Index (biojava 6.1.0 API)

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

A

A - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
A - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
A - Static variable in class org.biojava.nbio.aaproperties.Constraints
AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil: Valid Amino acids
aa2CTerminalPka - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2ExtinctionCoefficient - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2Hydrophathicity - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2MolecularWeight - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2NTerminalPka - Static variable in class org.biojava.nbio.aaproperties.Constraints
aa2PKa - Static variable in class org.biojava.nbio.aaproperties.Constraints
AAindexFactory - Class in org.biojava.nbio.core.alignment.matrices: Factory class to get Providers for substitution matrices that are provided by the AAINDEX database.
AAindexFactory() - Constructor for class org.biojava.nbio.core.alignment.matrices.AAindexFactory
AAIndexFileParser - Class in org.biojava.nbio.core.alignment.matrices
AAIndexFileParser() - Constructor for class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser
AAIndexProvider - Interface in org.biojava.nbio.core.alignment.matrices
aaScore(char, char) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
ABITrace - Class in org.biojava.nbio.core.sequence.io: Title: ABITrace
ABITrace(byte[]) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace: The byte[] constructor parses an ABI file represented as a byte array.
ABITrace(File) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace: The File constructor opens a local ABI file and parses the content.
ABITrace(URL) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace: The URL constructor opens an ABI file from any URL.
ABITracerCompoundSet - Class in org.biojava.nbio.core.sequence.compound
ABITracerCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet
AboutDialog - Class in org.biojava.nbio.structure.align.gui
AboutDialog() - Constructor for class org.biojava.nbio.structure.align.gui.AboutDialog
abs(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
abs(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
Absorbance_False - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
Absorbance_True - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
AbstractAlignmentJmol - Class in org.biojava.nbio.structure.align.gui.jmol: An Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol.
AbstractAlignmentJmol() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
AbstractAnnotation - Class in org.biojava.nbio.ontology.utils: A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
AbstractAnnotation() - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation: Protected no-args constructor intended for sub-classes.
AbstractAnnotation(Map) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation: Create a new Annotation by copying the key-value pairs from a map.
AbstractAnnotation(Annotation) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation: Copy-constructor.
AbstractCifFileSupplier<S> - Class in org.biojava.nbio.structure.io.cif: Convert a BioJava object to a CifFile.
AbstractCifFileSupplier() - Constructor for class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier
AbstractCifFileSupplier.WrappedAtom - Class in org.biojava.nbio.structure.io.cif: Wrapped atoms represent individual atoms enriched with model- and chain-level information.
AbstractCompound - Class in org.biojava.nbio.core.sequence.template: The details of a Compound
AbstractCompound() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound
AbstractCompound(String) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound
AbstractCompoundSet<C extends Compound> - Class in org.biojava.nbio.core.sequence.template
AbstractCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
AbstractCompoundTranslator<F extends Compound,T extends Compound> - Class in org.biojava.nbio.core.sequence.template
AbstractCompoundTranslator(SequenceCreatorInterface<T>, CompoundSet<F>, CompoundSet<T>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
AbstractEdit(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
AbstractEdit(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
AbstractFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features: A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that feature
AbstractFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.AbstractFeature: A feature has a type and a source
AbstractLocation - Class in org.biojava.nbio.core.sequence.location.template: Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand
AbstractLocation() - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation
AbstractLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation: Default constructor
AbstractLocation(Point, Point, Strand, boolean, boolean, AccessionID, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation: Default constructor
AbstractMatrixAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements common code for an Aligner which builds a score matrix during computation.
AbstractMatrixAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Before running an alignment, data must be sent in via calls to AbstractMatrixAligner.setGapPenalty(GapPenalty) and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Prepares for an alignment.
AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Prepares for an alignment.
AbstractNucleotideCompoundSet<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.template
AbstractNucleotideCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements common code for an Aligner for a pair of Sequences.
AbstractPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Prepares for a pairwise global sequence alignment.
AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Prepares for a pairwise sequence alignment.
AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements common code for an Aligner for a pair of Profiles.
AbstractProfileProfileAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Before running a profile-profile alignment, data must be sent in via calls to AbstractProfileProfileAligner.setQuery(Profile), AbstractProfileProfileAligner.setTarget(Profile), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Profile<S, C>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment.
AbstractReference - Class in org.biojava.nbio.core.sequence.reference
AbstractReference() - Constructor for class org.biojava.nbio.core.sequence.reference.AbstractReference
AbstractScorer - Class in org.biojava.nbio.alignment.template: Implements common code for algorithms which compute a score.
AbstractScorer() - Constructor for class org.biojava.nbio.alignment.template.AbstractScorer
AbstractScoresCache - Class in org.biojava.nbio.structure.align.multiple: Abstact implementation of the ScoresCache with the shared code used in all objects with a variables cache.
AbstractScoresCache() - Constructor for class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
AbstractScoresCache(AbstractScoresCache) - Constructor for class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
AbstractSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence.template: The base class for DNA, RNA and Protein sequences.
AbstractSequence() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence
AbstractSequence(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence: Create a Sequence from a simple string where the values should be found in compoundSet
AbstractSequence(SequenceReader<C>, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence: A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location of the sequence data.
AbstractSequence.AnnotationType - Enum in org.biojava.nbio.core.sequence.template
AbstractStructureAlignment - Class in org.biojava.nbio.structure.align
AbstractStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.AbstractStructureAlignment
AbstractTerm - Class in org.biojava.nbio.ontology: Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
AbstractTerm() - Constructor for class org.biojava.nbio.ontology.AbstractTerm
AbstractUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce: Base class for a new structure alignment CLI.
AbstractUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
Ac - org.biojava.nbio.structure.Element
AccesionedLocation - Interface in org.biojava.nbio.core.sequence.location.template: A location which is bound to an AccessionID.
ACCESSION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
Accessioned - Interface in org.biojava.nbio.core.sequence.template: Indicates an entity is accessioned
AccessionID - Class in org.biojava.nbio.core.sequence: Used in Sequences as the unique 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: Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Prepares for a pairwise global sequence alignment.
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Prepares for a pairwise global sequence alignment.
anchors - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
angle(Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions: Calculate the rotation angle component of the input unit quaternion.
angle(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: Gets the angle between two vectors
ANGLE - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
angleCheckOk(FragmentPair, FragmentPair, float) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
AngleOrderDetectorPlus - Class in org.biojava.nbio.structure.symmetry.internal: Guesses an order of rotational symmetry from the angle.
AngleOrderDetectorPlus(double) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
AngleOrderDetectorPlus(int) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
AngleOrderDetectorPlus(int, double) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
AngleOrderDetectorPlus(int, double, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus: Determine order by finding the order (up to the maxOrder) which has the closest rotation angle to the observed rotation.
Annotatable - Interface in org.biojava.nbio.ontology.utils: Indicates that an object has an associated annotation.
Annotation - Interface in org.biojava.nbio.ontology.utils: Arbitrary annotation associated with one or more objects.
antiparallel - org.biojava.nbio.structure.secstruc.BridgeType
ANY - Static variable in class org.biojava.nbio.ontology.OntoTools
ANYTHING_MATCHER - Static variable in class org.biojava.nbio.structure.AtomPositionMap: Matches all atoms
apairs_from_idxlst(JointFragments) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: Set apairs according to a list of (i,j) tuples.
apairs_from_seed(int, int, int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: Set apairs according to a seed position.
ApliphaticIndex - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
App - Class in org.biojava.nbio.genome: Hello world!
App - Class in org.biojava.nbio.ontology: Hello world!
App() - Constructor for class org.biojava.nbio.genome.App
App() - Constructor for class org.biojava.nbio.ontology.App
append(T, Iterable<Fastq>) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter: Append the specified FASTQ formatted sequences to the specified appendable.
append(T, Fastq...) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter: Append the specified FASTQ formatted sequences to the specified appendable.
appendQuality(String) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder: Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.
appendQuality(String) - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener: Notify this listener of a quality line.
appendSequence(String) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder: Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.
appendSequence(String) - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener: Notify this parse listener of an additional sequence line.
appendToSequence(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
appendWorkSheetColumns(WorkSheet) - Method in class org.biojava.nbio.survival.data.WorkSheet: Add columns from a second worksheet to be joined by common row.
appendWorkSheetRows(WorkSheet) - Method in class org.biojava.nbio.survival.data.WorkSheet: Add rows from a second worksheet to be joined by common column.
applyAlignment(Map<S, T>, Map<T, S>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Applies an alignment k times.
applyAlignment(Map<T, T>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Applies an alignment k times.
applyColumnFilter(String, ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet: Apply filter to a column to change values from say numberic to nominal based on some range
applyValues() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
approach_ap3(Atom[], Atom[], FragmentPair[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
Ar - org.biojava.nbio.structure.Element
Architecture - org.biojava.nbio.structure.cath.CathCategory
areInSameAxis(int, int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Returns true if both given transform ids belong to the same crystallographic axis (a, b or c) For two non-rotation transformations (i.e. identity operators) it returns true
arrayLeftDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element left division, C = A.
arrayLeftDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element left division in place, A = A.
ArrayListProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
ArrayListProxySequenceReader() - Constructor for class org.biojava.nbio.core.sequence.loader.ArrayListProxySequenceReader
ArrayListSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage: Stores a Sequence as a collection of compounds in an ArrayList
ArrayListSequenceReader() - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
ArrayListSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
ArrayListSequenceReader(List<C>, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
arrayRightDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element right division, C = A.
arrayRightDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element right division in place, A = A.
arrayTimes(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element multiplication, C = A.
arrayTimesEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element multiplication in place, A = A.
ARTIFACTUAL - org.biojava.nbio.protmod.ModificationOccurrenceType
As - org.biojava.nbio.structure.Element
AsaCalculator - Class in org.biojava.nbio.structure.asa: Class to calculate Accessible Surface Areas based on the rolling ball algorithm by Shrake and Rupley.
AsaCalculator(Point3d[], double, int, int, double) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator: Constructs a new AsaCalculator.
AsaCalculator(Atom[], double, int, int) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator: Constructs a new AsaCalculator.
AsaCalculator(Structure, double, int, int, boolean) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator: Constructs a new AsaCalculator.
asMap() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
asMap() - Method in interface org.biojava.nbio.ontology.utils.Annotation: Return a map that contains the same key/values as this Annotation.
AssertionFailure - Error in org.biojava.nbio.ontology.utils: An unchecked exception representing an Assertion failure.
AssertionFailure(String) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
AssertionFailure(String, Throwable) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
AssertionFailure(Throwable) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
assertLocation() - Method in class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
assertLocation() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
assignment - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
assignSecStruc(Structure, List<SecStrucInfo>) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools
Astral - Class in org.biojava.nbio.structure.scop: Provides programmatic access to ASTRAL representative sets.
Astral(String, Reader) - Constructor for class org.biojava.nbio.structure.scop.Astral: Constructs a new Astral object.
Astral(String, URL) - Constructor for class org.biojava.nbio.structure.scop.Astral: Constructs a new Astral object.
Astral(Astral.AstralSet) - Constructor for class org.biojava.nbio.structure.scop.Astral: Constructs a new Astral object.
Astral.AstralSet - Enum in org.biojava.nbio.structure.scop: An ASTRAL sequence-identity cutoff with an identifier such as:
ASYMMETRIC - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass
At - org.biojava.nbio.structure.Element
Atom - Interface in org.biojava.nbio.structure: A simple interface for an Atom.
ATOM_CA_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.FileParsingParameters: The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
ATOM_PLANE - org.biojava.nbio.structure.BondType
AtomCache - Class in org.biojava.nbio.structure.align.util: A utility class that provides easy access to Structure objects.
AtomCache() - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Default AtomCache constructor.
AtomCache(String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(String, String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Creates a new AtomCache object based on the provided UserConfiguration.
AtomContact - Class in org.biojava.nbio.structure.contact: A pair of atoms that are in contact
AtomContact(Pair<Atom>, double) - Constructor for class org.biojava.nbio.structure.contact.AtomContact
AtomContactSet - Class in org.biojava.nbio.structure.contact: A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations
AtomContactSet(double) - Constructor for class org.biojava.nbio.structure.contact.AtomContactSet
AtomIdentifier - Class in org.biojava.nbio.structure.contact
AtomIdentifier(int, String) - Constructor for class org.biojava.nbio.structure.contact.AtomIdentifier
AtomImpl - Class in org.biojava.nbio.structure: Implementation of an Atom of a PDB file.
AtomImpl() - Constructor for class org.biojava.nbio.structure.AtomImpl
AtomInfo - Class in org.biojava.nbio.structure.align.gui.jmol: This class uniquely describes an atom
AtomInfo() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
AtomInfoParser - Class in org.biojava.nbio.structure.align.gui.jmol
AtomInfoParser() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser
AtomIterator - Class in org.biojava.nbio.structure: an iterator over all atoms of a structure / group.
AtomIterator(Group) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object.
AtomIterator(Structure) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object over all models
AtomIterator(Structure, int) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object over a single model
atomn - org.biojava.nbio.structure.chem.ResidueType
AtomPositionMap - Class in org.biojava.nbio.structure: A map from ResidueNumbers to ATOM record positions in a PDB file.
AtomPositionMap(Atom[]) - Constructor for class org.biojava.nbio.structure.AtomPositionMap: Creates a new AtomPositionMap containing peptide alpha-carbon atoms
AtomPositionMap(Atom[], AtomPositionMap.GroupMatcher) - Constructor for class org.biojava.nbio.structure.AtomPositionMap: Creates a new AtomPositionMap containing only atoms matched by matcher.
AtomPositionMap(Structure) - Constructor for class org.biojava.nbio.structure.AtomPositionMap: Creates a new AtomPositionMap containing representative atoms from a structure.
AtomPositionMap.GroupMatcher - Interface in org.biojava.nbio.structure: Used as a Predicate to indicate whether a particular Atom should be mapped
ATOMRECORD - Static variable in interface org.biojava.nbio.structure.AminoAcid: Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
atoms - Variable in class org.biojava.nbio.structure.HetatomImpl
atomsToPoints(Collection<Atom>) - Static method in class org.biojava.nbio.structure.Calc: Convert an array of atoms into an array of vecmath points
atomsToPoints(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Convert an array of atoms into an array of vecmath points
ATTACHMENT - org.biojava.nbio.protmod.ModificationCategory
attribute(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
attribute(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Add an un-qualified attribute to an element.
attribute(String, String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
attribute(String, String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Add an attribute to an element.
attributes() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get the string of key/value attributes.
attributeValues(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a collection of the unique values for the specified key.
Au - org.biojava.nbio.structure.Element
AU - org.biojava.nbio.structure.xtal.TransformType
AugmentedResidueRange - Class in org.biojava.nbio.structure: Created by douglas on 1/23/15.
AugmentedResidueRange(String, String, String, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
AugmentedResidueRange(String, ResidueNumber, ResidueNumber, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
Author - Class in org.biojava.nbio.structure: Describes author attributes for author information in a PDB file.
Author() - Constructor for class org.biojava.nbio.structure.Author
AUTHORS_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
AUTO - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
AutoSuggestProvider - Interface in org.biojava.nbio.structure.align.gui.autosuggest: A class that provides auto-completion suggestions for JAutoSuggest
AV - org.biojava.nbio.phylo.TreeConstructorType: What does this stand for?
available() - Method in class org.biojava.nbio.core.util.UncompressInputStream
available() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
AverageHydropathyValue - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
AVGTM_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
Axis(Matrix4d, int, CESymmParameters.SymmetryType, int, int) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
AxisAligner - Class in org.biojava.nbio.structure.symmetry.axis
AxisAligner() - Constructor for class org.biojava.nbio.structure.symmetry.axis.AxisAligner
axisStroke - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

B

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

C

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