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
Constructor from an AFPChain instance.
MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
Copy constructor.
MultipleAlignmentGUI - Class in org.biojava.nbio.structure.align.gui
A JFrame that allows to trigger a multiple structure alignment, either from files in a directory or after manual upload.
MultipleAlignmentGUI() - Constructor for class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
 
MultipleAlignmentImpl - Class in org.biojava.nbio.structure.align.multiple
A general implementation of a MultipleAlignment.
MultipleAlignmentImpl() - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
Default Constructor.
MultipleAlignmentImpl(MultipleAlignmentEnsemble) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
Constructor linking to an existing ensemble.
MultipleAlignmentImpl(MultipleAlignmentImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
Copy constructor.
MultipleAlignmentJmol - Class in org.biojava.nbio.structure.align.gui.jmol
A class that provides a 3D visualization Frame in Jmol for MultipleAlignments.
MultipleAlignmentJmol() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
Default constructor creates an empty JmolPanel window, from where alignments can be made through the align menu.
MultipleAlignmentJmol(MultipleAlignment, List<Atom[]>) - Constructor for class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
The constructor displays the Mutltiple Alignment in a new JmolPanel Frame.
MultipleAlignmentJmolDisplay - Class in org.biojava.nbio.structure.align.gui
Utility Class that provides helper methods for the visualization of MultipleAlignments.
MultipleAlignmentJmolDisplay() - Constructor for class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
 
MultipleAlignmentScorer - Class in org.biojava.nbio.structure.align.multiple.util
Utility class for calculating common scores of MultipleAlignments.
MultipleAlignmentScorer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
 
MultipleAlignmentTools - Class in org.biojava.nbio.structure.align.multiple.util
Utility functions for working with MultipleAlignment.
MultipleAlignmentTools() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
 
MultipleAlignmentWriter - Class in org.biojava.nbio.structure.align.multiple.util
This class contains functions for the conversion of MultipleAlignment to various String outputs.
MultipleAlignmentWriter() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
 
MultipleAlignmentXMLConverter - Class in org.biojava.nbio.structure.align.xml
Helper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format.
MultipleAlignmentXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
 
MultipleAlignmentXMLParser - Class in org.biojava.nbio.structure.align.xml
Parse an XML file representing a MultipleAlignmentEnsemble, so that the original alignment can be recovered.
MultipleAlignmentXMLParser() - Constructor for class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
 
MultipleAligPanel - Class in org.biojava.nbio.structure.align.gui.aligpanel
A JPanel that can display the sequence alignment of a MultipleAlignment in a nice way and interact with Jmol by selecting the aligned atoms of the sequence selection.
MultipleAligPanel() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
Default constructor.
MultipleAligPanel(AFPChain, Atom[], Atom[], AbstractAlignmentJmol) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
Constructor using an afpChain and the atom arrays for pairwise alignments.
MultipleAligPanel(MultipleAlignment, AbstractAlignmentJmol) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
Constructor using a MultipleAlignment.
MultipleAligPanelMouseMotionListener - Class in org.biojava.nbio.structure.align.gui.aligpanel
Mouse Motion Listener for the MultipleAligPanel, which provides methods to obtain positions of the mouse and connect them to the sequence alignment positions using the information in MultipleAlignmentCoordManager.
MultipleAligPanelMouseMotionListener(MultipleAligPanel) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
 
multipleFrameTranslation(Sequence<NucleotideCompound>, Frame...) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
A way of translating DNA in a number of frames
MultipleMcMain - Class in org.biojava.nbio.structure.align.multiple.mc
Main class of the Java implementation of the Combinatorial Extension - Monte Carlo (CEMC) Algorithm, as it was originally described by C.Guda, E.D.Scheeff, P.E.
MultipleMcMain(StructureAlignment) - Constructor for class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
Default constructor.
MultipleMcOptimizer - Class in org.biojava.nbio.structure.align.multiple.mc
This class takes a MultipleAlignment seed previously generated and runs a Monte Carlo optimization in order to improve the overall score and highlight common structural motifs.
MultipleMcOptimizer(MultipleAlignment, MultipleMcParameters, int) - Constructor for class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer
Constructor.
MultipleMcParameters - Class in org.biojava.nbio.structure.align.multiple.mc
Contains the parameters to be sent to the MC optimization.
MultipleMcParameters() - Constructor for class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
Constructor with DEFAULT values of the parameters.
MultipleSequenceAlignment<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence
Implements a minimal data structure for reading and writing a sequence alignment.
MultipleSequenceAlignment() - Constructor for class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
 
MultipleStatusDisplay - Class in org.biojava.nbio.structure.align.gui.aligpanel
This class provides information of the selected positions in the MultipleAligPanel.
MultipleStatusDisplay(MultipleAligPanel) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
Constructor using an alignment panel as a parent, where the information will be displayed.
MultipleStructureAligner - Interface in org.biojava.nbio.structure.align
Interface for the Multiple Structure Alignment Algorithms.
MultipleSuperimposer - Interface in org.biojava.nbio.structure.align.multiple.util
Interface for Multiple Alignment superposition algorithms.
multiply(double[][], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
multiply(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
multiply(double[], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
MutableAlignedSequence<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.core.alignment.template
Defines a mutable (editable) data structure for an AlignedSequence.
MutableProfile<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.core.alignment.template
Defines a mutable (editable) data structure for a Profile.
MutableProfilePair<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.core.alignment.template
Defines a mutable (editable) data structure for a ProfilePair.
MutableSequencePair<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.core.alignment.template
Defines a mutable (editable) data structure for the results of pairwise sequence alignment.
mutate(Structure, String, String, String) - Method in class org.biojava.nbio.structure.Mutator
creates a new structure which is identical with the original one.
mutateResidue(AminoAcid, String) - Method in class org.biojava.nbio.structure.Mutator
create a new residue which is of the new type.
Mutator - Class in org.biojava.nbio.structure
A class that can change one amino acid to another.
Mutator() - Constructor for class org.biojava.nbio.structure.Mutator
 
MyAlignmentLoadListener - Class in org.biojava.nbio.structure.align.gui
Loads an alignment in an XML format and displays its content in a new Jmol panel.
MyAlignmentLoadListener() - Constructor for class org.biojava.nbio.structure.align.gui.MyAlignmentLoadListener
 
MyDistMaxListener - Class in org.biojava.nbio.structure.align.gui
Shows the interatomic Distance Matrices of all the Structures aligned in different Frames.
MyDistMaxListener(AbstractAlignmentJmol) - Constructor for class org.biojava.nbio.structure.align.gui.MyDistMaxListener
 
MyExportListener - Class in org.biojava.nbio.structure.align.gui
 
MyJmolStatusListener - Class in org.biojava.nbio.structure.align.gui.jmol
 
MyJmolStatusListener() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
MyOpenPdbFileListener - Class in org.biojava.nbio.structure.align.gui
 
MyOpenPdbFileListener() - Constructor for class org.biojava.nbio.structure.align.gui.MyOpenPdbFileListener
 
MySaveFileListener - Class in org.biojava.nbio.structure.align.gui
Save an alignment to a specified File by the user.
MySaveFileListener(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.MySaveFileListener
 
MySaveFileListener(AFPChain, MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.gui.MySaveFileListener
Constructor to avoid checking which of the two is null before instantiating this class.
MySaveFileListener(MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.gui.MySaveFileListener
 
MyTableRowSorter - Class in org.biojava.nbio.structure.align.gui
 
MyTableRowSorter(TableModel) - Constructor for class org.biojava.nbio.structure.align.gui.MyTableRowSorter
 
MyValidationEventHandler - Class in org.biojava.nbio.aaproperties.xml
 
MyValidationEventHandler() - Constructor for class org.biojava.nbio.aaproperties.xml.MyValidationEventHandler
 

N

n - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
last allowed n-term
N - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
N - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
N - org.biojava.nbio.structure.Element
 
N - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
N_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name for the backbone amide nitrogen
Na - org.biojava.nbio.structure.Element
 
name - Variable in enum org.biojava.nbio.phylo.TreeType
Description name of the Tree Type
name - Variable in class org.biojava.nbio.structure.align.client.StructureName
 
name - Variable in enum org.biojava.nbio.structure.secstruc.BridgeType
 
name - Variable in enum org.biojava.nbio.structure.secstruc.SecStrucType
 
NAME - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
Name2Count - Class in org.biojava.nbio.aaproperties.xml
 
Name2Count() - Constructor for class org.biojava.nbio.aaproperties.xml.Name2Count
 
Name2Count(String, int) - Constructor for class org.biojava.nbio.aaproperties.xml.Name2Count
 
NAMESPACE - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
NARROW_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
NARROW_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym
 
NATURAL - org.biojava.nbio.protmod.ModificationOccurrenceType
 
Nb - org.biojava.nbio.structure.Element
 
nBestTrace - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
nBestTrace - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
nBestTraces - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
nBestTraces - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
NBRF - org.biojava.nbio.core.sequence.DataSource
 
NCBI - org.biojava.nbio.core.sequence.DataSource
 
NCBI_GI - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
NCBIQBlastAlignmentProperties - Class in org.biojava.nbio.ws.alignment.qblast
This class wraps a QBlast search request parameter Map by adding several convenient parameter addition methods.
NCBIQBlastAlignmentProperties() - Constructor for class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
NCBIQBlastOutputProperties - Class in org.biojava.nbio.ws.alignment.qblast
This class wraps a QBlast output parameter Map by adding several convenient parameter addition methods.
NCBIQBlastOutputProperties() - Constructor for class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
This constructor builds the parameters for the output of the GET command sent to the QBlast service with default values:
NCBIQBlastService - Class in org.biojava.nbio.ws.alignment.qblast
Provides a simple way of submitting BLAST request to the QBlast service at NCBI.
NCBIQBlastService() - Constructor for class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
Constructs a service object that targets the public NCBI BLAST network service.
NCBIQBlastService(String) - Constructor for class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
Constructs a service object which targets a custom NCBI BLAST network service (e.g.: an instance of BLAST in the cloud).
NCBIQBlastServiceDemo - Class in demo
A simple demo showing NCBIQBlastService usage
NCBIQBlastServiceDemo() - Constructor for class demo.NCBIQBlastServiceDemo
 
ncens - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
NCS_CHAINID_SUFFIX_CHAR - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder
 
Nd - org.biojava.nbio.structure.Element
 
Ne - org.biojava.nbio.structure.Element
 
NeedlemanWunsch<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment
Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
NeedlemanWunsch() - Constructor for class org.biojava.nbio.alignment.NeedlemanWunsch
NeedlemanWunsch(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.NeedlemanWunsch
Prepares for a pairwise global sequence alignment.
needsQuotes() - Method in class org.biojava.nbio.core.sequence.features.Qualifier
 
NEGATIVE - org.biojava.nbio.core.sequence.Strand
 
NetCharge_pH_7 - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
NEUTRON_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique
 
nevents - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
newKey(String, String) - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener
found a new key in the file
newKey(String, String) - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
 
newline - Static variable in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
newline - Static variable in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
 
newline - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat
 
newline - Static variable in class org.biojava.nbio.structure.align.model.AFPChain
 
newline - Static variable in class org.biojava.nbio.structure.align.model.AfpChainWriter
 
newline - Static variable in class org.biojava.nbio.structure.PDBHeader
 
NEWLINE - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
 
newNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet
 
newNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.compound.DNACompoundSet
 
newNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.compound.RNACompoundSet
 
newNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
 
newOboFileHeader() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener
parsed a new OBO file header
newOboFileHeader() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
 
newStanza(String) - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener
parsed a new stanza in the file
newStanza(String) - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
 
newSynonym(Synonym) - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener
a new synonym has been found
newSynonym(Synonym) - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
 
next() - Method in class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator
 
next() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator
Get next window of default size, then increment position by default amount.
next() - Method in class org.biojava.nbio.structure.AtomIterator
Return next atom.
next() - Method in class org.biojava.nbio.structure.GroupIterator
get next Group.
next(int, int) - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator
Get next window of specified size, then increment position by specified amount.
nextStep(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
nextStep(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
Ni - org.biojava.nbio.structure.Element
 
NINETY_FIVE_175 - org.biojava.nbio.structure.scop.Astral.AstralSet
 
NINETY_FIVE_175A - org.biojava.nbio.structure.scop.Astral.AstralSet
 
NINETY_FIVE_175B - org.biojava.nbio.structure.scop.Astral.AstralSet
 
NINETY_FIVE_201 - org.biojava.nbio.structure.scop.Astral.AstralSet
 
NINETY_FIVE_202 - org.biojava.nbio.structure.scop.Astral.AstralSet
 
NINETY_FIVE_203 - org.biojava.nbio.structure.scop.Astral.AstralSet
 
nIter - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
nIter - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
NJ - org.biojava.nbio.phylo.TreeConstructorType
Neighbor Joining Algorithm
nnz() - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix
return the number of nonzero entries (not the most efficient implementation)
nnz() - Method in class org.biojava.nbio.structure.math.SparseVector
 
No - org.biojava.nbio.structure.Element
 
NO_ROTATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod
 
NOBLE_GAS - org.biojava.nbio.structure.ElementType
 
nodeListFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
 
NOHEADER - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
NON_AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
inversion of AA pattern
NON_NUCLEOTIDE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
Non nucleotide
none - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
 
NONE - Static variable in class org.biojava.nbio.ontology.OntoTools
 
nonOverlappingKmers(Sequence<C>, int) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
Produces kmers of the specified size e.g.
nonPolymer - org.biojava.nbio.structure.chem.ResidueType
 
NONPOLYMER - org.biojava.nbio.structure.EntityType
Non-polymeric entities: ligands, metal ions, buffer molecules, etc
nonredundant - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
NONWORD - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
Non word
norm() - Method in class org.biojava.nbio.structure.math.SparseVector
Calculates the 2-norm
norm(double) - Static method in class org.biojava.nbio.survival.cox.stats.ChiSq
 
norm1() - Method in class org.biojava.nbio.structure.jama.Matrix
One norm
norm2() - Method in class org.biojava.nbio.structure.jama.Matrix
Two norm
norm2() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
Two norm
normalizeMatrix(short) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
normalizeMatrix(short) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
 
normalizeMatrix(short) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
Rescales the matrix so that to SubstitutionMatrix.getMaxValue() - SubstitutionMatrix.getMinValue() = scale.
normF() - Method in class org.biojava.nbio.structure.jama.Matrix
Frobenius norm
normInf() - Method in class org.biojava.nbio.structure.jama.Matrix
Infinity norm
NOT_ALIGNED - Static variable in class org.biojava.nbio.structure.gui.util.AlignedPosition
they can be shown in the same column (for a compact display) , but they are not structurally equivalent
NOT_DOMAIN_ASSEMBLY - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
String for single-domain assemblies
NOT_REFINED - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
 
NOT_REPRESENTATIVE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
Indicates not a manual representative
notifyCalcFinished() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
 
notifyCalcFinished() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
 
notifyCalcFinished() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
 
notifyCallback(int, Object[]) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
notifyCallback(CBK, Object[]) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
notifyEnabled(int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
notifyEnabled(CBK) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
Np - org.biojava.nbio.structure.Element
 
nrisk - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
nrModels() - Method in interface org.biojava.nbio.structure.Structure
Return the number of models .
nrModels() - Method in class org.biojava.nbio.structure.StructureImpl
return number of models.
nrOpenWindows - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
nTrace - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
nTrace - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
nTraces - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
nTraces - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
NUC_CARBON_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
 
NUC_NITROGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
 
NUCLEOTIDE - org.biojava.nbio.structure.GroupType
The type for nucleotide groups (dna and rna)
NUCLEOTIDE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
Nucleotides a, t, g, c, u
NUCLEOTIDE_LETTERS - Static variable in class org.biojava.nbio.core.util.SequenceTools
 
NUCLEOTIDE_REPRESENTATIVE - Static variable in class org.biojava.nbio.structure.StructureTools
The atom used as representative for nucleotides, equivalent to StructureTools.CA_ATOM_NAME for proteins
NucleotideCompound - Class in org.biojava.nbio.core.sequence.compound
 
NucleotideCompound(String, CompoundSet<NucleotideCompound>, String) - Constructor for class org.biojava.nbio.core.sequence.compound.NucleotideCompound
 
NucleotideCompound(String, CompoundSet<NucleotideCompound>, String, NucleotideCompound[]) - Constructor for class org.biojava.nbio.core.sequence.compound.NucleotideCompound
 
NucleotideImpl - Class in org.biojava.nbio.structure
A nucleotide group is almost the same as a Hetatm group.
NucleotideImpl() - Constructor for class org.biojava.nbio.structure.NucleotideImpl
 
nullifyComments() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
Removes all of the comments (dir.com file) in order to free memory.
NullOutputStream - Class in org.biojava.nbio.ronn
The stream that void its input
NullOutputStream() - Constructor for class org.biojava.nbio.ronn.NullOutputStream
 
NUM_OVERVIEW - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
NUM_OVERVIEW - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
numberOfComponents() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
 
NumbersAtRiskPanel - Class in org.biojava.nbio.survival.kaplanmeier.figure
 
NumbersAtRiskPanel() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
 
numeric - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
 
numericalEntity(char) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 

O

O - org.biojava.nbio.structure.Element
 
O_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name for the backbone carbonyl oxygen
O2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the backbone O2' in RNA
O3_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the backbone O3' in RNA
O4_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the backbone O4' in RNA
O5_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the backbone O4' in RNA
OBLATE - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass
 
OboFileEventListener - Interface in org.biojava.nbio.ontology.obo
an interface for events that occur during parsing of .obo files
OboFileHandler - Class in org.biojava.nbio.ontology.obo
A file handler for .obo files
OboFileHandler(Ontology) - Constructor for class org.biojava.nbio.ontology.obo.OboFileHandler
 
OboFileParser - Class in org.biojava.nbio.ontology.obo
A class to parse the content of an OBO file.
OboFileParser() - Constructor for class org.biojava.nbio.ontology.obo.OboFileParser
 
OboFileParser.SOPair - Class in org.biojava.nbio.ontology.obo
 
OboParser - Class in org.biojava.nbio.ontology.io
Parses an OBO file.
OboParser() - Constructor for class org.biojava.nbio.ontology.io.OboParser
 
obtainAminoAcidCompositionTable(File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
 
obtainAminoAcidCompositionTable(File, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File, File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
 
Octahedron - Class in org.biojava.nbio.structure.symmetry.geometry
 
Octahedron() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Octahedron
 
of(String) - Static method in class org.biojava.nbio.protmod.Component
Get a Component that does not have to occur at terminals.
of(String, boolean, boolean) - Static method in class org.biojava.nbio.protmod.Component
Get or create a Component.
of(Set<String>) - Static method in class org.biojava.nbio.protmod.Component
Get a Component that does not have to occur at terminals.
of(Set<String>, boolean, boolean) - Static method in class org.biojava.nbio.protmod.Component
Get or create a Component.
offset(int) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
 
offset(int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
offset(int) - Method in interface org.biojava.nbio.core.sequence.location.template.Point
Returns a new point offset by the given distance
omitOverlapping(String, Location, boolean) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Create a list of all features that do not overlap the specified location on the specified sequence.
ONE - org.biojava.nbio.core.sequence.transcription.Frame
 
ONEBAR - org.biojava.nbio.structure.xtal.TransformType
 
oneDivide(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
oneDivide(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
OneOfLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation
 
OneOfLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation
 
Ontology - Interface in org.biojava.nbio.ontology
An ontology.
ONTOLOGY - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
Ontology.Impl - Class in org.biojava.nbio.ontology
A basic in-memory implementation of an ontology
OntologyException - Exception in org.biojava.nbio.ontology
Thrown to indicate an error in an Ontology object
OntologyException() - Constructor for exception org.biojava.nbio.ontology.OntologyException
 
OntologyException(String) - Constructor for exception org.biojava.nbio.ontology.OntologyException
 
OntologyException(String, Throwable) - Constructor for exception org.biojava.nbio.ontology.OntologyException
 
OntologyException(Throwable) - Constructor for exception org.biojava.nbio.ontology.OntologyException
 
OntologyFactory - Interface in org.biojava.nbio.ontology
A factory for Ontology instances.
OntologyOps - Interface in org.biojava.nbio.ontology
This is an interface for optimizing ontology operators.
OntologyTerm - Interface in org.biojava.nbio.ontology
A term in an ontology which identifies another ontology.
OntologyTerm.Impl - Class in org.biojava.nbio.ontology
Simple in-memory implementation of a remote ontology term.
OntoTools - Class in org.biojava.nbio.ontology
Tools for manipulating ontologies.
OP1_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the backbone O4' in RNA
OP2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the backbone O4' in RNA
OPEN - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
 
openFile(File) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
For a filename this code will check the extension of the file for a .gz extension.
openStringInline(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
 
openTag(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
openTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter
Open a new unqualified XML tag.
openTag(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
openTag(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter
Open a new namespace-qualified XML tag.
openURLConnection(URL) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
Open HttpURLConnection.
openURLConnection(URL, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
Open HttpURLConnection.
OperatorResolver - Class in org.biojava.nbio.structure.quaternary
A class to resolve the operators for transformations
OperatorResolver() - Constructor for class org.biojava.nbio.structure.quaternary.OperatorResolver
 
opposite() - Method in class org.biojava.nbio.genome.parsers.gff.Location
Return location that is in same position on opposite strand.
OptimalCECPMain - Class in org.biojava.nbio.structure.align.ce
A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.
OptimalCECPMain() - Constructor for class org.biojava.nbio.structure.align.ce.OptimalCECPMain
 
OptimalCECPParameters - Class in org.biojava.nbio.structure.align.ce
Contains the parameters that can be sent to CE
OptimalCECPParameters() - Constructor for class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
 
optimize() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer
Optimization method based in a Monte-Carlo approach.
optimize() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmOptimizer
Optimization method based in a Monte-Carlo approach.
optimizeAln(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
optimize the alignment by dynamic programming
optimizeResult(int[], int, int[][]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer
 
orange - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
 
order() - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup
The order of symmetry of the group is the number of connected residues.
OrderDetector - Interface in org.biojava.nbio.structure.symmetry.internal
A method to decide the order of symmetry (number of subunits) given a structure self-alignment, calculated by CE-Symm.
OrderedPair<T> - Class in org.biojava.nbio.structure.quaternary
An ordered pair represents a component of a cartesian product.
OrderLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
 
OrderLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
 
OrderLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
 
OrderLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
 
OrderLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
 
OrderLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
 
OrderLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
 
OrderLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
 
org.biojava.nbio.aaproperties - package org.biojava.nbio.aaproperties
Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
org.biojava.nbio.aaproperties.profeat - package org.biojava.nbio.aaproperties.profeat
Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
org.biojava.nbio.aaproperties.profeat.convertor - package org.biojava.nbio.aaproperties.profeat.convertor
Set of classes that enable the conversion protein sequences into various attributes.
org.biojava.nbio.aaproperties.xml - package org.biojava.nbio.aaproperties.xml
Set of classes that handles the reading and writing of xml files.
org.biojava.nbio.alignment - package org.biojava.nbio.alignment
 
org.biojava.nbio.alignment.io - package org.biojava.nbio.alignment.io
 
org.biojava.nbio.alignment.routines - package org.biojava.nbio.alignment.routines
 
org.biojava.nbio.alignment.template - package org.biojava.nbio.alignment.template
 
org.biojava.nbio.core.alignment - package org.biojava.nbio.core.alignment
 
org.biojava.nbio.core.alignment.matrices - package org.biojava.nbio.core.alignment.matrices
 
org.biojava.nbio.core.alignment.template - package org.biojava.nbio.core.alignment.template
 
org.biojava.nbio.core.exceptions - package org.biojava.nbio.core.exceptions
 
org.biojava.nbio.core.search.io - package org.biojava.nbio.core.search.io
 
org.biojava.nbio.core.search.io.blast - package org.biojava.nbio.core.search.io.blast
 
org.biojava.nbio.core.sequence - package org.biojava.nbio.core.sequence
 
org.biojava.nbio.core.sequence.compound - package org.biojava.nbio.core.sequence.compound
 
org.biojava.nbio.core.sequence.edits - package org.biojava.nbio.core.sequence.edits
 
org.biojava.nbio.core.sequence.features - package org.biojava.nbio.core.sequence.features
 
org.biojava.nbio.core.sequence.io - package org.biojava.nbio.core.sequence.io
 
org.biojava.nbio.core.sequence.io.embl - package org.biojava.nbio.core.sequence.io.embl
 
org.biojava.nbio.core.sequence.io.template - package org.biojava.nbio.core.sequence.io.template
 
org.biojava.nbio.core.sequence.io.util - package org.biojava.nbio.core.sequence.io.util
 
org.biojava.nbio.core.sequence.loader - package org.biojava.nbio.core.sequence.loader
 
org.biojava.nbio.core.sequence.location - package org.biojava.nbio.core.sequence.location
 
org.biojava.nbio.core.sequence.location.template - package org.biojava.nbio.core.sequence.location.template
 
org.biojava.nbio.core.sequence.reference - package org.biojava.nbio.core.sequence.reference
 
org.biojava.nbio.core.sequence.storage - package org.biojava.nbio.core.sequence.storage
 
org.biojava.nbio.core.sequence.template - package org.biojava.nbio.core.sequence.template
 
org.biojava.nbio.core.sequence.transcription - package org.biojava.nbio.core.sequence.transcription
 
org.biojava.nbio.core.sequence.views - package org.biojava.nbio.core.sequence.views
 
org.biojava.nbio.core.util - package org.biojava.nbio.core.util
 
org.biojava.nbio.data.sequence - package org.biojava.nbio.data.sequence
Set of classes that responsible for data handling.
org.biojava.nbio.genome - package org.biojava.nbio.genome
 
org.biojava.nbio.genome.homology - package org.biojava.nbio.genome.homology
 
org.biojava.nbio.genome.io.fastq - package org.biojava.nbio.genome.io.fastq
FASTQ and variants sequence format I/O.
org.biojava.nbio.genome.parsers.cytoband - package org.biojava.nbio.genome.parsers.cytoband
 
org.biojava.nbio.genome.parsers.geneid - package org.biojava.nbio.genome.parsers.geneid
 
org.biojava.nbio.genome.parsers.genename - package org.biojava.nbio.genome.parsers.genename
 
org.biojava.nbio.genome.parsers.gff - package org.biojava.nbio.genome.parsers.gff
 
org.biojava.nbio.genome.parsers.twobit - package org.biojava.nbio.genome.parsers.twobit
 
org.biojava.nbio.genome.query - package org.biojava.nbio.genome.query
 
org.biojava.nbio.genome.uniprot - package org.biojava.nbio.genome.uniprot
 
org.biojava.nbio.genome.util - package org.biojava.nbio.genome.util
 
org.biojava.nbio.ontology - package org.biojava.nbio.ontology
 
org.biojava.nbio.ontology.io - package org.biojava.nbio.ontology.io
org.biojava.nbio.ontology.obo - package org.biojava.nbio.ontology.obo
 
org.biojava.nbio.ontology.utils - package org.biojava.nbio.ontology.utils
 
org.biojava.nbio.phosphosite - package org.biojava.nbio.phosphosite
 
org.biojava.nbio.phylo - package org.biojava.nbio.phylo
 
org.biojava.nbio.proteincomparisontool - package org.biojava.nbio.proteincomparisontool
 
org.biojava.nbio.protmod - package org.biojava.nbio.protmod
 
org.biojava.nbio.protmod.io - package org.biojava.nbio.protmod.io
 
org.biojava.nbio.protmod.structure - package org.biojava.nbio.protmod.structure
 
org.biojava.nbio.ronn - package org.biojava.nbio.ronn
BioJava provide a module biojava-protein-disorder for prediction disordered regions from a protein sequence.
org.biojava.nbio.structure - package org.biojava.nbio.structure
org.biojava.nbio.structure.align - package org.biojava.nbio.structure.align
Classes for the alignment of structures.
org.biojava.nbio.structure.align.ce - package org.biojava.nbio.structure.align.ce
Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.client - package org.biojava.nbio.structure.align.client
This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.nbio.structure.align.fatcat - package org.biojava.nbio.structure.align.fatcat
Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
org.biojava.nbio.structure.align.fatcat.calc - package org.biojava.nbio.structure.align.fatcat.calc
 
org.biojava.nbio.structure.align.gui - package org.biojava.nbio.structure.align.gui
 
org.biojava.nbio.structure.align.gui.aligpanel - package org.biojava.nbio.structure.align.gui.aligpanel
 
org.biojava.nbio.structure.align.gui.autosuggest - package org.biojava.nbio.structure.align.gui.autosuggest
 
org.biojava.nbio.structure.align.gui.jmol - package org.biojava.nbio.structure.align.gui.jmol
Utility methods for better interaction with Jmol.
org.biojava.nbio.structure.align.helper - package org.biojava.nbio.structure.align.helper
Helper classes for structural alignment.
org.biojava.nbio.structure.align.model - package org.biojava.nbio.structure.align.model
 
org.biojava.nbio.structure.align.multiple - package org.biojava.nbio.structure.align.multiple
 
org.biojava.nbio.structure.align.multiple.mc - package org.biojava.nbio.structure.align.multiple.mc
 
org.biojava.nbio.structure.align.multiple.util - package org.biojava.nbio.structure.align.multiple.util
 
org.biojava.nbio.structure.align.pairwise - package org.biojava.nbio.structure.align.pairwise
Classes for the pairwise alignment of structures.
org.biojava.nbio.structure.align.quaternary - package org.biojava.nbio.structure.align.quaternary
 
org.biojava.nbio.structure.align.seq - package org.biojava.nbio.structure.align.seq
 
org.biojava.nbio.structure.align.util - package org.biojava.nbio.structure.align.util
 
org.biojava.nbio.structure.align.webstart - package org.biojava.nbio.structure.align.webstart
Classes related to Java Web Start
org.biojava.nbio.structure.align.xml - package org.biojava.nbio.structure.align.xml
Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
org.biojava.nbio.structure.asa - package org.biojava.nbio.structure.asa
 
org.biojava.nbio.structure.basepairs - package org.biojava.nbio.structure.basepairs
 
org.biojava.nbio.structure.cath - package org.biojava.nbio.structure.cath
 
org.biojava.nbio.structure.chem - package org.biojava.nbio.structure.chem
 
org.biojava.nbio.structure.cluster - package org.biojava.nbio.structure.cluster
 
org.biojava.nbio.structure.contact - package org.biojava.nbio.structure.contact
 
org.biojava.nbio.structure.domain - package org.biojava.nbio.structure.domain
 
org.biojava.nbio.structure.domain.pdp - package org.biojava.nbio.structure.domain.pdp
 
org.biojava.nbio.structure.ecod - package org.biojava.nbio.structure.ecod
 
org.biojava.nbio.structure.geometry - package org.biojava.nbio.structure.geometry
 
org.biojava.nbio.structure.gui - package org.biojava.nbio.structure.gui
org.biojava.nbio.structure.gui.events - package org.biojava.nbio.structure.gui.events
org.biojava.nbio.structure.gui.util - package org.biojava.nbio.structure.gui.util
org.biojava.nbio.structure.gui.util.color - package org.biojava.nbio.structure.gui.util.color
 
org.biojava.nbio.structure.io - package org.biojava.nbio.structure.io
Input and Output of Structures
org.biojava.nbio.structure.io.cif - package org.biojava.nbio.structure.io.cif
 
org.biojava.nbio.structure.io.mmtf - package org.biojava.nbio.structure.io.mmtf
 
org.biojava.nbio.structure.io.sifts - package org.biojava.nbio.structure.io.sifts
 
org.biojava.nbio.structure.io.util - package org.biojava.nbio.structure.io.util
 
org.biojava.nbio.structure.jama - package org.biojava.nbio.structure.jama
Matrix package for from JAMA
org.biojava.nbio.structure.math - package org.biojava.nbio.structure.math
 
org.biojava.nbio.structure.quaternary - package org.biojava.nbio.structure.quaternary
 
org.biojava.nbio.structure.scop - package org.biojava.nbio.structure.scop
org.biojava.nbio.structure.secstruc - package org.biojava.nbio.structure.secstruc
 
org.biojava.nbio.structure.symmetry.axis - package org.biojava.nbio.structure.symmetry.axis
 
org.biojava.nbio.structure.symmetry.core - package org.biojava.nbio.structure.symmetry.core
 
org.biojava.nbio.structure.symmetry.geometry - package org.biojava.nbio.structure.symmetry.geometry
 
org.biojava.nbio.structure.symmetry.gui - package org.biojava.nbio.structure.symmetry.gui
 
org.biojava.nbio.structure.symmetry.internal - package org.biojava.nbio.structure.symmetry.internal
 
org.biojava.nbio.structure.symmetry.jmolScript - package org.biojava.nbio.structure.symmetry.jmolScript
 
org.biojava.nbio.structure.symmetry.misc - package org.biojava.nbio.structure.symmetry.misc
 
org.biojava.nbio.structure.symmetry.utils - package org.biojava.nbio.structure.symmetry.utils
 
org.biojava.nbio.structure.xtal - package org.biojava.nbio.structure.xtal
 
org.biojava.nbio.structure.xtal.io - package org.biojava.nbio.structure.xtal.io
 
org.biojava.nbio.survival.cox - package org.biojava.nbio.survival.cox
 
org.biojava.nbio.survival.cox.comparators - package org.biojava.nbio.survival.cox.comparators
 
org.biojava.nbio.survival.cox.matrix - package org.biojava.nbio.survival.cox.matrix
 
org.biojava.nbio.survival.cox.stats - package org.biojava.nbio.survival.cox.stats
 
org.biojava.nbio.survival.data - package org.biojava.nbio.survival.data
 
org.biojava.nbio.survival.kaplanmeier.figure - package org.biojava.nbio.survival.kaplanmeier.figure
 
org.biojava.nbio.survival.kaplanmeier.metadata - package org.biojava.nbio.survival.kaplanmeier.metadata
 
org.biojava.nbio.ws.alignment - package org.biojava.nbio.ws.alignment
This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojava.nbio.ws.alignment.qblast - package org.biojava.nbio.ws.alignment.qblast
 
org.biojava.nbio.ws.hmmer - package org.biojava.nbio.ws.hmmer
 
ORGANISM_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
orientation(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions
The orientation represents the rotation of the principal axes with respect to the axes of the coordinate system (unit vectors [1,0,0], [0,1,0] and [0,0,1]).
orientationAngle(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions
The angle of the relative orientation of the two sets of points in 3D.
orientationAngle(Point3d[], Point3d[], boolean) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions
The angle of the relative orientation of the two sets of points in 3D.
orientationMetric(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions
The orientation metric is obtained by comparing the quaternion orientations of the principal axes of each set of points in 3D.
orientationMetric(Quat4d, Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions
The orientation metric is obtained by comparing two unit quaternion orientations.
oRmsdThr - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
ORonn - Class in org.biojava.nbio.ronn
Fully re-factored and enhanced version of RONN.
ORonnModel - Class in org.biojava.nbio.ronn
Fully re-factored version of RONN model.
ORonnModel(String, ModelLoader.Model, float) - Constructor for class org.biojava.nbio.ronn.ORonnModel
 
OrthologousSequenceFamily - org.biojava.nbio.structure.cath.CathCategory
 
ORTHORHOMBIC - org.biojava.nbio.structure.xtal.BravaisLattice
 
Os - org.biojava.nbio.structure.Element
 
OTHER_ADVANCED - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
OTHER_NONMETAL - org.biojava.nbio.structure.ElementType
 
otherChemComp - org.biojava.nbio.structure.chem.ResidueType
 
otherPolymer - org.biojava.nbio.structure.chem.PolymerType
other
OUTER - org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
 
outputFastaSequenceLengthGFF3(File, File) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
Output a gff3 feature file that will give the length of each scaffold/chromosome in the fasta file.
OutputHitsGFF - Class in org.biojava.nbio.genome.query
 
OutputHitsGFF() - Constructor for class org.biojava.nbio.genome.query.OutputHitsGFF
 
outputToStream(Document, OutputStream) - Static method in class org.biojava.nbio.core.util.XMLHelper
Given an org.w3c.dom.Document, writes it to the given outputStream
overlappingKmers(Sequence<C>, int) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
Used to generate overlapping k-mers such i.e.
overlaps(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Check if this location and other location overlap.
overlaps(BoundingBox, double) - Method in class org.biojava.nbio.structure.contact.BoundingBox
Returns true if this bounding box overlaps given one, i.e. they are within one cutoff distance in one of their 3 dimensions.
OXIGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
 

P

P - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
P - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
P - org.biojava.nbio.structure.Element
 
P - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
P_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name of the backbone phosphate in RNA
Pa - org.biojava.nbio.structure.Element
 
padding - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
padLeft(String, int) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
Adds padding to left of supplied string
padRight(String, int) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
Adds padding to right of supplied string
paint(Graphics) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
 
paint(Graphics) - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
 
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
 
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.gui.util.color.GradientPanel
 
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
paintComponent(Graphics) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
 
paintComponent(Graphics) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
paintComponent(Graphics) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
 
pair - Variable in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
 
pair - Variable in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
 
Pair<T> - Class in org.biojava.nbio.structure.contact
A Pair of objects.
Pair(T, T) - Constructor for class org.biojava.nbio.structure.contact.Pair
Creates a Pair from the specified elements.
pairingNames - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
pairingParameters - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
PairInProfileScorer<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.alignment.template
Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
pairParameters - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
PAIRS_ONLY - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
pairSequence - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
Pairwise - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
 
PAIRWISE_ALIGN - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
PairwiseSequenceAligner<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.alignment.template
Defines an Aligner for a pair of Sequences.
PairwiseSequenceScorer<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.alignment.template
Defines an algorithm which computes a score for a pair of sequences.
PAM250 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
 
PAM30 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
 
PAM70 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
 
pamMLdistance(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
The PAM (Point Accepted Mutations) distance is a measure of evolutionary distance in protein sequences.
parallel - org.biojava.nbio.structure.secstruc.BridgeType
 
ParameterGUI - Class in org.biojava.nbio.structure.align.gui
UI for ConfigStrucAligParams, for the AlignmentGUI.
ParameterGUI(ConfigStrucAligParams, String) - Constructor for class org.biojava.nbio.structure.align.gui.ParameterGUI
Constructor for a ParameterGUI.
params - Variable in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
 
params - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
params - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
params - Variable in class org.biojava.nbio.structure.align.ce.CeMain
 
params - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
 
params - Variable in class org.biojava.nbio.structure.align.util.AtomCache
 
parent - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
 
parentGeneSequence - Variable in class org.biojava.nbio.core.sequence.StartCodonSequence
 
parentGeneSequence - Variable in class org.biojava.nbio.core.sequence.StopCodonSequence
 
parse(BufferedReader, OntologyFactory) - Method in class org.biojava.nbio.ontology.io.TabDelimParser
Parse an ontology from a reader.
parse(InputStream) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser
parses InputStream and returns a the first contained alignment in a StockholmStructure object.
parse(InputStream) - Method in class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser
Parse an inputStream that points to an AAINDEX database file
parse(InputStream, int) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser
parses an InputStream and returns at maximum max objects contained in that file.
This method leaves the stream open for further calls of StockholmFileParser.parse(InputStream, int) (same function) or StockholmFileParser.parseNext(int).
parse(Readable, ParseListener) - Method in interface org.biojava.nbio.genome.io.fastq.FastqReader
Parse the specified readable.
parse(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser
Parses a Stockholm file and returns a StockholmStructure object with its content.
This function is meant to be used for single access to specific file and it closes the file after doing its assigned job.
parse(String) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser
Main method for parsing a location from a String instance
parse(String) - Static method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser
parses e.g.
parse(String) - Static method in class org.biojava.nbio.structure.ResidueRange
Parse the residue range from a string.
parse(String) - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
 
parse(String, int) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser
Parses a Stockholm file and returns a StockholmStructure object with its content.
This function doesn't close the file after doing its assigned job; to allow for further calls of StockholmFileParser.parseNext(int).
parse(String, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength
Parses a residue range.
parseBinaryOperatorExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
 
ParseFastaFileDemo - Class in demo
Created by andreas on 6/17/15.
ParseFastaFileDemo() - Constructor for class demo.ParseFastaFileDemo
 
parseFastqVariant(String) - Static method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Return the FASTQ sequence format variant with the specified name, if any.
parseFeatures(AbstractSequence<C>) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
parseFile(String, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser
Parse a DSSP output file and return the secondary structure annotation as a List of SecStrucState objects.
parseGO(BufferedReader, String, String, OntologyFactory) - Method in class org.biojava.nbio.ontology.io.GOParser
 
ParseGO - Class in demo
 
ParseGO() - Constructor for class demo.ParseGO
 
parseHeader(String, S) - Method in class org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser
Parse the header and set the values in the sequence
parseHeader(String, S) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
Parse the header and set the values in the sequence
parseHeader(String, S) - Method in class org.biojava.nbio.core.sequence.io.PlainFastaHeaderParser
Parse the header and set the values in the sequence
parseHeader(String, S) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface
 
parseInputStream(InputStream, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser
Parse a DSSP output file and return the secondary structure annotation as a List of SecStrucState objects.
ParseListener - Interface in org.biojava.nbio.genome.io.fastq
Low-level event based parser callback.
parseMultiple(String) - Static method in class org.biojava.nbio.structure.ResidueRange
 
parseMultiple(String, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength
 
parseMultiple(List<String>) - Static method in class org.biojava.nbio.structure.ResidueRange
 
parseMultiple(List<String>, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength
 
parseMultiXML(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
 
parseNext(int) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser
Tries to parse and return as maximum as max structures in the last used file or input stream.
Please consider calling either StockholmFileParser.parse(InputStream), StockholmFileParser.parse(InputStream, int), or StockholmFileParser.parse(String, int) before calling this function.
parseOBO(BufferedReader) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
parse an ontology file
parseOBO(BufferedReader, String, String) - Method in class org.biojava.nbio.ontology.io.OboParser
Parse a OBO file and return its content as a BioJava Ontology object
parseOperatorExpressionString(String) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver
Parses the operator expression and save the operators as a list of unary or binary operators (i.e. matrix multiplication, see below).
parsePDBFile(BufferedReader) - Method in class org.biojava.nbio.structure.io.PDBFileParser
Parse a PDB file and return a datastructure implementing PDBStructure interface.
parsePDBFile(InputStream) - Method in class org.biojava.nbio.structure.io.PDBFileParser
Parse a PDB file and return a datastructure implementing PDBStructure interface.
ParserException - Exception in org.biojava.nbio.core.exceptions
General abstraction of different parsing errors
ParserException(Exception) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException
 
ParserException(String) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException
 
ParserException(String, Exception) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException
 
parseSites(File) - Static method in class org.biojava.nbio.phosphosite.Site
 
parseSpaceGroup(String) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
Get the space group for the given international short name, using the PDB format, e.g.
parseSpaceGroupsXML(InputStream) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser
Load all SpaceGroup information from the file spacegroups.xml
parseString(String, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser
Parse a DSSP format String and return the secondary structure annotation as a List of SecStrucState objects.
parseSymopLib(InputStream) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser
A parser for the symop.lib file provided by CCP4.
parseUnaryOperatorExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
 
parseUniprotXMLString(String, CompoundSet<C>) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
The passed in xml is parsed as a DOM object so we know everything about the protein.
parseXmlFile(InputStream) - Method in class org.biojava.nbio.structure.io.sifts.SiftsXMLParser
 
parseXMLfile(String) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
Creates a list of MultipleAlignment ensembles from an XML file.
parseXref(String, int, int) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
 
PARSIMONY - org.biojava.nbio.phylo.TreeType
Parsimony Tree
PART_OF - Static variable in class org.biojava.nbio.ontology.OntoTools
 
PARTIAL_COMPLETE - org.biojava.nbio.structure.align.quaternary.QsRelation
All the Subunits of one Structure have an equivalent in the other Structure, but the other Structure contains additional non-matched Subunits.
PARTIAL_INCOMPLETE - org.biojava.nbio.structure.align.quaternary.QsRelation
Only a subset of Subunits of one Structure have an equivalent in the other Structure, and the other Structure also contains additional non-matched Subunits.
PARTIAL_ORDER - Static variable in class org.biojava.nbio.ontology.OntoTools
 
PARTITION_SINGLE - org.biojava.nbio.alignment.Alignments.RefinerType
 
PARTITION_SINGLE_ALL - org.biojava.nbio.alignment.Alignments.RefinerType
 
PARTITION_TREE - org.biojava.nbio.alignment.Alignments.RefinerType
 
PARTITION_TREE_ALL - org.biojava.nbio.alignment.Alignments.RefinerType
 
PartitionRefiner<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.alignment.template
Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning.
PassthroughIdentifier - Class in org.biojava.nbio.structure
A stub StructureIdentifier, representing the full structure in all cases.
PassthroughIdentifier(String) - Constructor for class org.biojava.nbio.structure.PassthroughIdentifier
 
PATENTS - org.biojava.nbio.core.sequence.DataSource
 
PATTERN_EXTENDED_PDBID - Static variable in class org.biojava.nbio.structure.PdbId
A regular expression that matches a PDB ID in the extended format.
PATTERN_SHORT_PDBID - Static variable in class org.biojava.nbio.structure.PdbId
A regular expression that matches a PDB ID in the short format.
PATTERN_SHORTABLE_EXTENDED_PDBID - Static variable in class org.biojava.nbio.structure.PdbId
/ * A regular expression that matches an extended PDB ID that is compatible with the short format.
Pb - org.biojava.nbio.structure.Element
 
Pd - org.biojava.nbio.structure.Element
 
PDB - org.biojava.nbio.structure.align.client.StructureName.Source
 
PDB - org.biojava.nbio.structure.io.StructureFiletype
 
PDB - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
PDB_AUTHOR_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
Secondary strucuture assigned by the PDB author
PDB_CACHE_DIR - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
 
PDB_DIR - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
 
PDB_FILE_SERVER_PROPERTY - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
 
pdb_flag - Variable in class org.biojava.nbio.structure.HetatomImpl
stores if 3d coordinates are available.
PDB_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
 
pdb_name - Variable in class org.biojava.nbio.structure.HetatomImpl
3 letter name of amino acid in pdb file.
PDB_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.PDBFileReader
 
pdb_REMARK_350_Handler(String) - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser
Parses REMARK 350 line.
PDB_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.PDBFileReader
 
PDB1 - org.biojava.nbio.core.sequence.DataSource
 
PDB2 - org.biojava.nbio.core.sequence.DataSource
 
PDBBioAssemblyParser - Class in org.biojava.nbio.structure.io
Parses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unit
PDBBioAssemblyParser() - Constructor for class org.biojava.nbio.structure.io.PDBBioAssemblyParser
 
PDBCrystallographicInfo - Class in org.biojava.nbio.structure
A class to hold crystallographic information about a PDB structure.
PDBCrystallographicInfo() - Constructor for class org.biojava.nbio.structure.PDBCrystallographicInfo
 
PDBDirPanel - Class in org.biojava.nbio.structure.gui.util
A class to define where a structure for the alignment is coming from
PDBDirPanel() - Constructor for class org.biojava.nbio.structure.gui.util.PDBDirPanel
load the PDB files from a local directory
PDBe - org.biojava.nbio.core.sequence.DataSource
 
PDBFileParser - Class in org.biojava.nbio.structure.io
This class implements the actual PDB file parsing.
PDBFileParser() - Constructor for class org.biojava.nbio.structure.io.PDBFileParser
 
PDBFileReader - Class in org.biojava.nbio.structure.io
The wrapper class for parsing a PDB file.
PDBFileReader() - Constructor for class org.biojava.nbio.structure.io.PDBFileReader
Constructs a new PDBFileReader, initializing the extensions member variable.
PDBFileReader(String) - Constructor for class org.biojava.nbio.structure.io.PDBFileReader
Constructs a new PDBFileReader, initializing the extensions member variable.
PDBHeader - Class in org.biojava.nbio.structure
A class that contains PDB Header information.
PDBHeader() - Constructor for class org.biojava.nbio.structure.PDBHeader
 
pdbId - Variable in class org.biojava.nbio.structure.align.client.StructureName
 
PdbId - Class in org.biojava.nbio.structure
A wrapper class for the PDB identifier.
PdbId(String) - Constructor for class org.biojava.nbio.structure.PdbId
 
PDBID_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier
URL parameter specifying the PDB ID
PdbPair - Class in org.biojava.nbio.structure.align.client
A pair for structure alignment.
PdbPair(String, String) - Constructor for class org.biojava.nbio.structure.align.client.PdbPair
 
PdbPair(StructureName, StructureName) - Constructor for class org.biojava.nbio.structure.align.client.PdbPair
 
PdbPairsMessage - Class in org.biojava.nbio.structure.align.xml
 
PdbPairsMessage() - Constructor for class org.biojava.nbio.structure.align.xml.PdbPairsMessage
 
PdbPairXMLConverter - Class in org.biojava.nbio.structure.align.xml
 
PdbPairXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
 
PDBParseException - Exception in org.biojava.nbio.structure.io
An exception during the parsing of a PDB file.
PDBParseException(String) - Constructor for exception org.biojava.nbio.structure.io.PDBParseException
Constructs a PDBParseException object.
PDBParseException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.io.PDBParseException
Constructs a PDBParseException object.
PDBParseException(Throwable) - Constructor for exception org.biojava.nbio.structure.io.PDBParseException
Constructs a PDBParseException object.
PDBRecord - Interface in org.biojava.nbio.structure
An interface implemented by all classes that represent PDB records.
PDBServerPanel - Class in org.biojava.nbio.structure.gui.util
A class to define where a structure for the alignment is coming from
PDBServerPanel() - Constructor for class org.biojava.nbio.structure.gui.util.PDBServerPanel
load the PDB files from a local directory
PDBStatus - Class in org.biojava.nbio.structure
Methods for getting the status of a PDB file (current, removed, unreleased) and for accessing different versions of the structure.
PDBStatus() - Constructor for class org.biojava.nbio.structure.PDBStatus
 
PDBStatus.Status - Enum in org.biojava.nbio.structure
Represents a simplified 3 state status of PDB IDs.
PDBTemporaryStorageUtils - Class in org.biojava.nbio.structure.io.util
Internal use only.
PDBTemporaryStorageUtils() - Constructor for class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils
 
PDBTemporaryStorageUtils.LinkRecord - Class in org.biojava.nbio.structure.io.util
Temporary data storage for LINK records.
PDBUploadPanel - Class in org.biojava.nbio.structure.gui.util
A JPanel to upload 2 custom PDB files.
PDBUploadPanel() - Constructor for class org.biojava.nbio.structure.gui.util.PDBUploadPanel
 
PDBUploadPanel(boolean) - Constructor for class org.biojava.nbio.structure.gui.util.PDBUploadPanel
 
PDBWEB - org.biojava.nbio.core.alignment.template.Profile.StringFormat
 
PDBWEB - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
 
PDPDistanceMatrix - Class in org.biojava.nbio.structure.domain.pdp
 
PDPDistanceMatrix() - Constructor for class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
 
PDPParameters - Class in org.biojava.nbio.structure.domain.pdp
 
PDPParameters() - Constructor for class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
peptide - org.biojava.nbio.structure.chem.PolymerType
polypeptide(L)
peptideLike - org.biojava.nbio.structure.chem.ResidueType
 
peptideNucleicAcid - org.biojava.nbio.structure.chem.PolymerType
Peptide nucleic acids
PeptideProperties - Class in org.biojava.nbio.aaproperties
This is an adaptor class which enable the ease of generating protein properties.
PeptideProperties() - Constructor for class org.biojava.nbio.aaproperties.PeptideProperties
 
PeptideProperties.SingleLetterAACode - Enum in org.biojava.nbio.aaproperties
Enumeration of 20 standard amino acid code
PeptidePropertiesImpl - Class in org.biojava.nbio.aaproperties
This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.
PeptidePropertiesImpl() - Constructor for class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
 
PERC_IDENT - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
percentageIdentity(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
BioJava implementation for percentage of identity (PID).
percentNucleotideSequence(String) - Static method in class org.biojava.nbio.core.util.SequenceTools
 
percentOverlap(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Return percent overlap of two locations.
PermutationGenerator - Class in org.biojava.nbio.structure.symmetry.utils
 
PermutationGenerator(int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
 
PermutationGroup - Class in org.biojava.nbio.structure.symmetry.core
 
PermutationGroup() - Constructor for class org.biojava.nbio.structure.symmetry.core.PermutationGroup
 
permuteCyclic(String, int) - Static method in class org.biojava.nbio.core.util.SequenceTools
Cyclically permute the characters in string forward by n elements.
permuteCyclic(T[], T[], int) - Static method in class org.biojava.nbio.core.util.SequenceTools
Cyclically permute array forward by n elements.
peto - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower
 
PFAM - org.biojava.nbio.core.sequence.DataSource
 
PFAM - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure
 
PFAMB - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
PHI_PATTERN - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
PHOSPHOROUS_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
 
PHOSPHORYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
 
PHYLOGENETIC_TREE - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
PID(String, String) - Static method in class org.biojava.nbio.phylo.Comparison
this is a gapped PID calculation
PID(String, String, int, int) - Static method in class org.biojava.nbio.phylo.Comparison
 
ping(String, int) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
Pings a HTTP URL.
plain - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
 
PlainFastaHeaderParser<S extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.io
The plain fasta header takes everything in the header as a single entity.
PlainFastaHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.PlainFastaHeaderParser
 
PLANAR - org.biojava.nbio.structure.BondType
 
PLASMID - org.biojava.nbio.core.sequence.DNASequence.DNAType
 
PLASTID - org.biojava.nbio.core.sequence.DNASequence.DNAType
 
playOrientations() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientations
playOrientations() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientations
playOrientations() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
plus() - Method in class org.biojava.nbio.genome.parsers.gff.Location
Return location that is in same position on plus strand.
plus(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
C = A + B
plus(SparseSquareMatrix) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix
return C = A + B
plus(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseVector
Calcualtes return a + b
plus(Structure, Matrix) - Static method in class org.biojava.nbio.structure.Calc
calculate structure + Matrix coodinates ...
plusEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
A = A + B
Pm - org.biojava.nbio.structure.Element
 
Po - org.biojava.nbio.structure.Element
 
Point - Interface in org.biojava.nbio.core.sequence.location.template
Holds a single point part of a location
Point.Resolver<T extends Point> - Interface in org.biojava.nbio.core.sequence.location.template
Used to resolve a position about a point
poissonDistance(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
The Poisson (correction) evolutionary distance (d) is a function of the fractional dissimilarity (D), given by:
POLARITY - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
 
POLARIZABILITY - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
 
Polyhedron - Interface in org.biojava.nbio.structure.symmetry.geometry
 
POLYMER - org.biojava.nbio.structure.EntityType
Polymeric entities: poly-peptides and nucleotide chains
polymerType - Variable in enum org.biojava.nbio.structure.chem.ResidueType
The associated PolymerType
PolymerType - Enum in org.biojava.nbio.structure.chem
Enumerates the classification of polymers.
polymerTypeFromString(String) - Static method in enum org.biojava.nbio.structure.chem.PolymerType
 
POLYNUCLEOTIDE_ONLY - Static variable in enum org.biojava.nbio.structure.chem.PolymerType
Convenience Set of polymer types classified as DNA.
polysaccharide - org.biojava.nbio.structure.chem.PolymerType
polysaccharide(D)
populate(String) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
Loops through the chars in a String and passes them onto BitSequenceReader.BitArrayWorker.setCompoundAt(char, int)
populate(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
Loops through the Compounds in a Sequence and passes them onto BitSequenceReader.BitArrayWorker.setCompoundAt(Compound, int)
populateMaps() - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
Populate the Maps for quick retrieval
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
positionSelected(AlignedPosition) - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
 
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
 
POSITIVE - org.biojava.nbio.core.sequence.Strand
 
POST_TRANSITION_METAL - org.biojava.nbio.structure.ElementType
 
postProcess(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
 
postProcessAlignment(AFPChain, Atom[], Atom[], CECalculator) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
Circular permutation specific code to be run after the standard CE alignment
postProcessAlignment(AFPChain, Atom[], Atom[], CECalculator, CECPParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
Circular permutation specific code to be run after the standard CE alignment
postProcessCompoundLists(List<List<AminoAcidCompound>>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator
Performs the trimming of stop codons and the conversion of a valid start amino acid to M
postProcessCompoundLists(List<List<NucleotideCompound>>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
 
postProcessCompoundLists(List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
POWDER_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique
 
powerSet(Set<T>) - Method in class org.biojava.nbio.structure.symmetry.utils.PowerSet
 
PowerSet<T> - Class in org.biojava.nbio.structure.symmetry.utils
In mathematics, the power set (or powerset) of any set S, written P(S), is the set of all subsets of S, including the empty set and S itself.
PowerSet() - Constructor for class org.biojava.nbio.structure.symmetry.utils.PowerSet
 
Pr - org.biojava.nbio.structure.Element
 
PredictDisorder - Class in demo
 
PredictDisorder() - Constructor for class demo.PredictDisorder
 
PREDICTED - org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
 
preferredLayoutSize(Container) - Method in class org.biojava.nbio.structure.gui.WrapLayout
Returns the preferred dimensions for this layout given the visible components in the specified target container.
prefetchStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Download a structure, but don't parse it yet or store it in memory.
prefix(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location
The part of this location before the specified position.
prefix(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
The part of this location before the other location (not inclusive).
prepare() - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
 
prepare() - Method in interface org.biojava.nbio.structure.io.cif.CifFileConsumer
Setup routine which initializes a new container.
prepare() - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
 
prepare() - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl
 
prepareGroupsForDisplay(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Rotate the Atoms/Groups so they are aligned for the 3D visualisation
prepareURLConnection(String, int) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
Prepare URLConnection with customised timeouts.
PrettyXMLWriter - Class in org.biojava.nbio.core.util
Implementation of XMLWriter which emits nicely formatted documents to a PrintWriter.
PrettyXMLWriter(PrintWriter) - Constructor for class org.biojava.nbio.core.util.PrettyXMLWriter
 
PRF - org.biojava.nbio.core.sequence.DataSource
 
PRIMARY - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
PRIME - Static variable in class org.biojava.nbio.core.util.Hashcoder
The prime number used to multiply any calculated hashcode seed by i.e. result = PRIME*result + c Where result is the result of the previous calculation (at first this will be seed) and c is the calculated int to add to result
print() - Method in class org.biojava.nbio.proteincomparisontool.HelloWorld
Prints hello world on command line
print(boolean[]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO
Print an array of booleans to standard output.
print(boolean[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO
Print the M-by-N array of booleans to standard output.
print(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO
Print an array of doubles to standard output.
print(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO
Print the M-by-N array of doubles to standard output.
print(int[]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO
Print an array of ints to standard output.
print(int[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO
Print the M-by-N array of ints to standard output.
print(int, int) - Method in class org.biojava.nbio.structure.jama.Matrix
Print the matrix to stdout.
print(Graphics, PageFormat, int) - Method in class org.biojava.nbio.structure.align.gui.JPrintPanel
 
print(PrintWriter, int, int) - Method in class org.biojava.nbio.structure.jama.Matrix
Print the matrix to the output stream.
print(PrintWriter, NumberFormat, int) - Method in class org.biojava.nbio.structure.jama.Matrix
Print the matrix to the output stream.
print(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
print(String) - Method in interface org.biojava.nbio.core.util.XMLWriter
Prints some textual content in an element.
print(String, File) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
Prints string to file.
print(NumberFormat, int) - Method in class org.biojava.nbio.structure.jama.Matrix
Print the matrix to stdout.
PRINT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
printAboutMe() - Static method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
 
printAttributeValue(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
printChars(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
printDomainsForPDB() - Method in class demo.DemoSCOP
 
printDSSP() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
Generate a DSSP file format ouput String of this SS prediction.
printDSSPline(int) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
printFASTA() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
Generate a FASTA sequence with the SS annotation letters in the aminoacid sequence order.
printFastaSequence() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
printFastaSequence(long) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
printFull() - Method in class org.biojava.nbio.structure.ResidueNumber
 
printHelixSummary() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
Generate a summary of this SS prediction with information about the three types of helix turns in different row sequences.
printHelp() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
 
printHelp() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
 
printHelp() - Method in interface org.biojava.nbio.structure.align.ce.UserArgumentProcessor
Print help about the arguments
println(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
println(String) - Method in interface org.biojava.nbio.core.util.XMLWriter
Prints some textual content, terminated with a newline character.
printRaw(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
printRaw(String) - Method in interface org.biojava.nbio.core.util.XMLWriter
Send raw data to the stream.
PRINTS - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
printScoresInLines(AFPChain, int, int, double, double, int, int, double, double, StringBuffer) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter
 
printSecStruc(Structure) - Static method in class demo.DemoLoadSecStruc
 
printSymmetryAxes(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
Generates a String that displays the symmetry axes of a structure.
printSymmetryAxes(CeSymmResult, boolean) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
Generates a String that displays the symmetry axes of a structure.
printSymmetryGroup(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
Given a symmetry alignment, it draws the symmetry group axes and the polyhedron box around the structure.
printTimeStamps - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
 
printXMLalignment(PrettyXMLWriter, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
 
printXMLblock(PrettyXMLWriter, Block) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
 
printXMLblockSet(PrettyXMLWriter, BlockSet) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
 
printXMLensemble(PrettyXMLWriter, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
 
printXMLEQRInferPositions(PrettyXMLWriter, AFPChain, int, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
 
printXMLheader(PrettyXMLWriter, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
 
printXMLHeader(PrettyXMLWriter, AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
 
printXMLmatrix4d(PrettyXMLWriter, Matrix4d) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
 
printXMLscoresCache(PrettyXMLWriter, ScoresCache) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
 
Prism - Class in org.biojava.nbio.structure.symmetry.geometry
 
Prism(int) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Prism
 
PROBABILITY - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
 
process() - Method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter
 
process() - Method in class org.biojava.nbio.core.sequence.io.FastaReader
The parsing is done in this method.
This method tries to process all the available fasta records in the File or InputStream, closes the underlying resource, and return the results in LinkedHashMap.
You don't need to call FastaReader.close() after calling this method.
process() - Method in class org.biojava.nbio.core.sequence.io.FastaWriter
 
process() - Method in class org.biojava.nbio.core.sequence.io.GenbankReader
The parsing is done in this method.
This method will return all the available Genbank records in the File or InputStream, closes the underlying resource, and return the results in LinkedHashMap.
You don't need to call GenbankReader.close() after calling this method.
process() - Method in class org.biojava.nbio.core.sequence.io.GenbankWriter
Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option
process() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
Parses the fasta file and loads it into memory.
process(double[][], double[][], double) - Static method in class org.biojava.nbio.survival.cox.WaldTest
 
process(double[][], double[], double) - Static method in class org.biojava.nbio.survival.cox.WaldTest
 
process(double[][], int, double) - Static method in class org.biojava.nbio.survival.cox.stats.Cholesky2
 
process(double[][], int, double[][], int) - Static method in class org.biojava.nbio.survival.cox.stats.Chsolve2
 
process(int) - Method in class org.biojava.nbio.core.sequence.io.FastaReader
This method tries to parse maximum max records from the open File or InputStream, and leaves the underlying resource open.
Subsequent calls to the same method continue parsing the rest of the file.
This is particularly useful when dealing with very big data files, (e.g.
process(int) - Method in class org.biojava.nbio.core.sequence.io.GenbankReader
This method tries to parse maximum max records from the open File or InputStream, and leaves the underlying resource open.
Subsequent calls to the same method continue parsing the rest of the file.
This is particularly useful when dealing with very big data files, (e.g.
process(File) - Static method in class org.biojava.nbio.core.sequence.io.embl.EmblReader
The parsing is done in this method.
This method tries to process all the Embl records in the File , closes the underlying resource, and return the results in object of EmblRecord.
process(File, double, LinkedHashMap<String, GeneSequence>, OutputStream) - Method in class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
 
process(File, File, File, double, double, boolean, boolean) - Method in class org.biojava.nbio.genome.query.OutputHitsGFF
 
process(String) - Method in interface org.biojava.nbio.core.sequence.io.util.IOUtils.ReaderProcessor
 
process(String[]) - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
 
process(String[]) - Method in interface org.biojava.nbio.structure.align.ce.UserArgumentProcessor
Process user arguments that have been provided from the command line
process(String, String) - Method in class org.biojava.nbio.genome.uniprot.UniprotToFasta
Convert a Uniprot sequence file to a fasta file.
process(String, String, String, String, String, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
 
process(String, String, String, String, String, String, ArrayList<String>, boolean, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxHelper
 
process(String, ArrayList<SurvivalInfo>, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
 
process(String, ArrayList<SurvivalInfo>, SurvFitKM.Method, SurvFitKM.Error, boolean, double, SurvFitKM.ConfType, SurvFitKM.ConfLower, Double, Double, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
 
process(ArrayList<String>, ArrayList<SurvivalInfo>, boolean, boolean, boolean, boolean) - Method in class org.biojava.nbio.survival.cox.CoxR
 
process(ArrayList<String>, ArrayList<SurvivalInfo>, int, CoxMethod, double, double, double[], int, boolean, boolean, boolean, boolean) - Method in class org.biojava.nbio.survival.cox.CoxR
 
process(LinkedHashMap<String, ArrayList<String>>, LinkedHashMap<String, GeneSequence>, OutputStream) - Method in class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
 
process(LinkedHashMap<String, ArrayList<CensorStatus>>, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
 
process(CoxInfo) - Static method in class org.biojava.nbio.survival.cox.CoxCC
 
process(CoxInfo, ResidualsCoxph.Type, boolean, ArrayList<String>) - Static method in class org.biojava.nbio.survival.cox.ResidualsCoxph
 
process(CoxMethod, ArrayList<SurvivalInfo>, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxMart
 
process(CoxMethod, ArrayList<SurvivalInfo>, CoxInfo, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxScore
 
process(CoxMethod, ArrayList<SurvivalInfo>, CoxInfo, boolean) - Static method in class org.biojava.nbio.survival.cox.stats.AgScore
 
process(WorkSheet, String) - Method in interface org.biojava.nbio.survival.kaplanmeier.metadata.DiscreteQuantizerInterface
 
process(WorkSheet, String) - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MeanQuantizer
 
process(WorkSheet, String, String, String, String, String, ArrayList<String>, boolean, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxHelper
 
process(WorkSheet, String, LinkedHashMap<String, String>, String, Double, ArrayList<MetaDataInfo>) - Static method in class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
 
processNucleotides(File, String, File) - Method in class org.biojava.nbio.genome.util.SplitFasta
 
processReader(BufferedReader, IOUtils.ReaderProcessor) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
Takes in a reader and a processor, reads every line from the given file and then invokes the processor.
processStrataInfo(String, ArrayList<SurvivalInfo>, SurvFitKM.Method, SurvFitKM.Error, boolean, double, SurvFitKM.ConfType, SurvFitKM.ConfLower, Double, Double, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
 
processUnknownCompound(C, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
Since bit encoding only supports a finite number of bases it is more than likely when processing sequence you will encounter a compound which is not covered by the encoding e.g.
ProfeatProperties - Class in org.biojava.nbio.aaproperties.profeat
This is an adaptor class which enable the ease of generating profeat properties.
ProfeatProperties() - Constructor for class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
 
ProfeatPropertiesImpl - Class in org.biojava.nbio.aaproperties.profeat
 
ProfeatPropertiesImpl() - Constructor for class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
 
profile - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
Profile<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.core.alignment.template
Defines a data structure for the results of sequence alignment.
Profile.StringFormat - Enum in org.biojava.nbio.core.alignment.template
List of output formats.
ProfilePair<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.core.alignment.template
Defines a data structure for the results of the alignment of a pair of Profiles.
ProfileProfileAligner<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.alignment.template
Defines an Aligner for a pair of Profiles.
ProfileProfileScorer<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.alignment.template
Defines an algorithm which computes a score for a pairing of alignment profiles.
ProfileView<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.core.alignment.template
Defines a data structure for a view of sequence alignment.
PROGRAM - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
PROLATE - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass
 
propertiesAllocated() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
A convenience method to see if we have allocated the properties Map.
propertiesAllocated() - Method in class org.biojava.nbio.ontology.utils.SmallAnnotation
 
PROSITE - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
PROSITE_PROFILE - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
PROTEIN_ONLY - Static variable in enum org.biojava.nbio.structure.chem.PolymerType
Convenience Set of polymer types classified as protein.
ProteinComplexSignature - Class in org.biojava.nbio.structure.symmetry.misc
 
ProteinComplexSignature(String, List<String>, BlastClustReader) - Constructor for class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
 
proteinCreator(SequenceCreatorInterface<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
 
ProteinMappingTools - Class in org.biojava.nbio.genome.util
 
ProteinMappingTools() - Constructor for class org.biojava.nbio.genome.util.ProteinMappingTools
 
ProteinModification - Interface in org.biojava.nbio.protmod
This interface defines information about a specific protein modification.
ProteinModificationIdentifier - Class in org.biojava.nbio.protmod.structure
Identify attachment modification in a 3-D structure.
ProteinModificationIdentifier() - Constructor for class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
 
ProteinModificationImpl - Class in org.biojava.nbio.protmod
This class contains information about a specific protein modification.
ProteinModificationImpl.Builder - Class in org.biojava.nbio.protmod
Uses Builder pattern to build a ProteinModification.
ProteinModificationRegistry - Class in org.biojava.nbio.protmod
This class serves as a instance registry by maintaining a pool of ProteinModification instances.
ProteinModificationRegistry() - Constructor for class org.biojava.nbio.protmod.ProteinModificationRegistry
 
ProteinModificationXmlReader - Class in org.biojava.nbio.protmod.io
 
ProteinSequence - Class in org.biojava.nbio.core.sequence
The representation of a ProteinSequence
ProteinSequence(String) - Constructor for class org.biojava.nbio.core.sequence.ProteinSequence
Create a protein from a string
ProteinSequence(String, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.ProteinSequence
Create a protein from a string with a user defined set of amino acids
ProteinSequence(ProxySequenceReader<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.ProteinSequence
A protein sequence where the storage of the sequence is somewhere else.
ProteinSequence(ProxySequenceReader<AminoAcidCompound>, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.ProteinSequence
A protein sequence where the storage of the sequence is somewhere else with user defined set of amino acids.
ProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io
Used to create a ProteinSequence from a String to allow for details about the location of the sequence etc.
ProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
 
ProxySequenceReader<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
 
PSSM - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
Pt - org.biojava.nbio.structure.Element
 
Pu - org.biojava.nbio.structure.Element
 
PUBMED_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
purgeTempFiles(String) - Static method in class org.biojava.nbio.structure.chem.ZipChemCompProvider
Cleanup chemical component (.cif.gz) files downloaded to tmpdir.
put(int, double) - Method in class org.biojava.nbio.structure.math.SparseVector
Setter method (should it be renamed to set?)
put(int, int, double) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix
set A[i][j] = value
put(Double, Color) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
Adds a gradient endpoint at the specified position.
put(Object, Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap
 
put(Object, Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
 
put(Key, Value) - Method in class org.biojava.nbio.structure.math.SymbolTable
Put key-value pair into the symbol table.
put(K, V) - Method in class org.biojava.nbio.core.util.SoftHashMap
Here we put the key, value pair into the HashMap using a SoftValue object.
putAll(Map<? extends Double, ? extends Color>) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
putCoxInfo(String, CoxInfo) - Method in class org.biojava.nbio.survival.cox.CoxVariables
 
putScore(String, Double) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
 
putScore(String, Double) - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache
Add a score to the list of scores.
Px - org.biojava.nbio.structure.scop.ScopCategory
 

Q

Q - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
Q - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
Q - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
Q - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc
constant for electrostatic energy
qr() - Method in class org.biojava.nbio.structure.jama.Matrix
QR Decomposition
QRDecomposition - Class in org.biojava.nbio.structure.jama
QR Decomposition.
QRDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.QRDecomposition
QR Decomposition, computed by Householder reflections. provides a data structure to access R and the Householder vectors and compute Q.
QsAlign - Class in org.biojava.nbio.structure.align.quaternary
Quaternary Structure Alignment (QS-Align).
QsAlign() - Constructor for class org.biojava.nbio.structure.align.quaternary.QsAlign
 
QsAlignParameters - Class in org.biojava.nbio.structure.align.quaternary
The parameter bean for the QsAlign algorithm.
QsAlignParameters() - Constructor for class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
 
QsAlignResult - Class in org.biojava.nbio.structure.align.quaternary
Result of a Quaternary Structure Alignment QsAlign.
QsAlignResult(List<Subunit>, List<Subunit>) - Constructor for class org.biojava.nbio.structure.align.quaternary.QsAlignResult
The Constructor of the result takes the same inputs as the QsAlign algorithm.
QsRelation - Enum in org.biojava.nbio.structure.align.quaternary
The Quaternary Structure Relation describes the pairwise relation between two quaternary structures.
Qualifier - Class in org.biojava.nbio.core.sequence.features
 
Qualifier(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.Qualifier
 
Qualifier(String, String, boolean) - Constructor for class org.biojava.nbio.core.sequence.features.Qualifier
 
QUALIFIER_INDENT - Static variable in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat
 
QUALIFIER_INDENT_STR - Static variable in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat
 
QUALIFIER_INDENT_TMP - Static variable in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat
 
quality(int) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Convert the specified quality score to a quality in ASCII format.
quality(String) - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
Notify this listener of a quality line.
QualityFeature<S extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.features
DNA Sequences produced by modern sequencers usually have quality informaion attached to them.
QualityFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.QualityFeature
 
qualityScore(char) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Convert the specified quality in ASCII format to a quality score.
qualityScore(double) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Convert the specified error probability to a quality score.
qualityScores(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
Return the quality scores from the specified FASTQ formatted sequence.
qualityScores(Fastq, int[]) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
Copy the quality scores from the specified FASTQ formatted sequence into the specified int array.
QuantityFeature<S extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.features
It is common to have a numerical value or values associated with a feature.
QuantityFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.QuantityFeature
 
QuatSuperpositionScorer - Class in org.biojava.nbio.structure.symmetry.core
 
QuatSuperpositionScorer() - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer
 
QuatSymmetryDetector - Class in org.biojava.nbio.structure.symmetry.core
Detects the symmetry (global, pseudo, internal and local) of protein structures.
QuatSymmetryParameters - Class in org.biojava.nbio.structure.symmetry.core
The QuatSymmetryParameters specify the options used for the detection of quaternary symmetry in structures using the QuatSymmetryDetector.
QuatSymmetryParameters() - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
QuatSymmetryResults - Class in org.biojava.nbio.structure.symmetry.core
Holds the results of quaternary symmetry perception obtained with QuatSymmetryDetector.
QuatSymmetryResults(Stoichiometry, HelixLayers, SymmetryPerceptionMethod) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
Constructor for roto-translational symmetries.
QuatSymmetryResults(Stoichiometry, RotationGroup, SymmetryPerceptionMethod) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
Constructor for rotational symmetries.
QuatSymmetryScores - Class in org.biojava.nbio.structure.symmetry.core
 
QuatSymmetryScores() - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
QuatSymmetrySolver - Interface in org.biojava.nbio.structure.symmetry.core
 
QuatSymmetrySubunits - Class in org.biojava.nbio.structure.symmetry.core
A bean to represent information about the set of Subunits being considered for symmetry detection.
QuatSymmetrySubunits(List<SubunitCluster>) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
Converts the List of SubunitCluster to a Subunit object.
QUERY - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
QUERY_BELIEVE_DEFLINE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
QUERY_FROM - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
QUERY_TO - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
QueryAnchored - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
 
QueryAnchoredNoIdentities - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
 
QueryIndexComparator() - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator
 
QUESTIONMARK - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy
Put '?'
quickSort(String[], int, int) - Static method in class org.biojava.nbio.structure.align.gui.SystemInfo
Stripped-down QuickSort.

R

R - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
R - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
R - org.biojava.nbio.structure.Element
R-group to represent generic groups that are sometimes present in MDL .sdf files.
R - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
Ra - org.biojava.nbio.structure.Element
 
RAINBOW_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
RAINBOW_INTENSITY_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
random(int, int) - Static method in class org.biojava.nbio.structure.jama.Matrix
Generate matrix with random elements
random(int, int) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
randomlyDivideSave(double, String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
Split a worksheet randomly.
randomPick(Collection<Number>) - Static method in class org.biojava.nbio.structure.align.util.CollectionTools
 
Range(int, int, float) - Constructor for class org.biojava.nbio.ronn.Jronn.Range
 
RANGE_REGEX - Static variable in class org.biojava.nbio.structure.ResidueRange
 
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
rangeSelected(AlignedPosition, AlignedPosition) - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
 
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
 
rank() - Method in class org.biojava.nbio.structure.jama.Matrix
Matrix rank
rank() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
Effective numerical matrix rank
RasmolCommandListener - Class in org.biojava.nbio.structure.align.gui.jmol
a utility class that listens to Ramsol script commands in the @link BiojavaJmol class
RasmolCommandListener(JmolPanel, JTextField) - Constructor for class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
 
RATIO_GAPS_FOR_MISMATCH - Static variable in class org.biojava.nbio.structure.io.EntityFinder
Above this ratio of mismatching residue types for same residue numbers we consider the 2 chains to have mismatching residue numbers and warn about it
RATIO_RESIDUES_TO_TOTAL - Static variable in class org.biojava.nbio.structure.StructureTools
Below this ratio of aminoacid/nucleotide residues to the sequence total, we use simple majority of aminoacid/nucleotide residues to decide the character of the chain (protein/nucleotide)
Rb - org.biojava.nbio.structure.Element
 
Re - org.biojava.nbio.structure.Element
 
read() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Reads a single character.
read() - Method in class org.biojava.nbio.core.util.UncompressInputStream
 
read() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
Method reads 1 nucleotide from sequence stream.
read(byte[], int, int) - Method in class org.biojava.nbio.core.util.UncompressInputStream
 
read(char[], int, int) - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Reads characters into a portion of an array.
read(BufferedReader) - Static method in class org.biojava.nbio.structure.jama.Matrix
Read a matrix from a stream.
read(File) - Method in interface org.biojava.nbio.genome.io.fastq.FastqReader
Read zero or more FASTQ formatted sequences from the specified file.
read(InputStream) - Method in interface org.biojava.nbio.genome.io.fastq.FastqReader
Read zero or more FASTQ formatted sequences from the specified input stream.
read(String) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
Read a file into a FeatureList.
read(String) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
Read a file into a FeatureList.
read(String) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Reader
 
read(String, List<String>) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Reader
Read a file into a FeatureList.
read(URL) - Method in interface org.biojava.nbio.genome.io.fastq.FastqReader
Read zero or more FASTQ formatted sequences from the specified url.
read(Path) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Reader
 
read(Path, List<String>) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Reader
Read a file into a FeatureList.
readableFiles - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
readCSV(File, char) - Static method in class org.biojava.nbio.survival.data.WorkSheet
 
readCSV(InputStream, char) - Static method in class org.biojava.nbio.survival.data.WorkSheet
Read a CSV/Tab delimited file where you pass in the delimiter
readCSV(String, char) - Static method in class org.biojava.nbio.survival.data.WorkSheet
Read a CSV/Tab delimitted file where you pass in the delimiter
readFasta(InputStream) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
Reads fasta sequences from inStream into the list of FastaSequence objects
readFastaDNASequence(File) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper
 
readFastaDNASequence(File, boolean) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper
Selecting lazySequenceLoad=true will parse the FASTA file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
readFastaDNASequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper
Read a fasta DNA sequence
readFastaProteinSequence(File) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper
Read a fasta file containing amino acids with setup that would handle most cases.
readFastaProteinSequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper
Read a fasta file containing amino acids with setup that would handle most cases.
readFastaRNASequence(File) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper
 
readFastaRNASequence(File, boolean) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper
Selecting lazySequenceLoad=true will parse the FASTA file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
readFastaRNASequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper
Read a fasta RNA sequence
readFromFile(Path) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions
Get a Structure object from a mmtf file.
readFromInputStream(InputStream) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions
Read a Biojava structure from an InputStream
readFromWeb(String) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions
Get a Biojava structure from the mmtf REST service.
readGenbankDNASequence(File) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
 
readGenbankDNASequence(File, boolean) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
readGenbankDNASequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
Read a Genbank DNA sequence
readGenbankProteinSequence(File) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
Read a Genbank file containing amino acids with setup that would handle most cases.
readGenbankProteinSequence(File, boolean) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
readGenbankProteinSequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
Read a Genbank file containing amino acids with setup that would handle most cases.
readGenbankRNASequence(File) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
 
readGenbankRNASequence(File, boolean) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
readGenbankRNASequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
Read a Genbank RNA sequence
readLine() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Reads a line of text.
readQuotedString(String, int, int, char, boolean, boolean) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
 
readResolve() - Method in class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder
 
readStructure(String, int) - Static method in class demo.DemoShowLargeAssembly
Load a specific biological assembly for a PDB entry
ready() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Tells whether this stream is ready to be read.
rebuildAFPChain(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
replace the PDB res nums with atom positions:
rebuildQuaternaryStructure(Structure, List<BiologicalAssemblyTransformation>, boolean, boolean) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
Builds a Structure object containing the quaternary structure built from given asymUnit and transformations, by adding symmetry partners as new models.
RectangularPrism - Class in org.biojava.nbio.structure.symmetry.geometry
 
RectangularPrism(double, double, double) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
 
RED_BLUE_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
reduce(Structure) - Method in class org.biojava.nbio.structure.align.client.StructureName
 
reduce(Structure) - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier
 
reduce(Structure) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
reduce(Structure) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
reduce(Structure) - Method in class org.biojava.nbio.structure.PassthroughIdentifier
 
reduce(Structure) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
reduce(Structure) - Method in interface org.biojava.nbio.structure.StructureIdentifier
Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
reduce(Structure) - Method in class org.biojava.nbio.structure.SubstructureIdentifier
Takes a complete structure as input and reduces it to residues present in the specified ranges
reduce(Structure) - Method in class org.biojava.nbio.structure.URLIdentifier
 
ReducedChemCompProvider - Class in org.biojava.nbio.structure.chem
Unlike the DownloadChemCompProvider, this ChemCompProvider does not download any chem comp definitions.
ReducedChemCompProvider() - Constructor for class org.biojava.nbio.structure.chem.ReducedChemCompProvider
 
reduceFragments(List<FragmentPair>, FragmentPair, Matrix) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
In helices often many similar fragments can be found.
reduceInitialFragments() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
if this is set to false, the time spent to joint the initial fragments (step 2) is increased. - particular for large structures this increases calc. time a lot.
reduceToRepresentativeAtoms(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
Remove all atoms but the representative atoms (C alphas or phosphates) from the given structure.
REF_RMSD - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
 
REFERENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
referenceFrames - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
ReferenceInterface - Interface in org.biojava.nbio.core.sequence.reference
 
ReferenceSuperimposer - Class in org.biojava.nbio.structure.align.multiple.util
Superimposes each structure in a MultipleAlignment onto a reference structure.
ReferenceSuperimposer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer
Default Constructor.
ReferenceSuperimposer(int) - Constructor for class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer
Constructor using a specified structure as reference.
refine(AFPChain, Atom[], int) - Method in class org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner
 
refine(AFPChain, Atom[], int) - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner
 
refine(AFPChain, Atom[], int) - Method in interface org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner
Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.
refine(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
Refinement procedure based on superposition and dynamic programming.
RefinerFailedException - Exception in org.biojava.nbio.structure.symmetry.internal
Refinement of the self-alignment failed.
RefinerFailedException() - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException
 
RefinerFailedException(String) - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException
 
RefinerFailedException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException
 
RefinerFailedException(Throwable) - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException
 
refineSymmetry(Map<Integer, Integer>, int) - Static method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner
Refines a CE-Symm alignment so that it is perfectly symmetric.
refineSymmetry(AFPChain, Atom[], Atom[], int) - Static method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner
Refines a CE-Symm alignment so that it is perfectly symmetric.
REFLEXIVE - Static variable in class org.biojava.nbio.ontology.OntoTools
 
refp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
refRange - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
REFTM_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
 
register(ProteinModification) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
Register a new ProteinModification.
registerProteinModificationFromXml(InputStream) - Static method in class org.biojava.nbio.protmod.io.ProteinModificationXmlReader
Read protein modifications from XML file and register them.
REGULATORY - Static variable in class org.biojava.nbio.phosphosite.Dataset
 
REL_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
RELATED_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym
 
RELATION - Static variable in class org.biojava.nbio.ontology.OntoTools
 
RELATIONSHIP - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
relativeOrientation(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions
Calculate the relative quaternion orientation of two arrays of points.
reloadFromFile() - Method in class org.biojava.nbio.structure.domain.SerializableCache
 
remainder() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator
Get portion of bounding location that has not yet been retrieved by next() method.
REMARK_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
remark800toPDB() - Method in class org.biojava.nbio.structure.Site
Provides REMARK 800 section pertaining to the site as a string.
remark800toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.Site
Appends the REMARK 800 section pertaining to the site onto the end of the StringBuffer provided.
RemoteHmmerScan - Class in org.biojava.nbio.ws.hmmer
Makes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence.
RemoteHmmerScan() - Constructor for class org.biojava.nbio.ws.hmmer.RemoteHmmerScan
 
RemotePairwiseAlignmentOutputProperties - Interface in org.biojava.nbio.ws.alignment
RemotePairwiseAlignmentOutputProperties: the simplest representation of an object capable of holding output formatting informations to be fed to a RemotePairwiseAlignmentService-implemented object.
RemotePairwiseAlignmentProperties - Interface in org.biojava.nbio.ws.alignment
RemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties.
RemotePairwiseAlignmentService - Interface in org.biojava.nbio.ws.alignment
This interface specifies minimal information needed to execute a pairwise alignment on a remote service.
RemoteTerm - Interface in org.biojava.nbio.ontology
A term in another ontology.
RemoteTerm.Impl - Class in org.biojava.nbio.ontology
Simple in-memory implementation of a remote ontology term.
remove() - Method in class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator
 
remove() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator
Unsupported.
remove() - Method in class org.biojava.nbio.structure.AtomIterator
does nothing.
remove() - Method in class org.biojava.nbio.structure.GroupIterator
does nothing .
remove(Object) - Method in class org.biojava.nbio.core.util.SoftHashMap
 
remove(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
removeAlgorithm(String) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
Removes the specified algorithm from the list of options
removeAlignedSequence(S) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
Remove a sequence
removeAlignmentOption(BlastAlignmentParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Removes given parameter
removeCDS(String) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
Remove a CDS or coding sequence from the transcript sequence
REMOVED - org.biojava.nbio.structure.PDBStatus.Status
 
removeExon(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence
Remove the exon sequence
removeFeature(FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Remove a feature from the sequence
removeGaps(ProteinSequence) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher
Removes all gaps ('-') from a protein sequence
removeGaps(T[][]) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher
Creates a new list consisting of all columns of gapped where no row contained a null value.
removeGeneSequence(String) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
 
removeInterfacesBelowArea() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Removes from this interface list all interfaces with areas below the default cutoff area.
removeInterfacesBelowArea(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Removes from this interface list all interfaces with areas below the given cutoff area.
removeIntron(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence
Remove the intron by accession
removeModels(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
Remove all models from a Structure and keep only the first
removeNote(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
removeOutputOption(BlastOutputParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
Removes given parameter
removeProperty(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
 
removeProperty(Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation
Delete a property.
removeRotation(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
removeSynonym(Object) - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
 
removeSynonym(Object) - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
 
removeSynonym(Object) - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
 
removeSynonym(Object) - Method in class org.biojava.nbio.ontology.Term.Impl
 
removeSynonym(Object) - Method in interface org.biojava.nbio.ontology.Term
Remove a synonym for this term.
removeSynonym(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl
 
removeTranscript(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence
Remove the transcript sequence from the gene
RenderStyle - Enum in org.biojava.nbio.structure.gui
 
repaint() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
repaint() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
 
repeatDescription(String) - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
Notify this parse listener of a repeat description line.
REPEATS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
replaceColumnValues(String, HashMap<String, String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
Change values in a column where 0 = something and 1 = something different
REPLACED_BY - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
replaceOptAln(int[][][], AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
It replaces an optimal alignment of an AFPChain and calculates all the new alignment scores and variables.
replaceOptAln(AFPChain, Atom[], Atom[], int, int[], int[][][]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
 
replaceOptAln(AFPChain, Atom[], Atom[], Map<Integer, Integer>) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Takes an AFPChain and replaces the optimal alignment based on an alignment map
requestUserConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
 
RESCORE_IDENTITIES - org.biojava.nbio.alignment.Alignments.RefinerType
 
RESCORE_SIMILARITIES - org.biojava.nbio.alignment.Alignments.RefinerType
 
RescoreRefiner<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.alignment.template
Defines an algorithm which computes a new alignment Profile by rescoring all pairs in an alignment and realigning.
reset() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Resets output fields; should be overridden to set max and min
reset() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
 
reset() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
 
reset() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Resets the stream to the most recent mark.
reset() - Method in class org.biojava.nbio.core.util.CRC64Checksum
 
reset() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
Method resets current position to the begining of sequence stream.
reset() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
 
reset() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
reset() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
Set the parameters to the default.
reset() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
 
reset() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
reset() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
reset() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
 
reset() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
reset() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
 
resetAlphas() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
Reassign alpha-strings for each cluster according to the current strategy.
resetDisplay() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
Return to the initial state of the alignment visualization.
resetDisplay() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
 
resetDisplay() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
 
resetModels() - Method in interface org.biojava.nbio.structure.Structure
Resets all models of this Structure
resetModels() - Method in class org.biojava.nbio.structure.StructureImpl
 
ResidualsCoxph - Class in org.biojava.nbio.survival.cox
 
ResidualsCoxph() - Constructor for class org.biojava.nbio.survival.cox.ResidualsCoxph
 
ResidualsCoxph.Type - Enum in org.biojava.nbio.survival.cox
 
ResidueGroup - Class in org.biojava.nbio.structure.symmetry.internal
A ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis.
ResidueGroup(Set<Integer>) - Constructor for class org.biojava.nbio.structure.symmetry.internal.ResidueGroup
Create a ResidueGroup object from a maximally connected component.
residueNumber - Variable in class org.biojava.nbio.structure.HetatomImpl
 
ResidueNumber - Class in org.biojava.nbio.structure
Everything that is needed to uniquely describe a residue position
ResidueNumber() - Constructor for class org.biojava.nbio.structure.ResidueNumber
 
ResidueNumber(String, Integer, Character) - Constructor for class org.biojava.nbio.structure.ResidueNumber
 
ResidueNumber(ResidueNumber) - Constructor for class org.biojava.nbio.structure.ResidueNumber
 
ResidueRange - Class in org.biojava.nbio.structure
A chainName, a start residue, and an end residue.
ResidueRange(String, String, String) - Constructor for class org.biojava.nbio.structure.ResidueRange
 
ResidueRange(String, ResidueNumber, ResidueNumber) - Constructor for class org.biojava.nbio.structure.ResidueRange
 
ResidueRangeAndLength - Class in org.biojava.nbio.structure
A chain, a start residue, and an end residue.
ResidueRangeAndLength(String, String, String, int) - Constructor for class org.biojava.nbio.structure.ResidueRangeAndLength
 
ResidueRangeAndLength(String, ResidueNumber, ResidueNumber, int) - Constructor for class org.biojava.nbio.structure.ResidueRangeAndLength
 
RESIDUES_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier
URL parameter specifying residue ranges to include, e.g.
ResidueType - Enum in org.biojava.nbio.structure.chem
Enumerates the possible classifications of residues.
resizeArray(Object, int) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
Reallocates an array with a new size, and copies the contents of the old array to the new array.
resizeArray(Object, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Reallocates an array with a new size, and copies the contents of the old array to the new array.
resizeInnerPanel(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
resolve(T) - Method in interface org.biojava.nbio.core.sequence.location.template.Point.Resolver
 
resolveInt(int) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
ResourceManager - Class in org.biojava.nbio.structure.align.util
A class that manages the Strings that are defined in the spice.properties file.
ResourceManager() - Constructor for class org.biojava.nbio.structure.align.util.ResourceManager
 
Result - Class in org.biojava.nbio.core.search.io
This class models a search result.
Result(String, String, String, String, HashMap<String, String>, int, String, String, int, List<Hit>, Sequence) - Constructor for class org.biojava.nbio.core.search.io.Result
 
ResultFactory - Interface in org.biojava.nbio.core.search.io
Designed by Paolo Pavan.
reverse(int) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
 
reverse(int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
reverse(int) - Method in interface org.biojava.nbio.core.sequence.location.template.Point
Returns the equivalent position on the reverse strand
reverse(int, int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
REVERSED_ONE - org.biojava.nbio.core.sequence.transcription.Frame
 
REVERSED_THREE - org.biojava.nbio.core.sequence.transcription.Frame
 
REVERSED_TWO - org.biojava.nbio.core.sequence.transcription.Frame
 
ReversedSequenceView<C extends Compound> - Class in org.biojava.nbio.core.sequence.views
For a given sequence this class will return the base at the reversed position i.e. in a sequence of size 10, if you request base 2 you will get back the base at position 9.
ReversedSequenceView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.views.ReversedSequenceView
 
reverseSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
Reverses and (if possible) complements the Sequence so as to represent the reverse strand (if one exists).
RFAM - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure
 
RG - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
RG1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
Rh - org.biojava.nbio.structure.Element
 
RIBBON - org.biojava.nbio.structure.gui.RenderStyle
 
RID - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
right - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
 
RIGHT - org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint
 
RING_MAP - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
RiskInfo - Class in org.biojava.nbio.survival.cox
 
RiskInfo() - Constructor for class org.biojava.nbio.survival.cox.RiskInfo
 
rms_dk_diag(double[], double[], int, int, int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils
Given distance matrix diagonals dk1, dk2, get the rmsd of a fpair.
rmsd(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
Calculate the RMSD of two point arrays, already superposed.
rmsd(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.Calc
Calculate the RMSD of two Atom arrays, already superposed.
RMSD - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
 
rmsdMin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
 
rmsdThr - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
rmsdThrJoin - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
Rn - org.biojava.nbio.structure.Element
 
rna - org.biojava.nbio.structure.chem.PolymerType
polyribonucleotide
RNA_ONLY - Static variable in enum org.biojava.nbio.structure.chem.PolymerType
Convenience Set of polymer types classified as RNA.
rna3PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType
 
rna5PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType
 
rnaAminoAcidTranslator(RNAToAminoAcidTranslator) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
 
rnaCompounds(CompoundSet<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
 
RNACompoundSet - Class in org.biojava.nbio.core.sequence.compound
 
RNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.RNACompoundSet
 
rnaCreator(SequenceCreatorInterface<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
 
rnaLinking - org.biojava.nbio.structure.chem.ResidueType
 
RNASequence - Class in org.biojava.nbio.core.sequence
RNASequence where RNACompoundSet are the allowed values
RNASequence(String) - Constructor for class org.biojava.nbio.core.sequence.RNASequence
Create a RNA sequence from a String
RNASequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.RNASequence
Create a RNA sequence from a string with a user defined RNA compound set
RNASequence(ProxySequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.RNASequence
Create a RNA aequence from a proxy reader
RNASequence(ProxySequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.RNASequence
Create a RNA sequence from a proxy reader and user-defined RNA compound set
RNASequenceCreator - Class in org.biojava.nbio.core.sequence.io
Used to create a RNA sequence
RNASequenceCreator(CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.RNASequenceCreator
 
RnaSequenceView - Class in org.biojava.nbio.core.sequence.views
Attempts to do on the fly translation of RNA by not requesting the compounds until asked.
RnaSequenceView(Sequence<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.views.RnaSequenceView
 
RnaSequenceView(Sequence<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.views.RnaSequenceView
 
RNAToAminoAcidTranslator - Class in org.biojava.nbio.core.sequence.transcription
Takes a Sequence of NucleotideCompound which should represent an RNA sequence (RNASequence is good for this) and returns a list of Sequence which hold AminoAcidCompound.
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound>, CompoundSet<NucleotideCompound>, CompoundSet<Table.Codon>, CompoundSet<AminoAcidCompound>, Table, boolean, boolean, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator
 
RonnConstraint - Class in org.biojava.nbio.ronn
A collection of various constrain values used by RONN
RonnConstraint() - Constructor for class org.biojava.nbio.ronn.RonnConstraint
 
RonnConstraint.Threshold - Enum in org.biojava.nbio.ronn
 
rotate(Atom[], double) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
 
rotate(Atom[], Matrix) - Static method in class org.biojava.nbio.structure.Calc
 
rotate(Atom, double[][]) - Static method in class org.biojava.nbio.structure.Calc
Rotate a single Atom aroud a rotation matrix.
rotate(Atom, Matrix) - Static method in class org.biojava.nbio.structure.Calc
Rotate an Atom around a Matrix object.
rotate(Group, double[][]) - Static method in class org.biojava.nbio.structure.Calc
Rotate a Group.
rotate(Group, Matrix) - Static method in class org.biojava.nbio.structure.Calc
Rotate a group object.
rotate(Structure, double[][]) - Static method in class org.biojava.nbio.structure.Calc
Rotate a structure.
rotate(Structure, Matrix) - Static method in class org.biojava.nbio.structure.Calc
Rotate a structure object.
rotateHue(Color, float) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
Rotate a color through HSB space
rotateJmol(Matrix) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
 
Rotation - Class in org.biojava.nbio.structure.symmetry.core
 
Rotation() - Constructor for class org.biojava.nbio.structure.symmetry.core.Rotation
 
ROTATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod
 
RotationAxis - Class in org.biojava.nbio.structure.align.util
Calculates the rotation axis for an alignment
RotationAxis(Matrix4d) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis
Create a rotation axis from a Matrix4d containing a rotational component and a translational component.
RotationAxis(AFPChain) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis
Calculate the rotation axis for the first block of an AFPChain
RotationAxis(Atom, Atom, double) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis
Create a rotation axis from a vector, a point, and an angle.
RotationAxis(Matrix, Atom) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis
Determine the location of the rotation axis based on a rotation matrix and a translation vector
RotationAxisAligner - Class in org.biojava.nbio.structure.symmetry.axis
 
RotationAxisAligner(QuatSymmetryResults) - Constructor for class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
 
RotationGroup - Class in org.biojava.nbio.structure.symmetry.core
 
RotationGroup() - Constructor for class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
RotationSolver - Class in org.biojava.nbio.structure.symmetry.core
 
RotationSolver(QuatSymmetrySubunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.RotationSolver
 
rotMatrixToString(Matrix4d) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
 
ROTO_TRANSLATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod
 
roundToDecimals(double, int) - Static method in class org.biojava.nbio.aaproperties.Utils
Returns a value with the desired number of decimal places.
row - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
Ru - org.biojava.nbio.structure.Element
 
run() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc
 
run() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
 
run() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
 
run() - Method in class org.biojava.nbio.structure.chem.AllChemCompProvider
Do the actual loading of the dictionary in a thread.
run() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc
 
run() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
 
run(String[]) - Static method in class org.biojava.nbio.aaproperties.CommandPrompt
 
runOptimization(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer
run the optimization
runPairwiseScorers(List<PairwiseSequenceScorer<S, C>>) - Static method in class org.biojava.nbio.alignment.Alignments
Factory method to run a list of scorers concurrently.

S

S - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
S - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
S - org.biojava.nbio.structure.Element
 
S - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
s_min - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
 
saccharide - org.biojava.nbio.structure.chem.ResidueType
 
SangerFastqReader - Class in org.biojava.nbio.genome.io.fastq
Reader for FastqVariant.FASTQ_SANGER formatted sequences.
SangerFastqReader() - Constructor for class org.biojava.nbio.genome.io.fastq.SangerFastqReader
 
SangerFastqWriter - Class in org.biojava.nbio.genome.io.fastq
Writer for FastqVariant.FASTQ_SANGER formatted sequences.
SangerFastqWriter() - Constructor for class org.biojava.nbio.genome.io.fastq.SangerFastqWriter
 
save(OutputStream, char, boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
SAVE_ALIGNMENT_XML - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
saveCSV(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
Save the worksheet as a csv file
savePNG(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
 
savePNG(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
savePNGKMNumRisk(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
Combine the KM and Num risk into one image
saveSurvivalData(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
Save data from survival curve to text file
saveTXT(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
Sb - org.biojava.nbio.structure.Element
 
Sc - org.biojava.nbio.structure.Element
 
scalarProduct(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
Scalar product (dot product).
scale(double) - Method in class org.biojava.nbio.structure.math.SparseVector
Calculates alpha * a
scale(double[][], double) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
scale(double[][], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
scale(Atom, double) - Static method in class org.biojava.nbio.structure.Calc
Multiply elements of a by s
SCALE_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
ScaleableMatrixPanel - Class in org.biojava.nbio.structure.gui
A JPanel that can display the underlying distance matrix data of the protein structure alignment algorithm.
ScaleableMatrixPanel() - Constructor for class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
ScaleableMatrixPanel.GradientRenderer - Class in org.biojava.nbio.structure.gui
A renderer for the the gradient dropdown menu at the top of scaleableMatrixPanes.
scaleAdd(double, Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
Perform linear transformation s*X+B, and store the result in b
ScaledSubstitutionMatrix - Class in org.biojava.nbio.core.alignment.matrices
The biojava-alignment module represents substitution matrices with short values.
ScaledSubstitutionMatrix() - Constructor for class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
scaleEquals(Atom, double) - Static method in class org.biojava.nbio.structure.Calc
Multiply elements of a by s (in place)
scan(ProteinSequence) - Method in interface org.biojava.nbio.ws.hmmer.HmmerScan
 
scan(ProteinSequence) - Method in class org.biojava.nbio.ws.hmmer.RemoteHmmerScan
 
scan(ProteinSequence, URL) - Method in class org.biojava.nbio.ws.hmmer.RemoteHmmerScan
Scans a protein sequence for Pfam profile matches.
SchemaGenerator - Class in org.biojava.nbio.aaproperties.xml
 
SchemaGenerator(String) - Constructor for class org.biojava.nbio.aaproperties.xml.SchemaGenerator
 
SCOP - org.biojava.nbio.structure.align.client.StructureName.Source
 
SCOP - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
SCOP_DOWNLOAD - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
 
SCOP_DOWNLOAD_ALTERNATE - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
 
SCOPAutoSuggestProvider - Class in org.biojava.nbio.structure.align.gui.autosuggest
 
SCOPAutoSuggestProvider() - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
 
ScopCategory - Enum in org.biojava.nbio.structure.scop
The various categories provided by SCOP.
ScopDatabase - Interface in org.biojava.nbio.structure.scop
General API how to interact with SCOP
ScopDescription - Class in org.biojava.nbio.structure.scop
Contains data from dir.des.scop.txt_1.75
ScopDescription() - Constructor for class org.biojava.nbio.structure.scop.ScopDescription
 
ScopDomain - Class in org.biojava.nbio.structure.scop
Container for the information for a domain.
ScopDomain() - Constructor for class org.biojava.nbio.structure.scop.ScopDomain
 
ScopFactory - Class in org.biojava.nbio.structure.scop
Controls the global ScopDatabase being used.
ScopFactory() - Constructor for class org.biojava.nbio.structure.scop.ScopFactory
 
ScopInstallation - Class in org.biojava.nbio.structure.scop
This class provides access to the SCOP protein structure classification.
ScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.ScopInstallation
Create a new SCOP installation, downloading the file to "the right place".
ScopInstallation(String) - Constructor for class org.biojava.nbio.structure.scop.ScopInstallation
Create a new SCOP installation.
ScopInstallationInstance - Class in org.biojava.nbio.structure.gui.util
 
ScopIOException - Exception in org.biojava.nbio.structure.scop
Indicates that an I/O error occurred with SCOP lazy initialization.
ScopIOException() - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException
 
ScopIOException(String) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException
 
ScopIOException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException
 
ScopIOException(Throwable) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException
 
ScopMirror - Class in org.biojava.nbio.structure.scop
Helper class to store paths to the four SCOP files The string "%s" is replaced with the version number.
ScopMirror() - Constructor for class org.biojava.nbio.structure.scop.ScopMirror
Use default MRC location
ScopMirror(String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror
 
ScopMirror(String, String, String, String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror
Specify all keys individually
ScopMirror(String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror
Specify a common root URL which is concatenated with individual filenames
ScopNode - Class in org.biojava.nbio.structure.scop
 
ScopNode() - Constructor for class org.biojava.nbio.structure.scop.ScopNode
 
ScopSelectPanel - Class in org.biojava.nbio.structure.gui.util
 
ScopSelectPanel() - Constructor for class org.biojava.nbio.structure.gui.util.ScopSelectPanel
 
ScopSelectPanel(boolean) - Constructor for class org.biojava.nbio.structure.gui.util.ScopSelectPanel
 
score - org.biojava.nbio.survival.cox.ResidualsCoxph.Type
 
score - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
score - Variable in class org.biojava.nbio.ronn.Jronn.Range
 
score() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
Get score.
Scorer - Interface in org.biojava.nbio.alignment.template
Defines an algorithm which computes a score.
scores - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Dynamic programming score matrix The first dimension has the length of the first (query) sequence + 1 The second has the length of the second (target) sequence + 1 The third has length 1 for linear gap penalty and 3 for affine/constant gap (one each for match/substitution, deletion, insertion)
ScoresCache - Interface in org.biojava.nbio.structure.align.multiple
Interface for classes which implement a temporary cache for various numeric scores, e.g.
scoresToRanges(float[], float) - Static method in class org.biojava.nbio.ronn.Jronn
Convert raw scores to ranges.
scoringStrategy - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
scoringStrategy - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
scroll - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
Se - org.biojava.nbio.structure.Element
 
SearchIO - Class in org.biojava.nbio.core.search.io
Designed by Paolo Pavan.
SearchIO(File) - Constructor for class org.biojava.nbio.core.search.io.SearchIO
Build a SearchIO reader and tries to select the appropriate parser inspecting file extension.
SearchIO(File, ResultFactory) - Constructor for class org.biojava.nbio.core.search.io.SearchIO
Build a SearchIO reader and specify a ResultFactory object to be used for parsing
SearchIO(File, ResultFactory, double) - Constructor for class org.biojava.nbio.core.search.io.SearchIO
Build a SearchIO reader, specify a ResultFactory object to be used for parsing and filter hsp retrieved by a e-value threshold.
SEARCHSP_EFF - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
SEC_STRUC - Static variable in interface org.biojava.nbio.structure.Group
Group property key for secondary structure annotation
SECONDARYSTRUCTURE - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
 
SecStrucCalc - Class in org.biojava.nbio.structure.secstruc
Calculate and assign the secondary structure (SS) to the Groups of a Structure object.
SecStrucCalc() - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucCalc
 
SecStrucElement - Class in org.biojava.nbio.structure.secstruc
A secondary structure element (SSE) is an object representing a block of sequential residues that share the same secondary structure type.
SecStrucElement(SecStrucType, ResidueNumber, ResidueNumber, int, int, String) - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucElement
Create a new SSE object.
SecStrucInfo - Class in org.biojava.nbio.structure.secstruc
Container for the secondary structure information of a single residue.
SecStrucInfo(Group, String, SecStrucType) - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucInfo
 
SecStrucState - Class in org.biojava.nbio.structure.secstruc
This class extends the basic container for secondary structure annotation, including all the information used in the DSSP algorithm.
SecStrucState(Group, String, SecStrucType) - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucState
 
SecStrucTools - Class in org.biojava.nbio.structure.secstruc
This class contains methods for obtaining and converting secondary structure information from BioJava Structures.
SecStrucTools() - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucTools
 
SecStrucType - Enum in org.biojava.nbio.structure.secstruc
This enum contains all of the secondary structure types found in the DSSP output.
SECTIONKEYNULL - Static variable in class org.biojava.nbio.core.exceptions.Messages
 
sectp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
sections start at a line and continue till the first line afterwards with a non-whitespace first character we want to match any of the following as a new section within a section \s{0,8} word \s{0,7} value \s{21} /word = value \s{21} /word
SEED - Static variable in class org.biojava.nbio.core.util.Hashcoder
An initial value for a hashCode, to which we add contributions from fields.
Segment - Class in org.biojava.nbio.structure.domain.pdp
 
Segment() - Constructor for class org.biojava.nbio.structure.domain.pdp.Segment
 
SegmentComparator - Class in org.biojava.nbio.structure.domain.pdp
 
SegmentComparator() - Constructor for class org.biojava.nbio.structure.domain.pdp.SegmentComparator
 
select(WorkSheet, String) - Method in interface org.biojava.nbio.survival.kaplanmeier.figure.CensorStatusSelect
 
SELECT_EQR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
selectByAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Create a list of all features that include the specified attribute key.
selectByAttribute(String, String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Create a list of all features that include the specified attribute key/value pair.
selectByGroup(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Create a list of all features that have the specified group id, as defined by the group() method of the features.
selectByType(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Create a list of all features that are of the specified type, as defined by the type() method of the features.
selectByUserData(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Create a list of all features that include the specified key in their userMap().
selectByUserData(String, Object) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Create a list of all features that include the specified key/value pair in their userMap().
selectElements(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper
Gets a list of elements matching xpathExpression.
Selection - Interface in org.biojava.nbio.structure.gui
 
SelectionImpl - Class in org.biojava.nbio.structure.gui
 
SelectionImpl() - Constructor for class org.biojava.nbio.structure.gui.SelectionImpl
 
selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
selectionLocked() - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
 
selectionLocked() - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
 
selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
selectionUnlocked() - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
 
selectionUnlocked() - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
 
SelectMultiplePanel - Class in org.biojava.nbio.structure.gui.util
A Text Panel that allows the user to specify multiple structure identifiers, space separated.
SelectMultiplePanel() - Constructor for class org.biojava.nbio.structure.gui.util.SelectMultiplePanel
 
SelectMultiplePanel(boolean) - Constructor for class org.biojava.nbio.structure.gui.util.SelectMultiplePanel
 
selectOverlapping(String, Location, boolean) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Create a list of all features that overlap the specified location on the specified sequence.
selectParentElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper
Given an element, searches upwards through ancestor Elements till the first Element matching the requests parentName is found.
SelectPDBPanel - Class in org.biojava.nbio.structure.align.gui
A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
SelectPDBPanel() - Constructor for class org.biojava.nbio.structure.align.gui.SelectPDBPanel
 
SelectPDBPanel(boolean) - Constructor for class org.biojava.nbio.structure.align.gui.SelectPDBPanel
 
selectSingleElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper
If xpathExpression is a plain string with no '/' characterr, this is interpreted as a child element name to search for.
sendAlignmentRequest(int, RemotePairwiseAlignmentProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
Sends the Blast request via the Put command of the CGI-BIN interface.
sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService
Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object
sendAlignmentRequest(Sequence<Compound>, RemotePairwiseAlignmentProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
sendAlignmentRequest(Sequence<Compound>, RemotePairwiseAlignmentProperties) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService
Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object
sendDeleteRequest(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
Sends a delete request for given request id.
seqArraySize(int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
seqFont - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
SeqMisMatch - Interface in org.biojava.nbio.structure
Created by andreas on 9/11/15.
SeqMisMatchImpl - Class in org.biojava.nbio.structure
Created by andreas on 9/11/15.
SeqMisMatchImpl() - Constructor for class org.biojava.nbio.structure.SeqMisMatchImpl
 
seqname() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
Get the sequence name.
seqname() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
Get the sequence name.
SeqRes2AtomAligner - Class in org.biojava.nbio.structure.io
Aligns the SEQRES residues to the ATOM residues.
SeqRes2AtomAligner() - Constructor for class org.biojava.nbio.structure.io.SeqRes2AtomAligner
 
SEQRESRECORD - Static variable in interface org.biojava.nbio.structure.AminoAcid
Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
sequence(String) - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
Notify this parse listener of a sequence line.
Sequence<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
Main interface for defining a collection of Compounds and accessing them using biological indexes
SEQUENCE - org.biojava.nbio.structure.cluster.SubunitClustererMethod
The SEQUENCE clustering method uses the residue sequence of the Subunit to calculate sequence alignments.
SEQUENCE_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
SEQUENCE_CONSERVATION - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
 
SEQUENCE_FUNCTION - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
 
SEQUENCE_FUNCTION - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
 
SEQUENCE_STRUCTURE - org.biojava.nbio.structure.cluster.SubunitClustererMethod
The SEQUENCE_STRUCTURE clustering method uses the residue sequence and the coordinates of its Atom representatives of the Subunit to calculate sequence and structure alignments.
sequenceAndQualityLengthsMatch() - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder
Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length.
SequenceAsStringHelper<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
This is a common method that can be used across multiple storage/proxy implementations to handle Negative strand and other interesting elements of sequence data.
SequenceAsStringHelper() - Constructor for class org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper
 
SequenceComparator - Class in org.biojava.nbio.core.sequence
Used to sort sequences in ascending order of bioBegin property.
SequenceComparator() - Constructor for class org.biojava.nbio.core.sequence.SequenceComparator
 
SequenceCreatorInterface<C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
 
SequenceDisplay - Class in org.biojava.nbio.structure.gui
A sequence display that can show the results of a protein structure alignment.
SequenceDisplay(StructurePairAligner) - Constructor for class org.biojava.nbio.structure.gui.SequenceDisplay
 
sequenceEquality(Sequence<C>, Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
A case-sensitive manner of comparing two sequence objects together.
sequenceEqualityIgnoreCase(Sequence<C>, Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
A case-insensitive manner of comparing two sequence objects together.
SequenceFamily - org.biojava.nbio.structure.cath.CathCategory
 
SequenceFileProxyLoader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
This class represents the storage container of a sequence stored in a fasta file where the initial parsing of the file we store the offset and length of the sequence.
SequenceFileProxyLoader(File, SequenceParserInterface, long, int, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
 
SequenceFunctionOrderDetector - Class in org.biojava.nbio.structure.symmetry.internal
Calls Spencer's method for determining order.
SequenceFunctionOrderDetector() - Constructor for class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector
 
SequenceFunctionOrderDetector(int, float) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector
 
SequenceFunctionRefiner - Class in org.biojava.nbio.structure.symmetry.internal
Creates a refined alignment with the CE-Symm alternative self-alignment.
SequenceFunctionRefiner() - Constructor for class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner
 
SequenceHeaderParserInterface<S extends Sequence<?>,​C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
 
SequenceIterator(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator
 
SequenceLocation<S extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.location
A location in a sequence that keeps a reference to its parent sequence
SequenceLocation(int, int, S) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation
 
SequenceLocation(int, int, S, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation
 
SequenceLocation(int, int, S, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation
 
SequenceLocation(Point, Point, S, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation
 
SequenceMixin - Class in org.biojava.nbio.core.sequence.template
Provides a set of static methods to be used as static imports when needed across multiple Sequence implementations but inheritance gets in the way.
SequenceMixin() - Constructor for class org.biojava.nbio.core.sequence.template.SequenceMixin
 
SequenceMixin.SequenceIterator<C extends Compound> - Class in org.biojava.nbio.core.sequence.template
A basic sequence iterator which iterates over the given Sequence by biological index.
SequenceMouseListener - Class in org.biojava.nbio.structure.gui.util
a mouse listener for the AbstractChainRenderer class it listens to all mouse events and triggeres appropriate SequenceListener and FeatureListener events
SequenceMouseListener(SequenceDisplay) - Constructor for class org.biojava.nbio.structure.gui.util.SequenceMouseListener
 
SequenceOptimizationHints - Class in org.biojava.nbio.core.sequence
A static class that provides optimization hints for memory or performance handling of sequence data.
SequenceOptimizationHints() - Constructor for class org.biojava.nbio.core.sequence.SequenceOptimizationHints
 
SequenceOptimizationHints.SequenceCollection - Enum in org.biojava.nbio.core.sequence
 
SequenceOptimizationHints.SequenceUsage - Enum in org.biojava.nbio.core.sequence
 
SequencePair<S extends Sequence<C>,​C extends Compound> - Interface in org.biojava.nbio.core.alignment.template
Defines a data structure for the results of pairwise sequence alignment.
SequenceParserInterface - Interface in org.biojava.nbio.core.sequence.io.template
 
SequenceProxyView<C extends Compound> - Class in org.biojava.nbio.core.sequence.template
 
SequenceProxyView() - Constructor for class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
SequenceProxyView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
SequenceProxyView(Sequence<C>, Integer, Integer) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceProxyView
Main constructor for working with SequenceProxyViews
SequenceReader<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
 
SequenceScalePanel - Class in org.biojava.nbio.structure.gui.util
A class that draws a Sequence as a rectangle, a scale display over it.
SequenceScalePanel(int) - Constructor for class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
SequenceTools - Class in org.biojava.nbio.core.util
 
SequenceTools() - Constructor for class org.biojava.nbio.core.util.SequenceTools
 
SequenceUtil - Class in org.biojava.nbio.data.sequence
Utility class for operations on sequences
SequenceView<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
 
seqWeight - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
SerializableCache<K,​V> - Class in org.biojava.nbio.structure.domain
A class that provides all that is necessary to create a Serializable Cache
SerializableCache(String) - Constructor for class org.biojava.nbio.structure.domain.SerializableCache
set cacheFileName to null to disable caching
serialize(File) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
serializedCache - Variable in class org.biojava.nbio.structure.domain.SerializableCache
 
serialVersionUID - Static variable in class org.biojava.nbio.structure.align.gui.ChooseDirAction
 
serialVersionUID - Static variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor
 
serialVersionUID - Static variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
 
serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathDomain
 
serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathFragment
 
serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathNode
 
serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathSegment
 
serialVersionUID - Static variable in exception org.biojava.nbio.structure.io.PDBParseException
 
serialVersionUID - Static variable in exception org.biojava.nbio.structure.StructureException
 
serialVersionUID - Static variable in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties
 
serialVersionUID - Static variable in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties
 
serverBaseUrl - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
The base URL to which the full path specified via DownloadChemCompProvider.setChemCompPathUrlTemplate(String) is appended.
set(int, int, double) - Method in class org.biojava.nbio.structure.jama.Matrix
Set a single element.
setA(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
setAAIndexProvider(AAIndexProvider) - Static method in class org.biojava.nbio.core.alignment.matrices.AAindexFactory
Sets the singleton provider.
setAbsoluteMinimumSequenceLength(int) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
setAcc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
setAccept1(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
setAccept2(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
setAcceptedAtomNames(String[]) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
By default the parser will read in all atoms (unless using the CAonly switch).
setAccession(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
The last accession passed to this routine will always be the one used.
setAccession(AccessionID) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
setAccession(AccessionID) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setAccessionNr(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setAccessionNumber(List<String>) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setAfpAftIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAfpBefIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAfpChain(AFPChain) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
setAFPChain(AFPChain) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
 
setAFPChain(AFPChain) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
setAfpChainLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAfpChainList(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAfpChainTwiBin(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAfpChainTwiList(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAfpChainTwiNum(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAfpDisCut(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setAfpDisCut0(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setAfpIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAfpSet(List<AFP>) - Method in class org.biojava.nbio.structure.align.model.AFPChain
Set the set of AFPs for this alignment.
setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
 
setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain
Caution has to be made when changing the algorithmName of an AFPChain, since downstream analysis methods (scores, display, etc) behave differently if the alignment is flexible (created with FatCat).
setAlgorithmName(String) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Set the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
setAligMap(List<AlignedPosition>) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
setAligMat(int, int, AligMatEl) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
setAligMat(AligMatEl[][]) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
setAligMat(AligMatEl[][]) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
setAlign_se1(int[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
setAlign_se1(int[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
setAlign_se2(int[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
setAlign_se2(int[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
setAlignementOption(String, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
setAlignementOption(String, String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties
Method to set the value for a specific alignment parameter using a key to store in a map.
setAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
The alignment that specifies the residue equivalencies of the equivalent Subunits.
setAlignmentJmol(AbstractAlignmentJmol) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
setAlignmentMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setAlignmentNumber(int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
Set the number of alignments to fetch
setAlignmentOption(BlastAlignmentParameterEnum, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the value of specified parameter
setAlignmentOutputFormat(BlastOutputAlignmentFormatEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
Sets the alignment output format to get from the QBlast service
setAlignments(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
we only keep the first alternative...
setAlignPairs(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setAlignRes(List<List<Integer>>) - Method in interface org.biojava.nbio.structure.align.multiple.Block
Set the double List containing the aligned residues for each structure.
setAlignRes(List<List<Integer>>) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
setAlignScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAlignScoreUpdate(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAlignSeqRes(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
Define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.
setAliLenth(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
setAllAtoms(List<Atom>) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
 
setAllChains(List<Chain>) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
 
setAlnbeg1(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAlnbeg2(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAlnLength(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAlnseq1(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAlnseq2(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAlnsymb(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setAlpha(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
setAlpha(String) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
A letter that is assigned to this cluster in stoichiometry.
setAlphabet(String) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
Change alphabet used for string representation of a stoichiometry.
setAltAligNumber(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
setAltAtomId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setAlternativeAlignment(AlternativeAlignment) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
 
setAlternativeAlignments(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
 
setAlternativeAligs(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
 
setAlternativeAligs(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
setAltLoc(Character) - Method in interface org.biojava.nbio.structure.Atom
Set alternate Location.
setAltLoc(Character) - Method in class org.biojava.nbio.structure.AtomImpl
 
setAltShortSymbol(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
setAminoacid(List<AminoAcidComposition>) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
 
setAminoType(Character) - Method in interface org.biojava.nbio.structure.AminoAcid
Set the name of the AA, in single letter code .
setAminoType(Character) - Method in class org.biojava.nbio.structure.AminoAcidImpl
Set the name of the AA, in single letter code .
setAnchors(int[]) - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
Sets the starting list of anchors before running the alignment routine.
setAngleDiff(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setAngleThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
setAnnotation(Annotation) - Method in class org.biojava.nbio.ontology.Term.Impl
 
setAnnotationType(AbstractSequence.AnnotationType) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setApprovedName(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setApprovedSymbol(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setArchitectureId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setArchitectureName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setAsaC(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
 
setAsaU(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
 
setAssemblyHeader(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setAssemblyId(Long) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setAssemblyInformation(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setAtcc(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setAtomArrays(List<Atom[]>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Sets the List of Atom arrays.
setAtomArrays(List<Atom[]>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
setAtomAsaCs(List<Double>) - Method in class org.biojava.nbio.structure.asa.GroupAsa
 
setAtomAsaUs(List<Double>) - Method in class org.biojava.nbio.structure.asa.GroupAsa
 
setAtomCache(AtomCache) - Static method in class org.biojava.nbio.structure.StructureIO
 
setAtomCaThreshold(int) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
setAtomGroups(List<Group>) - Method in interface org.biojava.nbio.structure.Chain
Set all Groups with observed density in the chain, i.e.
setAtomGroups(List<Group>) - Method in class org.biojava.nbio.structure.ChainImpl
 
setAtomicNumber(int) - Method in class org.biojava.nbio.aaproperties.xml.Element
 
setAtomId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setAtomId1(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
setAtomId2(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
setAtomInfo(String, int, char, float, float, float, float, float, String, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
 
setAtomLinkages(Set<StructureAtomLinkage>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
Set atom linkages
setAtomLinkages(Set<StructureAtomLinkage>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
setAtomName(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
 
setAtoms(List<Atom>) - Method in interface org.biojava.nbio.structure.Group
Set the atoms of this group.
setAtoms(List<Atom>) - Method in class org.biojava.nbio.structure.HetatomImpl
Set the atoms of this group.
setAtoms(List<ChemCompAtom>) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setAtoms(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
Create and set a new structure from a given atom array.
setAtoms(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
setAtomType1(String) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
 
setAtomType2(String) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
 
setAuthorList(List<Author>) - Method in class org.biojava.nbio.structure.JournalArticle
 
setAuthors(String) - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference
Set The authors are a list of Inventors that retrieved from the Reference section.
setAuthors(String) - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
 
setAuthors(String) - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface
Set the authors that retrieved from Reference section.
setAuthors(String) - Method in class org.biojava.nbio.structure.PDBHeader
 
setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setAutoSuggestProvider(AutoSuggestProvider) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
 
setAverageScore(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
 
setAxes(SymmetryAxes) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
setAxisAngle(AxisAngle4d) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
setAxisTransformation(RotationAxisAligner) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
setAxisTypes(int[]) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
setB(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
setBadRmsd(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setBbs(Structure, Matrix4d[], boolean) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox
 
setBend(boolean) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
setBeta(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
setBetweenCompounds(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
setBinaryOperators(List<OrderedPair<String>>) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver
 
setBioAssemblies(Map<Integer, BioAssemblyInfo>) - Method in class org.biojava.nbio.structure.PDBHeader
 
setBioAssemblyTrans(int, int[], double[], String) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
 
setBioBegin(Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setBioEnd(Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setBioEnd(Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
setBiologicalAssembly(boolean) - Method in interface org.biojava.nbio.structure.Structure
Set a flag to indicate if this structure is a biological assembly
setBiologicalAssembly(boolean) - Method in class org.biojava.nbio.structure.StructureImpl
Sets a flag to indicate if this structure is a biological assembly
setBiologicalUnit(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setBioStart(Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
setBlastAdvancedOptions(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
This method is to be used if a request is to use non-default values at submission.
setBlastDatabase(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the database to be used with blastall
setBlastExpect(double) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the EXPECT parameter to be use with blastall
setBlastFromToPosition(int, int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the QUERY_FROM and QUERY_TO parameters to be use by blast.
setBlastGapCosts(int, int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the GAPCOSTS parameter
setBlastMatrix(BlastMatrixEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the value for the MATRIX parameter to use for blastall
setBlastProgram(BlastProgramEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the program to be used with blastall
setBlastWordSize(int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the WORD_SIZE parameter to be use with blastall
setBlock2Afp(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setBlockGap(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setBlockNum(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setBlockNumClu(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setBlockNumIni(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setBlockNumSpt(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setBlockResList(int[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setBlockResSize(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setBlockRmsd(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setBlockRotationMatrix(Matrix[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setBlocks(List<Block>) - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
Set the List of alignment Blocks of the BlockSet.
setBlocks(List<Block>) - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
setBlockScore(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setBlockSet(BlockSet) - Method in interface org.biojava.nbio.structure.align.multiple.Block
Set the back-reference to its parent BlockSet.
setBlockSet(BlockSet) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
setBlockSets(List<BlockSet>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Sets the List of BlockSet List of the specified alignment.
setBlockSets(List<BlockSet>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
setBlockShiftVector(Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setBlockSize(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setbondLengthTolerance(double) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
 
setBonds(List<Bond>) - Method in interface org.biojava.nbio.structure.Atom
Sets the bonds
setBonds(List<Bond>) - Method in class org.biojava.nbio.structure.AtomImpl
Sets the bonds
setBonds(List<ChemCompBond>) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setBravLattice(BravaisLattice) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
setBridge1(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
setBridge2(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
setC(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
setC1(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
 
setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
setCa1Length(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setCa2(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
setCa2(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
setCa2Length(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setCache(AtomCache) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
 
setCacheDoubleValues(boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
 
setCacheLocation(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
setCacheLocation(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
Set an alternate download location for files
setCacheLocation(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
setCachePath(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
set the location at which utility data should be cached.
setCalculationTime(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setCalculationTime(long) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
setCalculationTime(Long) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Set the running time spent to calculate this alignment.
setCalculationTime(Long) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
setCallbackFunction(String, String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
setCategory(String) - Method in class org.biojava.nbio.ontology.Synonym
 
setCategory(ModificationCategory) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
 
setCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopDescription
 
setCath(CathDatabase) - Static method in class org.biojava.nbio.structure.cath.CathFactory
Sets the default (singleton) CathDatabase.
setCATH(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setCathDownloadUrl(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
setCathVersion(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
setCdsEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
setCdsStart(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
setCell(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setCellColor(ContinuousColorMapper) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
 
setCellColor(ContinuousColorMapper) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
setCellLine(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setCellularLocation(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setCenter1(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setCenter2(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setCentered(boolean) - Method in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
 
setChain(Chain) - Method in interface org.biojava.nbio.structure.Group
Sets the back-reference to its parent Chain.
setChain(Chain) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
 
setChain(Chain) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
setChain(Chain) - Method in class org.biojava.nbio.structure.HetatomImpl
Sets the back-reference to its parent Chain.
setChain1(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
setChain2(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
setChainId(String) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
setChainId(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
 
setChainId(String) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
 
setChainId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setChainId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
setChainId(String) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
Sets the chain identifier (asym id) that this transformation should be applied to.
setChainID1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
setChainID2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
setChainIdToIndexMap(Map<String, Integer>) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
 
setChainInfo(String, String, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
 
setChainLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setChainName(String) - Method in class org.biojava.nbio.structure.DBRef
The name of the corresponding chain.
setChainName(String) - Method in class org.biojava.nbio.structure.ResidueNumber
 
setChainOrigNamesMap(Map<String, String>) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Sets a map with mapping from NCS chain names to original chain names.
setChainRmsd(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
The RMSD of the chain of AFPs.
setChains(int, List<Chain>) - Method in interface org.biojava.nbio.structure.Structure
Set the chains for a model
setChains(int, List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl
Set the chains for a model
setChains(List<Chain>) - Method in class org.biojava.nbio.structure.EntityInfo
Set the chains for this EntityInfo
setChains(List<Chain>) - Method in class org.biojava.nbio.structure.Model
 
setChains(List<Chain>) - Method in interface org.biojava.nbio.structure.Structure
Set the chains of a structure, if this is a NMR structure, this will only set model 0.
setChains(List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl
Set the chains of a structure, if this is a NMR structure, this will only set model 0.
setCharge(int) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setCharge(short) - Method in interface org.biojava.nbio.structure.Atom
Set the charge of this atom
setCharge(short) - Method in class org.biojava.nbio.structure.AtomImpl
 
setChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.Group
Set the Chemical Component that closer describes this group.
setChemComp(ChemComp) - Method in class org.biojava.nbio.structure.HetatomImpl
 
setChemCompPathUrlTemplate(String) - Static method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
Set the path to append to the serverBaseUrl (settable in DownloadChemCompProvider.setServerBaseUrl(String)).
setChemCompProvider(ChemCompProvider) - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory
The new ChemCompProvider will be set in the static variable, so this provider will be used from now on until it is changed again.
setChildren(List<Integer>) - Method in class org.biojava.nbio.structure.scop.ScopNode
 
setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
Set the children features
setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Set the children features
setChrLoc(String) - Method in class org.biojava.nbio.phosphosite.Site
 
setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
 
setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitFacade
Sets a chromosome for TwoBitParser.
setChromosomeNumber(int) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
 
setCircular(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
Set the radius of a circumscribed sphere, that goes through all vertices
setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
Set the radius of a circumscribed sphere, that goes through all vertices
setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
Set the radius of a circumscribed sphere, that goes through all vertices
setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
Set the radius of a circumscribed sphere, that goes through all vertices
setClassId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
setClassId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setClassification(String) - Method in class org.biojava.nbio.structure.PDBHeader
 
setClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription
 
setClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
setCluster(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
set the number of the cluster this alignment belongs to.
setCluster(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setCluster(StructureInterfaceCluster) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
setClustererMethod(SubunitClustererMethod) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Method to cluster subunits.
setClusters(List<SubunitCluster>) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
 
setClusterValue(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
setCoeff(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
setCoefficient(String, CoxCoefficient) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
setCol(short) - Method in class org.biojava.nbio.structure.align.helper.IndexPair
 
setColor(Color) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
setColor(Color) - Method in interface org.biojava.nbio.structure.gui.StructureViewer
Apply this color to the current Selection
setColorByBlocks(boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
 
setColorSpace(ColorSpace) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
 
setColorSpace(ColorSpace, LinearColorInterpolator.InterpolationDirection[]) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
Sets the ColorSpace to use for interpolation.
setCols(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
setComment(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
setComment(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setComments(List<String>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Set comments.
setCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
setCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
 
setComplexFeaturesAppendMode(InsdcParser.complexFeaturesAppendEnum) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser
 
setCompositionId(String) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
 
setCompoundAt(char, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
Converts from char to Compound and sets it at the given biological index
setCompoundAt(C, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
Sets the compound at the specified biological index
setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
 
setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
Class is immutable & so this is unsupported
setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
 
setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
Unsupported
setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setCompoundSet(CompoundSet<C>) - Method in interface org.biojava.nbio.core.sequence.template.SequenceReader
 
setCompoundSet(CompoundSet<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
 
setCondition(ModificationCondition) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
 
setConn(Double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setConstructedSequence(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setContacts(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setContacts(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
setContacts(AtomContactSet) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
setContents(String) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
 
setContents(String) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
setContents(String) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
Once the sequence is retrieved set the contents and make sure everything this is valid Some uniprot records contain white space in the sequence.
setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
Class is immutable & so this is unsupported
setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
 
setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
Unsupported
setContents(String) - Method in interface org.biojava.nbio.core.sequence.template.SequenceReader
 
setContents(String) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
 
setContents(String, ArrayList) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
setContents(List<C>) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
setContig(int) - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
 
setConvergenceSteps(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
setCoordinateSystem(int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
 
setCoords(double[]) - Method in interface org.biojava.nbio.structure.Atom
Set the coordinates.
setCoords(double[]) - Method in class org.biojava.nbio.structure.AtomImpl
Set the coordinates.
setCovered(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setCoxInfo(ArrayList<String>, CoxInfo, String, LinkedHashMap<String, String>, Boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
setCPPoint(Integer) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
 
setCreate_co(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setCreateAtomBonds(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
Should we create bonds between atoms when parsing a file.
setCreateAtomCharges(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
Should we create charges on atoms when parsing a file?
setCreatedDate(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setCrystalCell(CrystalCell) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
Set the crystal cell
setCrystallographicInfo(PDBCrystallographicInfo) - Method in class org.biojava.nbio.structure.PDBHeader
 
setCrystallographicInfo(PDBCrystallographicInfo) - Method in interface org.biojava.nbio.structure.Structure
Set crystallographic information for this structure
setCrystallographicInfo(PDBCrystallographicInfo) - Method in class org.biojava.nbio.structure.StructureImpl
Sets crystallographic information for this structure
setCurrentSequence(String) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
Method open nucleotide stream for sequence with given name.
setCurrentSequencePosition(long) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
setCustomStringGenerator(Function<List<SubunitCluster>, String>) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
Let a user-defined function handle the entire string representation of a stoichiometry.
setCut_sites(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
 
setCutoff(double) - Method in class org.biojava.nbio.structure.contact.InterfaceFinder
Set the contact distance cutoff.
setCuts(int, AlignerHelper.Subproblem, AlignerHelper.Last[][], AlignerHelper.Cut[]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
 
setCutsPerSection(int) - Method in class org.biojava.nbio.alignment.routines.GuanUberbacher
Sets the number of cuts added to each section during each pass.
setData(TreeMap<Integer, SpaceGroup>) - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
 
setDatabase(String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
 
setDatabase(String) - Method in class org.biojava.nbio.structure.DBRef
Specifies the database value.
setDatabaseCrossReference(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setDatabaseReferences(List<Sequence>) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
Intended for use with run module.
setDatabaseReferences(List<Sequence>) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
 
setDatabaseReferences(List<Sequence>) - Method in interface org.biojava.nbio.core.search.io.ResultFactory
Specify the collection of sequences objects used as database in the Search run.
setDatabaseReferences(DatabaseReferenceInterface) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setDate(Date) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setDbAccession(String) - Method in class org.biojava.nbio.structure.DBRef
Sequence database accession code.
setDbComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setDbFile(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
setDbIdCode(String) - Method in class org.biojava.nbio.structure.DBRef
Sequence database identification code.
setDbReferences(Set<StockholmStructure.DatabaseReference>) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setDBRefs(List<DBRef>) - Method in interface org.biojava.nbio.structure.Structure
Set the list of database references for this structure
setDBRefs(List<DBRef>) - Method in class org.biojava.nbio.structure.StructureImpl
Set the list of database references for this structure
setDbSeqBegin(int) - Method in class org.biojava.nbio.structure.DBRef
Initial sequence number of the database seqment.
setDbSeqEnd(int) - Method in class org.biojava.nbio.structure.DBRef
The begin of the sequence position in the database
setDcl(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
setdCutoff(double) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
The maximum allowed distance between the centroids of two equivalent Subunits, in A.
setDefault() - Method in class org.biojava.nbio.structure.align.gui.ParameterGUI
 
setDefault() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
 
setDefaultColoring(String) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Sets a default Jmol script used for coloring.
setDefaultColoring(String) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
 
setDefaultColoring(String) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
setDefaultCutsPerSection(int) - Static method in class org.biojava.nbio.alignment.routines.GuanUberbacher
Sets the default number of cuts added to each section during each pass.
setDefaultExtensionPenalty(int) - Static method in class org.biojava.nbio.alignment.SimpleGapPenalty
Sets the default gap extension penalty.
setDefaultOpenPenalty(int) - Static method in class org.biojava.nbio.alignment.SimpleGapPenalty
Sets the default gap open penalty.
setDefaultSuperPosition(SuperPositionAbstract) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
 
setDefaultText(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
 
setDegreeFreedom(double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
setDensityCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setDepDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader
The deposition date of the structure in the PDB
setDesc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
setDescription(String) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
setDescription(String) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
 
setDescription(String) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
Sets the description of this matrix.
setDescription(String) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
 
setDescription(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
 
setDescription(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
setDescription(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Set the description that can be used to describe the feature
setDescription(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
setDescription(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
 
setDescription(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setDescription(String) - Method in interface org.biojava.nbio.core.sequence.template.Compound
 
setDescription(String) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
 
setDescription(String) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
setDescription(String) - Method in class org.biojava.nbio.ontology.AbstractTerm
 
setDescription(String) - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
 
setDescription(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
setDescription(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
setDescription(String) - Method in interface org.biojava.nbio.ontology.Ontology
set the description of this ontology
setDescription(String) - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
 
setDescription(String) - Method in interface org.biojava.nbio.ontology.Term
set the description of the term;
setDescription(String) - Method in class org.biojava.nbio.ontology.Triple.Impl
 
setDescription(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
 
setDescription(String) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
 
setDescription(String) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
setDescription(String) - Method in class org.biojava.nbio.structure.cath.CathNode
 
setDescription(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setDescription(String) - Method in class org.biojava.nbio.structure.PDBHeader
Deprecated.
will be removed later. Use PDBHeader.getKeywords() if you use description to keep the keywords.
setDescription(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription
 
setDescription(String) - Method in class org.biojava.nbio.structure.Site
sets the REMARK 800 description of the site
setDescription(String) - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
 
setDescription(String) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
 
setDescription2(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain
Set the textual description for protein 2.
setDescriptionNumber(int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
Sets the number of descriptions to fetch
setDescriptor(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
 
setDescriptors(List<ChemCompDescriptor>) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setDetails(String) - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord
 
setDetails(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setDetails(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch
 
setDetails(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
 
setDf(int) - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
 
setDiagonalDistance(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setDiagonalDistance2(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setDirection(int) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
setDiscreteValues(WorkSheet) - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
 
setDisCut(double) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
 
setDisCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setDisFilter(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setDisSmooth(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setDist(int[][]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
 
setDist1(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
setDist1(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
setDist2(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
setDist2(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
setDisTable1(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setDisTable2(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContact
 
setDistanceCutoff(Double) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
setDistanceCutoff(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setDistanceIncrement(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
setDistanceMatrix(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain
A matrix with ca1length rows and ca2length columns.
setDistanceMatrix(Matrix) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
The distance matrix this alignment is based on
setDNAType(DNASequence.DNAType) - Method in class org.biojava.nbio.core.sequence.DNASequence
 
setDoAngleCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setDoDensityCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setDoDistanceCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setDoi(String) - Method in class org.biojava.nbio.structure.JournalArticle
Set the value of doi
setDomainCounter(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setDomainId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
setDomainId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setDomainName(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setDomains(SortedSet<HmmerDomain>) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
setDomainSplit(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setDonor1(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
setDonor2(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
setDoRMSCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setDownloadAll(boolean) - Method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
By default this provider will download only some of the ChemComp files.
setDuplicationHint(CECPParameters.DuplicationHint) - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
 
setDuplicationHint(CECPParameters.DuplicationHint) - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
 
setDVar(Double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setEcNums(List<String>) - Method in class org.biojava.nbio.structure.EntityInfo
 
setEcodDatabase(String) - Static method in class org.biojava.nbio.structure.ecod.EcodFactory
Updates the default version
setEditorList(List<Author>) - Method in class org.biojava.nbio.structure.JournalArticle
 
setElement(List<Element>) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
 
setElement(Element) - Method in interface org.biojava.nbio.structure.Atom
Set element of the atom name, e.g.
setElement(Element) - Method in class org.biojava.nbio.structure.AtomImpl
Set element of the atom name, e.g.
setElement1(T) - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
Sets the first element of an ordered pair.
setElement2(T) - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
Sets the second element of an ordered pair.
setEmail(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
Set the email for QBlast.
setEmblId(EmblId) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setEmblReference(List<EmblReference>) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
 
setEnd(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
setEnd(Point) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
setEnergy(double) - Method in class org.biojava.nbio.structure.secstruc.HBond
 
setEngineered(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setEnsemble(MultipleAlignmentEnsemble) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Set the back-reference to its parent Ensemble.
setEnsemble(MultipleAlignmentEnsemble) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
setEnsemblGeneId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setEntityId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
 
setEntityInfo(int[], String, String, String) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
 
setEntityInfo(EntityInfo) - Method in interface org.biojava.nbio.structure.Chain
Sets the Entity information
setEntityInfo(EntityInfo) - Method in class org.biojava.nbio.structure.ChainImpl
 
setEntityInfos(List<EntityInfo>) - Method in interface org.biojava.nbio.structure.Structure
Set the EntityInfo
setEntityInfos(List<EntityInfo>) - Method in class org.biojava.nbio.structure.StructureImpl
Set the EntityInfo
setEquivalent(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
 
setEvalCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setEvalue(Float) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
setEvalue(Float) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
setEvCode(String) - Method in class org.biojava.nbio.structure.Site
sets the REMARK 800 EVIDENCE CODE for the site.
setExonCount(int) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
setExonEnds(List<Integer>) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
setExonStarts(List<Integer>) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
setExpectedExecutionTime(long) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
 
setExperimentalTechnique(String) - Method in class org.biojava.nbio.structure.PDBHeader
Adds the experimental technique to the set of experimental techniques of this header.
setExpressionSystem(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemAtccNumber(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemCell(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemCellLine(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemCellularLocation(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemGene(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemOrgan(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemOrganelle(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemOtherDetails(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemPlasmid(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemStrain(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemTaxId(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemTissue(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemVariant(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemVector(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExpressionSystemVectorType(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setExtensionPenalty(int) - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
 
setExtensionPenalty(int) - Method in interface org.biojava.nbio.alignment.template.GapPenalty
Sets penalty given when an already open gap elongates by a single element
setFalseDiscoveryRate(float) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setFamilyId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
setFeatureHeader(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setFeatureRetriever(FeatureRetriever) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setFeaturesKeyWord(FeaturesKeyWordInterface) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setFeatureTable(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Set the behavior for fetching files from the server
setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
 
setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Set the behavior for fetching files from the server.
setFGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setFGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setFigureLineInfo(ArrayList<String>) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
 
setFigureLineInfo(ArrayList<String>) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
setFile(File) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
 
setFile(File) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
 
setFile(File) - Method in interface org.biojava.nbio.core.search.io.ResultFactory
 
setFile1(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setFile2(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setFileFormat(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
 
setFileLocation(String) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
 
setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
 
setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.PDBFileParser
 
setFileParsingParameters(FileParsingParameters) - Method in interface org.biojava.nbio.structure.io.StructureProvider
Set the parameters that should be used for file parsing
setFileParsingParams(FileParsingParameters) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
setFiletype(StructureFiletype) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Set the file type that will be parsed.
setFirstGroupAsa(GroupAsa) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
setFirstGroupAsas(Map<ResidueNumber, GroupAsa>) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
setFirstRepeat(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
 
setFlexible(boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
 
setFocusAfpList(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setFocusAfpn(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setFocusRes1(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setFocusRes2(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setFocusResn(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setFold(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
setFold(int) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
setFoldId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
setFormat(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setFormat(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setFormula(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
Set the residue formula.
setFormula(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setFormulaWeight(double) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setFragCompat(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setFragLen(int) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
 
setFragLen(int) - Method in class org.biojava.nbio.structure.align.model.AFP
 
setFragLen(Integer) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setFragLenSq(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setFragment(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setFragmentId(Integer) - Method in class org.biojava.nbio.structure.cath.CathFragment
 
setFragmentLength(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setFragmentMiniDistance(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
 
setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
 
setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
setFragScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setFrom(Integer) - Method in class org.biojava.nbio.structure.domain.pdp.Segment
 
setFromFtp(JCheckBox) - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
 
setGamma(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
setGapCreate(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setGapExtCol(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
setGapExtCol(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
setGapExtend(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setGapExtend(short) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
 
setGapExtend(Short) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
 
setGapExtension(double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
setGapExtension(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setGapExtension(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
setGapExtension(Double) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
setGapExtRow(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
setGapExtRow(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
setGapLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setGapOpen(double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
setGapOpen(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setGapOpen(short) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
 
setGapOpen(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
setGapOpen(Double) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
setGapOpen(Short) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
 
setGapOpenCol(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
setGapOpenCol(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
setGapOpenRow(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
setGapOpenRow(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
setGapPenalty(GapPenalty) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Sets the gap penalties.
setGaps(Boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setGenbankDirectoryCache(String) - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
 
setGene(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setGenebankId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
setGeneName(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
setGeneSymb(String) - Method in class org.biojava.nbio.phosphosite.Site
 
setGFAccessionNumber(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFAuthors(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFClan(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFDBComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFDefinition(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFGatheringThreshs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFIdentification(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFKeywords(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFLocation(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFMembership(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFNoiseCutoffs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFNumSequences(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFPfamAccession(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFPreviousIDs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFRefComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFSearchMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFSourceSeed(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFSourceStructure(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFTrustedCutoffs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFTypeField(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGFWikipediaLink(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setGroup(String) - Method in class org.biojava.nbio.phosphosite.Site
 
setGroup(Group) - Method in interface org.biojava.nbio.structure.Atom
Set the back-reference to its parent Group.
setGroup(Group) - Method in class org.biojava.nbio.structure.AtomImpl
Set the back-reference to its parent Group.
setGroupBond(int, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
 
setGroupInfo(String, int, char, String, int, int, char, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
 
setGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setGroups(List<Group>) - Method in class org.biojava.nbio.structure.Site
 
setGroups(Set<StructureGroup>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
 
setGroups(Set<StructureGroup>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
setHazardRatio(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
setHazardRatioHiCI(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
setHazardRatioLoCI(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
setHeaderInfo(float, float, float, String, String, String, String[]) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
 
setHeaderOnly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
Parse only the PDB file header out of the files
setHeaderVars(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setHeight(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
 
setHelixRmsdThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
setHelixRmsdToRiseRatio(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
setHetAtomInFile(boolean) - Method in interface org.biojava.nbio.structure.Group
Sets the field isHetAtomInFile which is intented only for helping in infering if a polymeric group is in a ligand chain or in a polymeric chain.
setHetAtomInFile(boolean) - Method in class org.biojava.nbio.structure.HetatomImpl
 
setHgncId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setHGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setHGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setHide(boolean) - Method in class org.biojava.nbio.survival.data.HeaderInfo
 
setHitAccession(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
 
setHitDef(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
 
setHitId(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
 
setHitLen(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
 
setHitNum(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
 
setHits(List<Hit>) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
setHitSequence(Sequence) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
 
setHmmAcc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
setHmmDesc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
setHmmFrom(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
setHmmName(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
setHmmTo(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
setHomologyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setHspAlignLen(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspBitScore(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspEvalue(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspGaps(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspHitFrame(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspHitFrom(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspHitTo(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspHseq(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspIdentity(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspIdentityString(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspNum(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspPositive(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspQseq(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspQueryFrame(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspQueryFrom(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHspQueryTo(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setHsps(List<Hsp>) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
 
setHspScore(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setIclose(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
 
setId(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
setId(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
 
setId(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
 
setId(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
setId(long) - Method in class org.biojava.nbio.structure.align.model.AFP
 
setId(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setId(long) - Method in class org.biojava.nbio.structure.HetatomImpl
the Hibernate database ID
setId(Long) - Method in class org.biojava.nbio.structure.DBRef
Set the ID used by Hibernate.
setId(Long) - Method in class org.biojava.nbio.structure.EntityInfo
set the ID used by Hibernate
setId(String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
 
setId(String) - Method in interface org.biojava.nbio.structure.Chain
Set the 'private' asymId (internal chain IDs in mmCif) for this chain.
setId(String) - Method in class org.biojava.nbio.structure.ChainImpl
 
setId(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setId(String) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
 
setId(String) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
Sets the identifier for this biological assembly transformation.
setId(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
setId(String) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
 
setIdbnsBegin(char) - Method in class org.biojava.nbio.structure.DBRef
Insertion code of initial residue of the segment, if PDB is the reference.
setIdbnsEnd(char) - Method in class org.biojava.nbio.structure.DBRef
Insertion code of the ending residue of the segment, if PDB is the reference.
setIdCode(String) - Method in class org.biojava.nbio.structure.DBRef
Set the idCode for this entry.
setIdCode(String) - Method in class org.biojava.nbio.structure.PDBHeader
Deprecated.
setIdenticalSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setIdentifier(String) - Method in class org.biojava.nbio.core.sequence.AccessionID
 
setIdentifier(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
setIdentity(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setIdxlist(List<int[]>) - Method in class org.biojava.nbio.structure.align.helper.JointFragments
Stores the alignment between the residues of several fragments.
setIndex(int) - Method in class org.biojava.nbio.structure.align.helper.GapArray
 
setIndex(Integer) - Method in class org.biojava.nbio.survival.data.HeaderInfo
 
setIndexColumnName(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
setInitialK(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setInitials(String) - Method in class org.biojava.nbio.structure.Author
 
setInsCode(Character) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
setInsCode(Character) - Method in class org.biojava.nbio.structure.ResidueNumber
 
setInsCode(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch
 
setInsCode(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
 
setInsCode1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
setInsCode2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
Sets the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces
setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
Sets the radius of an inscribed sphere, that is tangent to each of the octahedron's faces
setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
Sets the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces
setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
Sets the radius of an inscribed sphere, that is tangent to each of the tetrahedron's faces
setInsertBegin(char) - Method in class org.biojava.nbio.structure.DBRef
Initial insertion code of the PDB sequence segment.
setInsertEnd(char) - Method in class org.biojava.nbio.structure.DBRef
Ending insertion code of the PDB sequence segment.
setInstalledDomainDescription(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
setInstalledDomainList(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
setInstalledDomall(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
setInstalledNodeList(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
setInterGroupBond(int, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
 
setInternalSymmetry(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
The internal symmetry option divides each Subunit of each SubunitCluster into its internally symmetric repeats.
setInterpolationDirection(int, LinearColorInterpolator.InterpolationDirection) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
 
setInterpolator(ColorInterpolator) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
setIoTime(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setIoTime(long) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
setIoTime(Long) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Set the IO time to load this object
setIoTime(Long) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
setIsAminoAcid(boolean) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
setIsotopes(List<Isotope>) - Method in class org.biojava.nbio.aaproperties.xml.Element
 
setIsPublished(Boolean) - Method in class org.biojava.nbio.structure.JournalArticle
Sets the publication state of a JournalArticle - TO BE PUBLISHED == false
setIterationNumber(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
setJclose(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
 
setJmolPanel(JmolPanel) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
Set the jmolPanel of the AlignmentJmol instance.
setJoinFast(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setJoinPlo(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setJoinRMSCutoff(double) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setJournal(String) - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference
Set The journal usually contains the Publication Number, Publication Date and Assignee
setJournal(String) - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
 
setJournal(String) - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface
Set the journal that retrieved from Reference section.
setJournalArticle(JournalArticle) - Method in class org.biojava.nbio.structure.PDBHeader
Set the associated publication as defined by the JRNL records in a PDB file.
setJournalArticle(JournalArticle) - Method in interface org.biojava.nbio.structure.Structure
Set the associated publication as defined by the JRNL records in a PDB file.
setJournalArticle(JournalArticle) - Method in class org.biojava.nbio.structure.StructureImpl
set the associated publication as defined by the JRNL records in a PDB file.
setJournalName(String) - Method in class org.biojava.nbio.structure.JournalArticle
 
setKaplanMeierFigure(KaplanMeierFigure) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
Pick up needed info and details from the KM Figure
setKappa(float) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
setKeyword(List<String>) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setKeywords(List<String>) - Method in class org.biojava.nbio.structure.PDBHeader
Sets the KEYWODS record of the structure.
setKMFigureInfo(KMFigureInfo) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
 
setKMFigureInfo(KMFigureInfo) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
setLastUpdatedDate(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setLcmp(int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
setLcmp(int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
setLength(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setLength(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
 
setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathFragment
 
setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathSegment
 
setLength1(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
setLength2(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
setLevel(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
 
setLigands(Set<String>) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setLikeSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setLinearPredictor(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
setLineLength(int) - Method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter
 
setLineLength(int) - Method in class org.biojava.nbio.core.sequence.io.FastaWriter
 
setLineLength(int) - Method in class org.biojava.nbio.core.sequence.io.GenbankWriter
 
setLineSeparator(String) - Method in class org.biojava.nbio.core.sequence.io.FastaWriter
Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option
setLocalTimeLimit(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
setLocation(AbstractLocation) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
setLocation(AbstractLocation) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
setLocation(AbstractLocation) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
The new location for this feature.
setLocationInAlignment(Location) - Method in interface org.biojava.nbio.core.alignment.template.MutableAlignedSequence
Sets the position of the AlignedSequence to the given Location (start, gaps, end).
setLocus(String) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
 
setLongName(String) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
 
setLongName(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
 
setLongName(String) - Method in interface org.biojava.nbio.core.sequence.template.Compound
 
setLongName(String) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
 
setLongName(String) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
setLookAndFeel() - Static method in class org.biojava.nbio.structure.align.webstart.AligUIManager
 
setLowercaseToNull(ProteinSequence, Object[]) - Static method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
setLowerLimit(float) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
 
setM(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFP
 
setMacromolecularSize(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
 
setMacromolecularSizes() - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser
Set the macromolecularSize fields of the parsed bioassemblies.
setManual(Boolean) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setMappingSequence(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
 
setMapProperty(TreeMap<Integer, SpaceGroup>) - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
 
setMass(double) - Method in class org.biojava.nbio.aaproperties.xml.Element
 
setMass(double) - Method in class org.biojava.nbio.aaproperties.xml.Isotope
 
setMatMatrix(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
setMatMatrix(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
setMatrix(int[], int[], Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Set a submatrix.
setMatrix(int[], int, int, Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Set a submatrix.
setMatrix(int, int, int[], Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Set a submatrix.
setMatrix(int, int, int, int, Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Set a submatrix.
setMatrix(short[][]) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
setMatrix(Matrix) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
sets the distance matrix to be displayed
setMatrix(Matrix) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
setMatTransform(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
 
setMax(short) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
setMaxAtoms(int) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
The maximum numbers of atoms to load in a protein structure (prevents memory overflows)
setMaxGap(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setMaxGapFrag(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setMaxGapSize(int) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
CE specific parameter: set the Max gap size parameter G (during AFP extension).
setMaxGapSize(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
Set the Max gap size parameter.
setMaximumLocalCombinations(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
setMaxIter(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setMaxNrIterationsForOptimization(int) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
Set the maximum nr of times the (slow) optimiziation of alignment should iterate.
setMaxNrSuggestions(int) - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
set the maximum number of suggestions to return
setMaxNrSuggestions(int) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
 
setMaxNrSuggestions(int) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
 
setMaxOptRMSD(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
set the maximum RMSD cutoff to be applied during alignment optimization.
setMaxOptRMSD(Double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
(jCE specific): maximum RMSD that shall be calculated for the alignment.
setMaxOrientationAngle(double) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
The maximum orientation angle between two equivalent Subunits, in radians.
setMaxPenalty(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setMaxPropeller(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
This method sets the maximum propeller allowed for a base pair, prior to analyze() call
setMaxPropeller(double) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
This method sets the maximum propeller allowed for a base pair, prior to analyze() call
setMaxrefine(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setMaxRmsd(double) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
The maximum allowed RMSD of the alignment, in A.
setMaxRmsd(double) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
 
setMaxRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
setMaxRmsd(Double) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
 
setMaxShear(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
This method sets the maximum shear allowed for a base pair, prior to analyze() call
setMaxStagger(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
This method sets the maximum stagger allowed for a base pair, prior to analyze() call
setMaxStagger(double) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
This method sets the maximum stagger allowed for a base pair, prior to analyze() call
setMaxStretch(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
This method sets the maximum stretch allowed for a base pair, prior to analyze() call.
setMaxSymmOrder(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setMaxTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
setMaxTra(int) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
 
setMaxTra(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
Set the maximum number of Twists that are allowed...
setMaxTra(Integer) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
set the maximum number of Twists that are allowed...
setMean(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
setMembers(List<StructureInterface>) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
 
setMetaDataColumns(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
Clears existing meta data columns and sets new ones
setMetaDataColumnsAfterColumn() - Method in class org.biojava.nbio.survival.data.WorkSheet
 
setMetaDataColumnsAfterColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
setMetaDataFilter(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
setMetaDataRows(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
setMetaDataRowsAfterRow() - Method in class org.biojava.nbio.survival.data.WorkSheet
 
setMetaDataRowsAfterRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
setMethod(String) - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
 
setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
Sets the radius of radius of a sphere, that is tangent to each of the icosahedron's edges
setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
Sets the radius of radius of a sphere, that is tangent to each of the octahedron's edges
setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
Sets the radius of radius of a sphere, that is tangent to each of the tetrahedron's edges
setMin(short) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
setMinAlignedStructures(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
setMinBlockLen(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
setMinCoreLength(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setMinCPLength(Integer) - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
 
setMinCPLength(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
 
setMinimumHelixAngle(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
setMinimumHelixRise(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
setMinimumSequenceLength(int) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Set the minimum number of residues of a subunits to be considered in the clusters.
setMinimumSequenceLengthFraction(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
setMinLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setMinLen(int) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
 
setMinLen(Integer) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
 
setMinRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
setMinTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
setMisCut(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setMisLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setMismatchCount(Integer) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setMisScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setModDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader
The latest modification date of the structure.
setModel(int, List<Chain>) - Method in interface org.biojava.nbio.structure.Structure
A convenience function if one wants to edit and replace the models in a structure.
setModel(int, List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl
A convenience function if one wants to edit and replace the models in a structure.
setModelCartnX(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setModelCartnY(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setModelCartnZ(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setModelInfo(int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
 
setModelNumber(int) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
 
setModification(ProteinModification) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
 
setModification(ProteinModification) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
setModType(String) - Method in class org.biojava.nbio.phosphosite.Site
 
setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
 
setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
 
setMolecularWeight(Float) - Method in interface org.biojava.nbio.core.sequence.template.Compound
 
setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
 
setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
setMoleculeIds(Pair<String>) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
setMolecules(Pair<Atom[]>) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
setMolId(int) - Method in class org.biojava.nbio.structure.EntityInfo
Set the molecule identifier, called entity_id in mmCIF dictionary.
setMonNstdFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setMonNstdParentCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setMultipleAlignment(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
Set the back-reference to its parent MultipleAlignment.
setMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
setMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
setMultipleAlignments(List<MultipleAlignment>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Set the List of MultipleAlignments in the ensemble.
setMultipleAlignments(List<MultipleAlignment>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
setMultiplicity(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
setMutation(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setNaiveVariance(double[][]) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
setName(String) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
 
setName(String) - Method in class org.biojava.nbio.aaproperties.xml.Element
 
setName(String) - Method in class org.biojava.nbio.aaproperties.xml.Isotope
 
setName(String) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
setName(String) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
 
setName(String) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
Sets the name (short description) of this matrix.
setName(String) - Method in class org.biojava.nbio.core.sequence.features.Qualifier
 
setName(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
setName(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
setName(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
setName(String) - Method in interface org.biojava.nbio.ontology.Ontology
Set the name for this ontology
setName(String) - Method in class org.biojava.nbio.ontology.Synonym
 
setName(String) - Method in interface org.biojava.nbio.structure.Atom
Set atom name, e.g.
setName(String) - Method in class org.biojava.nbio.structure.AtomImpl
Set atom name, e.g.
setName(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setName(String) - Method in interface org.biojava.nbio.structure.Chain
Set the 'public' authId (chain ID in PDB file)
setName(String) - Method in class org.biojava.nbio.structure.ChainImpl
 
setName(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setName(String) - Method in class org.biojava.nbio.structure.cluster.Subunit
The Name of a Subunit is a free-text field, user defined.
setName(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription
 
setName(String) - Method in interface org.biojava.nbio.structure.Structure
Set biological name of Structure .
setName(String) - Method in class org.biojava.nbio.structure.StructureImpl
Set biological name of Structure .
setName(String) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
setName(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
setName1(String) - Method in class org.biojava.nbio.structure.align.client.PdbPair
 
setName1(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setName2(String) - Method in class org.biojava.nbio.structure.align.client.PdbPair
 
setName2(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setnAtom(int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
setnAtom(int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
setNaturalPos(Integer) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
setNclose(int) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
 
setNcsOperators(Matrix4d[]) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
Set the NCS operators.
setNcuts(int) - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
 
setNdom(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
setNeedsQuotes(boolean) - Method in class org.biojava.nbio.core.sequence.features.Qualifier
 
setNeutronsNum(int) - Method in class org.biojava.nbio.aaproperties.xml.Isotope
 
setNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathNode
 
setNonStandardCoordFrameConvention(boolean) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
Set the non-standard coordinate frame convention field
setNonStandardSg(boolean) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
Set the non-standard space group field
setNormAlignScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setNotesList(ArrayList<String>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setNotObserved(Boolean) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
setNrCPU(int) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setNrCPUs(int) - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc
does not do anything here...
setNrCPUs(int) - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
 
setNrCPUs(int) - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
 
setNrCPUs(int) - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
 
setNreported(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
setNrThreads(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
setNseg(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
 
setnStart(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
setNullValue(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
 
setNumBonds(int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
 
setNumCells(int) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder
Set the number of neighboring crystal cells that will be used in the search for contacts
setNumRepeats(int) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
setNumRes(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setNumSequences(int) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.align.util.AtomCache
[Optional] This method changes the behavior when obsolete entries are requested.
setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
 
setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
[Optional] This method changes the behavior when obsolete entries are requested.
setOccupancy(float) - Method in interface org.biojava.nbio.structure.Atom
Set occupancy.
setOccupancy(float) - Method in class org.biojava.nbio.structure.AtomImpl
 
setOccurrenceType(ModificationOccurrenceType) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
 
setOffset(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
setOmega(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
setOmimId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setOneLetterCode(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
On-the-fly Jmol bioassembly generation.
setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Sets the type of bioassembly to be colored.
setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
 
setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
setOpenPenalty(int) - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
 
setOpenPenalty(int) - Method in interface org.biojava.nbio.alignment.template.GapPenalty
Sets penalty given when a deletion or insertion gap first opens
setOperator(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
 
setOptAln(int[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setOptimization(Boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setOptimizationSteps(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setOptimizeAlignment(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level.
setOptimizeAlignment(boolean) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.
setOptimizeAlignment(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.
setOptLen(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setOptLength(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
The length of the optimal alignment.
setOptRmsd(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setOrder(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
setOrderDetectorMethod(CESymmParameters.OrderDetectorMethod) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setOrgan(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setOrganelle(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setOrGanelle(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setOrganism(String) - Method in class org.biojava.nbio.phosphosite.Site
 
setOrganismClassification(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setOrganismCommon(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setOrganismScientific(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setOrganismSpecies(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setOrganismTaxId(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setOrientation(Character) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
setOrigGroup(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch
 
setOrigGroup(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
 
setOriginalHeader(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setORmsdThr(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
Set the Original RMSD threshold from which the alignment optimization is started
setOrthologousSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setOutFile(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setOutFile(SynchronizedOutFile) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
 
setOutputDir(File) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
 
setOutputFormat(BlastOutputFormatEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
Sets the stream output format to get from the QBlast service
setOutputOption(String, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
setOutputOption(String, String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties
Method to set the value for a specific output parameter using a key to store in a map.
setOutputOption(BlastOutputParameterEnum, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
Sets the value of specified output parameter
setOutputPDB(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
When writing the results to a file, don;t write as XML but write aligned PDB file
setP1(int) - Method in class org.biojava.nbio.structure.align.model.AFP
 
setP2(int) - Method in class org.biojava.nbio.structure.align.model.AFP
 
setPaintDefaults(Graphics2D) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
set some default rendering hints, like text antialiasing on
setPair(AlignedSequence<S, C>, AlignedSequence<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableSequencePair
Sets both AlignedSequences of the pair.
setPair(Profile<S, C>, Profile<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfilePair
Sets both Profiles of the pair.
setPair(PdbPair) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
 
setPair(Pair<Atom>) - Method in class org.biojava.nbio.structure.contact.AtomContact
 
setPair(Pair<Group>) - Method in class org.biojava.nbio.structure.contact.GroupContact
 
setPairs(SortedSet<PdbPair>) - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.CeMain
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
 
setParameters(ConfigStrucAligParams) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner
Set the parameters for this algorithm to use.
setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
 
setParameters(ConfigStrucAligParams) - Method in interface org.biojava.nbio.structure.align.StructureAlignment
Set the default parameters for this algorithm to use
setParams(StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
set the parameters to be used for the algorithm
setParams(CESymmParameters) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
setParent(Structure) - Method in class org.biojava.nbio.structure.DBRef
Set the structure object that this DBRef relates to.
setParentDNASequence(AbstractSequence<NucleotideCompound>, Integer, Integer) - Method in class org.biojava.nbio.core.sequence.ProteinSequence
A Protein sequence can be stand alone or loaded from a transcript sequence.
setParentFeature(FeatureInterface<S, C>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
A feature can be the child or contained by a parent feature.
setParentFeature(FeatureInterface<S, C>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
setParentFeature(FeatureInterface<S, C>) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Set the parent feature
setParentId(String) - Method in class org.biojava.nbio.structure.cath.CathNode
 
setParentSequence(AbstractSequence<?>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setParentSunid(int) - Method in class org.biojava.nbio.structure.scop.ScopNode
 
setParseBioAssembly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
Should the biological assembly info (REMARK 350) be parsed from the PDB file?
setParseCAOnly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
Flag if only the C-alpha atoms of the structure should be parsed.
setParseSecStruc(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
A flag to tell the parser to parse the Author's secondary structure assignment from the file default is set to false, i.e. do NOT parse.
setParsingConsistency(BlastTabularParser.PARSING_CONSISTENCY) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
Tries to define a different level of consistency during parsing.
setPartialOn3prime(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
setPartialOn5prime(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
setPartner(int) - Method in class org.biojava.nbio.structure.secstruc.HBond
 
setPath(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
Set the path that is used to cache PDB files.
setPath(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
Sets the path for the directory where PDB files are read/written
setPath(IndexPair[]) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
setPath(IndexPair[]) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
setPathSize(int) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
setPathSize(int) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
setPdb1(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
mandatory argument to set the first PDB (and optionally chain ID) to be aligned.
setPdb1(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
setPdb2(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
mandatory argument to set the second PDB (and optionally chain ID) to be aligned.
setPdb2(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
setPdbAln(String[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setPdbccId(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
Set the Protein Data Bank Chemical Component ID.
setPdbccName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
Set the Protein Data Bank Chemical Component name.
setPDBCode(String) - Method in interface org.biojava.nbio.structure.Structure
Deprecated.
use #setPDBCode(PdbId)
setPDBCode(String) - Method in class org.biojava.nbio.structure.StructureImpl
Deprecated.
use #setPDBCode(PdbId)
setPDBDirField(JTextField) - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
 
setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
mandatory argument to set the location of PDB files.
setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
 
setPDBFlag(boolean) - Method in interface org.biojava.nbio.structure.Group
Flag if group has 3D data .
setPDBFlag(boolean) - Method in class org.biojava.nbio.structure.HetatomImpl
 
setPdbGroup(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch
 
setPdbGroup(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
 
setPDBHeader(PDBHeader) - Method in interface org.biojava.nbio.structure.Structure
Set the the header information for this PDB file
setPDBHeader(PDBHeader) - Method in class org.biojava.nbio.structure.StructureImpl
Set the the header information for this PDB file
setPdbId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setPdbId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
setPdbId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain
setPdbId(PdbId) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setPdbId(PdbId) - Method in class org.biojava.nbio.structure.PDBHeader
Sets the PDB identifier code for this protein structure.
setPdbId(PdbId) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
setPdbId(PdbId) - Method in interface org.biojava.nbio.structure.Structure
Sets the PdbId identifier associated with this structure.
setPdbId(PdbId) - Method in class org.biojava.nbio.structure.StructureImpl
Sets the PdbId identifier associated with this structure.
setPDBName(String) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
setPDBName(String) - Method in class org.biojava.nbio.structure.AminoAcidImpl
set three character name of AminoAcid.
setPDBName(String) - Method in interface org.biojava.nbio.structure.Group
Set the PDB 3-letter name for this group.
setPDBName(String) - Method in class org.biojava.nbio.structure.HetatomImpl
 
setPDBResidueNumber(ResidueNumber) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
setPdbResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
setPdbResNum(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
setPdbResNum(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch
 
setPdbResNum(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
 
setPDBresnum1(String[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
setPDBresnum2(String[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
setPdbSerial(int) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
 
setPDBserial(int) - Method in interface org.biojava.nbio.structure.Atom
Set PDB atom number.
setPDBserial(int) - Method in class org.biojava.nbio.structure.AtomImpl
Set PDB atom number.
setPdbxAlign(int) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxAmbiguousFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxAromaticFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxAromaticFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
setPdbxComponentAtomId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxComponentCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxComponentId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxFormalCharge(int) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxIdealCoordinatesDetails(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxIdealCoordinatesMissingFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxInitialDate(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxLeavingAtomFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxModelCartnXIdeal(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxModelCartnYIdeal(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxModelCartnZIdeal(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxModelCoordinatesDbCode(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxModelCoordinatesDetails(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxModelCoordinatesMissingFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxModifiedDate(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxOrdinal(int) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxOrdinal(int) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
setPdbxPolymerType(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxProcessingSite(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxRefId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxReleaseStatus(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxReplacedBy(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxReplaces(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxResidueNumbering(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxStereoConfig(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setPdbxStereoConfig(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
setPdbxSubcomponentList(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxSynonyms(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPdbxType(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPercentage(Double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
setPercentageIdentity(Double) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
 
setPercId(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
setPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
setPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
setPermutationSize(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setPhase(int) - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos
 
setPhi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
setPmid(String) - Method in class org.biojava.nbio.structure.JournalArticle
Set the value of pmid
setPolyhedron(Polyhedron) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
setPolymerType(PolymerType) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setPos(int) - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos
 
setPos(int, int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
 
setPos1(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setPos1(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
 
setPos2(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setPos2(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
 
setPosition(int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
setPreferredSize() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
 
setPreviousNames(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setPreviousSymbols(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setPrimitiveMultiplicity(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
setPrintCE(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
Display the output string in CE style
setPrintConnections(boolean) - Method in class org.biojava.nbio.structure.io.FileConvert
enable/disable printing of connections connections are sometimes buggy in PDB files so there are some cases where one might turn this off.
setPrintFatCat(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setPrintXML(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setProbability(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
 
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.SimpleProfileProfileAligner
 
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.SmithWaterman
 
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
setProfile(Profile<S, C>) - Method in class org.biojava.nbio.alignment.GuideTree.Node
 
setProfile(Profile<S, C>) - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
Stores the given profile.
setProfileFuture(Future<ProfilePair<S, C>>) - Method in class org.biojava.nbio.alignment.GuideTree.Node
 
setProfileFuture(Future<ProfilePair<S, C>>) - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
Stores the given profile future.
setProgram(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
setProgram(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
 
setProgramSpecificParameters(HashMap<String, String>) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
setProgramVersion(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
 
setProjectIdentifier(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setProperties(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
 
setProperties(Map<String, Object>) - Method in interface org.biojava.nbio.structure.Group
Properties of this amino acid.
setProperties(Map<String, Object>) - Method in class org.biojava.nbio.structure.HetatomImpl
Properties of this amino acid.
setProperty(Object, Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
 
setProperty(Object, Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation
Set the value of a property.
setProperty(String, Object) - Method in interface org.biojava.nbio.structure.Group
Set a single property .
setProperty(String, Object) - Method in class org.biojava.nbio.structure.HetatomImpl
 
setProtein(String) - Method in class org.biojava.nbio.phosphosite.Site
 
setProxySequenceReader(SequenceReader<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Very important method that allows external mappings of sequence data and features.
setPsi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
setPsimodId(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
Set the PSI-MOD ID.
setPsimodName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
Set the PSI-MOD name.
setPublicationDate(int) - Method in class org.biojava.nbio.structure.JournalArticle
 
setPublished(boolean) - Method in class org.biojava.nbio.structure.JournalArticle
 
setPublisher(String) - Method in class org.biojava.nbio.structure.JournalArticle
 
setPvalue(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
setPvalue(Double) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
setPx(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
setQualifiers(Map<String, List<Qualifier>>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
 
setQualifiers(Map<String, List<Qualifier>>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
setQualifiers(Map<String, List<Qualifier>>) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Set the qualifiers
setQualities(List<Number>) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
 
setQuantities(List<Number>) - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature
 
setQuery(AlignedSequence<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableSequencePair
Sets the first AlignedSequence of the pair.
setQuery(Profile<S, C>) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
Sets the query Profile.
setQuery(Profile<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfilePair
Sets the first Profile of the pair.
setQuery(S) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
Sets the query Sequence.
setQueryDef(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
setQueryID(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
setQueryLength(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
setQueryReferences(List<Sequence>) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
Intended for use with run module.
setQueryReferences(List<Sequence>) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
 
setQueryReferences(List<Sequence>) - Method in interface org.biojava.nbio.core.search.io.ResultFactory
Specify the collection of sequences objects used as queries in the Search run.
setQuerySequence(Sequence) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
setRandomSeed(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
setRange(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setRanges(List<String>) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
setRecordAdditionalAttachments(boolean) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
 
setRecordType(String) - Method in interface org.biojava.nbio.structure.AminoAcid
Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
setRecordType(String) - Method in class org.biojava.nbio.structure.AminoAcidImpl
Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
setRecordUnidentifiableCompounds(boolean) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
 
setReduceInitialFragments(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setRef(String) - Method in class org.biojava.nbio.structure.JournalArticle
Set the value of the ref.
setRefAuthor(StringBuffer) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
 
setRefChainId(String) - Method in class org.biojava.nbio.structure.EntityInfo
Return the ref chain id value.
setReference(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
setReferenceAuthor(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
 
setReferenceComment(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
 
setReferenceCrossReference(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
 
setReferenceGroup(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
 
setReferenceLocation(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
 
setReferenceNumber(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
 
setReferencePosition(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
 
setReferences(List<AbstractReference>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Set the list of AbstractReference
setReferences(Vector<StockholmFileAnnotation.StockholmFileAnnotationReference>) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setReferenceTitle(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
 
setRefined(boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
setRefinedScoreThreshold(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setRefineMethod(CESymmParameters.RefineMethod) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setRefineResult(boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
Deprecated.
setRefLocation(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
 
setRefMedline(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
 
setRefn(String) - Method in class org.biojava.nbio.structure.JournalArticle
Set the value of the refn
setRefseqIds(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setRefTitle(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
 
setRelation(QsRelation) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
The quaternary structure relation QsRelation between the two groups of Subunits.
setRelDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader
The release date of the structure in the PDB.
setRemoveCif(boolean) - Method in class org.biojava.nbio.structure.chem.ZipChemCompProvider
Remove downloaded .cif.gz after adding to zip archive?
setRepeatUnits(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
setRepresentative(String) - Method in class org.biojava.nbio.structure.cath.CathNode
 
setResidId(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
Set the RESID ID.
setResidName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
Set the RESID name.
setResidual(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
setResidualVariable(String, Double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
Set the residual value for the variable for this sample.
setResidue(String) - Method in class org.biojava.nbio.phosphosite.Site
 
setResidueName(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
Including insertion code
setResidueNumber(int) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
setResidueNumber(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
 
setResidueNumber(String, Integer, Character) - Method in interface org.biojava.nbio.structure.Group
Utility method to temporarily set a chainID for a group, if a parent chain object does not exist yet.
setResidueNumber(String, Integer, Character) - Method in class org.biojava.nbio.structure.HetatomImpl
 
setResidueNumber(ResidueNumber) - Method in interface org.biojava.nbio.structure.Group
Sets the ResidueNumber for this Group
setResidueNumber(ResidueNumber) - Method in class org.biojava.nbio.structure.HetatomImpl
 
setResidues(List<SiftsResidue>) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
setResidueType(ResidueType) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setResNames(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setResnum1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
setResnum2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
setResolution(float) - Method in class org.biojava.nbio.structure.PDBHeader
 
setResolution(Double) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setResScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setRevisionRecords(List<DatabasePDBRevRecord>) - Method in class org.biojava.nbio.structure.PDBHeader
 
setRevNum(String) - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord
 
setRfree(float) - Method in class org.biojava.nbio.structure.PDBHeader
 
setRise(double) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
setRms(double) - Method in class org.biojava.nbio.structure.align.helper.JointFragments
 
setRms(double) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
the rms in the structurally equivalent regions
setRms(double) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setRmsd(double) - Method in class org.biojava.nbio.structure.align.model.AFP
 
setRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
setRmsdCenters(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
setRmsdCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
The cutoff to be used during AFP detection
setRmsdCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
 
setRmsdIntra(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
setRmsdThr(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
setRmsdThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
setRMSDThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.
setRmsdThrJoin(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
setRndSeed(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setRobustStdError(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
setRot(Matrix) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setRotationGroup(RotationGroup) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
setRotationMatrix(double[][]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
 
setRow(short) - Method in class org.biojava.nbio.structure.align.helper.IndexPair
 
setRowHeader(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
setRows(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
setRscore(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
setRscoreLogrankTestpvalue(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
setRwork(float) - Method in class org.biojava.nbio.structure.PDBHeader
 
setSaturation(float) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
 
setSaveOutputDir(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setScale(float) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
 
setScale(float) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
 
setScale(float) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
setScale(int) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
 
setScalevalue(double) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
 
setScopDatabase(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
Set the default scop version
setScopDatabase(ScopDatabase) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
Set the default scop version and instance
setScope(int) - Method in class org.biojava.nbio.ontology.Synonym
 
setScopId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
setScopVersion(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
Sets the scop version used.
setScopVersion(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
 
setScore(double) - Method in class org.biojava.nbio.structure.align.model.AFP
 
setScore(double) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
 
setScore(double) - Method in class org.biojava.nbio.structure.domain.pdp.Segment
 
setScore(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
setScore(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
 
setScore(float) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
setScore(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
setScore(Float) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
setScoreLogrankTest(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
setScoreLogrankTestpvalue(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
setScorePoint(int, int, int, int, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Calculates the optimal alignment score for the given sequence positions and a linear gap penalty
setScorePoint(int, int, int, int, int, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Calculate the optimal alignment score for the given sequence positions with an affine or constant gap penalty
setScores(QuatSymmetryScores) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
setScores(QuatSymmetryScores) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
setScoreVector(int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Score local alignment for a given position in the query sequence for a linear gap penalty
setScoreVector(int, int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Score local alignment for a given position in the query sequence
setScoreVector(int, int, int, int, int, int[], boolean, int[][][], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Score global alignment for a given position in the query sequence for a linear gap penalty
setScoreVector(int, int, int, int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Score local alignment for a given position in the query sequence for a linear gap penalty
setScoreVector(int, int, int, int, int, int, int[], boolean, int[][][], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Score global alignment for a given position in the query sequence
setScoreVector(int, int, int, int, int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Score local alignment for a given position in the query sequence
setScoreVector(int, AlignerHelper.Subproblem, int, int[], boolean, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Score global alignment for a given position in the query sequence for a linear gap penalty
setScoreVector(int, AlignerHelper.Subproblem, int, int, int[], boolean, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Score global alignment for a given position in the query sequence
setScoringStrategy(CeParameters.ScoringStrategy) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
Set the scoring strategy to use. 0 is default CE scoring scheme. 1 uses Side chain orientation.
setScoringStrategy(CeParameters.ScoringStrategy) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
setSearchFile(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setSecondGroupAsa(GroupAsa) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
setSecondGroupAsas(Map<ResidueNumber, GroupAsa>) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
setSecretion(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setSecStructType(Group, int) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Get the secondary structure as defined by DSSP.
setSeedFragmentLength(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setSeedRmsdCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setSegId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
setSegmentId(Integer) - Method in class org.biojava.nbio.structure.cath.CathSegment
 
setSegments(List<CathSegment>) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setSegments(List<Segment>) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
 
setSegments(List<SiftsSegment>) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
 
setSelectedAlignmentPos(int) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
 
setSelectedAlignmentPos(int) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
setSelection(List<AtomInfo>) - Method in interface org.biojava.nbio.structure.gui.Selection
 
setSelection(List<AtomInfo>) - Method in class org.biojava.nbio.structure.gui.SelectionImpl
 
setSelection(Selection) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
setSelection(Selection) - Method in interface org.biojava.nbio.structure.gui.StructureViewer
 
setSelfAlignment(AFPChain) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
setSeparatorSequence(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
 
setSeqBegin(int) - Method in class org.biojava.nbio.structure.DBRef
Initial sequence number of the PDB sequence segment.
setSeqEnd(int) - Method in class org.biojava.nbio.structure.DBRef
Ending sequence number of the PDB sequence segment.
setSeqIdRange(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setSeqMisMatches(List<SeqMisMatch>) - Method in interface org.biojava.nbio.structure.Chain
Sets annotated sequence mismatches for this chain.
setSeqMisMatches(List<SeqMisMatch>) - Method in class org.biojava.nbio.structure.ChainImpl
 
setSeqNum(Integer) - Method in class org.biojava.nbio.structure.ResidueNumber
 
setSeqNum(Integer) - Method in interface org.biojava.nbio.structure.SeqMisMatch
 
setSeqNum(Integer) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
 
setSeqResGroups(List<Group>) - Method in interface org.biojava.nbio.structure.Chain
Sets the list of SeqResGroups for this chain.
setSeqResGroups(List<Group>) - Method in class org.biojava.nbio.structure.ChainImpl
 
setSeqResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
setSequence(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setSequence(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setSequence(String) - Method in class org.biojava.nbio.structure.cath.CathSegment
 
setSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
 
setSequence(S) - Method in class org.biojava.nbio.core.sequence.location.SequenceLocation
 
setSequenceCircular(boolean) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser
 
setSequenceCollection(SequenceOptimizationHints.SequenceCollection) - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
 
setSequenceCoverageThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
The minimum coverage of the sequence alignment between two subunits to be clustered together.
setSequenceDescription(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setSequenceHeader(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
 
setSequenceHeader(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setSequenceHeader(String) - Method in class org.biojava.nbio.structure.cath.CathSegment
 
setSequenceIdentityThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Sequence identity threshold to consider for the sequence subunit clustering.
setSequenceLength(long) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser
 
setSequences(List<AlignedSequence<S, C>>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfile
Sets entirely new set of AlignedSequences.
setSequenceScore(Double) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setSequenceUsage(SequenceOptimizationHints.SequenceUsage) - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
 
setSequentialAlignment(boolean) - Method in class org.biojava.nbio.structure.align.model.AFPChain
Set whether this alignment has the normal topology, ie the residues aligned in each block increase sequentially over the original protein.
setSeqWeight(double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
Should sequence conservation be considered as part of the alignment?
setSerNum(int) - Method in class org.biojava.nbio.structure.io.SSBondImpl
get serial number of this SSBOND in PDB file
setServerBaseUrl(String) - Static method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
Set the base URL for the location of all chemical component CIF files, to which the chemCompPathUrlTemplate is appended, settable in DownloadChemCompProvider.setChemCompPathUrlTemplate(String).
setShortAlign(boolean) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setShortDescription(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
 
setShortDescription(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
setShortDescription(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Set the short description that can be used to describe the feature
setShortName(String) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
 
setShortName(String) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
 
setShortName(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
 
setShortName(String) - Method in interface org.biojava.nbio.core.sequence.template.Compound
 
setShortName(String) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
 
setShortName(String) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
setShortSymbol(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
setShow3d(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setShowAFPRanges(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
setShowAFPRanges(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
setShowDBresult(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setShowMenu(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
setSimCount(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
setSimilarity(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setSiteID(String) - Method in class org.biojava.nbio.structure.Site
 
setSites(List<Site>) - Method in interface org.biojava.nbio.structure.Structure
 
setSites(List<Site>) - Method in class org.biojava.nbio.structure.StructureImpl
 
setSize(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
 
setSOLID(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setSource(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
Set the feature source
setSource(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
setSource(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Change the source of the FeatureInterface.
setSource(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
Added support for the source of this sequence for GFF3 export
setSource(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setSpaceGroup(SpaceGroup) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
Set the SpaceGroup
setSparse(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setSpeciesId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
setSqFrom(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
setSqTo(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
setSSBonds(List<Bond>) - Method in interface org.biojava.nbio.structure.Structure
Set the list of SSBonds for this structure
setSSBonds(List<Bond>) - Method in class org.biojava.nbio.structure.StructureImpl
Set the list of SSBonds for this structure
setSSEThreshold(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setStandardDeviation(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
setStart(Integer) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
 
setStart(String) - Method in class org.biojava.nbio.structure.cath.CathFragment
 
setStart(String) - Method in class org.biojava.nbio.structure.cath.CathSegment
 
setStart(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
setStart(Point) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
setStartPage(String) - Method in class org.biojava.nbio.structure.JournalArticle
 
setStartTimestamp(long) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
 
setStatus(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
setStatus(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setStdError(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
setStdlow(ArrayList<Double>) - Method in class org.biojava.nbio.survival.cox.StrataInfo
 
setSteps(AlignerHelper.Last[][][], boolean, int[], AlignerHelper.Last, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Find alignment path through traceback matrix
setSteps(AlignerHelper.Last[][][], int[][][], List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Find global alignment path through traceback matrix
setSteps(AlignerHelper.Last[][][], int[], List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
Find local alignment path through traceback matrix
setStop(String) - Method in class org.biojava.nbio.structure.cath.CathFragment
 
setStop(String) - Method in class org.biojava.nbio.structure.cath.CathSegment
 
setStoringScoreMatrix(boolean) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Sets choice to cache the score matrix or to save memory by deleting score matrix after alignment.
setStrain(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setStrand(Strand) - Method in class org.biojava.nbio.core.sequence.GeneSequence
 
setStrand(Strand) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
setStrata(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
setStrataInfoHashMap(LinkedHashMap<String, StrataInfo>) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
 
setStrategy(Stoichiometry.StringOverflowStrategy) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
Change string representation of a stoichiometry in case number of clusters exceeds number of letters in the alphabet.
setStringSequence(String) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
 
setStructure(Structure) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
Set a new Structure to visualize in the AlignmentJmol window.
setStructure(Structure) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
 
setStructure(Structure) - Method in interface org.biojava.nbio.structure.Chain
Sets the back-reference to its parent Structure.
setStructure(Structure) - Method in class org.biojava.nbio.structure.ChainImpl
 
setStructure(Structure) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
 
setStructure(Structure) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
setStructure(Structure) - Method in interface org.biojava.nbio.structure.gui.StructureViewer
 
setStructure(Structure) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
 
setStructure(Structure, boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
 
setStructure1(Structure) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
 
setStructure1(Structure) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
 
setStructure2(Structure) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
 
setStructure2(Structure) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
 
setStructureAlignmentJmol(AbstractAlignmentJmol) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
setStructureCoverageThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
The minimum coverage of the structure alignment between two subunits to be clustered together.
setStructureId(StructureIdentifier) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
setStructureIdentifier(StructureIdentifier) - Method in interface org.biojava.nbio.structure.Structure
Set the identifier corresponding to this structure
setStructureIdentifier(StructureIdentifier) - Method in class org.biojava.nbio.structure.StructureImpl
 
setStructureIdentifiers(List<StructureIdentifier>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Set the List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
setStructureIdentifiers(List<StructureIdentifier>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
setStructurePairAligner(StructurePairAligner) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
 
setStructurePairAligner(StructurePairAligner) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
 
setStyle(RenderStyle) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
setStyle(RenderStyle) - Method in interface org.biojava.nbio.structure.gui.StructureViewer
Apply this style to the current selection
setSubLocations(List<Location>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
setSubstitutionMatrix(SubstitutionMatrix<C>) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Sets the substitution matrix.
setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound>) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
setSubunitMap(Map<Integer, Integer>) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
Map of Subunit equivalencies from the first to the second group.
setSubunitRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
setSunid(int) - Method in class org.biojava.nbio.structure.scop.ScopNode
 
setSunid(Integer) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
setSunID(int) - Method in class org.biojava.nbio.structure.scop.ScopDescription
 
setSuperfamilyId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
setSuperpositionAlgorithm(String) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Method to cluster subunits.
setSurname(String) - Method in class org.biojava.nbio.structure.Author
 
setSurvivalData(ArrayList<String>, LinkedHashMap<String, ArrayList<CensorStatus>>, Boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
The data will set the max time which will result in off time points for tick marks
setSurvivalData(ArrayList<String>, LinkedHashMap<String, ArrayList<CensorStatus>>, Double, Boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
 
setSurvivalData(ArrayList<String>, SurvFitInfo, Double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
Allow setting of points in the figure where weighted correction has been done and percentage has already been calculated.
setSurvivalInfo(ArrayList<String>, ArrayList<SurvivalInfo>, String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
 
setSurvivalInfoList(ArrayList<SurvivalInfo>) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
setSymbol(String) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
 
setSymbol(String) - Method in class org.biojava.nbio.aaproperties.xml.Element
 
setSymDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
setSymmetryDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
 
setSymmetryDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
setSymmGroup(String) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
setSymmLevels(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setSymmType(CESymmParameters.SymmetryType) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setSynonyms(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setSynonyms(List<String>) - Method in class org.biojava.nbio.structure.EntityInfo
 
setSynonyms(Set<Object>) - Method in class org.biojava.nbio.ontology.Term.Impl
 
setSynthetic(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setSystematicName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
Set the systematic name.
setT(double[]) - Method in class org.biojava.nbio.structure.align.model.AFP
 
setTarget(AlignedSequence<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableSequencePair
Sets the second AlignedSequence of the pair.
setTarget(Profile<S, C>) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
Sets the target Profile.
setTarget(Profile<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfilePair
Sets the second Profile of the pair.
setTarget(S) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
Sets the target Sequence.
setTaxonomy(TaxonomyID) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setTempFactor(float) - Method in interface org.biojava.nbio.structure.Atom
Set temp factor .
setTempFactor(float) - Method in class org.biojava.nbio.structure.AtomImpl
 
setText(String) - Method in class org.biojava.nbio.structure.align.gui.AlignmentTextPanel
 
setTextField(JTextField) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
setTextOutput(boolean) - Method in class org.biojava.nbio.structure.align.gui.MySaveFileListener
If true, the alignment format saved will be a text output (FASTA for MultipleAlignments and FatCat for pairwise alignments)
setTGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setThreadPool(ThreadPoolExecutor) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
Sets thread pool to any given ThreadPoolExecutor to allow use of an alternative execution style.
setThreadPoolCPUsAvailable(int) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
Sets thread pool to reserve a given number of processor cores for foreground or other use.
setThreadPoolCPUsFraction(float) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
Sets thread pool to a given fraction of the available processors.
setThreadPoolDefault() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
Sets thread pool to default of 1 background thread for each processor core.
setThreadPoolSingle() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
Sets thread pool to a single background thread.
setThreadPoolSize(int) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
Sets thread pool to given size.
setThreeLetterCode(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setTime(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
setTissue(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setTitle(String) - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference
Set The title that retrieved from the Reference section.
setTitle(String) - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
 
setTitle(String) - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface
Set the title that retrieved from Reference section.
setTitle(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
Set the title of the AlignmentJmol window.
setTitle(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setTitle(String) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
 
setTitle(String) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
setTitle(String) - Method in class org.biojava.nbio.structure.JournalArticle
Set the value of title
setTitle(String) - Method in class org.biojava.nbio.structure.PDBHeader
 
setTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
setTmIntra(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
setTMScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setTMThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.
setTo(Integer) - Method in class org.biojava.nbio.structure.domain.pdp.Segment
 
setTool(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
Set the tool identifier for QBlast.
setTopologyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setTorsionPenalty(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
setTotalArea(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
setTotalLenIni(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setTotalLenOpt(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setTotalRmsdIni(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
this is the init-RMSD, not the final RMSD after refinement.
setTotalRmsdOpt(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
The RMSD of the final alignment.
setTraceRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
setTraceTmScoreMin(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
setTrans(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setTranscriptionEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
setTranscriptionStart(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
setTransfAlgebraic(List<String>) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
setTransformation(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
setTransformation(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
setTransformationMatrix(Matrix4d) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
Sets the transformation using a 4x4 transformation matrix
setTransformations(List<Matrix4d>) - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
Set a new superposition for the structures.
setTransformations(List<Matrix4d>) - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
setTransformId(int) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
 
setTransforms(List<BiologicalAssemblyTransformation>) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
 
setTransforms(Pair<CrystalTransform>) - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
setTranslation(double[]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
 
setTryAllCPs(Boolean) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
 
setTurn(char, int) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
Set the turn column corresponding to 3,4 or 5 helix patterns.
setTwi(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setTwistedGroups(Group[]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
 
setType(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
Set the feature type
setType(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
setType(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
Change the type of this feature.
setType(String) - Method in class org.biojava.nbio.structure.chem.ChemComp
 
setType(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
 
setType(String) - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord
 
setType(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
 
setType(StainType) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
 
setType(EntityType) - Method in class org.biojava.nbio.structure.EntityInfo
Set the type of entity this EntityInfo describes.
setType(SecStrucType) - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
 
setTypeSymbol(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom
 
setUid(Long) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setUnaryOperators(List<String>) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver
 
setUncertain(boolean) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
setUniprot(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
setUniprot(String) - Method in class org.biojava.nbio.phosphosite.Site
 
setUniProtAccessionId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
setUniprotbaseURL(String) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
setUniprotDirectoryCache(String) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
setUniProtId(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch
 
setUniProtId(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
 
setUniProtPos(Integer) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
setUniProtResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
setUnitv(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setUnknown(boolean) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
setUnrefinedScoreThreshold(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setUnweightedStrataInfoHashMap(LinkedHashMap<String, StrataInfo>) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
 
setUpdateFrequency(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
The "latest" version will be re-downloaded if it is older than EcodInstallation.getUpdateFrequency() days.
setUpperLimit(float) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
 
setUrl(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
Specify a different mirror for the ECOD server.
setUsed(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
setUsedAtomNames(String[]) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
setUseEntityIdForSeqIdentityDetermination(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Whether to use the entity id of subunits to infer that sequences are identical.
setUseGlobalMetrics(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only
setUserCollection(Collection<Object>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
setUseRMSD(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Use RMSD for evaluating structure similarity
setUserObject(Object) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
Allow the user to associate an object with the feature.
setUserObject(Object) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
 
setUserObject(Object) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
 
setUserOrder(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
setUseSequenceCoverage(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Use sequence coverage for evaluating sequence similarity
setUseStructureCoverage(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Use structure coverage for evaluating sequence similarity
setUseTMScore(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Use TMScore for evaluating structure similarity
setValue(int) - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
 
setValue(int) - Method in class org.biojava.nbio.structure.align.helper.GapArray
 
setValue(String) - Method in class org.biojava.nbio.core.sequence.features.Qualifier
 
setValueOrder(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond
 
setVariableResiduals(double[][]) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
setVariance(double[][]) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
setVariant(String) - Method in class org.biojava.nbio.structure.EntityInfo
 
setVersion(int) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
The last accession passed to this routine will always be the one used.
setVersion(Integer) - Method in class org.biojava.nbio.core.sequence.AccessionID
 
setVersion(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
setVersion(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
 
setVersion(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
setVersion(String) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Sets the version of the algorithm used to generate the MultipleAlignment objects.
setVersion(String) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
setVersion(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
 
setVolume(String) - Method in class org.biojava.nbio.structure.JournalArticle
 
setWaldTestInfo(WaldTestInfo) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
setWeight(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
setWeighted(boolean) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
 
setWinSize(int) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
setWinSize(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
setX(double) - Method in interface org.biojava.nbio.structure.Atom
Set the X coordinate.
setX(double) - Method in class org.biojava.nbio.structure.AtomImpl
 
setXGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setXGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
setXtalInfo(String, float[], double[][]) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
 
setY(double) - Method in interface org.biojava.nbio.structure.Atom
Set the Y coordinate.
setY(double) - Method in class org.biojava.nbio.structure.AtomImpl
 
setZ(double) - Method in interface org.biojava.nbio.structure.Atom
Set the Z coordinate.
setZ(double) - Method in class org.biojava.nbio.structure.AtomImpl
 
setZ(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
setZoom(int) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
setZoom(int) - Method in interface org.biojava.nbio.structure.gui.StructureViewer
Set the Zoom level
shift(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc
Shift an array of atoms at once.
shift(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
Shift a vector.
shift(Group, Atom) - Static method in class org.biojava.nbio.structure.Calc
Shift a Group with a vector.
shift(Structure, Atom) - Static method in class org.biojava.nbio.structure.Calc
shift a structure with a vector.
shiftAtAlignmentLocation(Location, int) - Method in interface org.biojava.nbio.core.alignment.template.MutableAlignedSequence
Slides a part of the AlignedSequence.
shiftAtSequenceLocation(Location, int) - Method in interface org.biojava.nbio.core.alignment.template.MutableAlignedSequence
Slides a part of the AlignedSequence.
shiftCA2(AFPChain, Atom[], Matrix, Atom, Group[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
only shift CA positions.
SHORT_QUERY_ADJUST - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
SHORTER - org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint
 
ShortSegmentRemover - Class in org.biojava.nbio.structure.domain.pdp
 
ShortSegmentRemover() - Constructor for class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
 
shouldCreateAtomBonds() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
Should we create bonds between atoms when parsing a file?
shouldCreateAtomCharges() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
Should we create charges on atoms when parsing a file?
SHOW_CDS_FEATURE - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
SHOW_LINKOUT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
SHOW_OVERVIEW - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
 
showAboutDialog() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
Show some info about this GUI
showAFPRanges - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
showAFPRanges - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
showAlignmentGUI() - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
 
showAlignmentImage(AFPChain, String) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
 
showAlignmentImage(AFPChain, Atom[], Atom[], Object) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
 
showAlignmentImage(MultipleAlignment, String) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
Creates a new Frame with the String output representation of the MultipleAlignment.
showAlignmentPanel(AFPChain, Atom[], Atom[], AbstractAlignmentJmol) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
 
showAlternative(int) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
 
showAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
Returns a Jmol script to show axes
showAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
Returns a Jmol script to show axes
showAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
showConsole(boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
showDialog() - Method in class org.biojava.nbio.structure.align.gui.AboutDialog
 
showDialog() - Static method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
 
showDialog() - Method in class org.biojava.nbio.structure.align.gui.HelpDialog
 
showDialog() - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
 
showDistanceMatrix(int) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
 
showDocument(String) - Static method in class org.biojava.nbio.structure.align.webstart.BrowserOpener
open a URL in the browser that was used to launch SPICE
showDocument(URL) - Static method in class org.biojava.nbio.structure.align.webstart.BrowserOpener
open a URL in the browser that was used to launch SPICE
showDocument(URL) - Static method in class org.biojava.nbio.structure.align.webstart.JNLPProxy
 
showMemoryMonitor() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
showMultipleAligmentPanel(MultipleAlignment, AbstractAlignmentJmol) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
Creates a new Frame with the MultipleAlignment Sequence Panel.
ShowPDBIDListener - Class in org.biojava.nbio.structure.align.gui
 
ShowPDBIDListener() - Constructor for class org.biojava.nbio.structure.align.gui.ShowPDBIDListener
 
showPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
 
showPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
 
showPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
 
showProgressBar() - Static method in class org.biojava.nbio.structure.align.gui.StructureLoaderThread
 
showStructure(Structure) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
Shows a structure in Jmol
ShowStructureInJmol - Class in demo
Demo how to load and display a structure in Jmol
ShowStructureInJmol() - Constructor for class demo.ShowStructureInJmol
 
showSuggest() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
Force the suggestions to be displayed (Useful for buttons e.g. for using JSuggestionField like a ComboBox)
showSystemInfo() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
showUrl(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
shuffle(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
Implements sequence shuffling by first materializing the given Sequence into a List, applying Collections.shuffle(List) and then returning the shuffled elements in a new instance of SequenceBackingStore which behaves as a Sequence.
shuffleColumnsAndThenRows(ArrayList<String>, ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
Randomly shuffle the columns and rows.
shuffleColumnValues(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
Need to shuffle column values to allow for randomized testing.
shuffleRowValues(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
Need to shuffle rows values to allow for randomized testing.
shutdown() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
Disables new tasks from being submitted and closes the thread pool cleanly.
shutdownAndAwaitTermination() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
Closes the thread pool.
Si - org.biojava.nbio.structure.Element
 
SIDE_CHAIN_ANGLE_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
 
SIDE_CHAIN_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
 
sideChainScoringType - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
SiftsChainEntry - Class in org.biojava.nbio.structure.io.sifts
An entry in the chain-level SIFTS mapping between UniProt and the PDB.
SiftsChainEntry(String, String, String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
SiftsChainToUniprotMapping - Class in org.biojava.nbio.structure.io.sifts
A mapping between UniProt entries and PDB chains.
SiftsEntity - Class in org.biojava.nbio.structure.io.sifts
 
SiftsEntity() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsEntity
 
SiftsEntity(String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsEntity
 
SiftsMappingProvider - Class in org.biojava.nbio.structure.io.sifts
 
SiftsMappingProvider() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
 
SiftsResidue - Class in org.biojava.nbio.structure.io.sifts
 
SiftsResidue() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
SiftsSegment - Class in org.biojava.nbio.structure.io.sifts
 
SiftsSegment() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
SiftsSegment(String, String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
SiftsXMLParser - Class in org.biojava.nbio.structure.io.sifts
 
SiftsXMLParser() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsXMLParser
 
SigEva - Class in org.biojava.nbio.structure.align.fatcat.calc
 
SigEva() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.SigEva
 
signatureName - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
 
SIMILARITIES - org.biojava.nbio.alignment.Alignments.PairInProfileScorerType
 
SIMILARITY_COLOR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
SimpleAlignedSequence<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.alignment
Implements a data structure for a Sequence within an alignment.
SimpleAlignedSequence(AlignedSequence<S, C>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleAlignedSequence
Creates a new AlignedSequence for the given AlignedSequence in a global alignment.
SimpleAlignedSequence(AlignedSequence<S, C>, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.core.alignment.SimpleAlignedSequence
Creates a new AlignedSequence for the given AlignedSequence in a local alignment.
SimpleAlignedSequence(S, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleAlignedSequence
Creates an AlignedSequence for the given Sequence in a global alignment.
SimpleAlignedSequence(S, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.core.alignment.SimpleAlignedSequence
Creates an AlignedSequence for the given Sequence in a local alignment.
SimpleGapPenalty - Class in org.biojava.nbio.alignment
Implements a data structure for the gap penalties used during a sequence alignment routine.
SimpleGapPenalty() - Constructor for class org.biojava.nbio.alignment.SimpleGapPenalty
Creates a new set of gap penalties using the defaults.
SimpleGapPenalty(int, int) - Constructor for class org.biojava.nbio.alignment.SimpleGapPenalty
Creates a new set of gap penalties.
SimpleLocation - Class in org.biojava.nbio.core.sequence.location
Very basic implementation of the Location interface which defines a series of simple constructors.
SimpleLocation(int, int) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(int, int, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, boolean, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
 
SimplePoint - Class in org.biojava.nbio.core.sequence.location
Basic implementation of the Point interface.
SimplePoint() - Constructor for class org.biojava.nbio.core.sequence.location.SimplePoint
 
SimplePoint(int) - Constructor for class org.biojava.nbio.core.sequence.location.SimplePoint
 
SimplePoint(int, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.SimplePoint
 
SimpleProfile<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.alignment
Implements a data structure for the results of sequence alignment.
SimpleProfile(Collection<AlignedSequence<S, C>>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile
Creates a profile for the already aligned sequences.
SimpleProfile(AlignedSequence<S, C>, AlignedSequence<S, C>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile
Creates a pair profile for the given already aligned sequences.
SimpleProfile(Profile<S, C>, Profile<S, C>, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile
Creates a pair profile for the given profiles.
SimpleProfile(S) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile
Creates a profile from a single sequence.
SimpleProfile(S, S, List<AlignedSequence.Step>, int, int, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile
Creates a pair profile for the given sequences.
SimpleProfilePair<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.alignment
Implements a data structure for the results of the alignment of a pair of Profiles.
SimpleProfilePair(Profile<S, C>, Profile<S, C>, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfilePair
Creates a pair profile for the given profiles.
SimpleProfileProfileAligner<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment
Implements a simple (naive) Aligner for a pair of Profiles.
SimpleProfileProfileAligner() - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner
SimpleProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner
Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(Future<ProfilePair<S, C>>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner
Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(Profile<S, C>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner
Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner
Prepares for a profile-profile alignment.
SimpleSequencePair<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.alignment
Implements a data structure for the results of pairwise sequence alignment.
SimpleSequencePair(AlignedSequence<S, C>, AlignedSequence<S, C>) - Constructor for class org.biojava.nbio.core.alignment.SimpleSequencePair
Creates a pair profile for the given already aligned sequences.
SimpleSequencePair(S, S, List<AlignedSequence.Step>, int, int, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.core.alignment.SimpleSequencePair
Creates a pair profile for the given sequences with a local alignment.
SimpleSequencePair(S, S, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleSequencePair
Creates a pair profile for the given sequences with a global alignment.
SimpleSubstitutionMatrix<C extends Compound> - Class in org.biojava.nbio.core.alignment.matrices
Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.
SimpleSubstitutionMatrix(CompoundSet<C>, short, short) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
Creates an identity substitution matrix from match and replace values.
SimpleSubstitutionMatrix(CompoundSet<C>, File) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
Creates a substitution matrix by reading in a file.
SimpleSubstitutionMatrix(CompoundSet<C>, Reader, String) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
Creates a substitution matrix by parsing some input.
SimpleSubstitutionMatrix(CompoundSet<C>, String, String) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
Creates a substitution matrix by parsing a String.
SingleCompoundSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
An implementation of the SequenceReader interface which for every call will return only 1 compound (given to it during construction; a String is also valid but will require a CompoundSet).
SingleCompoundSequenceReader(C, CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
Build the object with a compound rather than a String
SingleCompoundSequenceReader(String, CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
Public constructor to be used with String based constructor
SingleLinkageClusterer - Class in org.biojava.nbio.core.util
An implementation of a single linkage clusterer See http://en.wikipedia.org/wiki/Single-linkage_clustering
SingleLinkageClusterer(double[][], boolean) - Constructor for class org.biojava.nbio.core.util.SingleLinkageClusterer
Constructs a new SingleLinkageClusterer Subsequently use SingleLinkageClusterer.getDendrogram() to get the full tree or SingleLinkageClusterer.getClusters(double) to get the clusters at a certain cutoff in the tree Please note that the matrix will be altered during the clustering procedure.
singleLocationPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser
parse a location. if group(1) is null than the feature is on the positive strand, group(2) start position, group(3) end position.
SingularValueDecomposition - Class in org.biojava.nbio.structure.jama
Singular Value Decomposition.
SingularValueDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.SingularValueDecomposition
Construct the singular value decomposition.
Site - Class in org.biojava.nbio.phosphosite
Created by ap3 on 31/10/2014.
Site - Class in org.biojava.nbio.structure
Holds the data of sites presented in PDB files.
Site() - Constructor for class org.biojava.nbio.phosphosite.Site
 
Site() - Constructor for class org.biojava.nbio.structure.Site
 
Site(String, List<Group>) - Constructor for class org.biojava.nbio.structure.Site
 
site2 - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
 
SIXBAR - org.biojava.nbio.structure.xtal.TransformType
 
SIXFOLD - org.biojava.nbio.structure.xtal.TransformType
 
SIXFOLDSCREW - org.biojava.nbio.structure.xtal.TransformType
 
size() - Static method in class org.biojava.nbio.core.util.FlatFileCache
Returns the number of items in the cache.
size() - Method in class org.biojava.nbio.core.util.SoftHashMap
 
size() - Method in class org.biojava.nbio.ontology.utils.SmallMap
 
size() - Method in interface org.biojava.nbio.structure.align.multiple.Block
Returns the number of aligned structures (rows) in the Block.
size() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
size() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
Returns the number of aligned structures in the BlockSet.
size() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
size() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Returns the number of aligned structures in the MultipleAlignment.
size() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
Returns the number of aligned structures in the MultipleAlignments.
size() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
 
size() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
size() - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
Returns the number of ChemComps in this dictionary
size() - Method in class org.biojava.nbio.structure.cluster.Subunit
The size of a Subunit is the number of residues it contains.
size() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
 
size() - Method in class org.biojava.nbio.structure.contact.AtomContactSet
 
size() - Method in class org.biojava.nbio.structure.contact.GroupContactSet
 
size() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
 
size() - Method in interface org.biojava.nbio.structure.Group
Get number of atoms.
size() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
size() - Method in class org.biojava.nbio.structure.HetatomImpl
Get number of atoms.
size() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
Returns the number of mapped entries.
size() - Method in class org.biojava.nbio.structure.math.SparseVector
 
size() - Method in class org.biojava.nbio.structure.math.SymbolTable
How many keys are in the table?
size() - Method in class org.biojava.nbio.structure.Model
Returns the total number of chains in this model: polymeric, non-polymeric and water
size() - Method in interface org.biojava.nbio.structure.Structure
Return number of polymer Chains in this Structure for first model.
size() - Method in class org.biojava.nbio.structure.StructureImpl
 
size() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
 
size(int) - Method in interface org.biojava.nbio.structure.Structure
Return number of chains of model.
size(int) - Method in class org.biojava.nbio.structure.StructureImpl
return number of chains of model.
SIZE - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
skip(long) - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Skips characters.
skip(long) - Method in class org.biojava.nbio.core.util.UncompressInputStream
 
skip(long) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
Method skips n nucleotides in sequence stream.
sleepAmount - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
 
slider - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
SLIDER_STEPS - Static variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
Sm - org.biojava.nbio.structure.Element
 
SmallAnnotation - Class in org.biojava.nbio.ontology.utils
Annotation that is optimized for memory usage.
SmallAnnotation() - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation
Return a new SmallAnnotation optimised for small sets of properties.
SmallAnnotation(Map) - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation
Return a new SmallAnnotation that copies all values from a Map.
SmallAnnotation(Annotation) - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation
Return a new SmallAnnotation that copies all values from another annoation.
SmallMap - Class in org.biojava.nbio.ontology.utils
Lightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability.
SmallMap() - Constructor for class org.biojava.nbio.ontology.utils.SmallMap
 
SmallMap(int) - Constructor for class org.biojava.nbio.ontology.utils.SmallMap
 
SmallMap(Map) - Constructor for class org.biojava.nbio.ontology.utils.SmallMap
 
SMART - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
smartAdapter - Static variable in class org.biojava.nbio.structure.gui.BiojavaJmol
 
smartAdapter - Static variable in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
SmithWaterman<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment
Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence).
SmithWaterman() - Constructor for class org.biojava.nbio.alignment.SmithWaterman
SmithWaterman(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SmithWaterman
Prepares for a pairwise local sequence alignment.
SmithWaterman3Daligner - Class in org.biojava.nbio.structure.align.seq
Provides a 3D superimposition of two structures based on their sequence alignment.
SmithWaterman3Daligner() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
 
SmithWaterman3DParameters - Class in org.biojava.nbio.structure.align.seq
 
SmithWaterman3DParameters() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
 
SmithWatermanStartupParams() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
 
SmithWatermanUserArgumentProcessor - Class in org.biojava.nbio.structure.align.seq
 
SmithWatermanUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
 
SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams - Class in org.biojava.nbio.structure.align.seq
 
Sn - org.biojava.nbio.structure.Element
 
SoftHashMap<K,​V> - Class in org.biojava.nbio.core.util
A in memory cache using soft references.
SoftHashMap() - Constructor for class org.biojava.nbio.core.util.SoftHashMap
 
SoftHashMap(int) - Constructor for class org.biojava.nbio.core.util.SoftHashMap
 
SolexaFastqReader - Class in org.biojava.nbio.genome.io.fastq
Reader for FastqVariant.FASTQ_SOLEXA formatted sequences.
SolexaFastqReader() - Constructor for class org.biojava.nbio.genome.io.fastq.SolexaFastqReader
 
SolexaFastqWriter - Class in org.biojava.nbio.genome.io.fastq
Writer for FastqVariant.FASTQ_SOLEXA formatted sequences.
SolexaFastqWriter() - Constructor for class org.biojava.nbio.genome.io.fastq.SolexaFastqWriter
 
SOLID_STATE_NMR - org.biojava.nbio.structure.ExperimentalTechnique
 
SOLUTION_NMR - org.biojava.nbio.structure.ExperimentalTechnique
 
SOLUTION_SCATTERING - org.biojava.nbio.structure.ExperimentalTechnique
 
solve(Matrix) - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition
Solve A*X = B
solve(Matrix) - Method in class org.biojava.nbio.structure.jama.LUDecomposition
Solve A*X = B
solve(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Solve A*X = B
solve(Matrix) - Method in class org.biojava.nbio.structure.jama.QRDecomposition
Least squares solution of A*X = B
SOLVENTACCESSIBILITY - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
 
solveTranspose(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Solve X*A = B, which is also A'*X' = B'
SOPair(String, int) - Constructor for class org.biojava.nbio.ontology.obo.OboFileParser.SOPair
 
SOPair(String, int, int) - Constructor for class org.biojava.nbio.ontology.obo.OboFileParser.SOPair
 
sort() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Sorts the interface list and reassigns ids based on new sorting
sortAfps(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
 
sortBlocks(List<Block>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Sort blocks so that the specified row is in sequential order.
sortByFoldDecending() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
sortByStart() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Create a new list that is ordered by the starting index of the features' locations.
source() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
Get source (aka method).
SOURCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
SpaceGroup - Class in org.biojava.nbio.structure.xtal
A crystallographic space group.
SpaceGroup(int, int, int, String, String, BravaisLattice) - Constructor for class org.biojava.nbio.structure.xtal.SpaceGroup
 
SpaceGroupMapElements - Class in org.biojava.nbio.structure.xtal.io
 
SpaceGroupMapElements(Integer, SpaceGroup) - Constructor for class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements
 
SpaceGroupMapRoot - Class in org.biojava.nbio.structure.xtal.io
 
SpaceGroupMapRoot() - Constructor for class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
 
SparseSquareMatrix - Class in org.biojava.nbio.structure.math
A sparse, square matrix, implementing using two arrays of sparse vectors, one representation for the rows and one for the columns.
SparseSquareMatrix(int) - Constructor for class org.biojava.nbio.structure.math.SparseSquareMatrix
initialize an N-by-N matrix of all 0s
SparseVector - Class in org.biojava.nbio.structure.math
A sparse vector, implemented using a symbol table.
SparseVector(int) - Constructor for class org.biojava.nbio.structure.math.SparseVector
Constructor. initialize the all 0s vector of length N
Species - org.biojava.nbio.structure.scop.ScopCategory
 
SPHERES - org.biojava.nbio.structure.gui.RenderStyle
 
SphereSampler - Class in org.biojava.nbio.structure.symmetry.geometry
Sample possible orientations.
splice(DNASequence) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Concatenate successive portions of the specified sequence using the feature locations in the list.
splitBlocksByTopology(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
 
SplitFasta - Class in org.biojava.nbio.genome.util
Utility to write each Fasta entry to a unique file
SplitFasta() - Constructor for class org.biojava.nbio.genome.util.SplitFasta
 
sqrt(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
sqrt(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
SqrtColorMapper - Class in org.biojava.nbio.structure.gui.util.color
Performs a sqrt transform on input before passing the values off to another colorMapper.
SqrtColorMapper(ContinuousColorMapper) - Constructor for class org.biojava.nbio.structure.gui.util.color.SqrtColorMapper
Creates a new SqrtColorMapper.
Sr - org.biojava.nbio.structure.Element
 
SSBondImpl - Class in org.biojava.nbio.structure.io
A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.
SSBondImpl() - Constructor for class org.biojava.nbio.structure.io.SSBondImpl
 
StainType - Enum in org.biojava.nbio.genome.parsers.cytoband
 
stalk - org.biojava.nbio.genome.parsers.cytoband.StainType
 
STANDARD_BASES - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
standardAASet - Static variable in class org.biojava.nbio.aaproperties.PeptideProperties
Contains the 20 standard AA code in a set
StandardAminoAcid - Class in org.biojava.nbio.structure
A class that provides a set of standard amino acids.
StandardRescoreRefiner<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment
 
StandardRescoreRefiner(Alignments.PairInProfileScorerType, Alignments.ProfileProfileAlignerType) - Constructor for class org.biojava.nbio.alignment.StandardRescoreRefiner
 
start() - Method in class org.biojava.nbio.genome.parsers.gff.Location
Get starting index (origin 0).
start() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
 
START_SEQUENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
StartCodonSequence - Class in org.biojava.nbio.core.sequence
Used to map the start codon feature on a gene
StartCodonSequence(TranscriptSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.StartCodonSequence
 
startElement(String, String, String, Attributes) - Method in class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
 
startingAlignment(String, Atom[], String, Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
 
startsAfter(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Check if this location starts after the other location starts.
startsBefore(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Check if this location starts before other location starts.
StartupParameters - Class in org.biojava.nbio.structure.align.ce
A simple bean that contains the parameters that can get set at startup
StartupParameters() - Constructor for class org.biojava.nbio.structure.align.ce.StartupParameters
 
stateChanged(ChangeEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
 
stateChanged(ChangeEvent) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
 
stateChanged(ChangeEvent) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
 
StaticMemberPlaceHolder - Class in org.biojava.nbio.ontology.utils
 
StaticMemberPlaceHolder() - Constructor for class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder
 
StaticMemberPlaceHolder(Field) - Constructor for class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder
 
status - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
STATUS_ENDPOINT - Static variable in class org.biojava.nbio.structure.PDBStatus
 
STATUS_LIST_ENDPOINT - Static variable in class org.biojava.nbio.structure.PDBStatus
 
StatusDisplay - Class in org.biojava.nbio.structure.align.gui.aligpanel
 
StatusDisplay() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
StdArrayIO - Class in org.biojava.nbio.survival.cox.matrix
Standard array IO.
StdArrayIO() - Constructor for class org.biojava.nbio.survival.cox.matrix.StdArrayIO
 
stepParameters - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
STICKS - org.biojava.nbio.structure.gui.RenderStyle
 
StockholmFileAnnotation - Class in org.biojava.nbio.alignment.io
Stores all the content parsed from the #=GF lines
StockholmFileAnnotation() - Constructor for class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
StockholmFileAnnotation.StockholmFileAnnotationReference - Class in org.biojava.nbio.alignment.io
 
StockholmFileAnnotationReference() - Constructor for class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
 
StockholmFileParser - Class in org.biojava.nbio.alignment.io
StockholmFileParser() - Constructor for class org.biojava.nbio.alignment.io.StockholmFileParser
 
StockholmStructure - Class in org.biojava.nbio.alignment.io
Stores all the content of a Stockholm file.
StockholmStructure() - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure
 
StockholmStructure.DatabaseReference - Class in org.biojava.nbio.alignment.io
 
Stoichiometry - Class in org.biojava.nbio.structure.symmetry.core
A utility object that describes Stoichiometry (composition of a protein assembly), determined via clustering procedure SubunitClusterer, and implements human-readable representation using various strategies.
Stoichiometry(List<SubunitCluster>) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry
Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster>, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry
Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster>, Function<List<SubunitCluster>, String>) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry
Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster>, Stoichiometry.StringOverflowStrategy) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry
Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster>, Stoichiometry.StringOverflowStrategy, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry
Constructor for Stoichiometry.
Stoichiometry.StringOverflowStrategy - Enum in org.biojava.nbio.structure.symmetry.core
What to do when the number of SubunitCluster exceeds the length of the alphabet.
stop() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
Interrupt searching for suggestions
stop() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
 
stop() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
 
stop() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
 
stopAtStopCodons(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
If set, then the last codon translated in the resulting peptide sequence will be the stop codon
StopCodonSequence - Class in org.biojava.nbio.core.sequence
Used to map the stop codon sequence on a gene
StopCodonSequence(TranscriptSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.StopCodonSequence
 
storeObjects(List<Result>) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
 
storeObjects(List<Result>) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
 
storeObjects(List<Result>) - Method in interface org.biojava.nbio.core.search.io.ResultFactory
The factory that implements this method will be able to save the Search results to a file in the same format that it is able to read.
storeParameters() - Method in class org.biojava.nbio.structure.align.gui.ParameterGUI
 
storeUnAlignedSeqRes(Structure, List<Chain>, boolean) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
Storing unaligned SEQRES groups in a Structure.
str - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair
 
Strand - Enum in org.biojava.nbio.core.sequence
Provides a way of representing the strand of a sequence, location hit or feature.
StrataInfo - Class in org.biojava.nbio.survival.cox
Information needed to represent a survival curve
StrataInfo() - Constructor for class org.biojava.nbio.survival.cox.StrataInfo
 
StrCompAlignment - Class in org.biojava.nbio.structure.align.pairwise
 
StrCompAlignment(int, int) - Constructor for class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
 
stream(Readable, StreamListener) - Method in interface org.biojava.nbio.genome.io.fastq.FastqReader
Stream the specified readable.
StreamListener - Interface in org.biojava.nbio.genome.io.fastq
Event based parser callback.
StringManipulationHelper - Class in org.biojava.nbio.core.util
A utility class for common String manipulation tasks.
StringProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
An example of a ProxySequenceReader that is created from a String.
StringProxySequenceReader() - Constructor for class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
StringProxySequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
stringToFloats(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
StrucAligParameters - Class in org.biojava.nbio.structure.align
A class that contains all the parameters of the structure alignment algorithm.
StrucAligParameters() - Constructor for class org.biojava.nbio.structure.align.StrucAligParameters
 
structuralDistance(double[][], double, double, double) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
The structural distance (dS) uses the structural similarity (or dissimilarity) from a the structural alignment of two protein strutures.
structure - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
structure - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
Structure - Interface in org.biojava.nbio.structure
Interface for a structure object.
STRUCTURE - org.biojava.nbio.structure.cluster.SubunitClustererMethod
The STRUCTURE clustering method uses the residue sequence and the coordinates of its Atom representatives of the Subunit to calculate sequence and structure alignments.
StructureAlignment - Interface in org.biojava.nbio.structure.align
 
StructureAlignmentDisplay - Class in org.biojava.nbio.structure.align.gui
 
StructureAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay
 
StructureAlignmentFactory - Class in org.biojava.nbio.structure.align
 
StructureAlignmentFactory() - Constructor for class org.biojava.nbio.structure.align.StructureAlignmentFactory
 
StructureAlignmentJmol - Class in org.biojava.nbio.structure.align.gui.jmol
A class that provides a simple GUI for Jmol
StructureAlignmentJmol() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
 
StructureAlignmentJmol(AFPChain, Atom[], Atom[]) - Constructor for class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
 
StructureAlignmentOptimizer - Class in org.biojava.nbio.structure.align.fatcat.calc
 
StructureAlignmentOptimizer(int, int, Atom[], int, int, Atom[], int, int[][]) - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer
optimize the structural alignment by update the equivalent residues and then run dynamic programming input: len1 the length of structure 1; c1: the structure information of 1 len2 the length of structure 2; c2: the structure information of 2 iniLen and iniSet is the length and list of initial equivalent residues
StructureAtom - Class in org.biojava.nbio.protmod.structure
Everything that is needed to uniquely describe a atom.
StructureAtom(StructureGroup, String) - Constructor for class org.biojava.nbio.protmod.structure.StructureAtom
 
StructureAtomLinkage - Class in org.biojava.nbio.protmod.structure
 
StructureAtomLinkage(StructureAtom, StructureAtom, double) - Constructor for class org.biojava.nbio.protmod.structure.StructureAtomLinkage
 
StructureAtomXMLConverter - Class in org.biojava.nbio.protmod.io
 
StructureAtomXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.StructureAtomXMLConverter
 
StructureException - Exception in org.biojava.nbio.structure
An exception during the parsing of a PDB file.
StructureException(String) - Constructor for exception org.biojava.nbio.structure.StructureException
Constructs a StructureException object.
StructureException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.StructureException
Constructs a StructureException object.
StructureException(Throwable) - Constructor for exception org.biojava.nbio.structure.StructureException
Constructs a StructureException object.
StructureFiletype - Enum in org.biojava.nbio.structure.io
An enum of supported file formats.
StructureGroup - Class in org.biojava.nbio.protmod.structure
Information of a group (residue or ligand) involved in a modification.
StructureGroup() - Constructor for class org.biojava.nbio.protmod.structure.StructureGroup
 
StructureGroup(ResidueNumber, String, boolean) - Constructor for class org.biojava.nbio.protmod.structure.StructureGroup
 
StructureGroupXMLConverter - Class in org.biojava.nbio.protmod.io
 
StructureGroupXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.StructureGroupXMLConverter
 
StructureIdentifier - Interface in org.biojava.nbio.structure
An identifier that uniquely identifies a whole Structure or arbitrary substructure.
StructureImpl - Class in org.biojava.nbio.structure
Implementation of a PDB Structure.
StructureImpl() - Constructor for class org.biojava.nbio.structure.StructureImpl
Constructs a StructureImpl object.
StructureImpl(Chain) - Constructor for class org.biojava.nbio.structure.StructureImpl
Construct a Structure object that contains a particular chain
StructureImpl(Group) - Constructor for class org.biojava.nbio.structure.StructureImpl
Construct a Structure object that only contains a single group
StructureInterface - Class in org.biojava.nbio.structure.contact
An interface between 2 molecules (2 sets of atoms).
StructureInterface() - Constructor for class org.biojava.nbio.structure.contact.StructureInterface
Constructs an empty StructureInterface
StructureInterface(Atom[], Atom[], String, String, AtomContactSet, CrystalTransform, CrystalTransform) - Constructor for class org.biojava.nbio.structure.contact.StructureInterface
Constructs a StructureInterface
StructureInterfaceCluster - Class in org.biojava.nbio.structure.contact
 
StructureInterfaceCluster() - Constructor for class org.biojava.nbio.structure.contact.StructureInterfaceCluster
 
StructureInterfaceList - Class in org.biojava.nbio.structure.contact
A list of interfaces between 2 molecules (2 sets of atoms)
StructureInterfaceList() - Constructor for class org.biojava.nbio.structure.contact.StructureInterfaceList
 
StructureIO - Class in org.biojava.nbio.structure
A class that provides static access methods for easy lookup of protein structure related components
StructureIO() - Constructor for class org.biojava.nbio.structure.StructureIO
 
StructureIOFile - Interface in org.biojava.nbio.structure.io
StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem.
StructureLoaderThread - Class in org.biojava.nbio.structure.align.gui
 
StructureName - Class in org.biojava.nbio.structure.align.client
A utility class that makes working with names of structures, domains and ranges easier.
StructureName(String) - Constructor for class org.biojava.nbio.structure.align.client.StructureName
Create a new StructureName from the given identifier, which may be a domain name, a substructure identifier, etc.
StructureName.Source - Enum in org.biojava.nbio.structure.align.client
 
StructurePairAligner - Class in org.biojava.nbio.structure.align
Perform a pairwise protein structure superimposition.
StructurePairAligner() - Constructor for class org.biojava.nbio.structure.align.StructurePairAligner
 
StructurePairSelector - Interface in org.biojava.nbio.structure.gui.util
To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.
StructureProvider - Interface in org.biojava.nbio.structure.io
A class that can provide a protein structure object from somewhere.
StructureSequenceMatcher - Class in org.biojava.nbio.structure.io
A utility class with methods for matching ProteinSequences with Structures.
StructureSequenceMatcher() - Constructor for class org.biojava.nbio.structure.io.StructureSequenceMatcher
 
StructureTools - Class in org.biojava.nbio.structure
A class that provides some tool methods.
StructureTools() - Constructor for class org.biojava.nbio.structure.StructureTools
 
StructureUtil - Class in org.biojava.nbio.protmod.structure
 
StructureViewer - Interface in org.biojava.nbio.structure.gui
 
SUB_SEQUENCE_DATA - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
 
submit(Callable<T>) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
Queues up a task and adds a default log entry.
submit(Callable<T>, String) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
Queues up a task and adds a log entry.
Subproblem(int, int, int, int) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
 
Subproblem(int, int, int, int, boolean) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
 
subSequence(int, int) - Method in class org.biojava.nbio.survival.data.CompactCharSequence
 
SUBSET - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
Substitute(String, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Substitute
 
Substitute(Sequence<C>, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Substitute
 
SUBSTITUTION - org.biojava.nbio.alignment.routines.AlignerHelper.Last
 
substitutionMatrix - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
SubstitutionMatrix<C extends Compound> - Interface in org.biojava.nbio.core.alignment.template
Defines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.
SubstitutionMatrixHelper - Class in org.biojava.nbio.core.alignment.matrices
Static utility to access substitution matrices that come bundled with BioJava.
SubstitutionMatrixScorer<S extends Sequence<C>,​C extends Compound> - Class in org.biojava.nbio.alignment
Scores using a substitution matrix.
SubstitutionMatrixScorer(SequencePair<S, C>, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SubstitutionMatrixScorer
 
SubstructureIdentifier - Class in org.biojava.nbio.structure
This is the canonical way to identify a part of a structure.
SubstructureIdentifier(String) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier
Create a new identifier from a string.
SubstructureIdentifier(String, List<ResidueRange>) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier
Create a new identifier based on a set of ranges.
SubstructureIdentifier(PdbId, List<ResidueRange>) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier
Create a new identifier based on a set of ranges.
subtract(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
subtract(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
subtract two atoms ( a - b).
Subunit - Class in org.biojava.nbio.structure.cluster
A Subunit consists of a set of residues from a Structure, which may correspond to an entire Chain, a Domain, or any subset or combination of residues from them.
Subunit(Atom[], String, StructureIdentifier, Structure) - Constructor for class org.biojava.nbio.structure.cluster.Subunit
A Subunit is solely defined by the coordinates of the representative Atoms of its residues.
SubunitCluster - Class in org.biojava.nbio.structure.cluster
A SubunitCluster contains a set of equivalent QuatSymmetrySubunits, the set of equivalent residues (EQR) between Subunit and a Subunit representative.
SubunitCluster(Subunit) - Constructor for class org.biojava.nbio.structure.cluster.SubunitCluster
A constructor from a single Subunit.
SubunitCluster(SubunitCluster, List<Integer>) - Constructor for class org.biojava.nbio.structure.cluster.SubunitCluster
A copy constructor with the possibility of removing subunits.
SubunitClusterer - Class in org.biojava.nbio.structure.cluster
The SubunitClusterer takes as input a collection of Subunit and returns a collection of SubunitCluster.
SubunitClustererMethod - Enum in org.biojava.nbio.structure.cluster
The SubunitClustererMethod ennummerates all methods that can be used to cluster Subunit in the SubunitCluster.
SubunitClustererParameters - Class in org.biojava.nbio.structure.cluster
The SubunitClustererParameters specifies the options used for the clustering of the subunits in structures using the SubunitClusterer.
SubunitClustererParameters() - Constructor for class org.biojava.nbio.structure.cluster.SubunitClustererParameters
Initialize with "local" metrics by default.
SubunitClustererParameters(boolean) - Constructor for class org.biojava.nbio.structure.cluster.SubunitClustererParameters
"Local" metrics are scoring SubunitClustererMethod.SEQUENCE: sequence identity of a local alignment (normalised by the number of aligned residues) sequence coverage of the alignment (normalised by the length of the longer sequence) SubunitClustererMethod.STRUCTURE: RMSD of the aligned substructures and structure coverage of the alignment (normalised by the length of the larger structure) Two thresholds for each method are required.
SubunitExtractor - Class in org.biojava.nbio.structure.cluster
The SubunitExtractor extracts the information of each protein Chain in a Structure and converts them into a List of Subunit.
suffix(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location
The part of this location after the specified position.
suffix(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
The part of this location after the other location (not inclusive).
suggestDomains(Atom[]) - Static method in class org.biojava.nbio.structure.domain.LocalProteinDomainParser
Suggest domains for a set of Calpha atoms
suggestDomains(Structure) - Static method in class org.biojava.nbio.structure.domain.LocalProteinDomainParser
Suggest domains for a protein structure
SULFUR_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
 
SUMMARY_POS - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
Position at which the alignment summary is printed
SUMMARY_POS - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
Position at which the alignment summary is printed
SUMOYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
 
Superfamily - org.biojava.nbio.structure.scop.ScopCategory
 
superimpose(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer
 
superimpose(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer
Superimpose all structures from a MultipleAlignment.
superimpose(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer
 
superpose(Point3d[], Point3d[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition
Obtain the superposition matrix that minimizes the RMSD between two arrays of equivalent points.
superpose(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP
 
superpose(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQuat
 
superpose(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
Use the SuperPosition.superpose(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.
superpose(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionSVD
 
superposeAfterRmsd() - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP
The QCP method can be used as a two-step calculation: first compute the RMSD (fast) and then compute the superposition.
superposeAndTransform(Point3d[], Point3d[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition
Transform an array of points so that the coordinates of its points minimize the RMSD to the other array of equivalent points, and return the transformation matrix applied.
superposeAndTransform(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
 
superposeAndTransform(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
Use the SuperPosition.superposeAndTransform(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.
superposeAndTransformAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
Use the SuperPosition.superposeAndTransform(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.
superposeAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
Use the SuperPosition.superpose(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.
SuperPosition - Interface in org.biojava.nbio.structure.geometry
The SuperPosition interface defines and documents the required methods for any superpostion algorithm implementation, so that the input and expected output are uniform.
SuperPositionAbstract - Class in org.biojava.nbio.structure.geometry
The SuperPositionAbstract contains common code shared by all SuperPosition algorithm implementations.
SuperPositionAbstract(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionAbstract
 
SuperPositionQCP - Class in org.biojava.nbio.structure.geometry
Implementation of the Quaternion-Based Characteristic Polynomial algorithm for RMSD and Superposition calculations.
SuperPositionQCP(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionQCP
Default constructor for the quaternion based superposition algorithm.
SuperPositionQCP(boolean, double, double) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionQCP
Constructor with option to set the precision values.
SuperPositionQuat - Class in org.biojava.nbio.structure.geometry
The SuperPositionQuat implements a quaternion based algorithm to superpose arrays of Points in 3D.
SuperPositionQuat(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionQuat
Constructor for the quaternion based superposition algorithm.
SuperPositions - Class in org.biojava.nbio.structure.geometry
SuperPositions is a Class that provides static helper methods and an easy access to the whole family of SuperPosition algorithms.
SuperPositionSVD - Class in org.biojava.nbio.structure.geometry
A class that calculates the superposition between two sets of points using an SVD Matrix Decomposition.
SuperPositionSVD(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionSVD
Constructor for the SVD superposition algorithm.
surf - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor
 
Surface() - Constructor for class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
 
SURFACE - org.biojava.nbio.structure.gui.RenderStyle
 
SurvFitInfo - Class in org.biojava.nbio.survival.cox
Contains info for graphing km figures
SurvFitInfo() - Constructor for class org.biojava.nbio.survival.cox.SurvFitInfo
 
SurvFitKM - Class in org.biojava.nbio.survival.kaplanmeier.figure
Ported from survfitKM.S When combining multiple entries with same time not sure how the weighting adds up
SurvFitKM() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
 
SurvFitKM.ConfLower - Enum in org.biojava.nbio.survival.kaplanmeier.figure
 
SurvFitKM.ConfType - Enum in org.biojava.nbio.survival.kaplanmeier.figure
 
SurvFitKM.Error - Enum in org.biojava.nbio.survival.kaplanmeier.figure
 
SurvFitKM.Method - Enum in org.biojava.nbio.survival.kaplanmeier.figure
 
SurvivalInfo - Class in org.biojava.nbio.survival.cox
Data class to represent a single sample where time and event/censor status is required Additionally each variable and data associated with that variable.
SurvivalInfo(double, int) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo
 
SurvivalInfo(double, int, String, double) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo
 
SurvivalInfo(double, int, LinkedHashMap<String, Double>) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo
 
SurvivalInfoComparator - Class in org.biojava.nbio.survival.cox.comparators
 
SurvivalInfoComparator() - Constructor for class org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator
 
SurvivalInfoHelper - Class in org.biojava.nbio.survival.cox
Used to work with SurvivalInfo
SurvivalInfoHelper() - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoHelper
 
SurvivalInfoIndex - Class in org.biojava.nbio.survival.cox
Not used and probably should be deleted
SurvivalInfoIndex(double, int, int) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoIndex
 
SurvivalInfoIndex(double, int, int, double) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoIndex
 
SurvivalInfoIndex(double, int, int, double[]) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoIndex
 
SurvivalInfoValueComparator - Class in org.biojava.nbio.survival.cox.comparators
 
SurvivalInfoValueComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator
 
svd() - Method in class org.biojava.nbio.structure.jama.Matrix
Singular Value Decomposition
swapRowAndColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
Swap the row and columns returning a new worksheet
SYM_CHAIN_ID_SEPARATOR - Static variable in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
The character separating the original chain identifier from the operator id.
SymbolTable<Key extends Comparable<Key>,​Value> - Class in org.biojava.nbio.structure.math
Sorted symbol table implementation using a java.util.TreeMap.
SymbolTable() - Constructor for class org.biojava.nbio.structure.math.SymbolTable
Create an empty symbol table.
SYMMETRIC - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass
 
SYMMETRIC - Static variable in class org.biojava.nbio.ontology.OntoTools
 
SymmetryAxes - Class in org.biojava.nbio.structure.symmetry.internal
Data Structure that stores all the symmetry axis that describe the symmetry of a structure.
SymmetryAxes() - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
Constructor.
SymmetryAxes.Axis - Class in org.biojava.nbio.structure.symmetry.internal
Represents an axis of symmetry
SymmetryCalc - Class in org.biojava.nbio.structure.symmetry.gui
Calculates a symmetry analysis and displays the results.
SymmetryCalc(SymmetryGui, Structure) - Constructor for class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
Requests for a structure to analyze.
symmetryCoefficient() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
 
SymmetryDisplay - Class in org.biojava.nbio.structure.symmetry.gui
Class that provides visualizations methods for symmetry alignments.
SymmetryDisplay() - Constructor for class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
 
SymmetryGui - Class in org.biojava.nbio.structure.symmetry.gui
A JFrame that allows to trigger a symmetry analysis, either from files in a directory or after manual upload Adapted from the AlignmentGui class in biojava.
SymmetryListener - Class in org.biojava.nbio.structure.symmetry.gui
Action Listener for the symmetry menu.
SymmetryListener(MultipleAlignmentJmol, CeSymmResult) - Constructor for class org.biojava.nbio.structure.symmetry.gui.SymmetryListener
 
SymmetryPerceptionMethod - Enum in org.biojava.nbio.structure.symmetry.core
Method used for symmetry perception in the QuatSymmetryDetector.
SymmetryRefiner - Interface in org.biojava.nbio.structure.symmetry.internal
Interface for all symmetry refinement implementations.
SymmetryTools - Class in org.biojava.nbio.structure.symmetry.utils
Utility methods for symmetry (quaternary and internal) detection and result manipulation.
SymmOptimizer - Class in org.biojava.nbio.structure.symmetry.internal
Optimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment.
SymmOptimizer(CeSymmResult) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmOptimizer
Constructor with a seed MultipleAligment storing a refined symmetry alignment of the repeats.
SymoplibParser - Class in org.biojava.nbio.structure.xtal
A class containing static methods to parse the symop.lib file from the CCP4 package.
SymoplibParser() - Constructor for class org.biojava.nbio.structure.xtal.SymoplibParser
 
SynchronizedOutFile - Class in org.biojava.nbio.structure.align.util
 
SynchronizedOutFile(File) - Constructor for class org.biojava.nbio.structure.align.util.SynchronizedOutFile
create a thread safe wrapper for working with this file
SynchronizedOutFile(File, boolean) - Constructor for class org.biojava.nbio.structure.align.util.SynchronizedOutFile
Create a thread safe wrapper for writing to this file, the file will be gzip compressed.
Synonym - Class in org.biojava.nbio.ontology
 
Synonym() - Constructor for class org.biojava.nbio.ontology.Synonym
 
SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
SystematicSolver - Class in org.biojava.nbio.structure.symmetry.core
 
SystematicSolver(QuatSymmetrySubunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.SystematicSolver
 
SystemInfo - Class in org.biojava.nbio.structure.align.gui
 
SystemInfo() - Constructor for class org.biojava.nbio.structure.align.gui.SystemInfo
 

T

T - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
T - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
T - org.biojava.nbio.structure.Element
Tritium
T - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
T0 - org.biojava.nbio.ronn.RonnConstraint.Threshold
 
T1 - org.biojava.nbio.ronn.RonnConstraint.Threshold
 
T2 - org.biojava.nbio.ronn.RonnConstraint.Threshold
 
T3 - org.biojava.nbio.ronn.RonnConstraint.Threshold
 
T4 - org.biojava.nbio.ronn.RonnConstraint.Threshold
 
T5 - org.biojava.nbio.ronn.RonnConstraint.Threshold
 
T6 - org.biojava.nbio.ronn.RonnConstraint.Threshold
 
T7 - org.biojava.nbio.ronn.RonnConstraint.Threshold
 
T8 - org.biojava.nbio.ronn.RonnConstraint.Threshold
 
T9 - org.biojava.nbio.ronn.RonnConstraint.Threshold
 
Ta - org.biojava.nbio.structure.Element
 
TabDelimParser - Class in org.biojava.nbio.ontology.io
Parse tab-delimited ontology files into Ontology objects.
TabDelimParser() - Constructor for class org.biojava.nbio.ontology.io.TabDelimParser
 
table(Integer) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by ID.
table(String) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by its String name
table(Table) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
 
Table - Interface in org.biojava.nbio.core.sequence.transcription
Provides a way of separating us from the specific IUPACParser.IUPACTable even though this is the only implementing class for the interface.
Table.CaseInsensitiveTriplet - Class in org.biojava.nbio.core.sequence.transcription
Class used to hold three nucleotides together and allow for equality to be assessed in a case insensitive manner.
Table.Codon - Class in org.biojava.nbio.core.sequence.transcription
Instance of a Codon which is 3 NucleotideCompounds, its corresponding AminoAcidCompound and if it is a start or stop codon.
Tabular - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
 
TaxonomyID - Class in org.biojava.nbio.core.sequence
A sequence can be associated with a species or Taxonomy ID
TaxonomyID(String, DataSource) - Constructor for class org.biojava.nbio.core.sequence.TaxonomyID
 
Tb - org.biojava.nbio.structure.Element
 
tblastn - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
 
tblastx - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
 
Tc - org.biojava.nbio.structure.Element
 
TD - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
TD1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
Te - org.biojava.nbio.structure.Element
 
techniquesToStringArray(Set<ExperimentalTechnique>) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
Converts the set of experimental techniques to an array of strings.
tempBuffer - Variable in class org.biojava.nbio.ontology.obo.OboFileParser
 
TEMPLATE_LENTH - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
TEMPLATE_TYPE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
Term - Interface in org.biojava.nbio.ontology
A term in an ontology.
TERM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
Term.Impl - Class in org.biojava.nbio.ontology
Simple in-memory implementation of an ontology term.
TertiaryBasePairParameters - Class in org.biojava.nbio.structure.basepairs
This class also finds the base pairing and base-pair step parameters but has a broader definition of a base pair so that non-canonical-WC base pairs will be detected and reported.
TertiaryBasePairParameters(Structure, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
 
TestDNANeedlemanWunsch - Class in demo
 
TestDNANeedlemanWunsch() - Constructor for class demo.TestDNANeedlemanWunsch
 
TETRAGONAL - org.biojava.nbio.structure.xtal.BravaisLattice
 
TETRAHEDRAL_CARBON_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
 
TETRAHEDRAL_NITROGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
 
Tetrahedron - Class in org.biojava.nbio.structure.symmetry.geometry
 
Tetrahedron() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
 
text - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
Text - org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum
 
TEXT_ONLY - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
 
TEXT_SCALE_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
TextFeature<S extends AbstractSequence<C>,​C extends Compound> - Class in org.biojava.nbio.core.sequence.features
A implmentation of AbstractFeature
TextFeature(String, String, String, String) - Constructor for class org.biojava.nbio.core.sequence.features.TextFeature
 
Th - org.biojava.nbio.structure.Element
 
thread - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
 
THREE - org.biojava.nbio.core.sequence.transcription.Frame
 
THREEBAR - org.biojava.nbio.structure.xtal.TransformType
 
THREEFOLD - org.biojava.nbio.structure.xtal.TransformType
 
THREEFOLDSCREW - org.biojava.nbio.structure.xtal.TransformType
 
Threshold(int) - Constructor for class org.biojava.nbio.ronn.ModelLoader.Threshold
 
THRESHOLD - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
THROW_EXCEPTION - org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
Throw a StructureException for obsolete entries.
Ti - org.biojava.nbio.structure.Element
 
time - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
time - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
Timer - Class in org.biojava.nbio.ronn
A simple timer, calculates the time interval between two events.
Timer() - Constructor for class org.biojava.nbio.ronn.Timer
 
Timer(TimeUnit) - Constructor for class org.biojava.nbio.ronn.Timer
 
times(double) - Method in class org.biojava.nbio.structure.jama.Matrix
Multiply a matrix by a scalar, C = s*A
times(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
Linear algebraic matrix multiplication, A * B
times(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix
 
timeScale - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
timesEquals(double) - Method in class org.biojava.nbio.structure.jama.Matrix
Multiply a matrix by a scalar in place, A = s*A
TITLE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
titleHeight - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
Tl - org.biojava.nbio.structure.Element
 
Tm - org.biojava.nbio.structure.Element
 
TMP_DIR - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
 
TMScore(Point3d[], Point3d[], int) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
Returns the TM-Score for two superimposed sets of coordinates Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
to - Variable in class org.biojava.nbio.ronn.Jronn.Range
The range ending position includes the last residue.
to3DFormat(MultipleAlignment, int, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
Outputs a pairwise alignment in I-TASSER's 3D Format for target-template alignment. http://zhanglab.ccmb.med.umich.edu/I-TASSER/option4.html
toAlignedPairs(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter
Prints the alignment in the simplest form: a list of aligned residues.
toAlignedResidues(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
Converts the alignment to its simplest form: a list of groups of aligned residues.
toAtomSite() - Static method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier
Collects AbstractCifFileSupplier.WrappedAtom instances into one AtomSite.
toBinary(Structure) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Convert a structure to BCIF format.
toBinaryFile(Structure, Path) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Write a structure to a BCIF file.
toCanonical() - Method in class org.biojava.nbio.structure.align.client.StructureName
 
toCanonical() - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier
 
toCanonical() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
toCanonical() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
toCanonical() - Method in class org.biojava.nbio.structure.PassthroughIdentifier
 
toCanonical() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
toCanonical() - Method in interface org.biojava.nbio.structure.StructureIdentifier
Convert to a canonical SubstructureIdentifier.
toCanonical() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
Return itself.
toCanonical() - Method in class org.biojava.nbio.structure.URLIdentifier
 
toCE(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter
 
toCE(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
toCIEXYZ(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
 
toCifFile(Chain) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Convert Chain to CifFile
toCifFile(Structure) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Convert Structure to CifFile.
toConciseAlignmentString(Map<S, T>, Map<T, S>) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Print an alignment map in a concise representation.
toConciseAlignmentString(Map<T, T>) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
 
toDASStructure(XMLWriter) - Method in class org.biojava.nbio.structure.io.FileConvert
Convert a protein Structure to a DAS Structure XML response .
toDBSearchResult() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
toDBSearchResult(AFPChain) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter
 
toDoubleArray(Collection<Number>) - Static method in class org.biojava.nbio.structure.align.util.CollectionTools
 
toExtendedId(String) - Static method in class org.biojava.nbio.structure.PdbId
Converts shortId to the PDB ID extended format.
toFASTA(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
Converts the MultipleAlignment into a multiple sequence alignment String in FASTA format.
toFatcat(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
toFatCat(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter
 
toFatCat(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
Converts the MultipleAlignment into a FatCat String format.
toFatCatCore(AFPChain, Atom[], Atom[], boolean, boolean, boolean, boolean) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter
Output in FatCatCore format
toFullAlignment(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Method that converts a repeats symmetric alignment into an alignment of whole structures.
toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
toggleSelection(AlignedPosition) - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
 
toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
 
toHexColor(Color) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
 
toIndex(int) - Method in class org.biojava.nbio.core.sequence.views.ReversedSequenceView
 
toIntArray(Collection<Number>) - Static method in class org.biojava.nbio.structure.align.util.CollectionTools
 
toList(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
For the given Sequence this will return a List filled with the Compounds of that Sequence.
toMMCIF() - Method in interface org.biojava.nbio.structure.Chain
Convert this Chain to a String in mmCIF format
toMMCIF() - Method in class org.biojava.nbio.structure.ChainImpl
 
toMMCIF() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Return a String representing the 2 molecules of this interface in mmCIF format.
toMMCIF() - Method in class org.biojava.nbio.structure.io.FileConvert
Convert this structure to its CIF representation.
toMMCIF() - Method in interface org.biojava.nbio.structure.Structure
Create a String that contains this Structure's contents in MMCIF file format.
toMMCIF() - Method in class org.biojava.nbio.structure.StructureImpl
Create a String that contains this Structure's contents in MMCIF file format.
toMMCIF(Chain) - Static method in class org.biojava.nbio.structure.io.FileConvert
Convert a chain to its CIF representation.
toMultimodelStructure(MultipleAlignment, List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
 
TOOL - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
Tools() - Constructor for class org.biojava.nbio.core.sequence.location.template.Location.Tools
 
top - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
 
toPDB() - Method in class org.biojava.nbio.structure.AtomImpl
 
toPDB() - Method in interface org.biojava.nbio.structure.Chain
Convert this Chain to a String in PDB format
toPDB() - Method in class org.biojava.nbio.structure.ChainImpl
 
toPDB() - Method in class org.biojava.nbio.structure.contact.StructureInterface
Return a String representing the 2 molecules of this interface in PDB format.
toPDB() - Method in class org.biojava.nbio.structure.DBRef
Convert the DBRef object to a DBREF record as it is used in PDB files
toPDB() - Method in class org.biojava.nbio.structure.io.FileConvert
Convert a structure into a PDB file.
toPDB() - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
toPDB() - Method in class org.biojava.nbio.structure.PDBHeader
Return a PDB representation of the PDB Header
toPDB() - Method in interface org.biojava.nbio.structure.PDBRecord
Returns a PDB file like representation of this record.
toPDB() - Method in class org.biojava.nbio.structure.ResidueNumber
 
toPDB() - Method in class org.biojava.nbio.structure.Site
 
toPDB() - Method in interface org.biojava.nbio.structure.Structure
Create a String that contains this Structure's contents in PDB file format.
toPDB() - Method in class org.biojava.nbio.structure.StructureImpl
Create a String that contains this Structure's contents in PDB file format.
toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.AtomImpl
 
toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.DBRef
Append the PDB representation of this DBRef to the provided StringBuffer
toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.io.SSBondImpl
Append the PDB representation of this SSBOND to the provided StringBuffer
toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.PDBHeader
Appends a PDB representation of the PDB header to the provided StringBuffer
toPDB(StringBuffer) - Method in interface org.biojava.nbio.structure.PDBRecord
Appends a PDB file like representation of this record to the provided StringBuffer.
toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.Site
 
toPDB(Atom) - Static method in class org.biojava.nbio.structure.io.FileConvert
Prints the content of an Atom object as a PDB formatted line.
toPDB(Atom, String) - Static method in class org.biojava.nbio.structure.io.FileConvert
 
toPDB(Atom, StringBuffer) - Static method in class org.biojava.nbio.structure.io.FileConvert
 
toPDB(Atom, StringBuffer, String) - Static method in class org.biojava.nbio.structure.io.FileConvert
Print ATOM record in the following syntax
toPDB(Chain) - Static method in class org.biojava.nbio.structure.io.FileConvert
Convert a Chain object to PDB representation
toPDB(Group) - Static method in class org.biojava.nbio.structure.io.FileConvert
Convert a Group object to PDB representation
toPDB(Structure, Structure) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
converts the alignment to a PDB file each of the structures will be represented as a model.
Topolgy - org.biojava.nbio.structure.cath.CathCategory
 
toPrettyAlignment(AFPChain, Atom[], Atom[], boolean, boolean) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter
 
toProteinMSA(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid residues.
toRepeatsAlignment(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Method that converts a symmetry alignment into an alignment of the repeats only, as new independent structures.
toRGB(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
 
toRotMat() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
toRotMat(AFPChain) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter
 
torsionAngle(Atom, Atom, Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
Calculate the torsion angle, i.e. the angle between the normal vectors of the two plains a-b-c and b-c-d.
toScoresList(AFPChain) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter
 
toSDF() - Method in interface org.biojava.nbio.structure.Group
Function to get the Group as an MDL molblock
toSDF() - Method in class org.biojava.nbio.structure.HetatomImpl
 
toShortId(String) - Static method in class org.biojava.nbio.structure.PdbId
Converts extendedId to the PDB ID short format.
toSsBond(Bond) - Static method in class org.biojava.nbio.structure.io.SSBondImpl
Converts the given Bond object into a SSBondImpl.
toStartIndex(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
Calculates start index according to the equation start = ( (index-1) - windowSize) +1
toString() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
 
toString() - Method in class org.biojava.nbio.aaproperties.xml.Element
 
toString() - Method in class org.biojava.nbio.alignment.GuideTree
 
toString() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
toString() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
toString() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
Returns in a format similar to the standard NCBI files.
toString() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
Returns in a format similar to the standard NCBI files.
toString() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
Provides standard Java language access to results of SimpleAlignedSequence.getSequenceAsString().
toString() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
 
toString() - Method in interface org.biojava.nbio.core.alignment.template.Profile
Returns a simple view of the alignment profile.
toString() - Method in class org.biojava.nbio.core.sequence.AccessionID
 
toString() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
 
toString() - Method in class org.biojava.nbio.core.sequence.features.Qualifier
 
toString() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
 
toString() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
toString() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
toString() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
 
toString() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
toString() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
String representation of the MSA
toString() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
 
toString() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
toString() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
Returns a simple view of the alignment profile.
toString() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
 
toString() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
toString() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
toString() - Method in class org.biojava.nbio.core.util.CRC64Checksum
Returns a zero-padded 16 character wide string containing the current value of this checksum in uppercase hexadecimal format.
toString() - Method in class org.biojava.nbio.data.sequence.FastaSequence
Same as oneLineFasta
toString() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
 
toString() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
toString() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
toString() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
 
toString() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
A string representation of the feature.
toString() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Return a string representation of all features in this list.
toString() - Method in class org.biojava.nbio.genome.parsers.gff.Location
Return a string representation of location.
toString() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator
Get string representation of iterator.
toString() - Method in class org.biojava.nbio.ontology.Ontology.Impl
 
toString() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
 
toString() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
 
toString() - Method in class org.biojava.nbio.ontology.Synonym
 
toString() - Method in class org.biojava.nbio.ontology.Term.Impl
 
toString() - Method in class org.biojava.nbio.ontology.Triple.Impl
 
toString() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
 
toString() - Method in class org.biojava.nbio.phosphosite.Site
 
toString() - Method in class org.biojava.nbio.protmod.Component
 
toString() - Method in enum org.biojava.nbio.protmod.ModificationCategory
 
toString() - Method in class org.biojava.nbio.protmod.ModificationConditionImpl
 
toString() - Method in class org.biojava.nbio.protmod.ModificationLinkage
 
toString() - Method in enum org.biojava.nbio.protmod.ModificationOccurrenceType
 
toString() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
 
toString() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
 
toString() - Method in class org.biojava.nbio.protmod.structure.StructureAtom
 
toString() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
 
toString() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
 
toString() - Method in class org.biojava.nbio.ronn.Jronn.Range
 
toString() - Method in class org.biojava.nbio.ronn.ModelLoader.Model
 
toString() - Method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint
 
toString() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
 
toString() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
 
toString() - Method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
 
toString() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
 
toString() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
toString() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
 
toString() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
 
toString() - Method in class org.biojava.nbio.structure.align.client.PdbPair
 
toString() - Method in class org.biojava.nbio.structure.align.client.StructureName
 
toString() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
 
toString() - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
 
toString() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
 
toString() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
 
toString() - Method in class org.biojava.nbio.structure.align.helper.IndexPair
 
toString() - Method in class org.biojava.nbio.structure.align.helper.JointFragments
 
toString() - Method in class org.biojava.nbio.structure.align.model.AFP
 
toString() - Method in class org.biojava.nbio.structure.align.model.AFPChain
 
toString() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
toString() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
toString() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
 
toString() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
Return a summary of the MultipleAlignment, containing the structures, the lengths and the cached scores.
toString() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
 
toString() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
 
toString() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
print the idx positions of this alignment
toString() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
toString() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
 
toString() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
 
toString() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
 
toString() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
 
toString() - Method in class org.biojava.nbio.structure.AminoAcidImpl
string representation.
toString() - Method in class org.biojava.nbio.structure.AtomImpl
 
toString() - Method in class org.biojava.nbio.structure.Author
 
toString() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
toString() - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier
 
toString() - Method in class org.biojava.nbio.structure.BondImpl
 
toString() - Method in enum org.biojava.nbio.structure.cath.CathCategory
 
toString() - Method in class org.biojava.nbio.structure.cath.CathDomain
 
toString() - Method in class org.biojava.nbio.structure.cath.CathNode
 
toString() - Method in class org.biojava.nbio.structure.cath.CathSegment
 
toString() - Method in interface org.biojava.nbio.structure.Chain
 
toString() - Method in class org.biojava.nbio.structure.ChainImpl
 
toString() - Method in class org.biojava.nbio.structure.chem.ChemComp
 
toString() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
 
toString() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance
 
toString() - Method in class org.biojava.nbio.structure.cluster.Subunit
 
toString() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
 
toString() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
 
toString() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
 
toString() - Method in class org.biojava.nbio.structure.contact.BoundingBox
 
toString() - Method in class org.biojava.nbio.structure.contact.GridCell
 
toString() - Method in class org.biojava.nbio.structure.contact.GroupContact
 
toString() - Method in class org.biojava.nbio.structure.contact.Pair
 
toString() - Method in class org.biojava.nbio.structure.contact.StructureInterface
 
toString() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
 
toString() - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord
 
toString() - Method in class org.biojava.nbio.structure.DBRef
String representation of a DBRef.
toString() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
 
toString() - Method in class org.biojava.nbio.structure.domain.pdp.CutValues
 
toString() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
 
toString() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
 
toString() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
 
toString() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
 
toString() - Method in class org.biojava.nbio.structure.EntityInfo
 
toString() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique
 
toString() - Method in enum org.biojava.nbio.structure.GroupType
 
toString() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
 
toString() - Method in class org.biojava.nbio.structure.HetatomImpl
 
toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
 
toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
 
toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
 
toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
 
toString() - Method in class org.biojava.nbio.structure.io.SSBondImpl
 
toString() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
 
toString() - Method in class org.biojava.nbio.structure.jama.Matrix
 
toString() - Method in class org.biojava.nbio.structure.JournalArticle
 
toString() - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix
 
toString() - Method in class org.biojava.nbio.structure.math.SparseVector
 
toString() - Method in class org.biojava.nbio.structure.Model
 
toString() - Method in class org.biojava.nbio.structure.NucleotideImpl
 
toString() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
 
toString() - Method in class org.biojava.nbio.structure.PDBHeader
String representation
toString() - Method in class org.biojava.nbio.structure.PdbId
 
toString() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
 
toString() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
 
toString() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
 
toString() - Method in class org.biojava.nbio.structure.ResidueNumber
 
toString() - Method in class org.biojava.nbio.structure.ResidueRange
 
toString() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
 
toString() - Method in enum org.biojava.nbio.structure.scop.ScopCategory
 
toString() - Method in class org.biojava.nbio.structure.scop.ScopDescription
 
toString() - Method in class org.biojava.nbio.structure.scop.ScopDomain
 
toString() - Method in class org.biojava.nbio.structure.scop.ScopNode
 
toString() - Method in enum org.biojava.nbio.structure.secstruc.BridgeType
 
toString() - Method in class org.biojava.nbio.structure.secstruc.HBond
 
toString() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
 
toString() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement
 
toString() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
 
toString() - Method in enum org.biojava.nbio.structure.secstruc.SecStrucType
 
toString() - Method in interface org.biojava.nbio.structure.SeqMisMatch
 
toString() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
 
toString() - Method in class org.biojava.nbio.structure.Site
 
toString() - Method in interface org.biojava.nbio.structure.Structure
String representation of object.
toString() - Method in class org.biojava.nbio.structure.StructureImpl
String representation.
toString() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
 
toString() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
 
toString() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
 
toString() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
 
toString() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
toString() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
 
toString() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
 
toString() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
 
toString() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
 
toString() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
 
toString() - Method in class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
 
toString() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
toString() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
 
toString() - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector
 
toString() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
 
toString() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
toString() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
 
toString() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
toString() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
 
toString() - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
toString() - Method in class org.biojava.nbio.survival.cox.CoxVariables
 
toString() - Method in class org.biojava.nbio.survival.cox.StrataInfo
 
toString() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
 
toString() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
toString() - Method in class org.biojava.nbio.survival.cox.SurvivalInfoIndex
 
toString() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
 
toString() - Method in class org.biojava.nbio.survival.data.CompactCharSequence
 
toString() - Method in class org.biojava.nbio.survival.data.HeaderInfo
 
toString() - Method in class org.biojava.nbio.survival.data.WorkSheet
 
toString() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
toString() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
 
toString() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
 
toString() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
toString(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
 
toString(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile
Returns a formatted view of the alignment profile.
toString(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
Get a string representation of the MSA with a fixed width
toString(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
Returns a formatted view of the alignment profile.
toString(String, String, String) - Method in class org.biojava.nbio.survival.cox.CoxInfo
 
toString(List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange
 
toString(Profile.StringFormat) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
 
toString(Profile.StringFormat) - Method in interface org.biojava.nbio.core.alignment.template.Profile
Returns a formatted view of the alignment profile.
toString(LightweightProfile.StringFormat) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
Support for different MSA formats
toString(LightweightProfile.StringFormat) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
Returns a formatted view of the alignment profile.
toString(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
Shortcut to SequenceMixin.toStringBuilder(org.biojava.nbio.core.sequence.template.Sequence) which calls toString() on the resulting object.
toStringBuilder(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
For the given Sequence this will return a StringBuilder object filled with the results of Compound#toString().
toStrings(List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange
 
totalSize - Variable in class org.biojava.nbio.ontology.obo.OboFileParser
 
toText(Chain) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Convert a chain to mmCIF format.
toText(Structure) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Convert a structure to mmCIF format.
toTextFile(Structure, Path) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter
Write a structure to a CIF file.
toTransformMatrices(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
Converts the transformation Matrices of the alignment into a String output.
toUnixPath(String) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
Converts path to Unix convention and adds a terminating slash if it was omitted.
toWebSiteDisplay(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter
Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.
toWebSiteDisplay(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter
Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.
toXML() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
 
toXML() - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
 
toXML() - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
 
toXML() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
toXML(PrintWriter) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
convert Configuration to an XML file so it can be serialized
toXML(PrettyXMLWriter) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
 
toXML(XMLWriter) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
convert Configuration to an XML file so it can be serialized add to an already existing xml file.
toXML(Component) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter
 
toXML(Component, PrettyXMLWriter) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter
 
toXML(ModifiedCompound) - Static method in class org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter
 
toXML(StructureAtom) - Static method in class org.biojava.nbio.protmod.io.StructureAtomXMLConverter
 
toXML(StructureAtom, PrettyXMLWriter) - Static method in class org.biojava.nbio.protmod.io.StructureAtomXMLConverter
 
toXML(StructureGroup, PrettyXMLWriter) - Static method in class org.biojava.nbio.protmod.io.StructureGroupXMLConverter
 
toXML(AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
 
toXML(AFPChain, StringWriter, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
Write the XML representation to a StringWriter
toXML(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
Convert an afpChain to a simple XML representation
toXML(MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
Converts all the information of a multiple alignment ensemble into an XML String format.
toXYZString() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
Expresses this transformation in terms of x,y,z fractional coordinates.
trace() - Method in class org.biojava.nbio.structure.jama.Matrix
Matrix trace.
trace1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
trace1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
trace2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
trace2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
tracebackToString(AlignerHelper.Last[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
 
traceFragmentMatrix(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
traceFragmentMatrix(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
TranscriptionEngine - Class in org.biojava.nbio.core.sequence.transcription
Used as a way of encapsulating the data structures required to parse DNA to a Protein sequence.
TranscriptionEngine.Builder - Class in org.biojava.nbio.core.sequence.transcription
This class is the way to create a TranslationEngine.
TranscriptSequence - Class in org.biojava.nbio.core.sequence
This is the sequence if you want to go from a gene sequence to a protein sequence.
TranscriptSequence(GeneSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.TranscriptSequence
Deprecated. 
TranscriptSequence(GeneSequence, AccessionID, int, int) - Constructor for class org.biojava.nbio.core.sequence.TranscriptSequence
 
TransfAlgebraicAdapter - Class in org.biojava.nbio.structure.xtal.io
 
TransfAlgebraicAdapter() - Constructor for class org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter
 
transform(double) - Method in class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform
An arbitrary transform over reals
transform(double) - Method in class org.biojava.nbio.structure.gui.util.color.LogColorMapper
Apply log transform.
transform(double) - Method in class org.biojava.nbio.structure.gui.util.color.SqrtColorMapper
Return sqrt(value).
transform(Map<?, ?>) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
Transforms Map to String, representing every entry as key mappingSequence value , joined by separatorSequence
transform(Matrix4d, Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
Transform all points with a 4x4 transformation matrix.
transform(Atom[], Matrix4d) - Static method in class org.biojava.nbio.structure.Calc
Transform an array of atoms at once.
transform(Atom, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc
Transforms an atom object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix).
transform(Chain, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc
Transforms a chain object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix).
transform(Group, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc
Transforms a group object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix).
transform(Structure, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc
Transforms a structure object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix).
transformAtoms(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
Transforms atoms according to the superposition stored in the alignment.
transformPoint(double[]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
Applies the transformation to given point.
TransformType - Enum in org.biojava.nbio.structure.xtal
 
transfToCrystal(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
Transform given Matrix4d in orthonormal basis to the crystal basis using the PDB axes convention (NCODE=1)
transfToCrystal(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
Transforms the given orthonormal basis coordinates into crystal coordinates.
transfToOriginCell(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
Converts the coordinates in pt so that they occur within the (0,0,0) unit cell
transfToOriginCell(Tuple3d[], Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
Converts a set of points so that the reference point falls in the unit cell.
transfToOriginCellCrystal(Matrix4d[], Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
transfToOriginCellOrthonormal(Matrix4d[], Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
transfToOrthonormal(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
Transform given Matrix4d in crystal basis to the orthonormal basis using the PDB axes convention (NCODE=1)
transfToOrthonormal(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
Transforms the given crystal basis coordinates into orthonormal coordinates.
TRANSITION_METAL - org.biojava.nbio.structure.ElementType
 
TRANSITIVE - Static variable in class org.biojava.nbio.ontology.OntoTools
 
translate(F) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
translate(F) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator
 
translate(Matrix4d, Vector3d) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder
 
translate(Point3i) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
 
translate(Vector3d) - Method in class org.biojava.nbio.structure.contact.BoundingBox
 
translate(Vector3d, Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
Translate all points with a translation vector.
translate(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
Quick method to let you go from a CDS to a Peptide quickly.
translate(Atom, Vector3d) - Static method in class org.biojava.nbio.structure.Calc
Translates an atom object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)
translate(Chain, Vector3d) - Static method in class org.biojava.nbio.structure.Calc
Translates a chain object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)
translate(Group, Vector3d) - Static method in class org.biojava.nbio.structure.Calc
Translates a group object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)
translate(Structure, Vector3d) - Static method in class org.biojava.nbio.structure.Calc
Translates a Structure object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)
translateMany(F) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
translateMany(F) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator
 
translateNCodons() - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator
Indicates if we want to force exact translation of compounds or not i.e.
translateNCodons(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
 
TranslationException - Exception in org.biojava.nbio.core.exceptions
Thrown from AbstractCompundTranslator
TranslationException(Exception) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException
 
TranslationException(String) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException
 
TranslationException(String, Exception) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException
 
translVecToString(Matrix4d) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
 
transpose() - Method in class org.biojava.nbio.structure.jama.Matrix
Matrix transpose.
transpose(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
traverseHierarchy() - Method in class demo.DemoSCOP
Traverse throught the SCOP hierarchy
TreeConstructor - Class in org.biojava.nbio.phylo
The TreeConstructor uses the forester library to build different types of phylogenetic trees.
TreeConstructorType - Enum in org.biojava.nbio.phylo
The TreeConstructorType specifies the aligorithm used to construct the tree (clustering algorithm).
TreeMapSpaceGroupWrapper - Class in org.biojava.nbio.structure.xtal.io
 
TreeMapSpaceGroupWrapper() - Constructor for class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
 
TreeType - Enum in org.biojava.nbio.phylo
The TreeType specifies the optimization criteria used to generate the tree.
TRICLINIC - org.biojava.nbio.structure.xtal.BravaisLattice
 
triggerMouseOverPosition(int, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
 
triggerSelectionLocked(boolean) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
triggerSelectionLocked(boolean) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
 
TRIGONAL - org.biojava.nbio.structure.xtal.BravaisLattice
 
TRIGONAL_CARBON_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
 
TRIGONAL_NITROGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
 
trimStop(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
 
trimStop(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator
Imperfect code.
trimToSize() - Method in interface org.biojava.nbio.structure.Group
Attempts to reduce the memory imprint of this group by trimming all internal Collection objects to the required size.
trimToSize() - Method in class org.biojava.nbio.structure.HetatomImpl
 
trimToValidResidues(ResidueRange) - Method in class org.biojava.nbio.structure.AtomPositionMap
Trims a residue range so that both endpoints are contained in this map.
Triple - Interface in org.biojava.nbio.ontology
A triple in an ontology.
Triple.Impl - Class in org.biojava.nbio.ontology
Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple
tryAllCPs - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
If true, ignores OptimalCECPParameters.cpPoint and tries all possible cp points.
tsiatis - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error
 
turn - org.biojava.nbio.structure.secstruc.SecStrucType
 
twistOptimized(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.AFPTwister
superimposing according to the optimized alignment
twistPDB(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.AFPTwister
calculate the total rmsd of the blocks output a merged pdb file for both proteins protein 1, in chain A protein 2 is twisted according to the twists detected, in chain B
TWO - org.biojava.nbio.core.sequence.transcription.Frame
 
TWO_HITS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
TWOBAR - org.biojava.nbio.structure.xtal.TransformType
 
TwoBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
 
TwoBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
 
TwoBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
 
TwoBitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
 
TwoBitFacade - Class in org.biojava.nbio.genome.parsers.twobit
A facade that makes it easier to work with a 2bit file.
TwoBitFacade(File) - Constructor for class org.biojava.nbio.genome.parsers.twobit.TwoBitFacade
Reads a genome from a locally stored .2bit file.
TwoBitParser - Class in org.biojava.nbio.genome.parsers.twobit
downloaded from http://storage.bioinf.fbb.msu.ru/~roman/TwoBitParser.java Class is a parser of UCSC Genome Browser file format .2bit used to store nucleotide sequence information.
TwoBitParser(File) - Constructor for class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
TwoBitSequenceReader<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.storage
Implementation of the 2bit encoding.
TwoBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader
 
TwoBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader
 
TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader
 
TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader
 
TwoBitSequenceReader(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader
 
TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.storage
Extension of the BitArrayWorker which provides the 2bit implementation code.
TWOFOLD - org.biojava.nbio.structure.xtal.TransformType
 
TWOFOLDSCREW - org.biojava.nbio.structure.xtal.TransformType
 
type - Variable in enum org.biojava.nbio.genome.parsers.cytoband.StainType
 
type - Static variable in class org.biojava.nbio.structure.AminoAcidImpl
this is an Amino acid. type is "amino".
type - Static variable in class org.biojava.nbio.structure.HetatomImpl
The GroupType is HETATM
type - Static variable in class org.biojava.nbio.structure.NucleotideImpl
this is a "nucleotide", a special occurance of a Hetatom.
type - Variable in enum org.biojava.nbio.structure.secstruc.BridgeType
 
type - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
 
type - Variable in enum org.biojava.nbio.structure.secstruc.SecStrucType
 
type() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
Get feature type, such as "exon" or "CDS".
type() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
Get the feature type, for example, "exon", "CDS", etc.
TYPE - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature
Sort features by type
TYPEDEF - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 

U

U - org.biojava.nbio.structure.Element
 
UBIQUITINATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
 
uminus() - Method in class org.biojava.nbio.structure.jama.Matrix
Unary minus
uncompress(InputStream, OutputStream) - Static method in class org.biojava.nbio.core.util.UncompressInputStream
Read an input stream and uncompress it to an output stream.
uncompress(String, FileOutputStream) - Static method in class org.biojava.nbio.core.util.UncompressInputStream
Read a named file and uncompress it.
UncompressFile - Class in demo
Uncompresses a single tarred or zipped file, writing output to stdandard out
UncompressFile() - Constructor for class demo.UncompressFile
 
UncompressInputStream - Class in org.biojava.nbio.core.util
This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant).
UncompressInputStream(InputStream) - Constructor for class org.biojava.nbio.core.util.UncompressInputStream
 
UNDEFINED - org.biojava.nbio.core.sequence.Strand
 
UNDEFINED - org.biojava.nbio.protmod.ModificationCategory
 
UNDEFINED - org.biojava.nbio.structure.BondType
 
UNDERSCORE - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
 
unescape(String) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
 
unescape(String, char, int, boolean) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
 
unescape(String, char, int, int, boolean) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
 
unescapeChars - Static variable in class org.biojava.nbio.ontology.obo.OboFileParser
 
union(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Return the union.
unionWorkSheetsRowJoin(String, String, char, boolean) - Static method in class org.biojava.nbio.survival.data.WorkSheet
Combine two work sheets where you join based on rows.
unionWorkSheetsRowJoin(WorkSheet, WorkSheet, boolean) - Static method in class org.biojava.nbio.survival.data.WorkSheet
* Combine two work sheets where you join based on rows.
UNIPROT - org.biojava.nbio.core.sequence.DataSource
 
uniProtEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
 
UniprotProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
Pass in a Uniprot ID and this ProxySequenceReader when passed to a ProteinSequence will get the sequence data and other data elements associated with the ProteinSequence by Uniprot.
UniprotProxySequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
The UniProt id is used to retrieve the UniProt XML which is then parsed as a DOM object so we know everything about the protein.
UniprotProxySequenceReader(Document, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
The xml is passed in as a DOM object so we know everything about the protein.
UniprotToFasta - Class in org.biojava.nbio.genome.uniprot
 
UniprotToFasta() - Constructor for class org.biojava.nbio.genome.uniprot.UniprotToFasta
 
UnitCellBoundingBox - Class in org.biojava.nbio.structure.xtal
A class to contain the BoundingBoxes of all polymeric molecules in a full unit cell.
UnitCellBoundingBox(int, int) - Constructor for class org.biojava.nbio.structure.xtal.UnitCellBoundingBox
 
UnitQuaternions - Class in org.biojava.nbio.structure.geometry
UnitQuaternions is a static Class that contains methods for calculating and using unit quaternions.
unitVector(Atom) - Static method in class org.biojava.nbio.structure.Calc
Returns the unit vector of vector a .
unknown - org.biojava.nbio.structure.chem.PolymerType
if all else fails...
UNKNOWN - org.biojava.nbio.core.sequence.DataSource
 
UNKNOWN - org.biojava.nbio.core.sequence.DNASequence.DNAType
 
UNKNOWN - org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
 
UNKNOWN - org.biojava.nbio.structure.ElementType
 
UNKNOWN - org.biojava.nbio.structure.io.StructureFiletype
 
UNKNOWN_ALGORITHM - Static variable in class org.biojava.nbio.structure.align.model.AFPChain
 
UNKNOWN_DNA - Static variable in interface org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface
 
UNKNOWN_GROUP_LABEL - Static variable in class org.biojava.nbio.structure.StructureTools
The character to use for unknown compounds in sequence strings
UNKNOWN_SCOPE - Static variable in class org.biojava.nbio.ontology.Synonym
 
unknownGroup - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
 
unmarshal(String[]) - Method in class org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter
 
unregister(ProteinModification) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
Remove a modification from registry.
UNRELEASED - org.biojava.nbio.structure.PDBStatus.Status
 
UP_AC_PATTERN - Static variable in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
update(byte[], int, int) - Method in class org.biojava.nbio.core.util.CRC64Checksum
Updates the CRC-64 checksum with the specified array of bytes.
update(int) - Method in class org.biojava.nbio.core.util.CRC64Checksum
 
update(int, AlignerHelper.Subproblem, AlignerHelper.Last[][]) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
 
update(String) - Method in class org.biojava.nbio.core.util.CRC64Checksum
 
updateAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
Force the atom arrays to regenerate based on MultipleAlignmentEnsembleImpl.getStructureIdentifiers().
updateAxis(Integer, Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
Updates an axis of symmetry, after the superposition changed.
updateCache() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
updateCache() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
Updates all cached properties
updateContinousVariable(String, Double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
updateCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
 
updateCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
updateCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
Force recalculation of the core length (ungapped columns) based on the BlockSet core lengths.
updateDisplay() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
 
updateDistanceMatrix() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
Force recalculation of the distance matrices.
updateLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
 
updateLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
Force recalculation of the length (aligned columns) based on the BlockSet lengths.
updateMatrixWithSequenceConservation(double[][], Atom[], Atom[], CeParameters) - Static method in class org.biojava.nbio.structure.align.ce.CECalculator
Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.
updateMatrixWithSequenceConservation(double[][], Atom[], Atom[], CeParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.
updateScore(FatCatParameters, AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
to update the chaining score after block delete and merge processed the blockScore value is important for significance evaluation
updateSuperposition(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
After the alignment changes (optAln, optLen, blockNum, at a minimum), many other properties which depend on the superposition will be invalid.
updateSymmetryScores(MultipleAlignment) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Update the scores (TM-score and RMSD) of a symmetry multiple alignment.
updateSymmetryTransformation(SymmetryAxes, MultipleAlignment) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Calculates the set of symmetry operation Matrices (transformations) of the new alignment, based on the symmetry relations in the SymmetryAxes object.
UPGMA - org.biojava.nbio.phylo.TreeConstructorType
Unweighted Pair-Group Method with Arithmetic mean
UPPER - org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
 
upstream(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Return the adjacent location of specified length directly upstream of this location.
URL - org.biojava.nbio.structure.align.client.StructureName.Source
 
URL - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
URLConnectionTools - Class in org.biojava.nbio.structure.align.util
A class that takes care about opening URLConnections and sets the proper timeouts
URLConnectionTools() - Constructor for class org.biojava.nbio.structure.align.util.URLConnectionTools
 
URLIdentifier - Class in org.biojava.nbio.structure
Represents a structure loaded from a URL (including a file URL) A few custom query parameters are supported: format=[pdb|cif] Specify the file format (will otherwise be guessed from the extension) pdbId=[String] Specify the PDB ID (also guessed from the filename) chainID=[String] A single chain from the structure residues=[String] Residue ranges, in a form understood by SubstructureIdentifier
URLIdentifier(String) - Constructor for class org.biojava.nbio.structure.URLIdentifier
 
URLIdentifier(URL) - Constructor for class org.biojava.nbio.structure.URLIdentifier
 
urlPropertyNames - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo
 
useLocalTimeLimit(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
USER_INPUT - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
 
UserArgumentProcessor - Interface in org.biojava.nbio.structure.align.ce
 
UserConfiguration - Class in org.biojava.nbio.structure.align.util
A container to persist config to the file system
UserConfiguration() - Constructor for class org.biojava.nbio.structure.align.util.UserConfiguration
Default UserConfiguration: split directory autofetch files default download location.
userData() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
Get HashMap of user data.
userData() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
Get HashMap of user data.
useRNA - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
 
usual - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower
 
Utils - Class in org.biojava.nbio.aaproperties
This is a utility class that contains utility methods which will facilitates the coding of other methods
Utils() - Constructor for class org.biojava.nbio.aaproperties.Utils
 

V

V - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
V - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
V - org.biojava.nbio.structure.Element
 
V - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
value - Variable in class org.biojava.nbio.structure.align.helper.GapArray
 
value - Variable in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements
 
value - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.PairInProfileScorerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.RefinerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.routines.AlignerHelper.Last
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.template.GapPenalty.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.core.alignment.template.AlignedSequence.Step
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.core.alignment.template.Profile.StringFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.DataSource
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.DNASequence.DNAType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.Strand
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.phylo.TreeConstructorType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.phylo.TreeType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.protmod.ModificationCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.align.client.StructureName.Source
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.align.quaternary.QsRelation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.BondType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.chem.PolymerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.chem.ResidueType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.cluster.SubunitClustererMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.Element
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.ElementType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.EntityType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.GroupType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.gui.RenderStyle
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.io.StructureFiletype
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.PDBStatus.Status
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.scop.ScopCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.xtal.TransformType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.survival.cox.CoxMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.survival.cox.ResidualsCoxph.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
Returns the enum constant of this type with the specified name.
valueOfIgnoreCase(String) - Static method in enum org.biojava.nbio.structure.Element
Returns the Element that corresponds to the specified element symbol.
values() - Static method in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.Alignments.PairInProfileScorerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.Alignments.RefinerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.routines.AlignerHelper.Last
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.template.GapPenalty.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.core.alignment.template.AlignedSequence.Step
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.core.alignment.template.Profile.StringFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.core.sequence.DataSource
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.core.sequence.DNASequence.DNAType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.core.sequence.Strand
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.phylo.TreeConstructorType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.phylo.TreeType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.protmod.ModificationCategory
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.align.client.StructureName.Source
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.align.quaternary.QsRelation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.BondType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.cath.CathCategory
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.chem.PolymerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.chem.ResidueType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.cluster.SubunitClustererMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.Element
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.ElementType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.EntityType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.GroupType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.gui.RenderStyle
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
values() - Static method in enum org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
 
values() - Static method in enum org.biojava.nbio.structure.io.StructureFiletype
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.PDBStatus.Status
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.scop.ScopCategory
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.structure.xtal.TransformType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.survival.cox.CoxMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.survival.cox.ResidualsCoxph.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
Returns an array containing the constants of this enum type, in the order they are declared.
VANDERWAALS - org.biojava.nbio.structure.BondType
 
Variable - Interface in org.biojava.nbio.ontology
 
VARIABLE_SEQUENCES - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
 
Variable.Impl - Class in org.biojava.nbio.ontology
 
vectorProduct(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
Vector product (cross product).
verbose - Static variable in class org.biojava.nbio.structure.domain.pdp.CutDomain
 
version - Static variable in class org.biojava.nbio.structure.align.ce.CeCPMain
version history: 1.5 - Added more parameters to the command line, including -maxOptRMSD 1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain 1.3 - Short CPs are now discarded 1.2 - now supports check AlignmentTools.isSequentialAlignment.
version - Static variable in class org.biojava.nbio.structure.align.ce.CeMain
version history: 1.2 - Added more parameters to the command line, including -maxOptRMSD 1.1 - Additional parameters 1.0 - Initial port from C code
version - Static variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
version history: 1.0 - Initial version
version - Static variable in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
Version history:
version - Static variable in class org.biojava.nbio.structure.symmetry.internal.CeSymm
Version History:
VERSION - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat
version history: 1.1 - Added more parameters to the command line 1.0 - Initial version
VERSION_1_55 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_57 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_59 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_61 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_63 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_65 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_67 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_69 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_71 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_73 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_75 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_75A - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_75B - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_1_75C - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_2_0_1 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_2_0_2 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_2_0_3 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_2_0_4 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_2_0_5 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_2_0_6 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_2_0_7 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_2_0_8 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
 
VERSION_3_5_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory
 
VERSION_4_0_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory
 
VERSION_4_1_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory
 
VERSION_4_2_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory
 
VERSION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
viewer - Static variable in class org.biojava.nbio.structure.gui.BiojavaJmol
 
viewer - Static variable in class org.biojava.nbio.structure.gui.JmolViewerImpl
 
VOLUME - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
 
vp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 

W

W - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
W - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
W - org.biojava.nbio.structure.Element
 
W - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
WAIT_INCREMENT - Static variable in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
Number of milliseconds by which expected job execution time is incremented if it is not finished yet.
waitForStartCodon(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
If set, then translation will not start until a start codon is encountered
WaldTest - Class in org.biojava.nbio.survival.cox
 
WaldTest() - Constructor for class org.biojava.nbio.survival.cox.WaldTest
 
WaldTestInfo - Class in org.biojava.nbio.survival.cox
 
WaldTestInfo() - Constructor for class org.biojava.nbio.survival.cox.WaldTestInfo
 
warn(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
 
warnEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
 
WATER - org.biojava.nbio.structure.EntityType
Water
WATERNAMES - Static variable in enum org.biojava.nbio.structure.GroupType
The 3-letter codes used in the PDB to identify water molecules
WeakValueHashMap - Class in org.biojava.nbio.ontology.utils
Map implementation which keeps weak references to values.
WeakValueHashMap() - Constructor for class org.biojava.nbio.ontology.utils.WeakValueHashMap
 
WebStartClientDemo - Class in demo
 
WebStartClientDemo() - Constructor for class demo.WebStartClientDemo
 
WebStartMain - Class in org.biojava.nbio.structure.align.webstart
 
WebStartMain() - Constructor for class org.biojava.nbio.structure.align.webstart.WebStartMain
 
weight - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
weightedSuperpose(Point3d[], Point3d[], double[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP
Weighted superposition.
WHITE_BLACK_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
WHITE_SPACE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
A whitespace character: [\t\n\x0B\f\r]
width - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
window(int, int) - Method in class org.biojava.nbio.genome.parsers.gff.Location
Enable a "sliding window" iteration over a location to use with Java's "for" loop construct.
windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
WindowedSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence.views
A sliding window view of a sequence which does not implement any interfaces like Sequence because they do not fit how this works.
WindowedSequence(Sequence<C>, int) - Constructor for class org.biojava.nbio.core.sequence.views.WindowedSequence
 
windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
 
windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
 
windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
 
windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
 
windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
winSize - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
winSize - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
WIREFRAME - org.biojava.nbio.structure.gui.RenderStyle
 
withDescription(String) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified description.
withQuality(String) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified quality scores.
withSequence(String) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified sequence.
withVariant(FastqVariant) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.
WORD_SIZE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 
workingListToSequences(List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
WorkSheet - Class in org.biojava.nbio.survival.data
Need to handle very large spreadsheets of expression data so keep memory footprint low
WorkSheet() - Constructor for class org.biojava.nbio.survival.data.WorkSheet
 
WorkSheet(String[][]) - Constructor for class org.biojava.nbio.survival.data.WorkSheet
 
WorkSheet(Collection<String>, Collection<String>) - Constructor for class org.biojava.nbio.survival.data.WorkSheet
 
WorkSheet(CompactCharSequence[][]) - Constructor for class org.biojava.nbio.survival.data.WorkSheet
 
wrap(Sequence<C>) - Method in enum org.biojava.nbio.core.sequence.transcription.Frame
Optionally wraps a Sequence in a reverse complementing view (if the frame is on the reverse strand) and creates a sub sequence view if it is required.
WrapLayout - Class in org.biojava.nbio.structure.gui
FlowLayout subclass that fully supports wrapping of components.
WrapLayout() - Constructor for class org.biojava.nbio.structure.gui.WrapLayout
Constructs a new WrapLayout with a left alignment and a default 5-unit horizontal and vertical gap.
WrapLayout(int) - Constructor for class org.biojava.nbio.structure.gui.WrapLayout
Constructs a new FlowLayout with the specified alignment and a default 5-unit horizontal and vertical gap.
WrapLayout(int, int, int) - Constructor for class org.biojava.nbio.structure.gui.WrapLayout
Creates a new flow layout manager with the indicated alignment and the indicated horizontal and vertical gaps.
WrappedAtom(int, String, String, Atom, int) - Constructor for class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom
Construct a new atoms.
wrapToRna(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
Takes in the given DNA Sequence and returns an instance of RNASequence which is using RnaSequenceView as a ProxySequenceReader.
write(int) - Method in class org.biojava.nbio.ronn.NullOutputStream
 
write(File, Iterable<Fastq>) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter
Write the specified FASTQ formatted sequences to the specified file.
write(File, Fastq...) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter
Write the specified FASTQ formatted sequences to the specified file.
write(OutputStream, Iterable<Fastq>) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter
Write the specified FASTQ formatted sequences to the specified output stream.
write(OutputStream, LinkedHashMap<String, ChromosomeSequence>) - Method in class org.biojava.nbio.genome.parsers.gff.GFF3Writer
Output gff3 format for a DNA Sequence
write(OutputStream, Fastq...) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter
Write the specified FASTQ formatted sequences to the specified output stream.
write(Appendable, Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
Used as a way of sending a Sequence to a writer without the cost of converting to a full length String and then writing the data out
write(String) - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
 
write(FeatureList, String) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
Write features in FeatureList to file.
writeFasta(OutputStream, List<FastaSequence>) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
Writes FastaSequence in the file, each sequence will take one line only
writeFasta(OutputStream, List<FastaSequence>, int) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line
writeGeneSequence(File, Collection<GeneSequence>, boolean) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper
Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence
writeGeneSequence(OutputStream, Collection<GeneSequence>, boolean) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper
Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence
writeIndent() - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
writeNucleotideSequence(File, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper
Write a collection of NucleotideSequences to a file
writeNucleotideSequence(File, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
Write a collection of NucleotideSequences to a file
writeNucleotideSequence(OutputStream, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper
Write a collection of NucleotideSequences to a file
writeNucleotideSequence(OutputStream, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
Write a collection of NucleotideSequences to a file
writeNucleotideSequence(OutputStream, Collection<DNASequence>, String) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
Write a collection of NucleotideSequences to a file
writeNucleotideSequenceOriginal(OutputStream, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
Write a collection of NucleotideSequences to a file using the NucleotideSequences original header as the LOCUS line rather than generating it
writeProteinSequence(File, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper
Write collection of protein sequences to a file
writeProteinSequence(File, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
Write collection of protein sequences to a file
writeProteinSequence(OutputStream, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper
Write collection of protein sequences to a stream
writeProteinSequence(OutputStream, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
Write collection of protein sequences to a stream
writeResults() - Method in class org.biojava.nbio.core.search.io.SearchIO
used to write a search report using the guessed or specified factory
writeSequence(File, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper
Write a sequence to a file
writeSequence(File, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
Write a sequence to a file
writeSequence(OutputStream, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper
Write a sequence to OutputStream
writeSequence(OutputStream, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
Write a sequence to OutputStream
writeSequences(OutputStream, Collection<Sequence<?>>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper
Method which will write your given Sequences to the specified OutputStream.
writeSequences(OutputStream, Collection<Sequence<?>>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
Method which will write your given Sequences to the specified OutputStream.
writeToFile(Structure, Path) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions
Write a Structure object to a file.
writeToOutputStream(Structure, OutputStream) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions
Write a Structure object to an OutputStream
WU_MANBER - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
 
WWW_BLAST_TYPE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
 

X

xAxisLabels - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
xAxisLegend - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
xaxisPercentIncrement - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
Xe - org.biojava.nbio.structure.Element
 
xmax - Variable in class org.biojava.nbio.structure.contact.BoundingBox
 
xmin - Variable in class org.biojava.nbio.structure.contact.BoundingBox
 
XML - org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum
 
XMLHelper - Class in org.biojava.nbio.core.util
Helper methods to simplify boilerplate XML parsing code for org.w3c.dom XML objects
XMLHelper() - Constructor for class org.biojava.nbio.core.util.XMLHelper
 
XMLWriter - Interface in org.biojava.nbio.core.util
Simple interface for building XML documents.
XRAY_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique
 
XREF_ANALOG - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
XTALTRANSL - org.biojava.nbio.structure.xtal.TransformType
 
xyMax - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
End position of the aligned sequence in the query and target respectively
xyStart - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Start position of the aligned sequence in the query and target respectively

Y

Y - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
 
Y - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
 
Y - org.biojava.nbio.structure.Element
 
Y - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
yAxisLegend - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
yaxisPercentIncrement - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
Yb - org.biojava.nbio.structure.Element
 
ymax - Variable in class org.biojava.nbio.structure.contact.BoundingBox
 
ymin - Variable in class org.biojava.nbio.structure.contact.BoundingBox
 

Z

ZipChemCompProvider - Class in org.biojava.nbio.structure.chem
This chemical component provider retrieves and caches chemical component definition files from a zip archive specified in its construction.
ZipChemCompProvider(String, String) - Constructor for class org.biojava.nbio.structure.chem.ZipChemCompProvider
ZipChemCompProvider is a Chemical Component provider that stores chemical components in a zip archive.
zmax - Variable in class org.biojava.nbio.structure.contact.BoundingBox
 
zmin - Variable in class org.biojava.nbio.structure.contact.BoundingBox
 
Zn - org.biojava.nbio.structure.Element
 
Zr - org.biojava.nbio.structure.Element
 
zscore - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
 
zStrAlign(int, int, double, int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
 
zStrAlign(int, int, double, int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 
zThr - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator
 
zThr - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
 

_

_split_multi_line(String, int) - Method in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat
Returns a list of strings.
_write_feature(FeatureInterface<AbstractSequence<C>, C>, int) - Method in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat
Write a single SeqFeature object to features table.
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