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A

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 the 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
 
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
 
absolutePercentialRNAsuiteness - Variable in class org.biojava.nbio.structure.validation.Entry
 
absolutePercentileClashscore - Variable in class org.biojava.nbio.structure.validation.Entry
 
absolutePercentileDCCRfree - Variable in class org.biojava.nbio.structure.validation.Entry
 
absolutePercentilePercentRamaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
 
absolutePercentilePercentRotaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
 
absolutePercentilePercentRSRZOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
 
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(Annotation) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation
Copy-constructor.
AbstractAnnotation(Map) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation
Create a new Annotation by copying the key-value pairs from a map.
AbstractBean - Class in org.biojava.nbio.structure.io.mmcif.model
a generic class that implements the toString method for a bean
AbstractBean() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AbstractBean
 
AbstractCompound - Class in org.biojava.nbio.core.sequence.template
The details of a Compound
AbstractCompound() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound
 
AbstractCompound(String) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound
 
AbstractCompoundSet<C extends Compound> - Class in org.biojava.nbio.core.sequence.template
 
AbstractCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
AbstractCompoundTranslator<F extends Compound,T extends Compound> - Class in org.biojava.nbio.core.sequence.template
 
AbstractCompoundTranslator(SequenceCreatorInterface<T>, CompoundSet<F>, CompoundSet<T>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
AbstractEdit(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
 
AbstractEdit(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
 
AbstractFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features
A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that feature
AbstractFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.AbstractFeature
A feature has a type and a source
AbstractLocation - Class in org.biojava.nbio.core.sequence.location.template
Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand
AbstractLocation() - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
AbstractLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation
Default constructor
AbstractLocation(Point, Point, Strand, boolean, boolean, AccessionID, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation
Default constructor
AbstractMatrixAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template
Implements common code for an Aligner which builds a score matrix during computation.
AbstractMatrixAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner
AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Prepares for an alignment.
AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Prepares for an alignment.
AbstractNucleotideCompoundSet<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.template
 
AbstractNucleotideCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
 
AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template
Implements common code for an Aligner for a pair of Sequences.
AbstractPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
Prepares for a pairwise global sequence alignment.
AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
Prepares for a pairwise sequence alignment.
AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template
Implements common code for an Aligner for a pair of Profiles.
AbstractProfileProfileAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
AbstractProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
Prepares for a profile-profile alignment.
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(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(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.
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
 
AccesionedLocation - Interface in org.biojava.nbio.core.sequence.location.template
A location which is bound to an AccessionID.
ACCESSION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
Accessioned - Interface in org.biojava.nbio.core.sequence.template
Indicates an entity is accessioned
AccessionID - Class in org.biojava.nbio.core.sequence
Used in Sequences as the unique indentifier.
AccessionID() - Constructor for class org.biojava.nbio.core.sequence.AccessionID
 
AccessionID(String) - Constructor for class org.biojava.nbio.core.sequence.AccessionID
 
AccessionID(String, DataSource) - Constructor for class org.biojava.nbio.core.sequence.AccessionID
 
AccessionID(String, DataSource, Integer, String) - Constructor for class org.biojava.nbio.core.sequence.AccessionID
 
acentricOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
 
ACETYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
 
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.DBResultTable
 
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
Invoked when the user presses the stop button.
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.RasmolCommandListener
Deprecated.
 
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(FeatureI) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
Add specified feature to the end of the list.
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(int, int, int, int) - Method in class org.biojava.nbio.structure.align.helper.JointFragments
 
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
 
add(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
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
 
addAlignmentProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
 
addAlignmentProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.FarmJob
 
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[], Atom[]) - Method in class org.biojava.nbio.structure.contact.Grid
Adds the i and j atoms and fills the grid.
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.
addAtoms(Atom[]) - Method in class org.biojava.nbio.structure.contact.Grid
Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts.
addAtoms(Atom[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid
Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts.
addAxis(Matrix4d, List<List<Integer>>, List<Integer>, Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
Deprecated.
Use #addAxis(Matrix4d, int, SymmetryType) instead. Repeats and Superposition are now inferred automatically.
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.Compound
Add new Chain to this Compound
addChain(Chain) - Method in interface org.biojava.nbio.structure.Structure
Add a new chain.
addChain(Chain, int) - Method in interface org.biojava.nbio.structure.Structure
Add a new chain, if several models are available.
addChain(Chain) - Method in class org.biojava.nbio.structure.StructureImpl
Add a new chain.
addChain(Chain, int) - Method in class org.biojava.nbio.structure.StructureImpl
Add a new chain, if several models are available.
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.io.mmcif.ChemicalComponentDictionary
add a new component to the dictionary
addChildElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper
 
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, C, Iterable<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) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
 
addCompound(Compound) - Method in interface org.biojava.nbio.structure.Structure
Add a Compound to this Structure
addCompound(Compound) - Method in class org.biojava.nbio.structure.StructureImpl
Add a Compound to this Structure
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
 
addDBReference(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
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
add a group to the list of ATOM record group of this chain.
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
 
addLigand(RCSBLigand) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigands
 
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
 
addMMcifConsumer(MMcifConsumer) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser
Add a MMcifConsumer that listens to even being triggered by the parser and processes the data into a backend provided by the Consumer.
addMMcifConsumer(MMcifConsumer) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
 
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
 
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, T) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
 
addPoint(Point3d, double) - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
 
addPolymer(RCSBPolymer) - Method in class org.biojava.nbio.structure.rcsb.RCSBDescription
 
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
 
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
 
addSeqResGroup(Group) - Method in class org.biojava.nbio.structure.ChainImpl
 
addSequence(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addSSBond(Bond) - Method in interface org.biojava.nbio.structure.Structure
Add a single disulfide Bond to this structure
addSSBond(Bond) - Method in class org.biojava.nbio.structure.StructureImpl
Adds a single disulfide Bond to this structure
addStartCodonSequence(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
 
addStopCodonSequence(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
 
addStrataInfoHashMap(LinkedHashMap<String, StrataInfo>, String) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
 
addStrings(String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
 
addSurfaceAccessibility(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
 
addSynonym(Object) - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
 
addSynonym(Object) - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
 
addSynonym(Object) - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
 
addSynonym(Object) - Method in interface org.biojava.nbio.ontology.Term
Add a synonym for this term.
addSynonym(Object) - Method in class org.biojava.nbio.ontology.Term.Impl
 
addSynonym(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl
 
addToCache(String, File) - Static method in class org.biojava.nbio.core.util.FlatFileCache
 
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
 
addUniqueSequenceList(UniqueSequenceList) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
 
addUnknownDataTypeVariable(String, String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
 
AFP - Class in org.biojava.nbio.structure.align.model
A class to represent a FATCAT 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() - Constructor for class org.biojava.nbio.structure.align.model.AFPChain
Deprecated.
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
 
AgScore - Class in org.biojava.nbio.survival.cox.stats
 
AgScore() - Constructor for class org.biojava.nbio.survival.cox.stats.AgScore
 
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(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
 
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
 
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
 
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[]) - Method in class org.biojava.nbio.structure.align.ce.CeMain
 
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[], boolean, FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
 
align(Atom[], Atom[], FatCatParameters, boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
 
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
 
align(Atom[], Atom[], Object) - 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[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
 
align(List<Atom[]>, Object) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
 
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 interface org.biojava.nbio.structure.align.MultipleStructureAligner
Run an alignment and also send a bean containing the parameters.
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
 
align(Atom[], Atom[], Object) - 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[], Object) - Method in interface org.biojava.nbio.structure.align.StructureAlignment
run an alignment and also send a bean containing the parameters.
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, 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(Atom[], Atom[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
calculate the protein structure superimposition, between two sets of atoms.
align(Structure, List<Chain>) - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
 
align(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
 
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
 
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(AlignmentGui, Structure, Structure, String, String) - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentCalc
requests an alignment of pdb1 vs pdb 2.
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.
AlignmentCalcDB - Class in org.biojava.nbio.structure.align.gui
 
AlignmentCalcDB(AlignmentGui, Structure, String, UserConfiguration, String, Boolean) - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
 
AlignmentCalculationRunnable - Interface in org.biojava.nbio.structure.align.gui
 
alignmentEnded() - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
 
alignmentEnded() - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
 
alignmentEnded() - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
 
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 - Interface in org.biojava.nbio.structure.align.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.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.
alignmentStarted(String, String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
 
alignmentStarted(String, String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
 
alignmentStarted(String, String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
 
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).
alignPair(String, String) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
 
alignPair(String, String, String) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
 
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
 
AlignTools - Class in org.biojava.nbio.structure.align.helper
 
AlignTools() - Constructor for class org.biojava.nbio.structure.align.helper.AlignTools
 
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
 
ALL_POLYMER_TYPES - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType
Convenience Set of all polymer types.
AllChemCompProvider - Class in org.biojava.nbio.structure.io.mmcif
A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.
AllChemCompProvider() - Constructor for class org.biojava.nbio.structure.io.mmcif.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
 
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
 
altcode - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
 
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
 
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 two additional letters - XU
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.
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.
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(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
Analyze the symmetries of the input Atom array using the DEFAULT parameters.
analyze(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
Analyze the symmetries of the input Atom array using the provided parameters.
analyzeLevel(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
Analyze a single level of symmetry.
Anchor(int, int) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
 
AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.routines
This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.
AnchoredPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
Prepares for a pairwise global sequence alignment.
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
Prepares for a pairwise global sequence alignment.
anchors - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
angle(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
Gets the angle between two vectors
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.
AngleOutlier - Class in org.biojava.nbio.structure.validation
Java class for anonymous complex type.
AngleOutlier() - Constructor for class org.biojava.nbio.structure.validation.AngleOutlier
 
angleOutlier - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
 
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.
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.
App - Class in org.biojava.nbio.genome
Hello world!
App() - Constructor for class org.biojava.nbio.genome.App
 
App - Class in org.biojava.nbio.ontology
Hello world!
App() - Constructor for class org.biojava.nbio.ontology.App
 
append(T, Fastq...) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter
Append the specified FASTQ formatted sequences to the specified appendable.
append(T, Iterable<Fastq>) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter
Append the specified FASTQ formatted sequences to the specified appendable.
appendQuality(String) - Method in class org.biojava.nbio.sequencing.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.sequencing.io.fastq.ParseListener
Notify this listener of a quality line.
appendSequence(String) - Method in class org.biojava.nbio.sequencing.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.sequencing.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<T, T>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
Applies an alignment k times.
applyAlignment(Map<S, T>, Map<T, S>, 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
 
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(List<C>, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
ArrayListSequenceReader(String, 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.
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(Structure, double, int, int, boolean) - 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.
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(Throwable) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
 
AssertionFailure(String, 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
 
AssignmentXMLSerializer - Class in org.biojava.nbio.structure.domain
 
AssignmentXMLSerializer() - Constructor for class org.biojava.nbio.structure.domain.AssignmentXMLSerializer
 
Astral - Class in org.biojava.nbio.structure.scop
Provides programmatic access to ASTRAL representative sets.
Astral(Astral.AstralSet) - 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(String, Reader) - 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: 1.75A_95 Also contains a URL pointing to a FASTA file containing the representatives.
Atom - Interface in org.biojava.nbio.structure
A simple interface for an Atom.
atom - Variable in class org.biojava.nbio.structure.validation.Clash
 
atom - Variable in class org.biojava.nbio.structure.validation.SymmClash
 
atom0 - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
 
atom0 - Variable in class org.biojava.nbio.structure.validation.BondOutlier
 
atom1 - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
 
atom1 - Variable in class org.biojava.nbio.structure.validation.BondOutlier
 
atom2 - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
 
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.
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(String, boolean) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache
Deprecated.
isSplit parameter is ignored (4.0.0)
AtomCache(String, String, boolean) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache
Deprecated.
isSplit parameter is ignored (4.0.0)
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(Structure) - Constructor for class org.biojava.nbio.structure.AtomIterator
Constructs an AtomIterator object.
AtomIterator(Group) - Constructor for class org.biojava.nbio.structure.AtomIterator
Constructs an AtomIterator object.
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
 
atoms - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier
 
atoms - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier
 
AtomSite - Class in org.biojava.nbio.structure.io.mmcif.model
 
AtomSite() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AtomSite
 
AtomSites - Class in org.biojava.nbio.structure.io.mmcif.model
A class containing the _atom_sites data.
AtomSites() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AtomSites
 
atomsToPoints(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
Convert an array of atoms into an array of vecmath points
attemptedValidationSteps - Variable in class org.biojava.nbio.structure.validation.Entry
 
attribute(String, String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
attribute(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.
attribute(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter
Add an un-qualified 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.
AuditAuthor - Class in org.biojava.nbio.structure.io.mmcif.model
 
AuditAuthor() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
 
AugmentedResidueRange - Class in org.biojava.nbio.structure
Created by douglas on 1/23/15.
AugmentedResidueRange(String, ResidueNumber, ResidueNumber, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
 
AugmentedResidueRange(String, String, String, 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
 
AutoSuggestProvider - Interface in org.biojava.nbio.structure.align.gui.autosuggest
A class that provides auto-completion suggestions for JAutoSuggest
available() - Method in class org.biojava.nbio.core.util.UncompressInputStream
 
available() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
avgoccu - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
 
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.core
 
AxisAligner() - Constructor for class org.biojava.nbio.structure.symmetry.core.AxisAligner
 
axisStroke - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 

B

BACKGROUND_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
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
 
baseURL - Static variable in class org.biojava.nbio.structure.rcsb.RCSBUpdates
 
basicLoad(PDBFileReader, boolean, String) - Method in class demo.DemoChangeChemCompProvider
 
basicLoad(String) - Method in class demo.DemoDomainsplit
 
basicLoad() - Method in class demo.DemoLoadStructure
 
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
 
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
 
BIO_ASSEMBLY - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
 
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
 
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.
BioUnitDataProvider - Interface in org.biojava.nbio.structure.quaternary.io
Provides access to the data that is needed in order to rebuild the correct biological assembly of a protein.
BioUnitDataProviderFactory - Class in org.biojava.nbio.structure.quaternary.io
Factory to create BioUnitDataProvider instances.
BitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
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
 
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.
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
 
BlastAlignmentParameterEnum - Enum in org.biojava.nbio.ws.alignment.qblast
Alignment request parameters accepted by QBlast service.
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
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.
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
 
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(BlockSet) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl
Constructor.
BlockImpl(BlockImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl
Copy 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(MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl
Constructor.
BlockSetImpl(BlockSetImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl
Copy constructor.
Blosum62 - Static variable in class org.biojava.nbio.ronn.RonnConstraint
 
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(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
 
BondLocation(List<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
 
BondOutlier - Class in org.biojava.nbio.structure.validation
Java class for anonymous complex type.
BondOutlier() - Constructor for class org.biojava.nbio.structure.validation.BondOutlier
 
bondOutlier - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
 
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(BoundingBox) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
 
BoundingBox(Atom[]) - 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
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.
BravaisLattice - Enum in org.biojava.nbio.structure.xtal
An enum to represent the 7 Bravais lattices
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, 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.
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.
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.protmod.ProteinModificationImpl.Builder
 
build() - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder
Build and return a new FASTQ formatted sequence configured from the properties of this builder.
build - Static variable in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
 
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.
builder() - Static method in class org.biojava.nbio.sequencing.io.fastq.Fastq
Create and return a new FastqBuilder.
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
 
bulkSolventB - Variable in class org.biojava.nbio.structure.validation.Entry
 
bulkSolventK - Variable in class org.biojava.nbio.structure.validation.Entry
 
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 - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
c - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
first allowed c-term
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
C2RotationSolver - Class in org.biojava.nbio.structure.symmetry.core
 
C2RotationSolver(Subunits, 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
C_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
The atom name for the backbone carbonyl
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
cache - Variable in class org.biojava.nbio.structure.align.client.FarmJobRunnable
 
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
 
CachedRemoteScopInstallation - Class in org.biojava.nbio.structure.scop
An extension of the RemoteScopInstallation that caches some of the data locally.
CachedRemoteScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
 
CachedRemoteScopInstallation(boolean) - Constructor for class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
 
CacheFactory - Class in org.biojava.nbio.structure.align.util
provides a SoftHashMap singleton.
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, etc.
Calc() - Constructor for class org.biojava.nbio.structure.Calc
 
calc_rmsd(Atom[], Atom[], int, boolean, boolean) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
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.
CalcBioAssemblySymmetry - Class in org.biojava.nbio.structure.symmetry.analysis
 
CalcBioAssemblySymmetry(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
 
calcCenterOfRotation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
 
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.
calcPairwiseAlignments() - Method in class org.biojava.nbio.structure.symmetry.core.ClusterMerger
Aligns all pairs of input clusters, calculating their pairwise alignments
calcQuatSymmetry(Subunits, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
 
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(Subunits, 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
 
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
 
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
 
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
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.
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_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(String, boolean, boolean) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
 
CathInstallation(String) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
 
CathInstallation() - 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
ccp4Version - Variable in class org.biojava.nbio.structure.validation.Entry
 
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_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
 
ceColumnNames - Static variable in class org.biojava.nbio.structure.align.gui.DBResultTable
 
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.
Cell - Class in org.biojava.nbio.structure.io.mmcif.model
 
Cell() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Cell
 
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.symmetry.geometry.SuperPosition
 
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.
centerOfMass(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
 
centerOfMass() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
 
centricOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
 
centroid(Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
 
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.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
 
Chain - Interface in org.biojava.nbio.structure
Defines the interface for a Chain.
chain - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
 
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
 
ChainClusterer - Class in org.biojava.nbio.structure.symmetry.core
Wraps a sequence clustering with structural information
ChainClusterer(List<SequenceAlignmentCluster>) - Constructor for class org.biojava.nbio.structure.symmetry.core.ChainClusterer
 
chainEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
 
chainId - Variable in class org.biojava.nbio.structure.align.client.StructureName
 
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.
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(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
changeColumnHeader(String, String) - 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(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
 
changeRowHeader(String, String) - 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
 
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.io.mmcif.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
 
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.io.mmcif.DownloadChemCompProvider
 
chem_comp_type - Variable in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType
String value of the type
chemComp - Variable in class org.biojava.nbio.structure.HetatomImpl
 
ChemComp - Class in org.biojava.nbio.structure.io.mmcif.model
A definition for a Chemical Component, as maintained by the wwPDB.
ChemComp() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemComp
 
ChemCompAtom - Class in org.biojava.nbio.structure.io.mmcif.model
stores these fields: _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_residue_numbering _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_polymer_type _chem_comp_atom.pdbx_ref_id _chem_comp_atom.pdbx_component_id _chem_comp_atom.pdbx_ordinal
ChemCompAtom() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
 
ChemCompBond - Class in org.biojava.nbio.structure.io.mmcif.model
 
ChemCompBond() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
 
ChemCompConsumer - Class in org.biojava.nbio.structure.io.mmcif
 
ChemCompConsumer() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
 
ChemCompDescriptor - Class in org.biojava.nbio.structure.io.mmcif.model
Container object for _pdbx_chem_comp_descriptor
ChemCompDescriptor() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
 
ChemCompDistribution - Class in demo
 
ChemCompDistribution() - Constructor for class demo.ChemCompDistribution
 
ChemCompGroupFactory - Class in org.biojava.nbio.structure.io.mmcif
 
ChemCompGroupFactory() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
 
ChemCompProvider - Interface in org.biojava.nbio.structure.io.mmcif
Interface that is implemented by all classes that can provide ChemComp definitions.
ChemCompTools - Class in org.biojava.nbio.structure.io.mmcif.chem
Some tools for working with chemical compounds.
ChemCompTools() - Constructor for class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
 
ChemicalComponentDictionary - Class in org.biojava.nbio.structure.io.mmcif
A representation of the Chemical Component Dictionary.
ChemicalComponentDictionary() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
 
children() - Method in class org.biojava.nbio.alignment.GuideTree.Node
 
ChiSq - Class in org.biojava.nbio.survival.cox.stats
 
ChiSq() - Constructor for class org.biojava.nbio.survival.cox.stats.ChiSq
 
chiSq(double, int) - Static method in 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 - 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(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(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>, 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
 
cid - Variable in class org.biojava.nbio.structure.validation.Clash
 
CIFLabel - Annotation Type in org.biojava.nbio.structure.io.mmcif.model
Annotation indicating that a specific field of a bean should be mapped to a different label
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.
claFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
 
Clash - Class in org.biojava.nbio.structure.validation
Java class for anonymous complex type.
Clash() - Constructor for class org.biojava.nbio.structure.validation.Clash
 
clash - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
 
clashmag - Variable in class org.biojava.nbio.structure.validation.Clash
 
clashmag - Variable in class org.biojava.nbio.structure.validation.SymmClash
 
clashscore - Variable in class org.biojava.nbio.structure.validation.Entry
 
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, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils
Returns a new sequence with all invalid characters being replaced by '-'.
cleanSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
Removes all whitespace chars in the sequence string
cleanup() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc
 
cleanup() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
 
cleanup() - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
 
cleanUp() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
 
cleanup() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
 
cleanUp() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
 
cleanup() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
 
cleanup(List<Domain>) - Static method in class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
 
cleanup() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc
 
cleanup() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
 
cleanUp() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
 
clear() - Method in class org.biojava.nbio.core.util.FlatFileCache
 
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
remove all atoms
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.PDBStatus
The status of PDB IDs are cached to reduce server overload.
clearConsumers() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser
Remove all consumers from the parser.
clearConsumers() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
 
clearExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
clear the supported file extensions
clearListeners() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
 
clearListeners() - Method in class org.biojava.nbio.structure.align.FarmJob
 
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(Object) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
Subclasses should override clone and use the copy constructor.
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
Returns an identical copy of this Chain .
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.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.core.SequenceAlignmentCluster
 
clone() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
 
clone() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
 
cloneAtomArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
Provides an equivalent copy of Atoms in a new array.
cloneCAArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
Deprecated.
Use the better-named StructureTools.cloneAtomArray(Atom[]) instead
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.symmetry.geometry.SuperPosition
 
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(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.
close() - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
close() - Method in interface org.biojava.nbio.core.util.XMLWriter
Close this XMLWriter, and it's underlying stream.
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
 
closeParser() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
Method closes random access file descriptor.
closeTag(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
closeTag(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
closeTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter
Closes an un-qualified element.
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(List<Domain>, PDPDistanceMatrix) - Static method in class org.biojava.nbio.structure.domain.pdp.ClusterDomains
 
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
 
ClusterMerger - Class in org.biojava.nbio.structure.symmetry.core
Merges clusters based on their sequence identity.
ClusterMerger(List<SequenceAlignmentCluster>, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ClusterMerger
 
ClusterProteinChains - Class in org.biojava.nbio.structure.symmetry.core
Clusters the chains of one or two structures by sequence.
ClusterProteinChains(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
 
ClusterProteinChains(Structure, Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
 
Codon(Table.CaseInsensitiveTriplet, AminoAcidCompound, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon
 
Codon(Table.CaseInsensitiveTriplet) - 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
 
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
 
CombinationGenerator - Class in org.biojava.nbio.structure.symmetry.utils
 
CombinationGenerator(int, int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
 
combine(BiologicalAssemblyTransformation, BiologicalAssemblyTransformation) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
Returns the combination (product) of two biological assembly transformations.
combine(List<Integer>, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
 
combineWith(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup
Combine the ResidueGroup with the alignment block.
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_CHAR - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
 
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(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(int[], int[]) - Method in class org.biojava.nbio.structure.align.helper.IdxComparator
 
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(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(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
 
compareTo(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber
 
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
 
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
 
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.sequencing.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.io.mmcif.AllChemCompProvider
 
ComponentXMLConverter - Class in org.biojava.nbio.protmod.io
 
ComponentXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.ComponentXMLConverter
 
Compound - Interface in org.biojava.nbio.core.sequence.template
 
Compound - Class in org.biojava.nbio.structure
An object to contain the info from the PDB header for a Molecule.
Compound() - Constructor for class org.biojava.nbio.structure.Compound
 
Compound(Compound) - Constructor for class org.biojava.nbio.structure.Compound
Constructs a new Compound copying all data from the given one but not setting the Chains
CompoundFinder - Class in org.biojava.nbio.structure.io
Heuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure.
CompoundFinder(Structure) - Constructor for class org.biojava.nbio.structure.io.CompoundFinder
 
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(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
 
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
 
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(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.
ConfigurationException() - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
 
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
 
constrain(double) - Method in enum org.biojava.nbio.sequencing.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.
contacts(Point3d[], Point3d[], double) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
 
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(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
Is the key in the table?
contains(ResidueNumber, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange
 
contains(Subunits) - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
 
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(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
Returns the converted sequence.
convert(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.ForesterWrapper
Convert a BioJava MultipleSequenceAlignment to a forester Msa.
convert(Fastq, FastqVariant) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools
Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.
convert(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriter
 
convert(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.SangerFastqWriter
 
convert(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriter
 
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
 
convert_3code_1code(String) - Static method in class org.biojava.nbio.structure.StructureTools
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
 
convertAtomToAtomSite(Atom, int, String, String) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
Converts an Atom object to an AtomSite object.
convertAtomToAtomSite(Atom, int, String, String, int) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
Converts an Atom object to an AtomSite object.
convertChainToAtomSites(Chain, int, String, String) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
Converts a Chain into a List of AtomSite objects
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
 
convertCrystalCellToCell(CrystalCell) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
Converts a CrystalCell object to a Cell object.
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.
convertSpaceGroupToSymmetry(SpaceGroup) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
Converts a SpaceGroup object to a Symmetry object.
convertStreamToString(InputStream) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
 
convertStreamToString(InputStream) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
 
convertStructureToAtomSites(Structure) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
Converts a Structure into a List of AtomSite objects
convertTo(FastqVariant) - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq
Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.
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(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.
copy(File, File) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils
Copy the content of file src to dst TODO since java 1.7 this is provided in java.nio.file.Files
copy() - Method in class org.biojava.nbio.structure.jama.Matrix
Make a deep copy of a matrix
copyFile(File, File) - Static method in class org.biojava.nbio.phosphosite.Dataset
 
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(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
countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
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
 
CountProgressListener - Class in org.biojava.nbio.structure.align.client
 
CountProgressListener() - Constructor for class org.biojava.nbio.structure.align.client.CountProgressListener
 
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(String, String, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
 
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(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 TODO make this a ResidueNumber
CPRange() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
 
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.
createAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
Create an instance of AngleOutlier
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
 
createBondOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
Create an instance of BondOutlier
createClash() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
Create an instance of Clash
createDNASequence(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools
Create and return a new DNASequence from the specified FASTQ formatted sequence.
createDNASequenceWithErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.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.sequencing.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.sequencing.io.fastq.FastqTools
Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence.
createEntry() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
Create an instance of Entry
createErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.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.
createModelledSubgroup() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
Create an instance of ModelledSubgroup
createMogAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
Create an instance of MogAngleOutlier
createMogBondOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
Create an instance of MogBondOutlier
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
 
createProgram() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
Create an instance of Program
createPrograms() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
Create an instance of Programs
createQualityScores(Fastq) - Static method in class org.biojava.nbio.sequencing.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>, Frame) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
 
createSequence(Sequence<NucleotideCompound>) - 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.
createSymmClash() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
Create an instance of SymmClash
createTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
createTerm(String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
 
createTerm(String, String, Object[]) - 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, String) - Method in interface org.biojava.nbio.ontology.Ontology
Create a new term in this ontology.
createTerm(String, String, Object[]) - 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.Ontology.Impl
 
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.
createWwPDBValidationInformation() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
Create an instance of WwPDBValidationInformation
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
 
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(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
CrystalTransform(CrystalTransform) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform
Copy constructor
CS_HSV - Static variable in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
The HSV color space
Cut(int, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
 
Cut - Class in org.biojava.nbio.structure.domain.pdp
 
Cut() - Constructor for class org.biojava.nbio.structure.domain.pdp.Cut
 
cut(Atom[], Domain, CutValues, int[][], PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.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 - Class in org.biojava.nbio.structure.domain.pdp
 
CutDomain(Atom[], PDPDistanceMatrix) - Constructor for class org.biojava.nbio.structure.domain.pdp.CutDomain
 
cutDomain(Domain, CutSites, PDPDistanceMatrix) - Method in 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
 
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 - 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.
dataAnisotropy - Variable in class org.biojava.nbio.structure.validation.Entry
 
DatabasePDBremark - Class in org.biojava.nbio.structure.io.mmcif.model
 
DatabasePDBremark() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
 
DatabasePDBrev - Class in org.biojava.nbio.structure.io.mmcif.model
 
DatabasePDBrev() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
 
DatabasePdbrevRecord - Class in org.biojava.nbio.structure.io.mmcif.model
 
DatabasePdbrevRecord() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
 
DatabaseReference(String, String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
 
DatabaseReference(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)
dataCompleteness - Variable in class org.biojava.nbio.structure.validation.Entry
 
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
 
DBL - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
 
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
DBResultTable - Class in org.biojava.nbio.structure.align.gui
 
DBResultTable() - Constructor for class org.biojava.nbio.structure.align.gui.DBResultTable
 
DBSearchGUI - Class in org.biojava.nbio.structure.align.gui
 
DBSearchGUI() - Constructor for class org.biojava.nbio.structure.align.gui.DBSearchGUI
 
dbxp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
dccr - Variable in class org.biojava.nbio.structure.validation.Entry
 
dccRefinementProgram - Variable in class org.biojava.nbio.structure.validation.Entry
 
dccRfree - Variable in class org.biojava.nbio.structure.validation.Entry
 
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(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
 
debug - Static variable in class org.biojava.nbio.structure.align.util.AlignmentTools
 
declareNamespace(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
 
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_BATCH_SIZE - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
 
DEFAULT_BUFFER_SIZE - Variable in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
 
DEFAULT_CHAIN_ID - Static variable in class org.biojava.nbio.structure.ChainImpl
The default chain identifier used to be an empty space
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_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.HTTPConnectionTools
 
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_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_JOB_TIME - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
 
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_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
 
DEFAULT_NR_ALIGNMENTS - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
 
DEFAULT_NR_THREADS - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
 
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_API_URL - Static variable in class org.biojava.nbio.structure.domain.PDBDomainProvider
 
DEFAULT_PDB_FILE_SERVER - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
The default server name, prefixed by the protocol string (http:// or ftp://).
DEFAULT_PDB_HOST - Static variable in class org.biojava.nbio.structure.domain.PDBDomainProvider
 
DEFAULT_PDB_PATH - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
 
DEFAULT_PDB_SERVER - Static variable in class org.biojava.nbio.structure.PDBStatus
 
DEFAULT_PROBE_SIZE - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
 
DEFAULT_PROVIDER_CLASS - Static variable in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
 
DEFAULT_PROVIDER_CLASSNAME - Static variable in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
 
DEFAULT_RANGE_PROBABILITY_THRESHOLD - Static variable in class org.biojava.nbio.ronn.RonnConstraint
 
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 - Static variable in class org.biojava.nbio.structure.domain.RemotePDPProvider
 
DEFAULT_SERVER - Static variable in class org.biojava.nbio.structure.scop.RemoteScopInstallation
 
DEFAULT_SERVER_URL - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
 
DEFAULT_SERVERNAME - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
 
DEFAULT_SERVERNAME - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
 
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_VARIANT - Static variable in class org.biojava.nbio.sequencing.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(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
 
delete(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
Delete the key (and paired value) from table.
deleteStructure(String) - 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
 
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
 
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
 
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
 
DemoOrientBioAssembly - Class in demo
Created by ap3 on 02/04/2015.
DemoOrientBioAssembly() - Constructor for class demo.DemoOrientBioAssembly
 
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
 
DemoShowValidationResults - Class in demo
 
DemoShowValidationResults() - Constructor for class demo.DemoShowValidationResults
 
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
 
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.sequencing.io.fastq.ParseListener
Notify this parse listener of a description line.
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() - Static method in class org.biojava.nbio.core.util.FlatFileCache
 
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.
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
 
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, 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(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay
Display an AFPChain alignment
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.
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 - Variable in class org.biojava.nbio.structure.validation.Clash
 
dist - Variable in class org.biojava.nbio.structure.validation.SymmClash
 
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_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.
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_ONLY - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType
Convenience Set of polymer types classified as DNA.
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
 
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(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(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>, 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
 
documentEnd() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
 
documentEnd() - Method in class org.biojava.nbio.structure.io.mmcif.MetalBondConsumer
 
documentEnd() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
called at end of document
documentEnd() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
 
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
 
documentStart() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
 
documentStart() - Method in class org.biojava.nbio.structure.io.mmcif.MetalBondConsumer
 
documentStart() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
called at start of document
documentStart() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
Start the parsing
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() - Constructor for class org.biojava.nbio.structure.domain.pdp.Domain
 
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
DomainProviderFactory - Class in org.biojava.nbio.structure.domain
A simple factory object that returns the system wide default DomainProvider
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.HTTPConnectionTools
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.HTTPConnectionTools
do a POST to a URL and return the response stream for further processing elsewhere.
doPOST(URL, String) - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
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(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseVector
Calculates the dot product of this vector a with b
dot(double[], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
 
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
 
download() - Method in class org.biojava.nbio.phosphosite.Dataset
 
DownloadChemCompProvider - Class in org.biojava.nbio.structure.io.mmcif
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.io.mmcif.DownloadChemCompProvider
 
DownloadChemCompProvider(String) - Constructor for class org.biojava.nbio.structure.io.mmcif.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(URL, File) - Method in class org.biojava.nbio.phosphosite.Dataset
 
downloadFile() - Static method in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider
Downloads the components.cif.gz file from the wwPDB site.
downloadFile(URL, File) - Static method in class org.biojava.nbio.structure.io.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
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
 
downloadingStructures(String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
 
downloadingStructures(String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
 
downloadingStructures(String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
 
downloadNodeListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
 
downloadPDB(String) - Method in class org.biojava.nbio.structure.io.PDBFileReader
Deprecated.
downloadStructure(String) - 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.
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
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
 

E

E - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
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(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(String) - 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(BufferedReader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
 
Edit<C extends Compound> - Interface in org.biojava.nbio.core.sequence.edits
Interface for carrying out edit operations on a Sequence.
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.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.
edsr - Variable in class org.biojava.nbio.structure.validation.Entry
 
edsResolution - Variable in class org.biojava.nbio.structure.validation.Entry
 
edsResolutionLow - Variable in class org.biojava.nbio.structure.validation.Entry
 
ef - Variable in class org.biojava.nbio.survival.cox.CoxInfo
 
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.
Element - Class in org.biojava.nbio.aaproperties.xml
One way to model the elements
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
 
Element - Enum in org.biojava.nbio.structure
Element is an enumeration of the elements of the periodic table.
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.
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.
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
 
ent - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
 
Entity - Class in org.biojava.nbio.structure.io.mmcif.model
A simple class to represent Entity records in mmCif files
Entity() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Entity
 
entity_poly_type - Variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType
 
EntityPolySeq - Class in org.biojava.nbio.structure.io.mmcif.model
Container for _entity_poly_seq records Field Name mmCIF Data Item Section n.a.
EntityPolySeq() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
 
EntitySrcGen - Class in org.biojava.nbio.structure.io.mmcif.model
Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated.
EntitySrcGen() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
 
EntitySrcNat - Class in org.biojava.nbio.structure.io.mmcif.model
Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue.
EntitySrcNat() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
 
EntitySrcSyn - Class in org.biojava.nbio.structure.io.mmcif.model
PDBX_ENTITY_SRC_SYN records the details about each chemically synthesized molecule (entity) in the asymmetric unit.
EntitySrcSyn() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
 
Entry - Class in org.biojava.nbio.structure.validation
Java class for anonymous complex type.
Entry() - Constructor for class org.biojava.nbio.structure.validation.Entry
 
entry - Variable in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
 
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(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(boolean, boolean) - 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.
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.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.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.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 - 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
 
equals(Object) - Method in class org.biojava.nbio.data.sequence.FastaSequence
 
equals(GeneName) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
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.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.mmcif.model.ChemComp
 
equals(Object) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
 
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(PDBHeader) - Method in class org.biojava.nbio.structure.PDBHeader
Compare two PDBHeader objects
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.misc.ChainSignature
 
equals(Object) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
 
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
 
equalsToIgnoreEndline(String, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
compares two strings 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
 
EQUIVALENCE - Static variable in class org.biojava.nbio.ontology.OntoTools
 
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.
equivalentAxes(Matrix4d, Matrix4d, double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Deprecated.
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.sequencing.io.fastq.FastqTools
Return the error probabilities from the specified FASTQ formatted sequence.
errorProbabilities(Fastq, double[]) - Static method in class org.biojava.nbio.sequencing.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.sequencing.io.fastq.FastqVariant
Convert the specified quality in ASCII format to an error probability.
errorProbability(int) - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant
Calculate the error probability given the specified quality score.
escape(String, boolean) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
 
escapeChars - Static variable in class org.biojava.nbio.ontology.obo.OboFileParser
 
eval(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
evalString(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
Execute a command String in the current Jmol panel.
evalString(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
 
evalString(String) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
 
evaluate(Phylogeny, DistanceMatrix) - Static method in class org.biojava.nbio.phylo.DistanceTreeEvaluator
Evaluate the goodness of fit of a given tree to the original distance matrix.
EXACT_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
 
EXACT_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym
 
execute(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative
This method uses iteratively CeSymm to calculate all symmetries in the input array of atoms and organize them in a multiple alignment of the repeats.
executeCmd(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
 
ExonComparator - Class in org.biojava.nbio.core.sequence
Sort Exon where it is a little confusing if exons shoud always be ordered left to right where a negative stranded gene should go the other direction.
ExonComparator() - Constructor for class org.biojava.nbio.core.sequence.ExonComparator
 
ExonSequence - Class in org.biojava.nbio.core.sequence
A gene contains a collection of Exon sequences
ExonSequence(GeneSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.ExonSequence
Need a parent gene sequence and the bioBegin and bioEnd.
expandUserHome(String) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils
Expands ~ in paths to the user's home directory.
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
 
Exptl - Class in org.biojava.nbio.structure.io.mmcif.model
 
Exptl() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Exptl
 
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
 
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
 

F

F - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
f(Double) - Method in class org.biojava.nbio.survival.cox.StrataInfo
 
f1Dot2(float) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
 
F_UNCLASSIFIED - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
String for unclassified F-groups
FarmJob - Class in org.biojava.nbio.structure.align
A job as it can be run on the farm.
FarmJob() - Constructor for class org.biojava.nbio.structure.align.FarmJob
 
FarmJobParameters - Class in org.biojava.nbio.structure.align.client
 
FarmJobParameters() - Constructor for class org.biojava.nbio.structure.align.client.FarmJobParameters
 
FarmJobRunnable - Class in org.biojava.nbio.structure.align.client
Contains the single thread for a job that can run multiple alignments.
FarmJobRunnable(FarmJobParameters) - Constructor for class org.biojava.nbio.structure.align.client.FarmJobRunnable
 
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(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.
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.
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(InputStream, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
 
FastaStructureParser(File, 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(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(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
TODO Write comment
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.
fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>, AminoAcidCompound>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
Provided only for convenience.
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 - Class in org.biojava.nbio.sequencing.io.fastq
FASTQ formatted sequence.
fastq(Fastq) - Method in interface org.biojava.nbio.sequencing.io.fastq.StreamListener
Notify this listener of a FASTQ formatted sequence.
FastqBuilder - Class in org.biojava.nbio.sequencing.io.fastq
Fluent builder API for creating FASTQ formatted sequences.
FastqBuilder() - Constructor for class org.biojava.nbio.sequencing.io.fastq.FastqBuilder
Create a new FASTQ formatted sequence builder.
FastqReader - Interface in org.biojava.nbio.sequencing.io.fastq
Reader for FASTQ formatted sequences.
FastqTools - Class in org.biojava.nbio.sequencing.io.fastq
Utility methods for FASTQ formatted sequences.
FastqVariant - Enum in org.biojava.nbio.sequencing.io.fastq
FASTQ sequence format variant.
FastqWriter - Interface in org.biojava.nbio.sequencing.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
 
fatColumnNames - Static variable in class org.biojava.nbio.structure.align.gui.DBResultTable
 
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
 
Feature - Class in org.biojava.nbio.genome.parsers.gff
A Feature corresponds to a single row in a GFF file.
Feature(Feature) - Constructor for class org.biojava.nbio.genome.parsers.gff.Feature
Make a copy of the specified feature.
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_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 - 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(String, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser
Fetch and parse the DSSP file of the specified pdb code from the PDB web server and return the secondary structure annotation as a List of SecStrucState objects.
FIELD_LINE - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
 
figureLineInfoLowerPercentX - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
figureLineInfoLowerPercentY - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
 
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.structure.io.util
 
FileDownloadUtils() - Constructor for class org.biojava.nbio.structure.io.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
fileSeparator - Static variable in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
 
FILESPLIT - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
 
FILESPLIT - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
 
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 class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
 
filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
 
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 class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
 
filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
 
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 class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
 
filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
 
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
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.
findChain(String) - Method in interface org.biojava.nbio.structure.Structure
Request a particular chain from a structure.
findChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
Request a particular chain from a particular model
findChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
Request a particular chain from a particular model
findChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
Request a particular chain from a structure.
findCompounds() - Method in class org.biojava.nbio.structure.io.CompoundFinder
Utility method that employs some heuristics to find the Compounds for this Structure in case the information is missing in PDB/mmCIF file
findGroup(String, String) - Method in interface org.biojava.nbio.structure.Structure
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.
findGroup(String, String) - 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.
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(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
 
first_cut - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
 
flagLoading(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
 
flagLoadingFinished(String) - 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.
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.
flippableSidechain - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
 
floor(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
Return the largest key in the table <= k.
flush() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
 
flushCache() - Method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
 
flushCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
 
flushCache() - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
 
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
 
foFcCorrelation - Variable in class org.biojava.nbio.structure.validation.Entry
 
ForesterWrapper - Class in org.biojava.nbio.phylo
This class contains wrapper methods for communication between BioJava and forester (e.g, Data Structure conversion).
FORMAT_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier
URL parameter specifying the file format (PDB or CIF)
formatExonStructure(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
Pretty print the details of a GeneChromosomePosition to a String
formBondsFromStructConn(List<StructConn>) - Method in class org.biojava.nbio.structure.io.BondMaker
 
formDisulfideBonds(List<SSBondImpl>) - Method in class org.biojava.nbio.structure.io.BondMaker
Creates disulfide bond objects and references in the corresponding Atoms objects, given a list of SSBondImpls parsed from a PDB/mmCIF file.
formLinkRecordBond(PDBTemporaryStorageUtils.LinkRecord) - Method in class org.biojava.nbio.structure.io.BondMaker
Creates bond objects from a LinkRecord as parsed from a PDB file
FourBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
FourBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
FourBitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
FourBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
FourBitSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
Four bit encoding of the bit formats.
FourBitSequenceReader(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader.FourBitArrayWorker<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
A four bit per compound implementation of the bit array worker code.
fractionalDissimilarity(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
The fractional dissimilarity (D) is defined as the percentage of sites that differ between two aligned sequences.
fractionalDissimilarityScore(MultipleSequenceAlignment<C, D>, SubstitutionMatrix<D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
The fractional dissimilarity score (Ds) is a relative measure of the dissimilarity between two aligned sequences.
FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
FractionalIdentityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityInProfileScorer
Creates a fractional identity scorer for an aligned pair of sequences in the given alignment profile.
FractionalIdentityScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
Implements an algorithm which computes a score for a sequence alignment pair.
FractionalIdentityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityScorer
Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
FractionalIdentityScorer(SequencePair<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityScorer
Creates a fractional identity scorer for an aligned pair of sequences.
FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
FractionalSimilarityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer
Creates a fractional similarity scorer for an aligned pair of sequences in the given alignment profile.
FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
Implements an algorithm which computes a score for a sequence alignment pair.
FractionalSimilarityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityScorer
Creates a fractional similarity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
FractionalSimilarityScorer(SequencePair<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityScorer
Creates a fractional similarity scorer for an aligned pair of sequences.
frag_pairwise_compat(FragmentPair[], int, float, int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
Calculate the pairwise compatibility of fpairs.
FragmentJoiner - Class in org.biojava.nbio.structure.align.pairwise
Joins the initial Fragments together to larger Fragments
FragmentJoiner() - Constructor for class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
 
FragmentPair - Class in org.biojava.nbio.structure.align.pairwise
a pair of fragments of two protein structures
FragmentPair(int, int, int) - Constructor for class org.biojava.nbio.structure.align.pairwise.FragmentPair
 
Frame - Enum in org.biojava.nbio.core.sequence.transcription
Indicates a way of translating a sequence.
frame() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
Get frame (aka phase).
frame - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
 
from - Variable in class org.biojava.nbio.ronn.Jronn.Range
Range starting position counts from 1 (the first position on the sequence is 1)
fromAFP(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Converts a refined symmetry AFPChain alignment into the standard representation of symmetry in a MultipleAlignment, that contains the entire Atom array of the strcuture and the symmetric repeats are orgaized in different rows in a single Block.
fromBio(int, int, char) - Static method in class org.biojava.nbio.genome.parsers.gff.Location
Create location from "biocoordinates", as in GFF file.
fromBioExt(int, int, char, int) - Static method in class org.biojava.nbio.genome.parsers.gff.Location
Create a location from MAF file coordinates, which represent negative strand locations as the distance from the end of the sequence.
fromCathCode(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory
 
fromCharacter(Character) - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType
 
fromCharacter(Character) - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType
Converts a Character representing a Secondary Structure type into the corresponding enum object.
fromCIEXYZ(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
 
fromConciseAlignmentString(String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
 
fromMultiXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
 
fromRGB(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
 
fromStartupParams(StartupParameters) - Static method in class org.biojava.nbio.structure.align.util.UserConfiguration
 
fromString(String) - Static method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
 
fromString(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory
 
fromString(String) - Static method in enum org.biojava.nbio.structure.PDBStatus.Status
 
fromString(String) - Static method in class org.biojava.nbio.structure.ResidueNumber
Convert a string representation of a residue number to a residue number object.
fromString(String) - Static method in enum org.biojava.nbio.structure.scop.ScopCategory
 
fromXML(String) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter
 
fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter
 
fromXML(String) - Static method in class org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter
 
fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.StructureAtomXMLConverter
 
fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.StructureGroupXMLConverter
 
fromXML(String, String, String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed
fromXML(String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
 
fromXML(String) - Method in class org.biojava.nbio.structure.align.xml.HasResultXMLConverter
 
fromXML(String) - Method in class org.biojava.nbio.structure.align.xml.PositionInQueueXMLConverter
 
fromXML(String) - Static method in class org.biojava.nbio.structure.align.xml.RepresentativeXMLConverter
 
fromXML(String) - Static method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer
 
fromXML(String) - Static method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
 
fromXML(String) - Static method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
 
fromXML(String) - Static method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
 
fromXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
 
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ListStringWrapper
 
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ScopDescriptions
 
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ScopDomains
 
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ScopNodes
 
fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper
 
fromXML(String) - Static method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
 
fromXML(String) - Static method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
 
functionXY(String, int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
functionXYZ(String, int, int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
 
FuzzyPoint - Class in org.biojava.nbio.core.sequence.location
Implementation for resolving fuzzy locations.
FuzzyPoint(int, int) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint
 
FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint
 
FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint
 

G

G - Static variable in class org.biojava.nbio.aaproperties.Constraints
 
GAP_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
 
GAP_COVERAGE_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.CompoundFinder
Gap coverage value (num gaps over length of sequence) for each chain of the match: 2 chains with more gap coverage than this value will not be considered part of the same entity
GapArray - Class in org.biojava.nbio.structure.align.helper
 
GapArray() - Constructor for class org.biojava.nbio.structure.align.helper.GapArray
 
gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
 
gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
 
gapPenalty - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
 
GapPenalty - Interface in org.biojava.nbio.alignment.template
Defines a data structure for the gap penalties used during a sequence alignment routine.
GapPenalty.Type - Enum in org.biojava.nbio.alignment.template
Defines the possible types of gap penalties.
GCStats - Class in org.biojava.nbio.genome.parsers.gff
 
GCStats() - Constructor for class org.biojava.nbio.genome.parsers.gff.GCStats
 
GENBANK_FORMAT - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
The name of this format
GenbankHeaderFormatInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
 
GenbankProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
 
GenbankProxySequenceReader(String, String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
 
GenbankReader<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank files
GenbankReader(InputStream, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReader
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.
GenbankReader(File, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReader
If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
GenbankReaderHelper - Class in org.biojava.nbio.core.sequence.io
 
GenbankReaderHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
 
GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
 
GenbankSequenceParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
 
genbankSplitPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser
Decodes a split pattern.
GenbankWriter<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
 
GenbankWriter(OutputStream, Collection<S>, GenbankHeaderFormatInterface<S, C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriter
Use default line length of 60
GenbankWriter(OutputStream, Collection<S>, GenbankHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriter
Set custom lineLength
GenbankWriterHelper - Class in org.biojava.nbio.core.sequence.io
The class that should be used to write out genbank file of a sequence collection
GenbankWriterHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
 
GeneChromosomePosition - Class in org.biojava.nbio.genome.parsers.genename
 
GeneChromosomePosition() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
 
GeneChromosomePositionParser - Class in org.biojava.nbio.genome.parsers.genename
A parser that parses a file from the UCSC genome browser that contains mapping of gene name to chromosome positions
GeneChromosomePositionParser() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
 
GeneFeatureHelper - Class in org.biojava.nbio.genome
 
GeneFeatureHelper() - Constructor for class org.biojava.nbio.genome.GeneFeatureHelper
 
GeneIDGFF2Reader - Class in org.biojava.nbio.genome.parsers.gff
http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneIDGFF2Reader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
 
GeneIDXMLReader - Class in org.biojava.nbio.genome.parsers.geneid
 
GeneIDXMLReader(String) - Constructor for class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
 
GeneMarkGTFReader - Class in org.biojava.nbio.genome.parsers.gff
http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneMarkGTFReader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
 
GeneName - Class in org.biojava.nbio.genome.parsers.genename
A simple bean that contains gene name information as available from www.genenames.org
GeneName() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneName
 
GeneNamesParser - Class in org.biojava.nbio.genome.parsers.genename
Parses a file from the www.genenames.org website that contains a mapping of human gene names to other databases
GeneNamesParser() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
 
generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
Returns what the value of a compound is in the backing bit storage i.e.
generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
Returns a Map which encodes the contents of CompoundSet.
generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
Returns a Map which encodes TCAG into positions 0,1,2,3.
generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
Should return the inverse information that BitSequenceReader.BitArrayWorker.generateCompoundsToIndex() returns i.e. if the Compound C returns 1 from compoundsToIndex then we should find that compound here in position 1
generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
Returns a List which reverse encodes the Compound, Integer map
generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
Returns a List which encodes TCAG into positions 0,1,2,3.
GenericFastaHeaderFormat<S extends AbstractSequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
We store the original header if the sequence is parsed from a fasta file and will use that exact sequence if we write out the sequences to a fasta file.
GenericFastaHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat
 
GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
The default fasta header parser where some headers are well defined based on the source database which allows us to set the source of the protein sequence and the identifier that can be used in future implementations to load features from external sources If the user has a custom header with local data then they can create their own implementation of a FastaHeaderParserInterface 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 sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE PDB EBI PDB:1ECY_A mol:protein length:142 ECOTIN 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
GenericFastaHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser
 
GenericGenbankHeaderFormat<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
 
GenericGenbankHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
 
GenericGenbankHeaderFormat(String) - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
 
GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
 
GenericGenbankHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
 
GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
 
GenericInsdcHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat
 
GeneSequence - Class in org.biojava.nbio.core.sequence
 
GeneSequence(ChromosomeSequence, int, int, Strand) - Constructor for class org.biojava.nbio.core.sequence.GeneSequence
A class that keeps track of the details of a GeneSequence which is difficult to properly model.
get(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
Returns the window specified at the given index in offsets i.e. asking for position 2 in a moving window sequence of size 3 will get you the window starting at position 4.
get(Object) - Method in class org.biojava.nbio.core.util.SoftHashMap
 
get(Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap
 
get(Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
 
get(Object) - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
 
get(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
Gets the interface corresponding to given id.
get(K) - Method in class org.biojava.nbio.structure.domain.SerializableCache
 
get(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
 
get(int, int) - Method in class org.biojava.nbio.structure.jama.Matrix
Get a single element.
get(int, int) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix
access a value at i,j
get(int) - Method in class org.biojava.nbio.structure.math.SparseVector
get a value
get(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
Return the value paired with given key; null if key is not in table.
get(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
 
get(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
 
get1LetterCode(String) - Static method in class org.biojava.nbio.structure.StructureTools
Convert a three letter amino acid or nucleotide code into a single character code.
get1LetterCodeAmino(String) - Static method in class org.biojava.nbio.structure.StructureTools
Convert three character amino acid codes into single character e.g.
GET_ASSEMBLY - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
 
GET_ASSEMBLY_GENS - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
 
GET_STRUCT_OPER - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
 
getA() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
 
getA() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
 
getAAComposition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
Returns the composition of the 20 standard amino acid in the sequence.
getAAComposition(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAAComposition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
 
getAACompositionChar(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAACompositionString(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAAIndexProvider() - Static method in class org.biojava.nbio.core.alignment.matrices.AAindexFactory
 
getAboutMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
 
getAbsoluteMinimumSequenceLength() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
 
getAbsolutePercentialRNAsuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
 
getAbsolutePercentileClashscore() - Method in class org.biojava.nbio.structure.validation.Entry
Gets the value of the absolutePercentileClashscore property.
getAbsolutePercentileDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry
 
getAbsolutePercentilePercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
Gets the value of the absolutePercentilePercentRamaOutliers property.
getAbsolutePercentilePercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
Gets the value of the absolutePercentilePercentRotaOutliers property.
getAbsolutePercentilePercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
Gets the value of the absolutePercentilePercentRSRZOutliers property.
getAbsorbance(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
Returns the absorbance (optical density) of sequence.
getAbsorbance(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
An adaptor method to returns the absorbance (optical density) of sequence.
getAbsorbance(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
 
getAbsorpt_coefficient_mu() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
 
getAbsorpt_correction_T_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
 
getAbsorpt_correction_T_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
 
getAbsorpt_correction_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
 
getAbsorpt_process_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
 
getAcc() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
 
getAccept1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
getAccept2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
 
getAcceptedAtomNames() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
By default the parser will read in all atoms (unless using the CAonly switch).
getAccession() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
 
getAccession() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
 
getAccession() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
 
getAccession() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
 
getAccession() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
 
getAccession() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
 
getAccession() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
 
getAccession() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
 
getAccession() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
Unsupoorted
getAccession() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
 
getAccession() - Method in interface org.biojava.nbio.core.sequence.template.Accessioned
Returns the AccessionID this location is currently bound with
getAccession() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
 
getAccessionNr() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
 
getAccessionNumber() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
 
getAccessions() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
Pull uniprot accessions associated with this sequence
getAccessions() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
Gets the protein accessions mapped from the Fasta file.
getAccessions() - Method in class org.biojava.nbio.structure.rcsb.RCSBMacromolecule
 
getAcentricOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
Gets the value of the acentricOutliers property.
getAdapter() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel