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All Classes All Packages
All Classes All Packages
A
- A - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
- A - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
- A - Static variable in class org.biojava.nbio.aaproperties.Constraints
- AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
-
Valid Amino acids
- aa2CTerminalPka - Static variable in class org.biojava.nbio.aaproperties.Constraints
- aa2ExtinctionCoefficient - Static variable in class org.biojava.nbio.aaproperties.Constraints
- aa2Hydrophathicity - Static variable in class org.biojava.nbio.aaproperties.Constraints
- aa2MolecularWeight - Static variable in class org.biojava.nbio.aaproperties.Constraints
- aa2NTerminalPka - Static variable in class org.biojava.nbio.aaproperties.Constraints
- aa2PKa - Static variable in class org.biojava.nbio.aaproperties.Constraints
- AAindexFactory - Class in org.biojava.nbio.core.alignment.matrices
-
Factory class to get Providers for substitution matrices that are provided by the AAINDEX database.
- AAindexFactory() - Constructor for class org.biojava.nbio.core.alignment.matrices.AAindexFactory
- AAIndexFileParser - Class in org.biojava.nbio.core.alignment.matrices
- AAIndexFileParser() - Constructor for class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser
- AAIndexProvider - Interface in org.biojava.nbio.core.alignment.matrices
- aaScore(char, char) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
- ABITrace - Class in org.biojava.nbio.core.sequence.io
-
Title: ABITrace
- ABITrace(byte[]) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace
-
The
byte[]
constructor parses an ABI file represented as a byte array. - ABITrace(File) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace
-
The File constructor opens a local ABI file and parses the content.
- ABITrace(URL) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace
-
The URL constructor opens an ABI file from any URL.
- ABITracerCompoundSet - Class in org.biojava.nbio.core.sequence.compound
- ABITracerCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet
- AboutDialog - Class in org.biojava.nbio.structure.align.gui
- AboutDialog() - Constructor for class org.biojava.nbio.structure.align.gui.AboutDialog
- abs(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
- abs(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
- Absorbance_False - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
- Absorbance_True - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
- AbstractAlignmentJmol - Class in org.biojava.nbio.structure.align.gui.jmol
-
An Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol.
- AbstractAlignmentJmol() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
- AbstractAnnotation - Class in org.biojava.nbio.ontology.utils
-
A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
- AbstractAnnotation() - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation
-
Protected no-args constructor intended for sub-classes.
- AbstractAnnotation(Map) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation
-
Create a new Annotation by copying the key-value pairs from a map.
- AbstractAnnotation(Annotation) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation
-
Copy-constructor.
- AbstractCifFileSupplier<S> - Class in org.biojava.nbio.structure.io.cif
-
Convert a BioJava object to a CifFile.
- AbstractCifFileSupplier() - Constructor for class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier
- AbstractCifFileSupplier.WrappedAtom - Class in org.biojava.nbio.structure.io.cif
-
Wrapped atoms represent individual atoms enriched with model- and chain-level information.
- AbstractCompound - Class in org.biojava.nbio.core.sequence.template
-
The details of a Compound
- AbstractCompound() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound
- AbstractCompound(String) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound
- AbstractCompoundSet<C extends Compound> - Class in org.biojava.nbio.core.sequence.template
- AbstractCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
- AbstractCompoundTranslator<F extends Compound,T extends Compound> - Class in org.biojava.nbio.core.sequence.template
- AbstractCompoundTranslator(SequenceCreatorInterface<T>, CompoundSet<F>, CompoundSet<T>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
- AbstractEdit(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
- AbstractEdit(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
- AbstractFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features
-
A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that feature
- AbstractFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.AbstractFeature
-
A feature has a type and a source
- AbstractLocation - Class in org.biojava.nbio.core.sequence.location.template
-
Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand
- AbstractLocation() - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation
- AbstractLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
Default constructor
- AbstractLocation(Point, Point, Strand, boolean, boolean, AccessionID, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
Default constructor
- AbstractMatrixAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template
-
Implements common code for an
Aligner
which builds a score matrix during computation. - AbstractMatrixAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Before running an alignment, data must be sent in via calls to
AbstractMatrixAligner.setGapPenalty(GapPenalty)
andAbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
. - AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Prepares for an alignment.
- AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Prepares for an alignment.
- AbstractNucleotideCompoundSet<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.template
- AbstractNucleotideCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
- AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template
- AbstractPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
Before running a pairwise global sequence alignment, data must be sent in via calls to
AbstractPairwiseSequenceAligner.setQuery(Sequence)
,AbstractPairwiseSequenceAligner.setTarget(Sequence)
,AbstractMatrixAligner.setGapPenalty(GapPenalty)
, andAbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
. - AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
Prepares for a pairwise global sequence alignment.
- AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
Prepares for a pairwise sequence alignment.
- AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template
- AbstractProfileProfileAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
Before running a profile-profile alignment, data must be sent in via calls to
AbstractProfileProfileAligner.setQuery(Profile)
,AbstractProfileProfileAligner.setTarget(Profile)
,AbstractMatrixAligner.setGapPenalty(GapPenalty)
, andAbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
. - AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
Prepares for a profile-profile alignment run concurrently.
- AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
Prepares for a profile-profile alignment run concurrently.
- AbstractProfileProfileAligner(Profile<S, C>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
Prepares for a profile-profile alignment run concurrently.
- AbstractProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
Prepares for a profile-profile alignment.
- AbstractReference - Class in org.biojava.nbio.core.sequence.reference
- AbstractReference() - Constructor for class org.biojava.nbio.core.sequence.reference.AbstractReference
- AbstractScorer - Class in org.biojava.nbio.alignment.template
-
Implements common code for algorithms which compute a score.
- AbstractScorer() - Constructor for class org.biojava.nbio.alignment.template.AbstractScorer
- AbstractScoresCache - Class in org.biojava.nbio.structure.align.multiple
-
Abstact implementation of the
ScoresCache
with the shared code used in all objects with a variables cache. - AbstractScoresCache() - Constructor for class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
- AbstractScoresCache(AbstractScoresCache) - Constructor for class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
- AbstractSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence.template
-
The base class for DNA, RNA and Protein sequences.
- AbstractSequence() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence
- AbstractSequence(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Create a Sequence from a simple string where the values should be found in compoundSet
- AbstractSequence(SequenceReader<C>, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence
-
A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location of the sequence data.
- AbstractSequence.AnnotationType - Enum in org.biojava.nbio.core.sequence.template
- AbstractStructureAlignment - Class in org.biojava.nbio.structure.align
- AbstractStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.AbstractStructureAlignment
- AbstractTerm - Class in org.biojava.nbio.ontology
-
Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
- AbstractTerm() - Constructor for class org.biojava.nbio.ontology.AbstractTerm
- AbstractUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
-
Base class for a new structure alignment CLI.
- AbstractUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
- Ac - org.biojava.nbio.structure.Element
- AccesionedLocation - Interface in org.biojava.nbio.core.sequence.location.template
-
A location which is bound to an AccessionID.
- ACCESSION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
- Accessioned - Interface in org.biojava.nbio.core.sequence.template
-
Indicates an entity is accessioned
- AccessionID - Class in org.biojava.nbio.core.sequence
-
Used in Sequences as the unique identifier.
- AccessionID() - Constructor for class org.biojava.nbio.core.sequence.AccessionID
-
Default constructor sets id t empty string
- AccessionID(String) - Constructor for class org.biojava.nbio.core.sequence.AccessionID
-
Creates an id with default DataSource.LOCAL source
- AccessionID(String, DataSource) - Constructor for class org.biojava.nbio.core.sequence.AccessionID
- AccessionID(String, DataSource, Integer, String) - Constructor for class org.biojava.nbio.core.sequence.AccessionID
- acen - org.biojava.nbio.genome.parsers.cytoband.StainType
- ACETYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
- ACTINOID - org.biojava.nbio.structure.ElementType
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.ChooseDirAction
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
The user selected one of the Combo boxes...
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.JPrintPanel
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyAlignmentLoadListener
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyDistMaxListener
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyExportListener
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyOpenPdbFileListener
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MySaveFileListener
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.ShowPDBIDListener
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
- actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryListener
- AD - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
- adapter - Static variable in class org.biojava.nbio.structure.gui.BiojavaJmol
- adapter - Static variable in class org.biojava.nbio.structure.gui.JmolViewerImpl
- add(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
- add(int, int, int, int) - Method in class org.biojava.nbio.structure.align.helper.JointFragments
- add(Collection<FeatureI>) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Add all features in the specified list or collection to this list.
- add(FeatureI) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Add specified feature to the end of the list.
- add(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
add two atoms ( a + b).
- add(AtomContact) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
- add(GroupContact) - Method in class org.biojava.nbio.structure.contact.GroupContactSet
- add(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
- addActiveSite(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addAlgorithm(StructureAlignment) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
-
Adds a new StructureAlignment algorithm to the list.
- addAlignedSequence(S) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
A sequence that has been aligned to other sequences will have inserts.
- addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
- addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
- addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
- addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
- addAligPosListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
- addAligPosListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
- addAll(Collection<AtomContact>) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
- addAltLoc(Group) - Method in interface org.biojava.nbio.structure.Group
-
Add a group that is an alternate location for this group.
- addAltLoc(Group) - Method in class org.biojava.nbio.structure.HetatomImpl
- addAnchor(int, int) - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
-
Adds an additional anchor to the set of anchored compounds
- addAnchors(AlignerHelper.Cut[], int[], boolean, int[]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
- addASPFamPredicted(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addASSwissProt(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addAtom(Atom) - Method in interface org.biojava.nbio.structure.Group
-
Add an atom to this group.
- addAtom(Atom) - Method in class org.biojava.nbio.structure.HetatomImpl
-
Add an atom to this group.
- addAtomAsaC(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
- addAtomAsaU(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
- addAtomContact(AtomContact) - Method in class org.biojava.nbio.structure.contact.GroupContact
- addAtomLinkage(StructureAtomLinkage) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
Add a linkage.
- addAtomLinkage(StructureAtomLinkage) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
- addAtomLinkages(Collection<StructureAtomLinkage>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
Add a collections of linkages.
- addAtomLinkages(Collection<StructureAtomLinkage>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
- addAtoms(Atom[]) - Method in class org.biojava.nbio.structure.contact.Grid
-
Adds a set of atoms, subsequent call to
Grid.getIndicesContacts()
orGrid.getAtomContacts()
will produce the interatomic contacts. - addAtoms(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.contact.Grid
-
Adds the i and j atoms and fills the grid.
- addAtoms(Atom[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid
-
Adds a set of atoms, subsequent call to
Grid.getIndicesContacts()
orGrid.getAtomContacts()
will produce the interatomic contacts. - addAtoms(Atom[], BoundingBox, Atom[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid
-
Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
- addAxis(Matrix4d, int, CESymmParameters.SymmetryType) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Adds a new axis of symmetry to the bottom level of the tree
- addBond(Bond) - Method in interface org.biojava.nbio.structure.Atom
-
Add a bond
- addBond(Bond) - Method in class org.biojava.nbio.structure.AtomImpl
- addBridge(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
Adds a Bridge to the residue.
- addCDS(AccessionID, int, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Add a Coding Sequence region with phase to the transcript sequence
- addCell(String, String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Add data to a cell
- addChain(Chain) - Method in class org.biojava.nbio.structure.EntityInfo
-
Add new Chain to this EntityInfo
- addChain(Chain) - Method in class org.biojava.nbio.structure.Model
- addChain(Chain) - Method in interface org.biojava.nbio.structure.Structure
-
Add a new chain to the first model
- addChain(Chain) - Method in class org.biojava.nbio.structure.StructureImpl
-
Add a new chain to the first model
- addChain(Chain, int) - Method in interface org.biojava.nbio.structure.Structure
-
Add a new chain to the model specified by the given index
- addChain(Chain, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Add a new chain to the model specified by the given index
- addCharges(Structure) - Static method in class org.biojava.nbio.structure.io.ChargeAdder
-
Function to add the charges to a given structure.
- addChemComp(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
-
Add a new component to the dictionary
- addChildElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper
-
Creates a new element called elementName and adds it to parentElement
- addColumn(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
- addColumns(ArrayList<String>, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Add columns to worksheet and set default value
- addCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
- addCompound(C, C, C...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
- addCompound(C, C, Iterable<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
- addCompounds(F, T...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
- addCompoundsToList(List<T>, List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
- addCompoundToLists(List<List<T>>, T) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
- addContinuousVariable(String, Double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
- addCoords(Point3d[]) - Method in class org.biojava.nbio.structure.contact.Grid
-
Adds a set of coordinates, subsequent call to
Grid.getIndicesContacts()
will produce the contacts, i.e. the set of points within distance cutoff. - addCoords(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.contact.Grid
-
Adds the i and j coordinates and fills the grid.
- addCoords(Point3d[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid
-
Adds a set of coordinates, subsequent call to
Grid.getIndicesContacts()
will produce the contacts, i.e. the set of points within distance cutoff. - addCoords(Point3d[], BoundingBox, Point3d[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid
-
Adds the i and j coordinates and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
- addDBReference(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
- addEntityInfo(EntityInfo) - Method in interface org.biojava.nbio.structure.Structure
-
Add an EntityInfo to this Structure
- addEntityInfo(EntityInfo) - Method in class org.biojava.nbio.structure.StructureImpl
-
Add an EntityInfo to this Structure
- addEquivalent(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
- addExon(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Add an ExonSequence mainly used to mark as a feature
- addExtension(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.
- addExtension(String) - Method in interface org.biojava.nbio.structure.io.StructureIOFile
-
Associates a file extension with this particular StructureIOFile, indicating that files of that type can be parsed.
- addFeature(int, int, FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Method to help set the proper details for a feature as it relates to a sequence where the feature needs to have a location on the sequence
- addFeature(FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Add a feature to this sequence.
- addGene(AccessionID, int, int, Strand) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0.
- addGeneIDGFF2GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
-
Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequences
- addGeneMarkGTFGeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
- addGFBuildMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
- addGFFalseDiscoveryRate(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
- addGFNewHampshire(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
- addGFTreeID(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
- addGlimmerGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
- addGmodGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
-
Load GFF3 file using mRNA as the gene feature as not all GFF3 files are complete
- addGroup(Group) - Method in interface org.biojava.nbio.structure.Chain
-
Add a group to the list of ATOM record group of this chain.
- addGroup(Group) - Method in class org.biojava.nbio.structure.ChainImpl
- addGroupsToStructure(Structure, Collection<Group>, int, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Add a list of groups to a new structure.
- addGroupToStructure(Structure, Group, int, Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Adds a particular group to a structure.
- addGSAccessionNumber(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addGSdbReference(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addGSDescription(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addGSLook(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addGSOrganismClassification(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addGSOrganismSpecies(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addHelix(Helix) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
- addIindex(int) - Method in class org.biojava.nbio.structure.contact.GridCell
- addIndex(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Add an attribute that will be used as index for queries
- addIndexes(List<String>) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Add a list of attributes that will be used as indexes for queries
- addInteraction(String, String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
-
To test for interactions use two variables and create a third variable where the two are multiplied together.
- addIntron(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addIntron(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Add an Intron Currently used to mark an IntronSequence as a feature
- addIntronsUsingExons() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Once everything has been added to the gene sequence where you might have added exon sequences only then you can infer the intron sequences and add them.
- addJindex(int) - Method in class org.biojava.nbio.structure.contact.GridCell
- addKeyword(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
Add a keyword associate with the PTM.
- addKeywords(Collection<String>) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
- addLigandBinding(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addMatrixListener(MatrixListener) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
- addMatrixListener(MatrixListener) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
- addMember(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
- addMirror(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- addModel(List<Chain>) - Method in interface org.biojava.nbio.structure.Structure
-
Add a new model.
- addModel(List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl
-
Add a new model.
- addMultipleAlignment(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Add a new MultipleAlignment to the end of the ensemble and set its parent ensemble to this.
- addMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
- addNcsEquivalent(StructureInterface, StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Add an interface to the list, possibly defining it as NCS-equivalent to an interface already in the list.
- addNote(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Add notes about this sequence that will get exported for GFF3
- addNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
- addOboFileEventListener(OboFileEventListener) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
- addOneSystemProperty(String) - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
- addPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
- addPoint(Point3d, double) - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
- addPoint(Point3d, T) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
- addPosteriorProbability(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
- addProperty(String, String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
-
Add a property and type to associate with this DBReferenceInfo
- addQualifier(String, Qualifier) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
- addQualifier(String, Qualifier) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
- addQualifier(String, Qualifier) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Add a qualifier
- addQuantity(Number) - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature
- addReference(AbstractReference) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
- addResidue(SiftsResidue) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
- addRotation(Rotation) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
- addRow(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
- addRows(ArrayList<String>, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Add rows to the worksheet and fill in default value
- addSecondaryStructure(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addSegment(SiftsSegment) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
- addSeqRes(Chain, String) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Add the missing groups to the SeqResGroups.
- addSSBond(Bond) - Method in interface org.biojava.nbio.structure.Structure
-
Add a single disulfide Bond to this structure
- addSSBond(Bond) - Method in class org.biojava.nbio.structure.StructureImpl
-
Adds a single disulfide Bond to this structure
- addStartCodonSequence(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Sets the start codon sequence at given begin / end location.
- addStopCodonSequence(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Sets the stop codon sequence at given begin / end location.
- addStrataInfoHashMap(LinkedHashMap<String, StrataInfo>, String) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
- addStrings(String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
- addSurfaceAccessibility(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addSynonym(Object) - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
- addSynonym(Object) - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
- addSynonym(Object) - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
- addSynonym(Object) - Method in interface org.biojava.nbio.ontology.Term
-
Add a synonym for this term.
- addSynonym(Object) - Method in class org.biojava.nbio.ontology.Term.Impl
- addSynonym(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl
- addToCache(String, File) - Static method in class org.biojava.nbio.core.util.FlatFileCache
-
The file is read and the bytes stored immediately.
- addToGFComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
- addToRefAuthor(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
- addToRefTitle(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
- addTranscript(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Add a transcription sequence to a gene which describes a ProteinSequence
- addTransformation(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
- addTransMembrane(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- addUnknownDataTypeVariable(String, String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
- AFFINE - org.biojava.nbio.alignment.template.GapPenalty.Type
- AFP - Class in org.biojava.nbio.structure.align.model
-
A class to represent a FATCAT aligned fragment pair (AFP)
- AFP() - Constructor for class org.biojava.nbio.structure.align.model.AFP
- afp2Res(AFPChain, int, int[], int) - Static method in class org.biojava.nbio.structure.align.AFPTwister
-
Set the list of equivalent residues in the two proteins given a list of AFPs WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain!
- AFPAlignmentDisplay - Class in org.biojava.nbio.structure.align.util
- AFPAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
- AFPCalculator - Class in org.biojava.nbio.structure.align.fatcat.calc
-
A class that performs calculations on AFPChains
- AFPCalculator() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
- AFPChain - Class in org.biojava.nbio.structure.align.model
-
A bean to contain the core of a structure alignment.
- AFPChain(String) - Constructor for class org.biojava.nbio.structure.align.model.AFPChain
-
Construction of an AFPChain needs the algorithm name, since downstream analysis methods (scores, display, etc) behave differently if the alignment is flexible (created with FatCat).
- AFPChain(AFPChain) - Constructor for class org.biojava.nbio.structure.align.model.AFPChain
-
Copy constructor
- AFPChainCoordManager - Class in org.biojava.nbio.structure.align.gui.aligpanel
- AFPChainCoordManager() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
- AFPChainer - Class in org.biojava.nbio.structure.align.fatcat.calc
-
a class to chain AFPs to an alignment
- AFPChainer() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
- AFPChainFlipper - Class in org.biojava.nbio.structure.align.xml
- AFPChainFlipper() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainFlipper
- AFPChainScorer - Class in org.biojava.nbio.structure.align.util
- AFPChainScorer() - Constructor for class org.biojava.nbio.structure.align.util.AFPChainScorer
- AfpChainWriter - Class in org.biojava.nbio.structure.align.model
-
A class to convert the data in an AfpChain object to various String outputs.
- AfpChainWriter() - Constructor for class org.biojava.nbio.structure.align.model.AfpChainWriter
- AFPChainXMLConverter - Class in org.biojava.nbio.structure.align.xml
- AFPChainXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
- AFPChainXMLParser - Class in org.biojava.nbio.structure.align.xml
- AFPChainXMLParser() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
- AFPFromFasta - Class in demo
-
Demo displaying a structural alignment from a FASTA file using
FastaAFPChainConverter
. - AFPFromFasta() - Constructor for class demo.AFPFromFasta
- AFPOptimizer - Class in org.biojava.nbio.structure.align.fatcat.calc
- AFPOptimizer() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
- afpPairConn(int, int, FatCatParameters, AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
-
//Key function: calculate the connectivity of AFP pairs //no compatibility criteria is executed //note: afp1 is previous to afp2 in terms of the position //this module must be optimized
- AFPPostProcessor - Class in org.biojava.nbio.structure.align.fatcat.calc
-
does post processing after alignment chaingin
- AFPPostProcessor() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
- AFPTwister - Class in org.biojava.nbio.structure.align
- AFPTwister() - Constructor for class org.biojava.nbio.structure.align.AFPTwister
- Ag - org.biojava.nbio.structure.Element
- AgScore - Class in org.biojava.nbio.survival.cox.stats
- AgScore() - Constructor for class org.biojava.nbio.survival.cox.stats.AgScore
- Al - org.biojava.nbio.structure.Element
- algorithmName - Static variable in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
- algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeCPMain
- algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeMain
- algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeSideChainMain
- algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
- algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat
- algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
- algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
- algorithmName - Static variable in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
- algorithmName - Static variable in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
- algorithmName - Static variable in class org.biojava.nbio.structure.symmetry.internal.CeSymm
- ALIGFACTOR - Static variable in class org.biojava.nbio.structure.align.pairwise.Gotoh
- AligMatEl - Class in org.biojava.nbio.structure.align.helper
- AligMatEl() - Constructor for class org.biojava.nbio.structure.align.helper.AligMatEl
- align() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Performs alignment
- align(List<Atom[]>) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
- align(List<Atom[]>) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner
-
Run an alignment while specifying the atoms to be aligned.
- align(List<Atom[]>, Object) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
- align(List<Atom[]>, Object) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner
-
Run an alignment and also send a bean containing the parameters.
- align(List<Subunit>, List<Subunit>, SubunitClustererParameters, QsAlignParameters) - Static method in class org.biojava.nbio.structure.align.quaternary.QsAlign
- align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
- align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
- align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeMain
- align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
- align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
- align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
- align(Atom[], Atom[]) - Method in interface org.biojava.nbio.structure.align.StructureAlignment
-
Run an alignment while specifying the atoms to be aligned.
- align(Atom[], Atom[], boolean, FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
- align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
- align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
- align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.CeCPMain
-
Aligns ca1 and ca2 using a heuristic to check for CPs.
- align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.CeMain
-
Align ca2 onto ca1.
- align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
-
Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
- align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
- align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
- align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
- align(Atom[], Atom[], Object) - Method in interface org.biojava.nbio.structure.align.StructureAlignment
-
run an alignment and also send a bean containing the parameters.
- align(Atom[], Atom[], FatCatParameters, boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
- align(Atom[], Atom[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
Calculate the protein structure superimposition, between two sets of atoms.
- align(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
- align(Structure, String, Structure, String) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
Align two chains from the structures.
- align(Structure, String, Structure, String, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
Aligns two chains from the structures using user provided parameters.
- align(Structure, List<Chain>) - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
- align(Structure, Structure) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
Calculate the alignment between the two full structures with default parameters
- align(Structure, Structure, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
Calculate the alignment between the two full structures with user provided parameters
- align(Structure, Structure, SubunitClustererParameters, QsAlignParameters) - Static method in class org.biojava.nbio.structure.align.quaternary.QsAlign
- align_NPE(Matrix, StrucAligParameters) - Static method in class org.biojava.nbio.structure.align.pairwise.AligNPE
-
Align without penalizing end-gaps.
- Alignable - Interface in org.biojava.nbio.structure.align.pairwise
- AlignedPosition - Class in org.biojava.nbio.structure.gui.util
- AlignedPosition() - Constructor for class org.biojava.nbio.structure.gui.util.AlignedPosition
- AlignedSequence<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template
-
Defines a data structure for a
Sequence
within an alignment. - AlignedSequence.Step - Enum in org.biojava.nbio.core.alignment.template
-
Defines an alignment step in order to pass alignment information from an
Aligner
to a constructor. - Aligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template
- AlignerHelper - Class in org.biojava.nbio.alignment.routines
-
Static utility to construct alignment routines from a common library of methods.
- AlignerHelper() - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper
- AlignerHelper.Anchor - Class in org.biojava.nbio.alignment.routines
-
Compounds in query and target sequences that must align
- AlignerHelper.Anchor.QueryIndexComparator - Class in org.biojava.nbio.alignment.routines
- AlignerHelper.Cut - Class in org.biojava.nbio.alignment.routines
-
Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
- AlignerHelper.Last - Enum in org.biojava.nbio.alignment.routines
-
Define a traceback pointer for the three edit operations: substitution (match/replacement of a query compound with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and insertion (addition of a target compound opening a gap in the query sequence).
- AlignerHelper.Subproblem - Class in org.biojava.nbio.alignment.routines
-
Alignment subproblem.
- alignFlexible(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
- ALIGNMENT_PANEL - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
- ALIGNMENT_VIEW - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
- alignmentAsMap(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Creates a Map specifying the alignment as a mapping between residue indices of protein 1 and residue indices of protein 2.
- AlignmentCalc - Class in org.biojava.nbio.structure.align.gui
-
A class that obtains two structures via DAS and aligns them This is done in a separate thread.
- AlignmentCalc - Class in org.biojava.nbio.structure.gui.util
-
A class that obtains two structures via DAS and aligns them This is done in a separate thread.
- AlignmentCalc(AlignmentGui, Structure, Structure) - Constructor for class org.biojava.nbio.structure.gui.util.AlignmentCalc
-
requests an alignment of pdb1 vs pdb 2.
- AlignmentCalc(AlignmentGui, Structure, Structure, String, String) - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentCalc
-
requests an alignment of pdb1 vs pdb 2.
- AlignmentCalculationRunnable - Interface in org.biojava.nbio.structure.align.gui
- AlignmentGui - Class in org.biojava.nbio.structure.align.gui
-
A JFrame that allows to trigger a pairwise structure alignment, either from files in a directory, or after manual upload.
- AlignmentGui() - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentGui
- AlignmentGuiDemo - Class in demo
-
Get an instance of the two alignment GUIs.
- AlignmentGuiDemo() - Constructor for class demo.AlignmentGuiDemo
- AlignmentPositionListener - Interface in org.biojava.nbio.structure.gui.events
- AlignmentProgressListener - Class in org.biojava.nbio.structure.align.pairwise
-
A class to listen to progress of the structure alignment calculations
- AlignmentProgressListener() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
- AlignmentResult - Class in org.biojava.nbio.structure.align.pairwise
-
A class to track the alignment results in a flat file
- AlignmentResult() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlignmentResult
- Alignments - Class in org.biojava.nbio.alignment
-
Static utility to easily run alignment routines.
- ALIGNMENTS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- ALIGNMENTS - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
- Alignments.PairInProfileScorerType - Enum in org.biojava.nbio.alignment
-
List of implemented sequence pair in a profile scoring routines.
- Alignments.PairwiseSequenceAlignerType - Enum in org.biojava.nbio.alignment
-
List of implemented pairwise sequence alignment routines.
- Alignments.PairwiseSequenceScorerType - Enum in org.biojava.nbio.alignment
-
List of implemented pairwise sequence scoring routines.
- Alignments.ProfileProfileAlignerType - Enum in org.biojava.nbio.alignment
-
List of implemented profile-profile alignment routines.
- Alignments.RefinerType - Enum in org.biojava.nbio.alignment
-
List of implemented profile refinement routines.
- AlignmentTextPanel - Class in org.biojava.nbio.structure.align.gui
- AlignmentTextPanel() - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentTextPanel
- AlignmentTools - Class in org.biojava.nbio.structure.align.util
-
Methods for analyzing and manipulating AFPChains and for other pairwise alignment utilities.
- AlignmentTools() - Constructor for class org.biojava.nbio.structure.align.util.AlignmentTools
- AlignmentTools.IdentityMap<K> - Class in org.biojava.nbio.structure.align.util
-
A Map
can be viewed as a function from K to V. - alignmentToSIF(Writer, AFPChain, Atom[], Atom[], String, String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Creates a simple interaction format (SIF) file for an alignment.
- alignOptimal(Atom[], Atom[], Object, AFPChain[]) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
-
Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
- AligNPE - Class in org.biojava.nbio.structure.align.pairwise
- AligNPE() - Constructor for class org.biojava.nbio.structure.align.pairwise.AligNPE
- alignPermuted(Atom[], Atom[], Object, int) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
-
Aligns ca1 with ca2 permuted by cp residues.
- alignRigid(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
- alignRigid(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
- alignSuperfamily() - Method in class demo.DemoSCOP
- AlignUtils - Class in org.biojava.nbio.structure.align.helper
-
Low level helper methods for CE and FATCAT algorithms.
- AlignUtils() - Constructor for class org.biojava.nbio.structure.align.helper.AlignUtils
- AligPanel - Class in org.biojava.nbio.structure.align.gui.aligpanel
-
A JPanel that can display an AFPChain in a nice way and interact with Jmol.
- AligPanel() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
- AligPanelMouseMotionListener - Class in org.biojava.nbio.structure.align.gui.aligpanel
- AligPanelMouseMotionListener(AligPanel) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
- AligUIManager - Class in org.biojava.nbio.structure.align.webstart
- AligUIManager() - Constructor for class org.biojava.nbio.structure.align.webstart.AligUIManager
- ALKALI_METAL - org.biojava.nbio.structure.ElementType
- ALKALINE_EARTH_METAL - org.biojava.nbio.structure.ElementType
- ALL - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
- ALL_CURRENT_ENDPOINT - Static variable in class org.biojava.nbio.structure.PDBStatus
- ALL_POLYMER_TYPES - Static variable in enum org.biojava.nbio.structure.chem.PolymerType
-
Convenience Set of all polymer types.
- ALL_SEQUENCES - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
- AllChemCompProvider - Class in org.biojava.nbio.structure.chem
-
A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.
- AllChemCompProvider() - Constructor for class org.biojava.nbio.structure.chem.AllChemCompProvider
- allComponents() - Static method in class org.biojava.nbio.protmod.Component
- allComponents() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
- allIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
- allKeywords() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
- allModifications() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
- allPdbccIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
- allPsimodIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
- allResidIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
- ALN - org.biojava.nbio.core.alignment.template.Profile.StringFormat
- ALN - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
- AlreadyExistsException - Exception in org.biojava.nbio.ontology
-
Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
- AlreadyExistsException() - Constructor for exception org.biojava.nbio.ontology.AlreadyExistsException
- AlreadyExistsException(String) - Constructor for exception org.biojava.nbio.ontology.AlreadyExistsException
- ALT_ID - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
- AltAligComparator - Class in org.biojava.nbio.structure.align.pairwise
-
A comparator to sort AlternativeAlignments based on their number of equivalent residues and RMSD.
- AltAligComparator() - Constructor for class org.biojava.nbio.structure.align.pairwise.AltAligComparator
- AlternativeAlignment - Class in org.biojava.nbio.structure.align.pairwise
-
Implements a class which handles one possible (alternative) solution.
- AlternativeAlignment() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
- AlternativeAlignmentFrame - Class in org.biojava.nbio.structure.gui.util
-
a frame showing the alternative alignments, which are the result of a structure superimposition
- AlternativeAlignmentFrame(Structure, Structure) - Constructor for class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
- Am - org.biojava.nbio.structure.Element
- AmbiguityDNACompoundSet - Class in org.biojava.nbio.core.sequence.compound
- AmbiguityDNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet
- AmbiguityDNARNAHybridCompoundSet - Class in org.biojava.nbio.core.sequence.compound
-
Ambiguity set for hybrid DNA/RNA sequences.
- AmbiguityDNARNAHybridCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet
- AmbiguityRNACompoundSet - Class in org.biojava.nbio.core.sequence.compound
- AmbiguityRNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet
- AMBIGUOUS_AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
-
Same as AA pattern but with one additional letters - X
- AMBIGUOUS_NUCLEOTIDE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
-
Ambiguous nucleotide
- AMINO_ACID_MATCHER - Static variable in class org.biojava.nbio.structure.AtomPositionMap
-
Matches CA atoms of protein groups
- AminoAcid - Interface in org.biojava.nbio.structure
-
A
Group
that represents an AminoAcid. - AMINOACID - org.biojava.nbio.structure.GroupType
-
The type for amino acids (L-peptides)
- AminoAcidComposition - Class in org.biojava.nbio.aaproperties.xml
- AminoAcidComposition() - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
- AminoAcidComposition(String, String, String, List<Name2Count>, List<Name2Count>) - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
- AminoAcidCompositionTable - Class in org.biojava.nbio.aaproperties.xml
- AminoAcidCompositionTable() - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
- AminoAcidCompositionTable(List<AminoAcidComposition>) - Constructor for class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
- AminoAcidCompound - Class in org.biojava.nbio.core.sequence.compound
-
Used to describe an Amino Acid.
- AminoAcidCompound(AminoAcidCompoundSet, String, String, String, Float) - Constructor for class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
- AminoAcidCompoundSet - Class in org.biojava.nbio.core.sequence.compound
-
Set of proteinogenic amino acids.
- AminoAcidCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
- AminoAcidImpl - Class in org.biojava.nbio.structure
-
AminoAcid inherits most from Hetatom.
- AminoAcidImpl() - Constructor for class org.biojava.nbio.structure.AminoAcidImpl
-
inherits most from Hetero and has just a few extensions.
- AminoAcidProperties - Class in org.biojava.nbio.aaproperties
-
This class provides the protein properties at the level of individual amino acids.
- AminoAcidProperties() - Constructor for class org.biojava.nbio.aaproperties.AminoAcidProperties
- aminoAcidsCompounds(CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
- amount(Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Gets the length of the vector (2-norm)
- analyze() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method is the main function call to extract all step parameters, pairing parameters, and sequence information from the Structure object provided to the constructor.
- analyze(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
-
Analyze the symmetries of the input Atom array using the DEFAULT parameters.
- analyze(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
-
Analyze the symmetries of the input Atom array using the provided parameters.
- analyzeLevel(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
-
Analyze a single level of symmetry.
- Anchor(int, int) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
- AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.routines
- AnchoredPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
-
Before running a pairwise global sequence alignment, data must be sent in via calls to
AbstractPairwiseSequenceAligner.setQuery(Sequence)
,AbstractPairwiseSequenceAligner.setTarget(Sequence)
,AbstractMatrixAligner.setGapPenalty(GapPenalty)
, andAbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
. - AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
-
Prepares for a pairwise global sequence alignment.
- AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
-
Prepares for a pairwise global sequence alignment.
- anchors - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
- angle(Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions
-
Calculate the rotation angle component of the input unit quaternion.
- angle(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Gets the angle between two vectors
- ANGLE - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
- angleCheckOk(FragmentPair, FragmentPair, float) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
- AngleOrderDetectorPlus - Class in org.biojava.nbio.structure.symmetry.internal
-
Guesses an order of rotational symmetry from the angle.
- AngleOrderDetectorPlus(double) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
- AngleOrderDetectorPlus(int) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
- AngleOrderDetectorPlus(int, double) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
- AngleOrderDetectorPlus(int, double, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
-
Determine order by finding the order (up to the maxOrder) which has the closest rotation angle to the observed rotation.
- Annotatable - Interface in org.biojava.nbio.ontology.utils
-
Indicates that an object has an associated annotation.
- Annotation - Interface in org.biojava.nbio.ontology.utils
-
Arbitrary annotation associated with one or more objects.
- antiparallel - org.biojava.nbio.structure.secstruc.BridgeType
- ANY - Static variable in class org.biojava.nbio.ontology.OntoTools
- ANYTHING_MATCHER - Static variable in class org.biojava.nbio.structure.AtomPositionMap
-
Matches all atoms
- apairs_from_idxlst(JointFragments) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
Set apairs according to a list of (i,j) tuples.
- apairs_from_seed(int, int, int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
Set apairs according to a seed position.
- ApliphaticIndex - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
- App - Class in org.biojava.nbio.genome
-
Hello world!
- App - Class in org.biojava.nbio.ontology
-
Hello world!
- App() - Constructor for class org.biojava.nbio.genome.App
- App() - Constructor for class org.biojava.nbio.ontology.App
- append(T, Iterable<Fastq>) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter
-
Append the specified FASTQ formatted sequences to the specified appendable.
- append(T, Fastq...) - Method in interface org.biojava.nbio.genome.io.fastq.FastqWriter
-
Append the specified FASTQ formatted sequences to the specified appendable.
- appendQuality(String) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder
-
Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.
- appendQuality(String) - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
-
Notify this listener of a quality line.
- appendSequence(String) - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder
-
Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.
- appendSequence(String) - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
-
Notify this parse listener of an additional sequence line.
- appendToSequence(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
- appendWorkSheetColumns(WorkSheet) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Add columns from a second worksheet to be joined by common row.
- appendWorkSheetRows(WorkSheet) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Add rows from a second worksheet to be joined by common column.
- applyAlignment(Map<S, T>, Map<T, S>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Applies an alignment k times.
- applyAlignment(Map<T, T>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Applies an alignment k times.
- applyColumnFilter(String, ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Apply filter to a column to change values from say numberic to nominal based on some range
- applyValues() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
- approach_ap3(Atom[], Atom[], FragmentPair[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
- Ar - org.biojava.nbio.structure.Element
- Architecture - org.biojava.nbio.structure.cath.CathCategory
- areInSameAxis(int, int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Returns true if both given transform ids belong to the same crystallographic axis (a, b or c) For two non-rotation transformations (i.e. identity operators) it returns true
- arrayLeftDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Element-by-element left division, C = A.
- arrayLeftDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Element-by-element left division in place, A = A.
- ArrayListProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
- ArrayListProxySequenceReader() - Constructor for class org.biojava.nbio.core.sequence.loader.ArrayListProxySequenceReader
- ArrayListSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
-
Stores a Sequence as a collection of compounds in an ArrayList
- ArrayListSequenceReader() - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
- ArrayListSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
- ArrayListSequenceReader(List<C>, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
- arrayRightDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Element-by-element right division, C = A.
- arrayRightDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Element-by-element right division in place, A = A.
- arrayTimes(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Element-by-element multiplication, C = A.
- arrayTimesEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Element-by-element multiplication in place, A = A.
- ARTIFACTUAL - org.biojava.nbio.protmod.ModificationOccurrenceType
- As - org.biojava.nbio.structure.Element
- AsaCalculator - Class in org.biojava.nbio.structure.asa
-
Class to calculate Accessible Surface Areas based on the rolling ball algorithm by Shrake and Rupley.
- AsaCalculator(Point3d[], double, int, int, double) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator
-
Constructs a new AsaCalculator.
- AsaCalculator(Atom[], double, int, int) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator
-
Constructs a new AsaCalculator.
- AsaCalculator(Structure, double, int, int, boolean) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator
-
Constructs a new AsaCalculator.
- asMap() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
- asMap() - Method in interface org.biojava.nbio.ontology.utils.Annotation
-
Return a map that contains the same key/values as this Annotation.
- AssertionFailure - Error in org.biojava.nbio.ontology.utils
-
An unchecked exception representing an Assertion failure.
- AssertionFailure(String) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
- AssertionFailure(String, Throwable) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
- AssertionFailure(Throwable) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure
- assertLocation() - Method in class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
- assertLocation() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
- assignment - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
- assignSecStruc(Structure, List<SecStrucInfo>) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools
- Astral - Class in org.biojava.nbio.structure.scop
-
Provides programmatic access to ASTRAL representative sets.
- Astral(String, Reader) - Constructor for class org.biojava.nbio.structure.scop.Astral
-
Constructs a new Astral object.
- Astral(String, URL) - Constructor for class org.biojava.nbio.structure.scop.Astral
-
Constructs a new Astral object.
- Astral(Astral.AstralSet) - Constructor for class org.biojava.nbio.structure.scop.Astral
-
Constructs a new Astral object.
- Astral.AstralSet - Enum in org.biojava.nbio.structure.scop
-
An ASTRAL sequence-identity cutoff with an identifier such as:
- ASYMMETRIC - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass
- At - org.biojava.nbio.structure.Element
- Atom - Interface in org.biojava.nbio.structure
-
A simple interface for an Atom.
- ATOM_CA_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.FileParsingParameters
-
The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
- ATOM_PLANE - org.biojava.nbio.structure.BondType
- AtomCache - Class in org.biojava.nbio.structure.align.util
-
A utility class that provides easy access to Structure objects.
- AtomCache() - Constructor for class org.biojava.nbio.structure.align.util.AtomCache
-
Default AtomCache constructor.
- AtomCache(String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache
-
Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
- AtomCache(String, String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache
-
Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
- AtomCache(UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache
-
Creates a new AtomCache object based on the provided UserConfiguration.
- AtomContact - Class in org.biojava.nbio.structure.contact
-
A pair of atoms that are in contact
- AtomContact(Pair<Atom>, double) - Constructor for class org.biojava.nbio.structure.contact.AtomContact
- AtomContactSet - Class in org.biojava.nbio.structure.contact
-
A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations
- AtomContactSet(double) - Constructor for class org.biojava.nbio.structure.contact.AtomContactSet
- AtomIdentifier - Class in org.biojava.nbio.structure.contact
- AtomIdentifier(int, String) - Constructor for class org.biojava.nbio.structure.contact.AtomIdentifier
- AtomImpl - Class in org.biojava.nbio.structure
-
Implementation of an Atom of a PDB file.
- AtomImpl() - Constructor for class org.biojava.nbio.structure.AtomImpl
- AtomInfo - Class in org.biojava.nbio.structure.align.gui.jmol
-
This class uniquely describes an atom
- AtomInfo() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
- AtomInfoParser - Class in org.biojava.nbio.structure.align.gui.jmol
- AtomInfoParser() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser
- AtomIterator - Class in org.biojava.nbio.structure
-
an iterator over all atoms of a structure / group.
- AtomIterator(Group) - Constructor for class org.biojava.nbio.structure.AtomIterator
-
Constructs an AtomIterator object.
- AtomIterator(Structure) - Constructor for class org.biojava.nbio.structure.AtomIterator
-
Constructs an AtomIterator object over all models
- AtomIterator(Structure, int) - Constructor for class org.biojava.nbio.structure.AtomIterator
-
Constructs an AtomIterator object over a single model
- atomn - org.biojava.nbio.structure.chem.ResidueType
- AtomPositionMap - Class in org.biojava.nbio.structure
-
A map from
ResidueNumbers
to ATOM record positions in a PDB file. - AtomPositionMap(Atom[]) - Constructor for class org.biojava.nbio.structure.AtomPositionMap
-
Creates a new AtomPositionMap containing peptide alpha-carbon atoms
- AtomPositionMap(Atom[], AtomPositionMap.GroupMatcher) - Constructor for class org.biojava.nbio.structure.AtomPositionMap
-
Creates a new AtomPositionMap containing only atoms matched by
matcher
. - AtomPositionMap(Structure) - Constructor for class org.biojava.nbio.structure.AtomPositionMap
-
Creates a new AtomPositionMap containing representative atoms from a structure.
- AtomPositionMap.GroupMatcher - Interface in org.biojava.nbio.structure
-
Used as a Predicate to indicate whether a particular Atom should be mapped
- ATOMRECORD - Static variable in interface org.biojava.nbio.structure.AminoAcid
-
Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
- atoms - Variable in class org.biojava.nbio.structure.HetatomImpl
- atomsToPoints(Collection<Atom>) - Static method in class org.biojava.nbio.structure.Calc
-
Convert an array of atoms into an array of vecmath points
- atomsToPoints(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
-
Convert an array of atoms into an array of vecmath points
- ATTACHMENT - org.biojava.nbio.protmod.ModificationCategory
- attribute(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
- attribute(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter
-
Add an un-qualified attribute to an element.
- attribute(String, String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
- attribute(String, String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter
-
Add an attribute to an element.
- attributes() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
Get the string of key/value attributes.
- attributeValues(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Create a collection of the unique values for the specified key.
- Au - org.biojava.nbio.structure.Element
- AU - org.biojava.nbio.structure.xtal.TransformType
- AugmentedResidueRange - Class in org.biojava.nbio.structure
-
Created by douglas on 1/23/15.
- AugmentedResidueRange(String, String, String, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
- AugmentedResidueRange(String, ResidueNumber, ResidueNumber, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
- Author - Class in org.biojava.nbio.structure
-
Describes author attributes for author information in a PDB file.
- Author() - Constructor for class org.biojava.nbio.structure.Author
- AUTHORS_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
- AUTO - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
- AutoSuggestProvider - Interface in org.biojava.nbio.structure.align.gui.autosuggest
-
A class that provides auto-completion suggestions for JAutoSuggest
- AV - org.biojava.nbio.phylo.TreeConstructorType
-
What does this stand for?
- available() - Method in class org.biojava.nbio.core.util.UncompressInputStream
- available() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
- AverageHydropathyValue - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
- AVGTM_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
- Axis(Matrix4d, int, CESymmParameters.SymmetryType, int, int) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
- AxisAligner - Class in org.biojava.nbio.structure.symmetry.axis
- AxisAligner() - Constructor for class org.biojava.nbio.structure.symmetry.axis.AxisAligner
- axisStroke - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
B
- B - org.biojava.nbio.structure.Element
- Ba - org.biojava.nbio.structure.Element
- BACKGROUND_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
- BALL_AND_STICK - org.biojava.nbio.structure.gui.RenderStyle
- BASE_COUNT_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
- BASE_COUNT_TAG_FULL - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
- BASE_LIST_DNA - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
- BASE_LIST_RNA - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
- BASE_MAP - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
- BasePairParameters - Class in org.biojava.nbio.structure.basepairs
-
This module calculates the el Hassan-Calladine Base Pairing and Base-pair Step Parameters for any nucleic acid containing structure that has the information about the core base-pair rings.
- BasePairParameters(Structure) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure for only canonical DNA pairs.
- BasePairParameters(Structure, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This constructor takes a Structure object, and whether to use the RNA standard bases.
- BasePairParameters(Structure, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This constructor takes a Structure object, whether to use RNA, and whether to remove duplicate sequences.
- BasePairParameters(Structure, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure.
- basePairReferenceFrame(Pair<Group>) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method calculates the central frame (4x4 transformation matrix) of a single base pair.
- basicLoad() - Method in class demo.DemoLoadStructure
- basicLoad(String) - Method in class demo.DemoDomainsplit
- basicLoad(PDBFileReader, String) - Method in class demo.DemoChangeChemCompProvider
- BasicSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence
-
Bare bones version of the Sequence object to be used sparingly.
- BasicSequence(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.BasicSequence
- BasicSequence(ProxySequenceReader<C>) - Constructor for class org.biojava.nbio.core.sequence.BasicSequence
- BCIF - org.biojava.nbio.structure.io.StructureFiletype
- BCIF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
- BcifFileReader - Class in org.biojava.nbio.structure.io
-
Parse binary Cif files and provide capabilities to store them locally.
- BcifFileReader() - Constructor for class org.biojava.nbio.structure.io.BcifFileReader
-
Constructs a new BcifFileReader, initializing the extensions member variable.
- BcifFileReader(String) - Constructor for class org.biojava.nbio.structure.io.BcifFileReader
-
Constructs a new BcifFileReader, initializing the extensions member variable.
- Be - org.biojava.nbio.structure.Element
- bend - org.biojava.nbio.structure.secstruc.SecStrucType
- BerkeleyScopInstallation - Class in org.biojava.nbio.structure.scop
-
SCOPe: The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop.berkeley.edu/).
- BerkeleyScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.BerkeleyScopInstallation
- bestTrace1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
- bestTrace1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
- bestTrace2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
- bestTrace2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
- bestTraces1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
- bestTraces1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
- bestTraces2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
- bestTraces2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
- bestTraceScore - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
- bestTraceScore - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
- bestTracesN - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
- bestTracesN - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
- bestTracesScores - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
- bestTracesScores - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
- BetaBridge - Class in org.biojava.nbio.structure.secstruc
-
Container that represents a beta Bridge between two residues.
- BetaBridge(int, int, BridgeType) - Constructor for class org.biojava.nbio.structure.secstruc.BetaBridge
- BETTER_PERFORMANCE_MORE_MEMORY - org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior
-
use a built-in HashMap for faster access to memory, at the price of more memory consumption
- BETWEEN_11 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
- BETWEEN_12 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
- BETWEEN_13 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
- BETWEEN_22 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
- BETWEEN_23 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
- BETWEEN_33 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
- Bi - org.biojava.nbio.structure.Element
- BIO - org.biojava.nbio.structure.align.client.StructureName.Source
- BIO_NAME_PATTERN - Static variable in class org.biojava.nbio.structure.BioAssemblyIdentifier
- BioAssemblyIdentifier - Class in org.biojava.nbio.structure
- BioAssemblyIdentifier(String) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
- BioAssemblyIdentifier(String, int) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
- BioAssemblyIdentifier(PdbId, int) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
- BioAssemblyInfo - Class in org.biojava.nbio.structure.quaternary
-
Representation of a Biological Assembly annotation as provided by the PDB.
- BioAssemblyInfo() - Constructor for class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
-
Empty constructor
- BioAssemblyTools - Class in org.biojava.nbio.structure.quaternary
- BioAssemblyTools() - Constructor for class org.biojava.nbio.structure.quaternary.BioAssemblyTools
- bioEnd() - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Get end index, in biocoordinates.
- BIOJAVA_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
-
Secondary strucuture calculated and assigned by DSSP of BioJava
- BioJavaAADemo - Class in demo
-
Created by andreas on 8/9/14.
- BioJavaAADemo() - Constructor for class demo.BioJavaAADemo
- BiojavaJmol - Class in org.biojava.nbio.structure.gui
-
A class that provides a simple GUI for Jmol
- BiojavaJmol() - Constructor for class org.biojava.nbio.structure.gui.BiojavaJmol
- BioJavaStructureAlignment - Class in org.biojava.nbio.structure.align
-
Wrapper for the BioJava Structure Alignment Implementation
- BioJavaStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.BioJavaStructureAlignment
- BIOL_ASSEMBLY_IDENTIFIER - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
- BiologicalAssemblyBuilder - Class in org.biojava.nbio.structure.quaternary
-
Reconstructs the quaternary structure of a protein from an asymmetric unit
- BiologicalAssemblyBuilder() - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
- BiologicalAssemblyTransformation - Class in org.biojava.nbio.structure.quaternary
-
The transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file.
- BiologicalAssemblyTransformation() - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Default Constructor
- BiologicalAssemblyTransformation(BiologicalAssemblyTransformation) - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Copy Constructor
- bioStart() - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Get start index, in biocoordinates.
- bioStrand() - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Get character representation of strand.
- BitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
- BitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
- BitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
- BitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
- bitMask() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
This method should return the bit mask to be used to extract the bytes you are interested in working with.
- bitMask() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
- bitMask() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
- BitSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
-
An implementation of the popular bit encodings.
- BitSequenceReader(BitSequenceReader.BitArrayWorker<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Instance which allows you to supply a different @{BitArrayWorker} object.
- BitSequenceReader.BitArrayWorker<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
-
The logic of working with a bit has been separated out into this class to help developers create the bit data structures without having to put the code into an intermediate format and to also use the format without the need to copy this code.
- bitsPerCompound() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Returns how many bits are used to represent a compound e.g. 2 if using 2bit encoding.
- Bk - org.biojava.nbio.structure.Element
- BLACK_WHITE_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper
- blankOutBreakFlag(AFPChain, Atom[], int, int, CECalculator, boolean[][], int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
- blankOutCEOrig(Atom[], int, int, CECalculator, Matrix, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
- blankOutPreviousAlignment(AFPChain, Atom[], int, int, CECalculator, Matrix, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
- BLAST_PROGRAM - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- BlastAlignmentParameterEnum - Enum in org.biojava.nbio.ws.alignment.qblast
-
Alignment request parameters accepted by QBlast service.
Not all are mandatory. - BlastClustReader - Class in org.biojava.nbio.structure.symmetry.utils
- BlastClustReader(int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
- BlastHitBuilder - Class in org.biojava.nbio.core.search.io.blast
-
Designed by Paolo Pavan.
- BlastHitBuilder() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
- BlastHomologyHits - Class in org.biojava.nbio.genome.homology
- BlastHomologyHits() - Constructor for class org.biojava.nbio.genome.homology.BlastHomologyHits
- BlastHspBuilder - Class in org.biojava.nbio.core.search.io.blast
-
Designed by Paolo Pavan.
- BlastHspBuilder() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
- BlastJob - Class in org.biojava.nbio.ws.alignment.qblast
-
Information about QBlast search job
- BlastJob() - Constructor for class org.biojava.nbio.ws.alignment.qblast.BlastJob
- BlastMatrixEnum - Enum in org.biojava.nbio.ws.alignment.qblast
-
Enum representing matrices supported by QBlast
- blastn - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
- BlastOutputAlignmentFormatEnum - Enum in org.biojava.nbio.ws.alignment.qblast
-
Enum representing available output alignment types.
- BlastOutputFormatEnum - Enum in org.biojava.nbio.ws.alignment.qblast
-
Enum representing available output formats.
- BlastOutputParameterEnum - Enum in org.biojava.nbio.ws.alignment.qblast
-
Output parameters accepted by QBlast service.
- blastp - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
- BlastProgramEnum - Enum in org.biojava.nbio.ws.alignment.qblast
-
Enum representing available blast programs.
- BlastResult - Class in org.biojava.nbio.core.search.io.blast
-
This class models a Blast/Blast plus result.
- BlastResult(String, String, String, String, HashMap<String, String>, int, String, String, int, List<Hit>, Sequence) - Constructor for class org.biojava.nbio.core.search.io.blast.BlastResult
- BlastResultBuilder - Class in org.biojava.nbio.core.search.io.blast
-
Designed by Paolo Pavan.
- BlastResultBuilder() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
- BlastTabularParser - Class in org.biojava.nbio.core.search.io.blast
-
Designed by Paolo Pavan.
- BlastTabularParser() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastTabularParser
- blastx - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
- BlastXMLParser - Class in org.biojava.nbio.core.search.io.blast
-
Re-designed by Paolo Pavan on the footprint of: org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis
You may want to find my contacts on Github and LinkedIn for code info or discuss major changes. - BlastXMLParser() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastXMLParser
- BlastXMLQuery - Class in org.biojava.nbio.genome.query
- BlastXMLQuery(String) - Constructor for class org.biojava.nbio.genome.query.BlastXMLQuery
- Block - Interface in org.biojava.nbio.structure.align.multiple
-
A Block is a Data Structure that stores aligned positions of a
MultipleAlignment
with the condition that residues are in a sequential order. - BlockImpl - Class in org.biojava.nbio.structure.align.multiple
-
General implementation of a
Block
that supports any type of sequential alignment with gaps. - BlockImpl(BlockImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl
-
Copy constructor.
- BlockImpl(BlockSet) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl
-
Constructor.
- blockInfo(AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
-
get the afp list and residue list for each block
- BlockSet - Interface in org.biojava.nbio.structure.align.multiple
-
A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment.
- BlockSetImpl - Class in org.biojava.nbio.structure.align.multiple
-
A general implementation of a BlockSet to store a flexible part of a multiple alignment.
- BlockSetImpl(BlockSetImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl
-
Copy constructor.
- BlockSetImpl(MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl
-
Constructor.
- BLOSUM45 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
- BLOSUM50 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
- Blosum62 - Static variable in class org.biojava.nbio.ronn.RonnConstraint
- BLOSUM62 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
- BLOSUM80 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
- BLOSUM90 - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
- Bond - Interface in org.biojava.nbio.structure
-
A simple bond -- it stores information about two atoms as well as information about its bond order.
- BOND_TYPES_TO_PARSE - Static variable in class org.biojava.nbio.structure.io.BondMaker
-
The types of bonds that are read from struct_conn (type specified in field conn_type_id)
- BondImpl - Class in org.biojava.nbio.structure
-
A simple bond -- it stores information about two atoms as well as information about its bond order.
- BondImpl(Atom, Atom, int) - Constructor for class org.biojava.nbio.structure.BondImpl
-
Constructs a new bond from a pair of atoms and the bond order of the bond between them.
- BondImpl(Atom, Atom, int, boolean) - Constructor for class org.biojava.nbio.structure.BondImpl
-
Constructs a new bond from a pair of atoms and the bond order of the bond between them.
- BondLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
- BondLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
- BondMaker - Class in org.biojava.nbio.structure.io
-
Adds polymer bonds for peptides and nucleotides based on distance cutoffs and intra-group (residue) bonds based on data from the Chemical Component Dictionary to the Structure object.
- BondMaker(Structure, FileParsingParameters) - Constructor for class org.biojava.nbio.structure.io.BondMaker
- BONDS_INITIAL_CAPACITY - Static variable in class org.biojava.nbio.structure.AtomImpl
-
The inital capacity of the bonds list.
- BondType - Enum in org.biojava.nbio.structure
-
Work in progress - NOT final!
- bottom - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
- BoundingBox - Class in org.biojava.nbio.structure.contact
-
A bounding box for short cutting some geometrical calculations.
- BoundingBox(double, double, double, double, double, double) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
- BoundingBox(Point3d[]) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
-
Constructs a BoundingBox by calculating maxs and mins of given array of atoms.
- BoundingBox(BoundingBox) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
- BoundingBox(BoundingBox[]) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
-
Given a set of bounding boxes returns a bounding box that bounds all of them.
- bounds() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
The union of all locations of all features in this list, mapped to the positive strand.
- Br - org.biojava.nbio.structure.Element
- BRANCHED - org.biojava.nbio.structure.EntityType
-
The 'branched' type use mainly to represent carbohydrates.
- BravaisLattice - Enum in org.biojava.nbio.structure.xtal
-
An enum to represent the 7 Bravais lattices
- Breslow - org.biojava.nbio.survival.cox.CoxMethod
- bridge - org.biojava.nbio.structure.secstruc.SecStrucType
- BridgeType - Enum in org.biojava.nbio.structure.secstruc
-
A bridge is formed by two non-overlapping stretches of three residues each (i-1,i,i+1) and (j-1,j,j+1), where i
- BROAD_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
- BROAD_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym
- BrowserOpener - Class in org.biojava.nbio.structure.align.webstart
- BrowserOpener() - Constructor for class org.biojava.nbio.structure.align.webstart.BrowserOpener
- BufferedReaderBytesRead - Class in org.biojava.nbio.core.sequence.io
Need to keep track of actual bytes read and take advantage of buffered reader performance.- BufferedReaderBytesRead(Reader) - Constructor for class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Creates a buffering character-input stream that uses a default-sized input buffer.- BufferedReaderBytesRead(Reader, int) - Constructor for class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
Creates a buffering character-input stream that uses an input buffer of the specified size.- build() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
The method to finish any calls to the builder with which returns a transcription engine.- build() - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder
Build and return a new FASTQ formatted sequence configured from the properties of this builder.- build() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
- build() - Static method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
Builds the mapping by reading SIFTS the tsv file set inSiftsChainToUniprotMapping.DEFAULT_FILE
variable.- builder() - Static method in class org.biojava.nbio.genome.io.fastq.Fastq
Create and return a new FastqBuilder.- builder(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.Fastq
Create and return a new FastqBuilder configured from the specified FASTQ formatted sequence.- Builder() - Constructor for class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
- Builder(String, ModificationCategory, ModificationOccurrenceType, ModificationCondition) - Constructor for class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
- Builder(ProteinModification) - Constructor for class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
Create a Builder from an existing ProteinModification.- buildFeatureAtrributeIndex(String, FeatureList) - Static method in class org.biojava.nbio.genome.parsers.gff.FeatureHelper
Build a list of individual features to allow easy indexing and to avoid iterating through large genome gff3 files The index for the returned HashMap is the value of the attribute used to build the index- buildSymmetryGraph(List<AFPChain>, Atom[], boolean) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Converts a set of AFP alignments into a Graph of aligned residues, where each vertex is a residue and each edge means the connection between the two residues in one of the alignments.- buildSymmetryGraph(AFPChain) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
Converts a self alignment into a directed jGraphT of aligned residues, where each vertex is a residue and each edge means the equivalence between the two residues in the self-alignment.- buildTranslators() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
- BYTES_PER_INT - Static variable in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
- bytesRead - Variable in class org.biojava.nbio.ontology.obo.OboFileParser
C
- c - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
-
first allowed c-term
- C - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
- C - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
- C - org.biojava.nbio.structure.Element
- C - Static variable in class org.biojava.nbio.aaproperties.Constraints
- C_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name for the backbone carbonyl
- C1_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name of the backbone C1' in RNA
- C2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name of the backbone C2' in RNA
- C2_ROTATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod
- C2RotationSolver - Class in org.biojava.nbio.structure.symmetry.core
- C2RotationSolver(QuatSymmetrySubunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.C2RotationSolver
- C3_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name of the backbone C3' in RNA
- C4_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name of the backbone C4' in RNA
- Ca - org.biojava.nbio.structure.Element
- CA_AND_SIDE_CHAIN_ANGLE_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
- CA_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name of the backbone C-alpha atom.
- CA_MIN_DIST - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc
-
min distance of two CA atoms if H-bonds are allowed to form
- CA_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
- cache(K, V) - Method in class org.biojava.nbio.structure.domain.SerializableCache
-
This will not cache null values.
- CACHE_PROPERTY - Static variable in class org.biojava.nbio.core.util.InputStreamProvider
- cacheFileName - Variable in class org.biojava.nbio.structure.domain.SerializableCache
- CAConverter - Class in org.biojava.nbio.structure.io
-
Converts full atom representations to Calpha only ones.
- CAConverter() - Constructor for class org.biojava.nbio.structure.io.CAConverter
- calAfpRmsd(int, int[], int, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
-
//return the rmsd of the residues from the segments that form the given AFP list //this value can be a measurement (1) for the connectivity of the AFPs
- Calc - Class in org.biojava.nbio.structure
-
Utility operations on Atoms, AminoAcids, Matrices, Point3d, etc.
- Calc() - Constructor for class org.biojava.nbio.structure.Calc
- calc_rmsd(Atom[], Atom[], int, boolean) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
superimpose and get rmsd
- calc_rmsd(Atom[], Atom[], int, boolean, boolean) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
superimpose and get rmsd
- calcAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together.
- calcAsas(int, int, int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together.
- calcCenterOfRotation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
- calcGlobalSymmetry(List<Subunit>, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Calculate GLOBAL symmetry results.
- calcGlobalSymmetry(Structure, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Calculate GLOBAL symmetry results.
- calcGlobalSymmetry(Stoichiometry, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Calculate GLOBAL symmetry results.
- calcIdSimilarity(char[], char[], int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
- calcLength(List<ResidueRangeAndLength>) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength
-
Calculates the combined number of residues of the ResidueRanges in
rrs
. - calcLocalSymmetries(List<Subunit>, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Returns a List of LOCAL symmetry results.
- calcLocalSymmetries(Structure, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Returns a List of LOCAL symmetry results.
- calcLocalSymmetries(Stoichiometry, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Returns a List of LOCAL symmetry results.
- CalcPoint - Class in org.biojava.nbio.structure.geometry
-
Utility operations on Point3d.
- calcRotationAngleInDegrees(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Calculates the angle from centerPt to targetPt in degrees.
- calcScale(int) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
a value of 100 means that the whole sequence should be displayed in the current visible window a factor of 1 means that one amino acid shoud be drawn as big as possible
- calcScores(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
calculates scores for this alignment ( %id )
- calcScores(QuatSymmetrySubunits, Matrix4d, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer
-
Returns minimum, mean, and maximum RMSD and TM-Score for two superimposed sets of subunits TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
- calcSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain
- calculate(Structure, boolean) - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
-
Predicts the secondary structure of this Structure object, using a DSSP implementation.
- calculateAsas() - Method in class org.biojava.nbio.structure.asa.AsaCalculator
-
Calculates the Accessible Surface Areas for the atoms given in constructor and with parameters given.
- calculateBlockGap(int[][][]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Method that calculates the number of gaps in each subunit block of an optimal AFP alignment.
- calculatedFragmentPairs(List<FragmentPair>) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
- calculateDsspSecondaryStructure(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Generate the secondary structure for a Biojava structure object.
- calculateIndirectAmbiguities() - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
-
Loops through all known nucleotides and attempts to find which are equivalent to each other.
- calculateInterfaces(Structure) - Static method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Calculates the interfaces for a structure using default parameters
- calculateMinCP(int[], int, int, int) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
-
Finds the alignment index of the residues minCPlength before and after the duplication.
- calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
- calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector
- calculateOrder(AFPChain, Atom[]) - Method in interface org.biojava.nbio.structure.symmetry.internal.OrderDetector
- calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector
- calculateScores(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
-
Calculates and puts the RMSD and the average TM-Score of the MultipleAlignment.
- calculateSuperpositionByIdx(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
- calculateTp(Matrix4d) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method calculates pairing and step parameters from 4x4 transformation matrices (used internally) that comes out as a Matrix4d.
- calculateWaldTestInfo(CoxInfo) - Static method in class org.biojava.nbio.survival.cox.CoxR
- calculator - Variable in class org.biojava.nbio.structure.align.ce.CeMain
- call() - Method in class org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner
- call() - Method in class org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer
- call() - Method in class org.biojava.nbio.alignment.template.CallableProfileProfileAligner
- call() - Method in class org.biojava.nbio.ronn.ORonn
- call() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
- call() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer
- CallablePairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template
-
Implements a concurrency wrapper for a
PairwiseSequenceAligner
. - CallablePairwiseSequenceAligner(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner
-
Creates a pairwise sequence alignment task for simplified parallel execution.
- CallablePairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template
-
Implements a concurrency wrapper for a
PairwiseSequenceScorer
. - CallablePairwiseSequenceScorer(PairwiseSequenceScorer<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer
-
Creates a pairwise sequence scoring task for simplified parallel execution.
- CallableProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template
-
Implements a concurrency wrapper for a
ProfileProfileAligner
. - CallableProfileProfileAligner(ProfileProfileAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallableProfileProfileAligner
-
Creates a profile-profile alignment task for simplified parallel execution.
- CallableStructureAlignment - Class in org.biojava.nbio.structure.align
-
Simple Callable Class that calculates a pairwise alignment in a different thread, so that multiple pairwise alignments can be run in parallel (examples: all-to-all alignments, DB search alignments).
- CallableStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment
-
Default constructor.
- CallableStructureAlignment(Atom[], Atom[], String, ConfigStrucAligParams) - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment
-
Constructor for all-to-all alignment calculation.
- calNS(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
- calSigAll(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
- canComplement(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
Uses the Sequence's CompoundSet to decide if a compound can be assgined to ComplementCompound meaning it can complement
- canonical - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
- CartesianProduct<T> - Class in org.biojava.nbio.structure.quaternary
-
A cartesian product between two lists A and B is the set of all ordered pairs of the elements of both sets.
- CartesianProduct(List<T>, List<T>) - Constructor for class org.biojava.nbio.structure.quaternary.CartesianProduct
-
Class constructor specifying the two lists of a cartesian product.
- CARTOON - org.biojava.nbio.structure.gui.RenderStyle
- CaseFreeAminoAcidCompoundSet - Class in org.biojava.nbio.aaproperties.xml
-
Set of proteinogenic amino acids.
- CaseFreeAminoAcidCompoundSet() - Constructor for class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
- CaseInsensitiveCompound - Class in org.biojava.nbio.core.sequence.transcription
-
Attempts to wrap compounds so it is possible to view them in a case insensitive manner
- CaseInsensitiveCompound(NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
- CaseInsensitiveTriplet(NucleotideCompound, NucleotideCompound, NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
- CasePreservingProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io
-
A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.
- CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
- categorizeData(ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
-
Take a collection of categorical data and convert it to numeric to be used in cox calculations
- CATH - org.biojava.nbio.structure.align.client.StructureName.Source
- CATH_DOWNLOAD_ALL_RELEASES_DIR - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
- CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
- CATH_DOWNLOAD_URL - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
- CathCategory - Enum in org.biojava.nbio.structure.cath
-
The categories found within CATH.
- CathDatabase - Interface in org.biojava.nbio.structure.cath
-
General API for interacting with CATH.
- CathDomain - Class in org.biojava.nbio.structure.cath
-
A class which represents a single CATH domain.
- CathDomain() - Constructor for class org.biojava.nbio.structure.cath.CathDomain
- CathFactory - Class in org.biojava.nbio.structure.cath
-
Controls global
CathDatabases
being used. - CathFragment - Class in org.biojava.nbio.structure.cath
- CathFragment() - Constructor for class org.biojava.nbio.structure.cath.CathFragment
- CathInstallation - Class in org.biojava.nbio.structure.cath
- CathInstallation() - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
- CathInstallation(String) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
- CathInstallation(String, boolean, boolean) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
- CathNode - Class in org.biojava.nbio.structure.cath
-
Represents a node in the CATH hierarchy.
- CathNode() - Constructor for class org.biojava.nbio.structure.cath.CathNode
- CathSegment - Class in org.biojava.nbio.structure.cath
- CathSegment() - Constructor for class org.biojava.nbio.structure.cath.CathSegment
- CB_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name of the side-chain C-beta atom
- Cd - org.biojava.nbio.structure.Element
- CDD_SEARCH - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- CDS - Static variable in class org.biojava.nbio.genome.util.ChromosomeMappingTools
- CDSComparator - Class in org.biojava.nbio.core.sequence
- CDSComparator() - Constructor for class org.biojava.nbio.core.sequence.CDSComparator
- CDSSequence - Class in org.biojava.nbio.core.sequence
-
Represents a exon or coding sequence in a gene.
- CDSSequence(TranscriptSequence, int, int, int) - Constructor for class org.biojava.nbio.core.sequence.CDSSequence
- Ce - org.biojava.nbio.structure.Element
- CE_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
- CECalculator - Class in org.biojava.nbio.structure.align.ce
-
This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
- CECalculator(CeParameters) - Constructor for class org.biojava.nbio.structure.align.ce.CECalculator
- CeCalculatorEnhanced - Class in org.biojava.nbio.structure.align.ce
-
This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
- CeCalculatorEnhanced(CeParameters) - Constructor for class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
- CeCPMain - Class in org.biojava.nbio.structure.align.ce
-
A wrapper for
CeMain
which sets default parameters to be appropriate for finding circular permutations. - CeCPMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain
- CeCPMain.CPRange - Class in org.biojava.nbio.structure.align.ce
-
Tiny wrapper for the disallowed regions of an alignment.
- CECPParameters - Class in org.biojava.nbio.structure.align.ce
-
Provides parameters to
CeCPMain
- CECPParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CECPParameters
- CECPParameters.DuplicationHint - Enum in org.biojava.nbio.structure.align.ce
- CeCPStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
- CeCPUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
- CeCPUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
- CeCPUserArgumentProcessor.CeCPStartupParams - Class in org.biojava.nbio.structure.align.ce
- ceil(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
-
Return the smallest key in the table >= k.
- CELLTRANSL - org.biojava.nbio.structure.xtal.TransformType
- CeMain - Class in org.biojava.nbio.structure.align.ce
-
The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.
- CeMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeMain
- censored - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
- CensorStatus - Class in org.biojava.nbio.survival.kaplanmeier.figure
- CensorStatus() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
- CensorStatus(String, Double, String) - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
- CensorStatusSelect - Interface in org.biojava.nbio.survival.kaplanmeier.figure
- center(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
-
Center a cloud of points.
- centerAtoms(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
-
Center the atoms at the Centroid.
- centerAtoms(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Center the atoms at the Centroid, if the centroid is already know.
- centered - Variable in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
- centerOfMass(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
-
Returns the center of mass of the set of atoms.
- centroid(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
-
Calculate the centroid of the point cloud.
- CeParameters - Class in org.biojava.nbio.structure.align.ce
-
Contains the parameters that can be sent to CE
- CeParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CeParameters
- CeParameters.ScoringStrategy - Enum in org.biojava.nbio.structure.align.ce
- CeSideChainMain - Class in org.biojava.nbio.structure.align.ce
- CeSideChainMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainMain
- CeSideChainUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
- CeSideChainUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
- CeStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
- CeSymm - Class in org.biojava.nbio.structure.symmetry.internal
-
Identify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment.
- CeSymmIterative - Class in org.biojava.nbio.structure.symmetry.internal
-
Iterative version of CeSymm that aims at identifying all symmetry axis of a structure.
- CeSymmIterative(CESymmParameters) - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative
-
For the iterative algorithm to work properly the refinement and optimization options should be turned on, because the alignment has to be consistent at every recursive step.
- CESymmParameters - Class in org.biojava.nbio.structure.symmetry.internal
-
Provides parameters to
CeSymm
. - CESymmParameters() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
- CESymmParameters(CESymmParameters) - Constructor for class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
- CESymmParameters.OrderDetectorMethod - Enum in org.biojava.nbio.structure.symmetry.internal
- CESymmParameters.RefineMethod - Enum in org.biojava.nbio.structure.symmetry.internal
- CESymmParameters.SymmetryType - Enum in org.biojava.nbio.structure.symmetry.internal
-
The internal symmetry detection can be divided into two types: CLOSE: includes the circular and dihedral symmetries, and OPEN: includes the helical and protein repeats symmetries.
- CeSymmResult - Class in org.biojava.nbio.structure.symmetry.internal
-
This Class stores all the relevant information of an internal symmetry result obtained with CeSymm.
- CeSymmResult() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
- CeUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
-
process the arguments from command line
- CeUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
- CeUserArgumentProcessor.CeStartupParams - Class in org.biojava.nbio.structure.align.ce
- Cf - org.biojava.nbio.structure.Element
- Chain - Interface in org.biojava.nbio.structure
-
Defines the interface for a Chain.
- CHAIN_NR_SYMBOL - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
- CHAIN_REGEX - Static variable in class org.biojava.nbio.structure.ResidueRange
- CHAIN_SPLIT_SYMBOL - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
- chainEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
- CHAINID_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier
-
URL parameter specifying a single chain to include; overridden by residues
- ChainImpl - Class in org.biojava.nbio.structure
-
A Chain in a PDB file.
- ChainImpl() - Constructor for class org.biojava.nbio.structure.ChainImpl
-
Constructs a ChainImpl object.
- chainName - Variable in class org.biojava.nbio.structure.align.client.StructureName
- ChainSignature - Class in org.biojava.nbio.structure.symmetry.misc
- ChainSignature(String, int, List<String>) - Constructor for class org.biojava.nbio.structure.symmetry.misc.ChainSignature
- change(String) - Method in interface org.biojava.nbio.survival.data.ChangeValue
- changeColumnHeader(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
- changeColumnHeader(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
- changeColumnsHeaders(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Change the columns in the HashMap Key to the name of the value
- changeRowHeader(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
- changeRowHeader(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
- ChangeValue - Interface in org.biojava.nbio.survival.data
- charAt(int) - Method in class org.biojava.nbio.survival.data.CompactCharSequence
- CHARGE - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
- ChargeAdder - Class in org.biojava.nbio.structure.io
-
A class to add appropriate charge information to a structure.
- ChargeAdder() - Constructor for class org.biojava.nbio.structure.io.ChargeAdder
- checkDoFirstInstall() - Method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
-
Checks if the chemical components already have been installed into the PDB directory.
- checkFileExists(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
- checkFileExists(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
- checkInput(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
-
Check that the input to the superposition algorithms is valid.
- checkPoint() - Method in class org.biojava.nbio.ronn.Timer
- checkScaleMatrix(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
Given a scale matrix parsed from a PDB entry (SCALE1,2,3 records), compares it to our calculated Mtranspose matrix to see if they coincide and returns true if they do.
- checkScaleMatrixConsistency(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
Given a scale matrix parsed from the PDB entry (SCALE1,2,3 records), checks that the matrix is a consistent scale matrix by comparing the cell volume to the inverse of the scale matrix determinant (tolerance of 1/100).
- checkSequence(String) - Static method in class org.biojava.nbio.aaproperties.Utils
-
Checks if the sequence contains invalid characters.
- checkSequence(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils
-
Checks if the sequence contains invalid characters.
- checksum(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Performs a simple CRC64 checksum on any given sequence.
- CHEM_COMP_CACHE_DIRECTORY - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
- chem_comp_type - Variable in enum org.biojava.nbio.structure.chem.ResidueType
-
String value of the type
- chemComp - Variable in class org.biojava.nbio.structure.HetatomImpl
- ChemComp - Class in org.biojava.nbio.structure.chem
-
Properties of a chemical component.
- ChemComp() - Constructor for class org.biojava.nbio.structure.chem.ChemComp
- ChemCompAtom - Class in org.biojava.nbio.structure.chem
-
Properties of an atom of a chemical component.
- ChemCompAtom() - Constructor for class org.biojava.nbio.structure.chem.ChemCompAtom
- ChemCompBond - Class in org.biojava.nbio.structure.chem
-
Properties of a bond in a chemical component.
- ChemCompBond() - Constructor for class org.biojava.nbio.structure.chem.ChemCompBond
- ChemCompConsumer - Interface in org.biojava.nbio.structure.io.cif
-
Create the
ChemicalComponentDictionary
from CIF data. - ChemCompConsumerImpl - Class in org.biojava.nbio.structure.io.cif
-
Consumes a CCD file to create the
ChemicalComponentDictionary
. - ChemCompConsumerImpl() - Constructor for class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
- ChemCompConverter - Class in org.biojava.nbio.structure.io.cif
-
Convert CifFiles to chem comps.
- ChemCompConverter() - Constructor for class org.biojava.nbio.structure.io.cif.ChemCompConverter
- ChemCompDescriptor - Class in org.biojava.nbio.structure.chem
-
Properties of the chemical component descriptor.
- ChemCompDescriptor() - Constructor for class org.biojava.nbio.structure.chem.ChemCompDescriptor
- ChemCompDistribution - Class in demo
- ChemCompDistribution() - Constructor for class demo.ChemCompDistribution
- ChemCompGroupFactory - Class in org.biojava.nbio.structure.chem
- ChemCompGroupFactory() - Constructor for class org.biojava.nbio.structure.chem.ChemCompGroupFactory
- ChemCompProvider - Interface in org.biojava.nbio.structure.chem
-
Interface that is implemented by all classes that can provide
ChemComp
definitions. - ChemCompTools - Class in org.biojava.nbio.structure.chem
- ChemCompTools() - Constructor for class org.biojava.nbio.structure.chem.ChemCompTools
- CHEMICAL_MODIFICATION - org.biojava.nbio.protmod.ModificationCategory
- ChemicalComponentDictionary - Class in org.biojava.nbio.structure.chem
-
A representation of the Chemical Component Dictionary.
- ChemicalComponentDictionary() - Constructor for class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
- children() - Method in class org.biojava.nbio.alignment.GuideTree.Node
- chiSq(double, int) - Static method in class org.biojava.nbio.survival.cox.stats.ChiSq
- ChiSq - Class in org.biojava.nbio.survival.cox.stats
- ChiSq() - Constructor for class org.biojava.nbio.survival.cox.stats.ChiSq
- chol() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Cholesky Decomposition
- Cholesky2 - Class in org.biojava.nbio.survival.cox.stats
- Cholesky2() - Constructor for class org.biojava.nbio.survival.cox.stats.Cholesky2
- CholeskyDecomposition - Class in org.biojava.nbio.structure.jama
-
Cholesky Decomposition.
- CholeskyDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.CholeskyDecomposition
-
Cholesky algorithm for symmetric and positive definite matrix.
- ChooseDirAction - Class in org.biojava.nbio.structure.align.gui
-
Ask the user to provide a directory containting PDB files.
- ChooseDirAction(JTextField, UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.gui.ChooseDirAction
- CHROMOSOME - org.biojava.nbio.core.sequence.DNASequence.DNAType
- CHROMOSOME - Static variable in class org.biojava.nbio.genome.util.ChromosomeMappingTools
- ChromosomeMappingTools - Class in org.biojava.nbio.genome.util
-
A class that can map chromosomal positions to mRNA (coding sequence) positions.
- ChromosomeMappingTools() - Constructor for class org.biojava.nbio.genome.util.ChromosomeMappingTools
- ChromosomeSequence - Class in org.biojava.nbio.core.sequence
-
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
- ChromosomeSequence() - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Empty constructor used by tools that need a proper Bean that allows the actual sequence data to be set after construction.
- ChromosomeSequence(String) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
-
String is king and assume DNA
- ChromosomeSequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet
- ChromosomeSequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Fairly important constructor given the size of a ChromsomeSequence where the ProxySequenceReader could load from disk via RandomAccessFile so that the sequence doesn't need to be kept in memory.
- ChromosomeSequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet
- ChromPos - Class in org.biojava.nbio.genome.parsers.genename
-
Created by ap3 on 27/10/2014.
- ChromPos(int, int) - Constructor for class org.biojava.nbio.genome.parsers.genename.ChromPos
- Chsolve2 - Class in org.biojava.nbio.survival.cox.stats
- Chsolve2() - Constructor for class org.biojava.nbio.survival.cox.stats.Chsolve2
- CIF - org.biojava.nbio.structure.io.StructureFiletype
- CIF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.BcifFileReader
- CIF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.CifFileReader
- CIF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.BcifFileReader
- CIF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.CifFileReader
- CifBean - Interface in org.biojava.nbio.structure.io.cif
-
Flag for BioJava beans that resemble categories defined by the mmCIF schema.
- CifChainSupplierImpl - Class in org.biojava.nbio.structure.io.cif
-
Convert a chain to a
CifFile
. - CifChainSupplierImpl() - Constructor for class org.biojava.nbio.structure.io.cif.CifChainSupplierImpl
- CifFileConsumer<S> - Interface in org.biojava.nbio.structure.io.cif
-
Defines a rather generic interface which allows to populate some data structure with data parsed from a CIF file.
- CifFileReader - Class in org.biojava.nbio.structure.io
-
Parse text Cif files and provide capabilities to store them locally.
- CifFileReader() - Constructor for class org.biojava.nbio.structure.io.CifFileReader
-
Constructs a new CifFileReader, initializing the extensions member variable.
- CifFileReader(String) - Constructor for class org.biojava.nbio.structure.io.CifFileReader
-
Constructs a new CifFileReader, initializing the extensions member variable.
- CifFileSupplier<S> - Interface in org.biojava.nbio.structure.io.cif
-
Create a CifFile instance for a given container of structure data.
- CifStructureConsumer - Interface in org.biojava.nbio.structure.io.cif
-
Defines the categories to consume during CIF parsing.
- CifStructureConsumerImpl - Class in org.biojava.nbio.structure.io.cif
-
An implementation of a CifFileConsumer for BioJava.
- CifStructureConsumerImpl(FileParsingParameters) - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- CifStructureConverter - Class in org.biojava.nbio.structure.io.cif
-
Convert BioJava structures to CifFiles and vice versa.
- CifStructureConverter() - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureConverter
- CifStructureSupplierImpl - Class in org.biojava.nbio.structure.io.cif
-
Convert a structure to a CifFile.
- CifStructureSupplierImpl() - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureSupplierImpl
- CIRCULAR_DNA - Static variable in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
- circularLocation(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
- circularLocation(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
-
Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
- Cl - org.biojava.nbio.structure.Element
- claFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
- Class - org.biojava.nbio.structure.cath.CathCategory
- Class - org.biojava.nbio.structure.scop.ScopCategory
- classEqual(Object, Object) - Static method in class org.biojava.nbio.core.util.Equals
-
This method should be called before beginning any equals methods.
- ClasspathResource - Class in org.biojava.nbio.core.sequence.io.util
-
This object represents a classpath resource on the local system.
- ClasspathResource(String) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource
-
Basic constructor only allowing you to specify where to find the file.
- ClasspathResource(String, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource
-
Advanced constructor which allows you to optionally pre-cache the data
- ClasspathResource(String, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource
-
Advanced constructor which lets you set the preCache variable and to force the type of file we are decompressing.
- cleanSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
-
Removes all whitespace chars in the sequence string
- cleanSequence(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils
-
Returns a new sequence with all invalid characters being replaced by '-'.
- cleanup() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc
- cleanup() - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
- cleanup() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
- cleanup() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc
- cleanup() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
- cleanup(List<Domain>) - Static method in class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
- cleanUp() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
- cleanUp() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
- cleanUp() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
- cleanUpAltLocs(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Cleans up the structure's alternate location (altloc) groups.
- clear() - Static method in class org.biojava.nbio.core.util.FlatFileCache
-
Removes all elements from the cache
- clear() - Method in class org.biojava.nbio.core.util.SoftHashMap
- clear() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
-
reset all suggestions
- clear() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
- clear() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
- clear() - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
-
Clear the cached scores.
- clear() - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Clear scores and other properties which depend on the specific alignment.
- clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
- clear() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
-
Clear scores and other properties which depend on the specific alignment.
- clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
- clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Clear scores and other properties which depend on the specific alignment.
- clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Clear scores and other properties which depend on the specific alignment.
- clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
- clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
- clear() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
Clears all domains, requiring the file to be reparsed for subsequent accesses
- clear() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
- clear() - Method in interface org.biojava.nbio.structure.gui.Selection
- clear() - Method in class org.biojava.nbio.structure.gui.SelectionImpl
- clear() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
-
Clear the current display
- clear() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
Clears all finite endpoints
- clear() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
- clear() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
See if we can free up memory
- clearAlgorithms() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
-
Removes all algorithms from the list
- clearAtoms() - Method in interface org.biojava.nbio.structure.Group
-
Remove all atoms from this group.
- clearAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl
- clearCache() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
- clearCache() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Nullifies cached arrays/objects.
- clearCache() - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory
-
Force the in-memory cache to be reset.
- clearExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
clear the supported file extensions
- clearListeners() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
- clearListeners() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
- clearListeners() - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
- ClinicalMetaDataOutcome - Class in org.biojava.nbio.survival.kaplanmeier.metadata
- ClinicalMetaDataOutcome() - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
- CliTools - Class in org.biojava.nbio.structure.align.util
-
Utilities for autoconfiguring javabeans based on command line arguments.
- clone() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Creates and returns a copy of this object.
- clone() - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Creates and returns an identical copy of this block.
- clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
- clone() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
-
Creates and returns an identical copy of this blockset, including a deep copy of all constituent
Block
s. - clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
- clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Creates and returns an identical copy of this alignment, including a deep copy of all constituent BlockSets.
- clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Creates and returns an identical copy of this ensemble, including a deep clone of all constituent alignments.
- clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
- clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
- clone() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
- clone() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
returns and identical copy of this Group object .
- clone() - Method in class org.biojava.nbio.structure.asa.GroupAsa
- clone() - Method in interface org.biojava.nbio.structure.Atom
-
Return an identical copy of this object .
- clone() - Method in class org.biojava.nbio.structure.AtomImpl
-
returns and identical copy of this object .
- clone() - Method in interface org.biojava.nbio.structure.Chain
-
Returns an identical copy of this Chain.
- clone() - Method in class org.biojava.nbio.structure.ChainImpl
- clone() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
- clone() - Method in interface org.biojava.nbio.structure.Group
-
Returns and identical copy of this Group object .
- clone() - Method in class org.biojava.nbio.structure.GroupIterator
-
Creates and returns a copy of this object.
- clone() - Method in class org.biojava.nbio.structure.HetatomImpl
-
returns and identical copy of this Group object .
- clone() - Method in class org.biojava.nbio.structure.io.SSBondImpl
- clone() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Clone the Matrix object.
- clone() - Method in class org.biojava.nbio.structure.NucleotideImpl
- clone() - Method in class org.biojava.nbio.structure.PdbId
- clone() - Method in class org.biojava.nbio.structure.scop.ScopDescription
- clone() - Method in class org.biojava.nbio.structure.scop.ScopDomain
- clone() - Method in class org.biojava.nbio.structure.secstruc.HBond
- clone() - Method in interface org.biojava.nbio.structure.Structure
-
Return an identical copy of this Structure object
- clone() - Method in class org.biojava.nbio.structure.StructureImpl
-
Returns an identical copy of this structure .
- clone() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
- clone(Object) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
-
Subclasses should override clone and use the copy constructor.
- cloneAtomArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Provides an equivalent copy of Atoms in a new array.
- cloneAtomsAndBonds(Group) - Method in class org.biojava.nbio.structure.HetatomImpl
- cloneDM(BasicSymmetricalDistanceMatrix) - Static method in class org.biojava.nbio.phylo.ForesterWrapper
-
Helper function to clone a forester symmetrical DistanceMatrix.
- cloneGroups(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Clone a set of representative Atoms, but returns the parent groups
- clonePoint() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
- clonePoint() - Method in interface org.biojava.nbio.core.sequence.location.template.Point
-
Returns a copy of this point
- clonePoint3dArray(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
-
Clone an array of points.
- close() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
- close() - Method in class org.biojava.nbio.core.sequence.io.FastaReader
- close() - Method in class org.biojava.nbio.core.sequence.io.GenbankReader
- close() - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
- close() - Method in interface org.biojava.nbio.core.util.XMLWriter
-
Close this XMLWriter, and its underlying stream.
- close() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitFacade
-
Closes .2bit file twoBitParser.
- close() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
Method closes current sequence and it's necessary to invoke it before setting new current sequence.
- close() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
- close(Closeable) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Closes any Object which implements the interface
Closeable
and sending any error to the logger but not forcing any explicit catching of stream errors. - CLOSED - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
- closeParser() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
Method closes random access file descriptor.
- closeTag(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
- closeTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter
-
Closes an un-qualified element.
- closeTag(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
- closeTag(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter
-
Closes an element
- CLUSTALW - org.biojava.nbio.core.alignment.template.Profile.StringFormat
- CLUSTALW - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
- cluster(List<Subunit>, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.cluster.SubunitClusterer
- cluster(List<Domain>, PDPDistanceMatrix) - Static method in class org.biojava.nbio.structure.domain.pdp.ClusterDomains
- cluster(AlternativeAlignment[]) - Static method in class org.biojava.nbio.structure.align.ClusterAltAligs
- cluster(AlternativeAlignment[], int) - Static method in class org.biojava.nbio.structure.align.ClusterAltAligs
- cluster(Structure, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.cluster.SubunitClusterer
- ClusterAltAligs - Class in org.biojava.nbio.structure.align
-
A class that clusters alternative alignments according to their similarity.
- ClusterAltAligs() - Constructor for class org.biojava.nbio.structure.align.ClusterAltAligs
- ClusterDomains - Class in org.biojava.nbio.structure.domain.pdp
- ClusterDomains() - Constructor for class org.biojava.nbio.structure.domain.pdp.ClusterDomains
- Cm - org.biojava.nbio.structure.Element
- CMD - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- Co - org.biojava.nbio.structure.Element
- Codon(Table.CaseInsensitiveTriplet) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon
- Codon(Table.CaseInsensitiveTriplet, AminoAcidCompound, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon
- CodonCompound - Class in org.biojava.nbio.core.sequence.compound
-
Define a codon
- CodonCompound(NucleotideCompound, NucleotideCompound, NucleotideCompound, boolean) - Constructor for class org.biojava.nbio.core.sequence.compound.CodonCompound
- coil - org.biojava.nbio.structure.secstruc.SecStrucType
- CollectionTools - Class in org.biojava.nbio.structure.align.util
-
Utilities for working with collections.
- CollectionTools() - Constructor for class org.biojava.nbio.structure.align.util.CollectionTools
- colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that colors subunits by their sequence cluster ids.
- colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script that colors subunits by their sequence cluster ids.
- colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
- colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that colors the subunits of a structure by different colors
- colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script that colors the subunits of a structure by different colors
- colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
- colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that colors subunits to highlight the symmetry within a structure
- colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script that colors subunits to highlight the symmetry within a structure Different subunits should have a consistent color scheme or different shade of the same colors
- colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
- ColorConverter - Class in org.biojava.nbio.structure.symmetry.jmolScript
- ColorConverter() - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
- coloring - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
- ColorInterpolator - Interface in org.biojava.nbio.structure.gui.util.color
- colorPalette - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
- ColorUtils - Class in org.biojava.nbio.structure.gui.util.color
- ColorUtils() - Constructor for class org.biojava.nbio.structure.gui.util.color.ColorUtils
- colorWheel - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
- column - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
- combine(List<Integer>, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
- combine(BiologicalAssemblyTransformation, BiologicalAssemblyTransformation) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Returns the combination (product) of two biological assembly transformations.
- combineWith(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup
-
Combine the ResidueGroup with the alignment block.
- combineWith(Stoichiometry) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Make a combined Stoichiometry object of this> and the other>.
- comFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
- COMMAND_LINE_HELP - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
- CommandPrompt - Class in org.biojava.nbio.aaproperties
- CommandPrompt() - Constructor for class org.biojava.nbio.aaproperties.CommandPrompt
- CommandPrompt.PropertyName - Enum in org.biojava.nbio.aaproperties
- COMMENT - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
- COMMENT_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
- CompactCharSequence - Class in org.biojava.nbio.survival.data
-
http://www.javamex.com/tutorials/memory/ascii_charsequence.shtml
- CompactCharSequence(String) - Constructor for class org.biojava.nbio.survival.data.CompactCharSequence
- COMPARATOR - Static variable in class org.biojava.nbio.ontology.Synonym
- compare(int[], int[]) - Method in class org.biojava.nbio.structure.align.helper.IdxComparator
- compare(AlignerHelper.Anchor, AlignerHelper.Anchor) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator
- compare(CDSSequence, CDSSequence) - Method in class org.biojava.nbio.core.sequence.CDSComparator
-
Used to sort two CDSSequences where Negative Strand makes it tough
- compare(ExonSequence, ExonSequence) - Method in class org.biojava.nbio.core.sequence.ExonComparator
- compare(AbstractSequence<?>, AbstractSequence<?>) - Method in class org.biojava.nbio.core.sequence.SequenceComparator
- compare(AlternativeAlignment, AlternativeAlignment) - Method in class org.biojava.nbio.structure.align.pairwise.AltAligComparator
- compare(Segment, Segment) - Method in class org.biojava.nbio.structure.domain.pdp.SegmentComparator
- compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator
- compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
- compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.MeanModelComparator
- compare(SurvivalInfo, SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator
- compare(SurvivalInfo, SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator
- compareTo(Point) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
- compareTo(Point) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
- compareTo(FastaSequence) - Method in class org.biojava.nbio.data.sequence.FastaSequence
- compareTo(Cytoband) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
- compareTo(GeneChromosomePosition) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
- compareTo(GeneName) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
- compareTo(Synonym) - Method in class org.biojava.nbio.ontology.Synonym
- compareTo(ProteinModification) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
- compareTo(ModifiedCompound) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
- compareTo(StructureGroup) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
- compareTo(PdbPair) - Method in class org.biojava.nbio.structure.align.client.PdbPair
- compareTo(StructureName) - Method in class org.biojava.nbio.structure.align.client.StructureName
-
Orders identifiers lexicographically by PDB ID and then full Identifier
- compareTo(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemComp
- compareTo(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterface
- compareTo(Domain) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
- compareTo(Segment) - Method in class org.biojava.nbio.structure.domain.pdp.Segment
- compareTo(PdbId) - Method in class org.biojava.nbio.structure.PdbId
- compareTo(BiologicalAssemblyTransformation) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
- compareTo(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber
-
Compare residue numbers by chain, sequence number, and insertion code
- compareTo(Site) - Method in class org.biojava.nbio.structure.Site
- compareTo(ChainSignature) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
- compareTo(SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
- compareTo(SurvivalInfoIndex) - Method in class org.biojava.nbio.survival.cox.SurvivalInfoIndex
- compareTo(CensorStatus) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
- compareTo(HmmerDomain) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
- compareTo(HmmerResult) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
- compareToPositional(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber
-
Compare residue numbers by sequence number and insertion code, ignoring the chain
- Comparison - Class in org.biojava.nbio.phylo
-
This class provides static methods for the calculation of the percentage of identity between two aligned sequences.
- Comparison() - Constructor for class org.biojava.nbio.phylo.Comparison
- complementBase(char, boolean) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the complement of a base.
- ComplementCompound - Interface in org.biojava.nbio.core.sequence.template
- ComplementSequenceView<C extends ComplementCompound> - Class in org.biojava.nbio.core.sequence.views
-
For a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlying base e.g. base A will become base T
- ComplementSequenceView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.views.ComplementSequenceView
- complete() - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
-
Notify this listener the FASTQ formatted sequence is complete.
- complete() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
- completeCircularPasses(int, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e. if we have a sequence of length 10 and the location 3..52 we make 4 complete passes through the genome to go from position 3 to position 52.
- completeCircularPasses(int, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
-
Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e. if we have a sequence of length 10 and the location 3..52 we make 4 complete passes through the genome to go from position 3 to position 52.
- completeGroup() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
-
Starts with an incomplete set of group generators in `permutations` and expands it to include all possible combinations.
- Component - Class in org.biojava.nbio.protmod
-
contains information about a certain Component.
- COMPONENTS_FILE_LOCATION - Static variable in class org.biojava.nbio.structure.chem.AllChemCompProvider
- ComponentXMLConverter - Class in org.biojava.nbio.protmod.io
- ComponentXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.ComponentXMLConverter
- COMPOSED_OPERATOR_SEPARATOR - Static variable in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
-
The character separating operator ids that are composed.
- COMPOSITION_BASED_STATISTICS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- Compound - Interface in org.biojava.nbio.core.sequence.template
- COMPOUND - org.biojava.nbio.core.alignment.template.AlignedSequence.Step
- CompoundNotFoundException - Exception in org.biojava.nbio.core.exceptions
- CompoundNotFoundException(String) - Constructor for exception org.biojava.nbio.core.exceptions.CompoundNotFoundException
- compoundsEqual(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
- compoundsEquivalent(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
- compoundsEquivalent(C, C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
- compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
- compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
- compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
- CompoundSet<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
- compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Should return the maximum amount of compounds we can encode per int
- compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
- compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
- compoundToInt(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
- CompoundTranslator<F extends Compound,T extends Compound> - Interface in org.biojava.nbio.core.sequence.template
- computeMolecularWeight(ElementTable) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
-
Computes and store the molecular weight of each amino acid by its symbol in aaSymbol2MolecularWeight.
- ConcurrencyTools - Class in org.biojava.nbio.core.util
-
Static utility to easily share a thread pool for concurrent/parallel/lazy execution.
- cond() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Matrix condition (2 norm)
- cond() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Two norm condition number
- ConfigPDBInstallPanel - Class in org.biojava.nbio.structure.align.gui
- ConfigStrucAligParams - Interface in org.biojava.nbio.structure.align.ce
- ConfigurationException - Exception in org.biojava.nbio.structure.align.util
- ConfigurationException() - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
- ConfigurationException(String) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
-
Constructs a ConfigurationException object.
- ConfigurationException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
- ConfigurationException(Throwable) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
-
Constructs a ConfigurationException object.
- configureBean(Object, String[]) - Static method in class org.biojava.nbio.structure.align.util.CliTools
-
Configure a JavaBean based on a set of command line arguments.
- configureParameters() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
- configureParameters() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
- ConfigXMLHandler - Class in org.biojava.nbio.structure.align.webstart
-
XML content handler for serialisation of RegistryConfiguration class
- ConfigXMLHandler() - Constructor for class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
- consistentAccessions(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Scans a list of locations and returns true if all the given locations are linked to the same sequence.
- CONSORTIUM_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
- CONSTANT - org.biojava.nbio.alignment.template.GapPenalty.Type
- constrain(double) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
-
Constrain the specified quality score in double precision to the minimum and maximum quality scores in int precision.
- Constraints - Class in org.biojava.nbio.aaproperties
-
This class is used to support the implementation of properties stated in IPeptideProperties.
- Constraints() - Constructor for class org.biojava.nbio.aaproperties.Constraints
- constructWithCopy(double[][]) - Static method in class org.biojava.nbio.structure.jama.Matrix
-
Construct a matrix from a copy of a 2-D array.
- consume(Category) - Method in interface org.biojava.nbio.structure.io.cif.MetalBondConsumer
- consume(Category) - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl
- consumeAtomSite(AtomSite) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeAtomSite(AtomSite) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeAtomSites(AtomSites) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeAtomSites(AtomSites) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeAuditAuthor(AuditAuthor) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeAuditAuthor(AuditAuthor) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeCell(Cell) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeCell(Cell) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer
-
Consume a particular Cif category.
- consumeChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
- consumeChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeChemCompAtom(ChemCompAtom) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer
-
Consume a particular Cif category.
- consumeChemCompAtom(ChemCompAtom) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
- consumeChemCompBond(ChemCompBond) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer
-
Consume a particular Cif category.
- consumeChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
- consumeChemCompBond(ChemCompBond) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeDatabasePDBRemark(DatabasePDBRemark) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeDatabasePDBRemark(DatabasePDBRemark) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeDatabasePDBRev(DatabasePDBRev) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeDatabasePDBRev(DatabasePDBRev) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeDatabasePDBRevRecord(DatabasePDBRevRecord) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeDatabasePDBRevRecord(DatabasePDBRevRecord) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeEm3dReconstruction(Em3dReconstruction) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume Electron Microscopy 3D reconstruction data
- consumeEm3dReconstruction(Em3dReconstruction) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeEntity(Entity) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeEntity(Entity) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeEntityPoly(EntityPoly) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeEntityPoly(EntityPoly) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeEntityPolySeq(EntityPolySeq) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeEntityPolySeq(EntityPolySeq) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeEntitySrcGen(EntitySrcGen) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeEntitySrcGen(EntitySrcGen) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeEntitySrcNat(EntitySrcNat) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeEntitySrcNat(EntitySrcNat) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeEntitySrcSyn(PdbxEntitySrcSyn) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeEntitySrcSyn(PdbxEntitySrcSyn) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeExptl(Exptl) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeExptl(Exptl) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxAuditRevisionHistory(PdbxAuditRevisionHistory) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxAuditRevisionHistory(PdbxAuditRevisionHistory) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxChemCompIdentifier(PdbxChemCompIdentifier) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxChemCompIdentifier(PdbxChemCompIdentifier) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxDatabaseStatus(PdbxDatabaseStatus) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxDatabaseStatus(PdbxDatabaseStatus) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxEntityBranchDescriptor(PdbxEntityBranchDescriptor) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxEntityBranchDescriptor(PdbxEntityBranchDescriptor) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxMolecule(PdbxMolecule) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxMolecule(PdbxMolecule) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxMoleculeFeatures(PdbxMoleculeFeatures) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxMoleculeFeatures(PdbxMoleculeFeatures) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxNonpolyScheme(PdbxNonpolyScheme) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxNonpolyScheme(PdbxNonpolyScheme) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxReferenceEntityLink(PdbxReferenceEntityLink) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxReferenceEntityLink(PdbxReferenceEntityLink) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxReferenceEntityList(PdbxReferenceEntityList) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxReferenceEntityList(PdbxReferenceEntityList) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxReferenceEntityPolyLink(PdbxReferenceEntityPolyLink) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxReferenceEntityPolyLink(PdbxReferenceEntityPolyLink) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxStructAssembly(PdbxStructAssembly) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxStructAssembly(PdbxStructAssembly) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxStructAssemblyGen(PdbxStructAssemblyGen) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxStructAssemblyGen(PdbxStructAssemblyGen) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxStructModResidue(PdbxStructModResidue) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxStructModResidue(PdbxStructModResidue) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumePdbxStructOperList(PdbxStructOperList) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumePdbxStructOperList(PdbxStructOperList) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeRefine(Refine) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeRefine(Refine) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStruct(Struct) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStruct(Struct) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStructAsym(StructAsym) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructAsym(StructAsym) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStructConf(StructConf) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructConf(StructConf) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStructConn(StructConn) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructConn(StructConn) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStructConnType(StructConnType) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructConnType(StructConnType) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStructKeywords(StructKeywords) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructKeywords(StructKeywords) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStructNcsOper(StructNcsOper) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructNcsOper(StructNcsOper) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStructRef(StructRef) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructRef(StructRef) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStructRefSeq(StructRefSeq) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructRefSeq(StructRefSeq) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStructRefSeqDif(StructRefSeqDif) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructRefSeqDif(StructRefSeqDif) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStructSheetRange(StructSheetRange) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructSheetRange(StructSheetRange) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStructSite(StructSite) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructSite(StructSite) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeStructSiteGen(StructSiteGen) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeStructSiteGen(StructSiteGen) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- consumeSymmetry(Symmetry) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer
-
Consume a particular Cif category.
- consumeSymmetry(Symmetry) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- Contact - Class in org.biojava.nbio.structure.contact
-
A simple class to store contacts in the form of pairs of indices and a distance associated to them.
- Contact(int, int, double) - Constructor for class org.biojava.nbio.structure.contact.Contact
- contacts(Point3d[], Point3d[], double) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
- contains(Point3d) - Method in class org.biojava.nbio.structure.contact.BoundingBox
-
Check if a given point falls within this box
- contains(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
-
Is the key in the table?
- contains(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Check if this location contains the other.
- contains(ResidueNumber) - Method in class org.biojava.nbio.structure.AugmentedResidueRange
- contains(ResidueNumber, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange
- containsChainId(String, String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
- containsKey(Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap
- containsKey(Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
- containsKey(Object) - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
- containsKey(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
- containsProperty(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
- containsProperty(Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation
-
Returns whether there the property is defined.
- containsTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
- containsTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Determines if this ontology currently contains a term named
name
- containsTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
- containsTriple(Term, Term, Term) - Method in class org.biojava.nbio.ontology.IntegerOntology
- containsTriple(Term, Term, Term) - Method in interface org.biojava.nbio.ontology.Ontology
-
See if a triple exists in this ontology
- containsTriple(Term, Term, Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl
- containsUniProtId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
- containsValue(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
- ContinuousColorMapper - Interface in org.biojava.nbio.structure.gui.util.color
-
Provides a mapping between real numbers and Colors.
- ContinuousColorMapperTransform - Class in org.biojava.nbio.structure.gui.util.color
-
Maps colors by performing a transform of the input data and then passing the transformed value to a ContinuousColorMapper for rendering.
- ContinuousColorMapperTransform(ContinuousColorMapper) - Constructor for class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform
-
Creates a transform.
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
-
Class for the conversion of protein sequence into charge
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
-
Class for the conversion of protein sequence into hydrophobicity
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
-
Class for the conversion of protein sequence into normalized van der waals volume
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
-
Class for the conversion of protein sequence into polarity
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
-
Class for the conversion of protein sequence into polarizability
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
-
Class for the conversion of protein sequence into secondary structure
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
-
Class for the conversion of protein sequence into solvent accessibility
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
Returns the grouping of the amino acid character.
- convert(File, File) - Static method in class demo.DemoMmcifToPdbConverter
- convert(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.ForesterWrapper
-
Convert a BioJava
MultipleSequenceAlignment
to a foresterMsa
. - convert(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
Returns the converted sequence.
- convert(Fastq) - Method in class org.biojava.nbio.genome.io.fastq.IlluminaFastqWriter
- convert(Fastq) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqWriter
- convert(Fastq) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqWriter
- convert(Fastq, FastqVariant) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.
- Convert2Charge - Class in org.biojava.nbio.aaproperties.profeat.convertor
- Convert2Charge() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
- Convert2Hydrophobicity - Class in org.biojava.nbio.aaproperties.profeat.convertor
- Convert2Hydrophobicity() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
- Convert2NormalizedVanDerWaalsVolume - Class in org.biojava.nbio.aaproperties.profeat.convertor
- Convert2NormalizedVanDerWaalsVolume() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
- Convert2Polarity - Class in org.biojava.nbio.aaproperties.profeat.convertor
- Convert2Polarity() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
- Convert2Polarizability - Class in org.biojava.nbio.aaproperties.profeat.convertor
- Convert2Polarizability() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
- Convert2SecondaryStructure - Class in org.biojava.nbio.aaproperties.profeat.convertor
- Convert2SecondaryStructure() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
- Convert2SolventAccessibility - Class in org.biojava.nbio.aaproperties.profeat.convertor
- Convert2SolventAccessibility() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
- convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
copy data from this class into AFPChain container object.
- convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
copy data from this class into AFPChain container object.
- convertAtomsToSeq(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
- convertColor4f(Color) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
- convertColor4f(Color[]) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
- convertDNAtoProteinSequence(String) - Static method in class org.biojava.nbio.genome.util.ProteinMappingTools
-
Converts the DNA sequence to protein sequence.
- convertDNAtoProteinSequence(DNASequence) - Static method in class org.biojava.nbio.genome.util.ProteinMappingTools
-
Converts the DNA sequence to protein sequence.
- Convertor - Class in org.biojava.nbio.aaproperties.profeat.convertor
- Convertor() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
- convertPairsToXML(SortedSet<PdbPair>, String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
- convertProteinSequencetoFasta(ProteinSequence) - Static method in class org.biojava.nbio.ronn.Jronn
-
Utility method to convert a BioJava ProteinSequence object to the FastaSequence object used internally in JRonn.
- convertStreamToString(InputStream) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
-
Converts an InputStream of text to a String, closing the stream before returning.
- convertTo(FastqVariant) - Method in class org.biojava.nbio.genome.io.fastq.Fastq
-
Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.
- convertToDoubleArray(Matrix4d) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Convert a four-d matrix to a double array.
- convertXMLtoPairs(String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
- CookBook - Class in demo
- CookBook() - Constructor for class demo.CookBook
- CookbookMSA - Class in demo
- CookbookMSA() - Constructor for class demo.CookbookMSA
- CoordManager - Class in org.biojava.nbio.structure.gui.util
-
a class that manages the conversion of sequence coordinate system to JPanel drawing coordinates
- CoordManager() - Constructor for class org.biojava.nbio.structure.gui.util.CoordManager
- copy() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Make a deep copy of a matrix
- copy(File, File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
-
Copy the content of file src to dst TODO since java 1.7 this is provided in java.nio.file.Files
- copy(InputStream, OutputStream) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Moves the bytes from input to output using a 4KB byte array.
- copyEmblReference(EmblReference) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
-
return copy of EmblReference
- copyFile(File, File) - Static method in class org.biojava.nbio.phosphosite.Dataset
- copyLigandsByProximity(Structure, Structure) - Static method in class org.biojava.nbio.structure.SubstructureIdentifier
-
Supplements the reduced structure with ligands from the full structure based on a distance cutoff.
- copyLigandsByProximity(Structure, Structure, double, int, int) - Static method in class org.biojava.nbio.structure.SubstructureIdentifier
-
Supplements the reduced structure with ligands from the full structure based on a distance cutoff.
- CoreSuperimposer - Class in org.biojava.nbio.structure.align.multiple.util
-
Superimposes the core aligned residues of every structure in a
MultipleAlignment
onto a reference structure. - CoreSuperimposer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer
-
Default Constructor.
- CoreSuperimposer(int) - Constructor for class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer
-
Constructor using a specified structure as reference.
- countAT(Sequence<NucleotideCompound>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Returns the count of AT in the given sequence
- countCompounds(C...) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Counts the number of times a compound appears in this sequence store
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Delegates to
SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[])
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
- countCompounds(C...) - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Returns the number of times we found a compound in the Sequence
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
- countCompounds(Sequence<C>, C...) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
For the given vargs of compounds this method counts the number of times those compounds appear in the given sequence
- countGC(Sequence<NucleotideCompound>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Returns the count of GC in the given sequence
- countMatchesInSequence(String, String) - Static method in class org.biojava.nbio.data.sequence.FastaSequence
- COVALENT - org.biojava.nbio.structure.BondType
- CoxCC - Class in org.biojava.nbio.survival.cox
- CoxCC() - Constructor for class org.biojava.nbio.survival.cox.CoxCC
- CoxCoefficient - Class in org.biojava.nbio.survival.cox
- CoxCoefficient() - Constructor for class org.biojava.nbio.survival.cox.CoxCoefficient
- CoxComparatorInterface - Interface in org.biojava.nbio.survival.cox.comparators
- CoxHelper - Class in org.biojava.nbio.survival.cox
-
The CoxHelper class is provided to start with a tab delimited file in a similar process in R and return the results as a CoxInfo class.
- CoxHelper() - Constructor for class org.biojava.nbio.survival.cox.CoxHelper
- CoxInfo - Class in org.biojava.nbio.survival.cox
-
Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R
- CoxInfo() - Constructor for class org.biojava.nbio.survival.cox.CoxInfo
- CoxMart - Class in org.biojava.nbio.survival.cox
- CoxMart() - Constructor for class org.biojava.nbio.survival.cox.CoxMart
- CoxMethod - Enum in org.biojava.nbio.survival.cox
- coxphfitSCleanup(CoxInfo, boolean, boolean, ArrayList<String>) - Method in class org.biojava.nbio.survival.cox.CoxR
- CoxR - Class in org.biojava.nbio.survival.cox
-
This is a port of the R survival code used for doing Cox Regression.
- CoxR() - Constructor for class org.biojava.nbio.survival.cox.CoxR
- coxsafe(double) - Method in class org.biojava.nbio.survival.cox.CoxR
- CoxScore - Class in org.biojava.nbio.survival.cox
- CoxScore() - Constructor for class org.biojava.nbio.survival.cox.CoxScore
- CoxVariables - Class in org.biojava.nbio.survival.cox
- CoxVariables(String, String, String) - Constructor for class org.biojava.nbio.survival.cox.CoxVariables
- CoxVariablesOverallModelFitComparator - Class in org.biojava.nbio.survival.cox.comparators
- CoxVariablesOverallModelFitComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator
-
Variables are stored as a string representation of an ArrayList [META_GENE] or [trtg, META_GENE] add variables used in cox regression to an array and then do toString.
- CoxVariablesVariableComparator - Class in org.biojava.nbio.survival.cox.comparators
- CoxVariablesVariableComparator(String, String) - Constructor for class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
- cpFastaToAfpChain(File, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site
cpSite
residues to the right. - cpFastaToAfpChain(String, String, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
- cpFastaToAfpChain(ProteinSequence, ProteinSequence, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site
cpSite
residues to the right. - cpPoint - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
The CP point, specified as a residue index
- CPRange() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
- Cr - org.biojava.nbio.structure.Element
- CRC64Checksum - Class in org.biojava.nbio.core.util
-
Utility class that calculates a CRC64 checksum on a stream of bytes.
- CRC64Checksum() - Constructor for class org.biojava.nbio.core.util.CRC64Checksum
- createAFPChain(Atom[], Atom[], ResidueNumber[], ResidueNumber[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Fundamentally, an alignment is just a list of aligned residues in each protein.
- createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.
- createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
- createBlastHit() - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
- createBlastHsp() - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
- createBlastResult() - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
- createDNASequence(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Create and return a new
DNASequence
from the specified FASTQ formatted sequence. - createDNASequenceWithErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Create and return a new
DNASequence
with error probabilities from the specified FASTQ formatted sequence. - createDNASequenceWithQualityScores(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Create and return a new
DNASequence
with quality scores from the specified FASTQ formatted sequence. - createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Create and return a new
DNASequence
with quality scores and error probabilities from the specified FASTQ formatted sequence. - createErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Create and return a new
QuantityFeature
from the error probabilities of the specified FASTQ formatted sequence. - createGradients() - Static method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
- createImage(String, String, Object, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
- createImageIcon(String) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
Returns an ImageIcon, or null if the path was invalid.
- createIterator(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Creates a simple sequence iterator which moves through a sequence going from 1 to the length of the Sequence.
- createObjects(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
- createObjects(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
- createObjects(double) - Method in interface org.biojava.nbio.core.search.io.ResultFactory
-
Launch the parsing and get back a list of Result objects representing the search result in the specified file.
- createOntology(String, String) - Method in interface org.biojava.nbio.ontology.OntologyFactory
-
Creates a new Ontology
- createOntologyTerm(Ontology) - Method in class org.biojava.nbio.ontology.Ontology.Impl
- createOutput(String, String) - Method in class org.biojava.nbio.aaproperties.xml.SchemaGenerator
- createPurelyNonPolyEntities(List<List<Chain>>, List<List<Chain>>, List<EntityInfo>) - Static method in class org.biojava.nbio.structure.io.EntityFinder
-
Given all chains of all models find entities for the nonpolymers and water chains within them, assigning entity ids, types and descriptions to them.
- createQualityScores(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Create and return a new
QualityFeature
from the quality scores of the specified FASTQ formatted sequence. - createSequence(Sequence<F>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
- createSequence(Sequence<F>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator
- createSequence(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
- createSequence(Sequence<NucleotideCompound>, Frame) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
- createSequences(Sequence<F>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
- createSequences(Sequence<F>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator
- createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
-
Overloaded local version which delegates to an optional translator when told to (specified during construction).
- createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator
-
Performs the core conversion of RNA to Peptide.
- createSubSequence(Sequence<C>, int, int) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Creates a simple sub sequence view delimited by the given start and end.
- createTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
- createTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Create a new term in this ontology.
- createTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
- createTerm(String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
- createTerm(String, String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Create a new term in this ontology.
- createTerm(String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
- createTerm(String, String, Object[]) - Method in class org.biojava.nbio.ontology.IntegerOntology
- createTerm(String, String, Object[]) - Method in interface org.biojava.nbio.ontology.Ontology
-
Create a new term in this ontology.
- createTerm(String, String, Object[]) - Method in class org.biojava.nbio.ontology.Ontology.Impl
- createTriple(Term, Term, Term, String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
- createTriple(Term, Term, Term, String, String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Creates a new Triple.
- createTriple(Term, Term, Term, String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
- createVariable(String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
- createVariable(String, String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Create a new term in this ontology that is used as a variable.
- createVariable(String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
- createVirtualCBAtom(AminoAcid) - Static method in class org.biojava.nbio.structure.Calc
-
creates a virtual C-beta atom. this might be needed when working with GLY thanks to Peter Lackner for a python template of this method.
- CROSS_LINK_1 - org.biojava.nbio.protmod.ModificationCategory
- CROSS_LINK_2 - org.biojava.nbio.protmod.ModificationCategory
- CROSS_LINK_3 - org.biojava.nbio.protmod.ModificationCategory
- CROSS_LINK_4 - org.biojava.nbio.protmod.ModificationCategory
- CROSS_LINK_5 - org.biojava.nbio.protmod.ModificationCategory
- CROSS_LINK_6 - org.biojava.nbio.protmod.ModificationCategory
- CROSS_LINK_7 - org.biojava.nbio.protmod.ModificationCategory
- CROSS_LINK_8_OR_LARGE - org.biojava.nbio.protmod.ModificationCategory
- crossChains() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
- crossChains() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
- CrystalBuilder - Class in org.biojava.nbio.structure.xtal
-
A class containing methods to find interfaces in a given crystallographic Structure by reconstructing the crystal lattice through application of symmetry operators
- CrystalBuilder(Structure) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder
- CrystalBuilder(Structure, Map<String, String>, Map<String, Matrix4d>) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder
-
Special constructor for NCS-aware CrystalBuilder.
- CrystalCell - Class in org.biojava.nbio.structure.xtal
-
A crystal cell's parameters.
- CrystalCell() - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell
- CrystalCell(double, double, double, double, double, double) - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell
- CrystalTransform - Class in org.biojava.nbio.structure.xtal
-
Representation of a transformation in a crystal: - a transformation id (each of the transformations in a space group, 0 to m) - a crystal translation The transformation matrix in crystal basis is stored, representing the basic transformation together with the crystal translation.
- CrystalTransform(CrystalTransform) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform
-
Copy constructor
- CrystalTransform(SpaceGroup) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform
-
Creates a new CrystalTransform representing the identity transform in cell (0,0,0)
- CrystalTransform(SpaceGroup, int) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform
-
Represents the n-th transform
- Cs - org.biojava.nbio.structure.Element
- CS_HSV - Static variable in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
-
The HSV color space
- Cu - org.biojava.nbio.structure.Element
- CUBIC - org.biojava.nbio.structure.xtal.BravaisLattice
- CURATED - org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
- CURRENT - org.biojava.nbio.structure.PDBStatus.Status
- CUSTOM - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy
-
The strategy is defined via an external function, we do not have to do anything.
- cut(Atom[], Domain, CutValues, int[][], PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.Cut
- Cut - Class in org.biojava.nbio.structure.domain.pdp
- Cut() - Constructor for class org.biojava.nbio.structure.domain.pdp.Cut
- Cut(int, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
- CUT_OFF_VALUE - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
- CUT_OFF_VALUE1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
- CUT_OFF_VALUE1M - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
- CUT_OFF_VALUE1S - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
- CUT_OFF_VALUE2 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
- cutDomain(Domain, CutSites, PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.CutDomain
- CutDomain - Class in org.biojava.nbio.structure.domain.pdp
- CutDomain(Atom[], PDPDistanceMatrix) - Constructor for class org.biojava.nbio.structure.domain.pdp.CutDomain
- CutSites - Class in org.biojava.nbio.structure.domain.pdp
- CutSites() - Constructor for class org.biojava.nbio.structure.domain.pdp.CutSites
- cutsPerSection - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
- CutValues - Class in org.biojava.nbio.structure.domain.pdp
- CutValues() - Constructor for class org.biojava.nbio.structure.domain.pdp.CutValues
- cyan - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
- CYCLE - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy
-
Cycle through the alphabet (e.g., ...xyzABC...)
- cyclicPeptide - org.biojava.nbio.structure.chem.PolymerType
-
cyclic peptides
- Cytoband - Class in org.biojava.nbio.genome.parsers.cytoband
- Cytoband() - Constructor for class org.biojava.nbio.genome.parsers.cytoband.Cytoband
- CytobandParser - Class in org.biojava.nbio.genome.parsers.cytoband
-
Parses the cytoband (karyotype) file from UCSC.
- CytobandParser() - Constructor for class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
D
- D - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
- D - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
- D - org.biojava.nbio.structure.Element
-
Deuterium
- D - Static variable in class org.biojava.nbio.aaproperties.Constraints
- d2 - Static variable in class org.biojava.nbio.structure.io.FileConvert
- d3 - Static variable in class org.biojava.nbio.structure.io.FileConvert
- darker(Color, double) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
-
Make a color darker.
- DATABASE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- DATABASE_PREFIX - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- DATABASE_SORT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
- DatabasePDBRevRecord - Class in org.biojava.nbio.structure
-
Represents revision records for use by
PDBHeader
. - DatabasePDBRevRecord() - Constructor for class org.biojava.nbio.structure.DatabasePDBRevRecord
- DatabasePDBRevRecord(String, String, String) - Constructor for class org.biojava.nbio.structure.DatabasePDBRevRecord
- DatabasePDBRevRecord(DatabasePDBRevRecord, int) - Constructor for class org.biojava.nbio.structure.DatabasePDBRevRecord
- DatabaseReference(String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
- DatabaseReference(String, String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
- DatabaseReferenceInterface - Interface in org.biojava.nbio.core.sequence.features
-
If a SequenceProxyReader implements this interface then that external source has a list of cross reference id(s)
- Dataset - Class in org.biojava.nbio.phosphosite
-
Phosphosite is available under the PhosphoSitePlus® is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from http://www.phosphosite.org/staticDownloads.do Please acknowledge PhosphoSitePlus®, www.phosphosite.org" at appropriate locations.
- Dataset() - Constructor for class org.biojava.nbio.phosphosite.Dataset
- DataSource - Enum in org.biojava.nbio.core.sequence
-
GenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT UNIPROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier
- dateFormat - Variable in class org.biojava.nbio.ontology.obo.OboFileParser
- dateToIsoString(Date) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Covert a Date object to ISO time format.
- DB_GENETIC_CODE - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- dBetaPeptideCGammaLinking - org.biojava.nbio.structure.chem.ResidueType
- DBL - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
- DBLINK - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
- DBRef - Class in org.biojava.nbio.structure
-
A class to represent database cross references.
- DBRef() - Constructor for class org.biojava.nbio.structure.DBRef
- DBReferenceInfo - Class in org.biojava.nbio.core.sequence.features
-
If you have a uniprot ID then it is possible to get a collection of other id(s) that the protein is known by.
- DBReferenceInfo(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.DBReferenceInfo
-
The source database and id
- DBSOURCE - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
- dbxp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
- DDBJ - org.biojava.nbio.core.sequence.DataSource
- debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
- debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
- debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
- debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
- debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
- debug - Static variable in class org.biojava.nbio.structure.align.util.AlignmentTools
- debug(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
- declareNamespace(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
-
Declare a namespace for current and following elements 'prefixHint' is ignored entirely in this implementation
- declareNamespace(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter
-
Hints that a namespace is going to be used in a sub-tree.
- decorateRna(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
-
Performs an optimisation where RNASequences are not translated into their own objects but are views onto the base DNA sequence.
- deepCleanSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
-
Removes all special characters and digits as well as whitespace chars from the sequence
- DEF - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
- DEF_NUM_CELLS - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder
- DEFAULT - Static variable in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
- DEFAULT - Static variable in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
- DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
- DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
- DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
- DEFAULT_ALGORITHM_NAME - Static variable in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
- DEFAULT_ASA_SPHERE_POINTS - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Default number of points to use when calculating ASAs
- DEFAULT_BCIF_FILE_SERVER - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
The default server to retrieve BinaryCIF files.
- DEFAULT_BIOASSEMBLY_STYLE - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
-
The default output bioassembly style: if true the bioassemblies are multimodel, if false the bioassemblies are flat with renamed chains for symmetry-partners.
- DEFAULT_BUFFER_SIZE - Variable in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
- DEFAULT_CHAR_SIZE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
size per character
- DEFAULT_CHAR_SIZE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Size per character
- DEFAULT_CHEMCOMP_PATHURL_TEMPLATE - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
- DEFAULT_CLUSTER_CUTOFF - Static variable in class org.biojava.nbio.structure.align.ClusterAltAligs
- DEFAULT_CONNECTION_TIMEOUT - Static variable in class org.biojava.nbio.structure.align.util.URLConnectionTools
-
The default connection timeout in ms - 15 seconds
- DEFAULT_CONTACT_CUTOFF - Static variable in class org.biojava.nbio.structure.contact.InterfaceFinder
- DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Any 2 interfaces with contact overlap score larger than this value will be considered to be clustered
- DEFAULT_DISORDER - Static variable in class org.biojava.nbio.ronn.RonnConstraint
- DEFAULT_FILE - Static variable in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
- DEFAULT_FRAGLEN - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
- DEFAULT_GAP_EXTENSION - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
- DEFAULT_GAP_OPEN - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
- DEFAULT_GENENAMES_URL - Static variable in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
- DEFAULT_HEIGHT - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
- DEFAULT_INTERFACE_DISTANCE_CUTOFF - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder
-
Default maximum distance between two chains to be considered an interface.
- DEFAULT_LIGAND_PROXIMITY_CUTOFF - Static variable in class org.biojava.nbio.structure.StructureTools
-
Threshold for plausible binding of a ligand to the selected substructure
- DEFAULT_LIMIT - Static variable in class org.biojava.nbio.core.util.SoftHashMap
- DEFAULT_LINE_LENGTH - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
number of chars per line
- DEFAULT_LINE_LENGTH - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Number of chars per line
- DEFAULT_LINE_SEPARATION - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
separation of line 1 and 2 in alignment
- DEFAULT_LINE_SEPARATION - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Separation between sequences in the alignment
- DEFAULT_LOCATION - Static variable in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
- DEFAULT_MAPPING_URL - Static variable in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
- DEFAULT_MAX_PROPELLER - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
- DEFAULT_MAX_PROPELLER - Static variable in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
- DEFAULT_MAX_SHEAR - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
- DEFAULT_MAX_STAGGER - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
- DEFAULT_MAX_STAGGER - Static variable in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
- DEFAULT_MAX_STRETCH - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
- DEFAULT_METHOD_NAME - Static variable in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
- DEFAULT_MIN_COFACTOR_SIZE - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Default minimum size of cofactor molecule (non-chain HET atoms) that will be used
- DEFAULT_MIN_CP_LENGTH - Static variable in class org.biojava.nbio.structure.align.ce.CECPParameters
- DEFAULT_MINIMUM_INTERFACE_AREA - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Default minimum area for a contact between two chains to be considered a valid interface.
- DEFAULT_N_SPHERE_POINTS - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
-
The default value for number of sphere points to sample.
- DEFAULT_NTHREADS - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
- DEFAULT_ORDER - Static variable in class org.biojava.nbio.ronn.RonnConstraint
- DEFAULT_oRmsdThr - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
- DEFAULT_PDB_FILE_SERVER - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
The default server name, prefixed by the protocol string (http://, https:// or ftp://).
- DEFAULT_PROBE_SIZE - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
- DEFAULT_RANGE_PROBABILITY_THRESHOLD - Static variable in class org.biojava.nbio.ronn.RonnConstraint
- DEFAULT_RCSB_DATA_API_SERVER - Static variable in class org.biojava.nbio.structure.PDBStatus
- DEFAULT_RESOLUTION - Static variable in class org.biojava.nbio.structure.PDBHeader
- DEFAULT_RFREE - Static variable in class org.biojava.nbio.structure.PDBHeader
- DEFAULT_RIGHT_SPACER - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
Space on the right side between sequence and legend.
- DEFAULT_RIGHT_SPACER - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Space on the right side between sequence and legend.
- DEFAULT_SCORING_STRATEGY - Static variable in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
- DEFAULT_SCRIPT - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
- DEFAULT_SERVER_URL - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
- DEFAULT_SUBSTITUTION_MATRIX - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
- DEFAULT_SYMMETRY_THRESHOLD - Static variable in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
- DEFAULT_UNIPROT_BASE_URL - Static variable in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
- DEFAULT_VARIANT - Static variable in class org.biojava.nbio.genome.io.fastq.FastqBuilder
-
Default FASTQ sequence format variant,
FastqVariant.FASTQ_SANGER
. - DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathFactory
- DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
- DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.ecod.EcodFactory
- DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
- DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
- DEFAULT_WIDTH - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
- DEFAULT_X_RIGHT_BORDER - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
- DEFAULT_X_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
left boundary
- DEFAULT_X_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Left boundary
- DEFAULT_X_START - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
- DEFAULT_Y_BOTTOM - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
- DEFAULT_Y_HEIGHT - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
- DEFAULT_Y_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
top boundary
- DEFAULT_Y_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Top boundary
- DEFAULT_Y_START - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
- DEFAULT_Y_STEP - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
size of space between rows
- DEFAULT_Y_STEP - Variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Size of space between rows.
- DEFAULT_Y_STEP - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
- DefaultAAIndexProvider - Class in org.biojava.nbio.core.alignment.matrices
-
The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directory
- DefaultAAIndexProvider() - Constructor for class org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider
- DefaultAutoSuggestProvider - Class in org.biojava.nbio.structure.align.gui.autosuggest
- DefaultAutoSuggestProvider() - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
- DefaultMatrixMapper - Class in org.biojava.nbio.structure.gui.util.color
-
Color Mapper which mimics the default coloring of JMatrixPanel pixels.
- DefaultMatrixMapper(double, float) - Constructor for class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
- DefaultOps - Class in org.biojava.nbio.ontology
-
Default implementation of OntologyOps.
- DefaultOps() - Constructor for class org.biojava.nbio.ontology.DefaultOps
- defaultProperties - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo
- DEFINITION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
- delete(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
-
Delete the key (and paired value) from table.
- Delete(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Delete
- Delete(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Delete
- deleteColumn(AFPChain, Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Delete an alignment position from the original alignment object.
- deleteDirectory(String) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
-
Recursively delete a folder & contents
- deleteDirectory(Path) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
-
Recursively delete a folder & contents
- deleteHighestDistanceColumn(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Find the alignment position with the highest atomic distance between the equivalent atomic positions of the arrays and remove it from the alignment.
- deleteStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Attempts to delete all versions of a structure from the local directory.
- deleteStructure(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Attempts to delete all versions of a structure from the local directory.
- deleteTerm(Term) - Method in class org.biojava.nbio.ontology.IntegerOntology
- deleteTerm(Term) - Method in interface org.biojava.nbio.ontology.Ontology
-
Remove a term from an ontology, together with all triples which refer to it.
- deleteTerm(Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl
- DELETION - org.biojava.nbio.alignment.routines.AlignerHelper.Last
- DELTA - Static variable in class org.biojava.nbio.structure.xtal.SpaceGroup
- deltaComp(double, double, double) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
- demo - package demo
- DemoAlignmentFromFasta - Class in demo
-
Demo of how to use the
FastaStructureParser
class to read protein structures from a FASTA file. - DemoAlignmentFromFasta() - Constructor for class demo.DemoAlignmentFromFasta
- DemoAlignProteins - Class in demo
- DemoAlignProteins() - Constructor for class demo.DemoAlignProteins
- DemoAsa - Class in demo
- DemoAsa() - Constructor for class demo.DemoAsa
- DemoAtomCache - Class in demo
-
Example of how to load PDB files using the AtomCache class.
- DemoAtomCache() - Constructor for class demo.DemoAtomCache
- DemoBerkeleyScop - Class in demo
-
A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP
- DemoBerkeleyScop() - Constructor for class demo.DemoBerkeleyScop
- DemoBioAssemblies - Class in demo
- DemoBioAssemblies() - Constructor for class demo.DemoBioAssemblies
- DemoCATH - Class in demo
-
An example for how to access CATH data.
- DemoCATH() - Constructor for class demo.DemoCATH
- DemoCE - Class in demo
-
Example of how to run a structure alignment using the CE algorithm.
- DemoCE() - Constructor for class demo.DemoCE
- DemoCeSymm - Class in demo
-
Quick demo of how to call CE-Symm programmatically.
- DemoCeSymm() - Constructor for class demo.DemoCeSymm
- DemoChangeChemCompProvider - Class in demo
-
This demo shows how to use an alternative ChemCompProvider.
- DemoChangeChemCompProvider() - Constructor for class demo.DemoChangeChemCompProvider
- DemoCommandLineStartup - Class in demo
- DemoCommandLineStartup() - Constructor for class demo.DemoCommandLineStartup
- DemoContacts - Class in demo
- DemoContacts() - Constructor for class demo.DemoContacts
- DemoCrystalInterfaces - Class in demo
- DemoCrystalInterfaces() - Constructor for class demo.DemoCrystalInterfaces
- DemoDistanceTree - Class in demo
-
This demo contains the CookBook example to create a phylogenetic tree from a multiple sequence alignment (MSA).
- DemoDistanceTree() - Constructor for class demo.DemoDistanceTree
- DemoDomainsplit - Class in demo
- DemoDomainsplit() - Constructor for class demo.DemoDomainsplit
- DemoFATCAT - Class in demo
- DemoFATCAT() - Constructor for class demo.DemoFATCAT
- DemoLoadSecStruc - Class in demo
-
Demonstration of how to load a Structure with the SS information, either from the PDB file annotation (Author's assignment) or from the DSSP file in the PDB servers (DSSP assignment).
- DemoLoadSecStruc() - Constructor for class demo.DemoLoadSecStruc
- DemoLoadStructure - Class in demo
-
Example for how to load protein structures (from PDB files).
- DemoLoadStructure() - Constructor for class demo.DemoLoadStructure
- DemoLoadSubstMax - Class in demo
- DemoLoadSubstMax() - Constructor for class demo.DemoLoadSubstMax
- DemoMMCIFReader - Class in demo
-
An example of how to read MMcif files
- DemoMMCIFReader() - Constructor for class demo.DemoMMCIFReader
- DemoMmcifToPdbConverter - Class in demo
-
An example of how to convert mmCIF file to PDB file
- DemoMmcifToPdbConverter() - Constructor for class demo.DemoMmcifToPdbConverter
- DemoMmtfReader - Class in demo
-
Class to show how to read a Biojava structure using MMTF
- DemoMmtfReader() - Constructor for class demo.DemoMmtfReader
- DemoMmtfWriter - Class in demo
- DemoMmtfWriter() - Constructor for class demo.DemoMmtfWriter
- DemoMultipleMC - Class in demo
-
Demo for running the MultipleMC Algorithm on a protein family.
- DemoMultipleMC() - Constructor for class demo.DemoMultipleMC
- DemoNWALignment - Class in demo
- DemoNWALignment() - Constructor for class demo.DemoNWALignment
- DemoQsAlign - Class in demo
-
Demo on how to use programatically
QsAlign
for the alignment of quaternary structures. - DemoQsAlign() - Constructor for class demo.DemoQsAlign
- DemoQuatSymmetryJmol - Class in demo
-
This demo shows how to display the
QuatSymmetryResults
of a structure. - DemoQuatSymmetryJmol() - Constructor for class demo.DemoQuatSymmetryJmol
- DemoRotationAxis - Class in demo
-
A demo for how to use
RotationAxis
to display the rotation for an alignment. - DemoRotationAxis() - Constructor for class demo.DemoRotationAxis
- DemoSCOP - Class in demo
-
A class demonstrating the use of the SCOP parsing tools
- DemoSCOP() - Constructor for class demo.DemoSCOP
- DemoSecStrucCalc - Class in demo
-
Demonstration on how to use the Secondary Structure Prediction (DSSP) implementation in BioJava and obtain different SS representations and outputs.
- DemoSecStrucCalc() - Constructor for class demo.DemoSecStrucCalc
- DemoShowBiolAssembly - Class in demo
- DemoShowBiolAssembly() - Constructor for class demo.DemoShowBiolAssembly
- DemoShowCATHDomain - Class in demo
- DemoShowCATHDomain() - Constructor for class demo.DemoShowCATHDomain
- DemoShowLargeAssembly - Class in demo
- DemoShowLargeAssembly() - Constructor for class demo.DemoShowLargeAssembly
- DemoSixFrameTranslation - Class in demo
-
Created by andreas on 8/10/15.
- DemoSixFrameTranslation() - Constructor for class demo.DemoSixFrameTranslation
- DemoStructureFromFasta - Class in demo
-
Demo of how to use the
FastaStructureParser
class to read protein structures from a FASTA file. - DemoStructureFromFasta() - Constructor for class demo.DemoStructureFromFasta
- DemoSW3DAligner - Class in demo
- DemoSW3DAligner() - Constructor for class demo.DemoSW3DAligner
- DemoSymmetry - Class in demo
-
A demo on how to use the quaternary symmetry detection algorithms.
- DemoSymmetry() - Constructor for class demo.DemoSymmetry
- description - Variable in class org.biojava.nbio.ontology.AbstractTerm
- description() - Method in enum org.biojava.nbio.protmod.ModificationCategory
- description(String) - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
-
Notify this parse listener of a description line.
- DESCRIPTIONS - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- DESCRIPTIONS - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
- deserialize(File) - Static method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
- desFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
- destroy() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
- destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
- destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
- destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
- destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
- destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
- destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
- destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
Set all the member variables to null.
- destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
Clean up this instance for garbage collection, to avoid memory leaks...
- destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
- destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
- det() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
-
Determinant
- det() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Matrix determinant
- detectCicular(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Loops through the given list of locations and returns true if it looks like they represent a circular location.
- detectEnd(List<Location>, boolean) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
This will attempt to find what the last point is and returns that position.
- detectStart(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Assumes that the first element is the start & clones it
- detectStrand(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Loops through the given list of locations and returns the consensus Strand class.
- dfbeta - org.biojava.nbio.survival.cox.ResidualsCoxph.Type
- dfbetas - org.biojava.nbio.survival.cox.ResidualsCoxph.Type
- dGammaPeptideCDeltaLinking - org.biojava.nbio.structure.chem.ResidueType
- diAA2Instability - Static variable in class org.biojava.nbio.aaproperties.Constraints
- diag(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
- diag(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
- dialogAsk(String, String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
- DIFFERENT - org.biojava.nbio.structure.align.quaternary.QsRelation
-
None of the Subunits of one Structure have an equivalent in the other Structure.
- DIGIT - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
-
A digit
- disableCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
- discreteQuantizer - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
- DiscreteQuantizerInterface - Interface in org.biojava.nbio.survival.kaplanmeier.metadata
- DISEASE_ASSOC - Static variable in class org.biojava.nbio.phosphosite.Dataset
- DISJOINT_FROM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
- display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
- display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay
-
Display an AFPChain alignment
- display(AFPChain, Group[], Atom[], Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
- display(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
-
Display a MultipleAlignment with a JmolPanel.
- display(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
-
Displays a single structure in a cartoon representation with each symmetric repeat colored differently.
- DISPLAY_SORT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
- DisplayAFP - Class in org.biojava.nbio.structure.align.gui
-
A utility class for visualistion of structure alignments
- DisplayAFP() - Constructor for class org.biojava.nbio.structure.align.gui.DisplayAFP
- displayFull(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
-
Displays a multiple alignment of the whole structure transformations colored by blocks, corresponding to the symmetric protodomains.
- displayRepeats(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
-
Displays a multiple alignment of the symmetry repeats
- dissimilarityScore(MultipleSequenceAlignment<C, D>, SubstitutionMatrix<D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
-
The dissimilarity score is the additive inverse of the similarity score (sum of scores) between two aligned sequences using a substitution model (Substitution Matrix).
- DIST_MATRICES - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
- distance(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Return distance between this location and the other location.
- DISTANCE - org.biojava.nbio.phylo.TreeType
-
Distance Tree
- DISTANCE_INCREMENT - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
- DistanceBox<T> - Class in org.biojava.nbio.structure.symmetry.geometry
- DistanceBox(double) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
-
Creates a new instance of DistanceBox
- distanceIncrement - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
- DistanceMatrixCalculator - Class in org.biojava.nbio.phylo
-
The DistanceMatrixCalculator methods generate a
DistanceMatrix
from aMultipleSequenceAlignment
or other indirect distance infomation (RMSD). - distanceTree(BasicSymmetricalDistanceMatrix, TreeConstructorType) - Static method in class org.biojava.nbio.phylo.TreeConstructor
- DistanceTreeEvaluator - Class in org.biojava.nbio.phylo
-
Check the accuracy of a Distance Tree by least squares error (LSE) of the Tree branch lengths and the original Distance Matrix.
- divideInternally(SubunitClustererParameters) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
Analyze the internal symmetry of the SubunitCluster and divide its
Subunit
into the internal repeats (domains) if they are internally symmetric. - divideStructure(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
Method that converts the symmetric units of a structure into different structures, so that they can be individually visualized.
- dna - org.biojava.nbio.structure.chem.PolymerType
-
polydeoxyribonucleotide
- DNA_ONLY - Static variable in enum org.biojava.nbio.structure.chem.PolymerType
-
Convenience Set of polymer types classified as DNA.
- dna3PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType
- dna5PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType
- dnaCompounds(CompoundSet<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
- DNACompoundSet - Class in org.biojava.nbio.core.sequence.compound
- DNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.DNACompoundSet
- dnaLinking - org.biojava.nbio.structure.chem.ResidueType
- dnarna - org.biojava.nbio.structure.chem.PolymerType
-
polydeoxyribonucleotide/polyribonucleotide hybrid
- dnaRnaTranslator(DNAToRNATranslator) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
- DNASequence - Class in org.biojava.nbio.core.sequence
-
This is class should model the attributes associated with a DNA sequence
- DNASequence() - Constructor for class org.biojava.nbio.core.sequence.DNASequence
-
Shouldn't be used but makes it bean happy
- DNASequence(String) - Constructor for class org.biojava.nbio.core.sequence.DNASequence
-
String is king and create a sequence from DNA with default DNA compound set
- DNASequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence
-
Create a sequence from a string with user defined compound set
- DNASequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence
-
Create a sequence where the actual storage of the sequence data is somewhere else
- DNASequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence
-
Create a sequence from a ProxySequencereader and user defined compound set
- DNASequence.DNAType - Enum in org.biojava.nbio.core.sequence
-
The type of DNA sequence
- DNASequenceCreator - Class in org.biojava.nbio.core.sequence.io
-
A helper class that allows different ways to read a string and create a DNA sequence.
- DNASequenceCreator(CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.DNASequenceCreator
- DNAToRNATranslator - Class in org.biojava.nbio.core.sequence.transcription
-
Performs the first stage of transcription by going from DNA to RNA.
- DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound>, CompoundSet<NucleotideCompound>, CompoundSet<NucleotideCompound>, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
- doChainAfp(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
-
// Key function: chain (assembly) the AFPs // a AFP (k) is defined as (i, j, k), with i and j are staring points // AFP extension (eg.
- documentEnd() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener
-
end of parsing a new OBO file
- documentEnd() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
- documentStart() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener
-
starting to parse a new OBO file
- documentStart() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
- doesSequenceContainInvalidChar(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils
-
Checks if given sequence contains invalid characters.
- doInBackground() - Method in class org.biojava.nbio.structure.align.gui.StructureLoaderThread
- doIter0(int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
- doIter0(int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
- Domain - Class in org.biojava.nbio.structure.domain.pdp
- Domain - org.biojava.nbio.structure.scop.ScopCategory
- Domain() - Constructor for class org.biojava.nbio.structure.domain.pdp.Domain
- DomainCounter - org.biojava.nbio.structure.cath.CathCategory
- domainDescriptionFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
- domainListFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
- DomainProvider - Interface in org.biojava.nbio.structure.domain
-
Decomposes a structure from the PDB into representative domains
- DOMAINS_PATH - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
- domallFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
- doPOST(URL, String) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
-
Do a POST to a URL and return the response stream for further processing elsewhere.
- doPOST(URL, String, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
-
Do a POST to a URL and return the response stream for further processing elsewhere.
- doPrintConnections() - Method in class org.biojava.nbio.structure.io.FileConvert
-
Returns if the Connections should be added default is true;
- dot(double[], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
- dot(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseVector
-
Calculates the dot product of this vector a with b
- DOT_PLOT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
- DotPlotListener(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener
- DotPlotPanel - Class in org.biojava.nbio.structure.align.gui
-
Displays the dot plot trace for an alignment.
- DotPlotPanel(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.DotPlotPanel
- dotProduct(Quat4d, Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions
-
Compute the dot (inner) product of two quaternions.
- DOUBLE - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy
-
Represent every cluster with two symbols from the alphabet, this forces us to specify number of subunits for every subunit (e.g., AA1AB1AC1...).
- download() - Method in class org.biojava.nbio.phosphosite.Dataset
- DownloadChemCompProvider - Class in org.biojava.nbio.structure.chem
-
This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.
- DownloadChemCompProvider() - Constructor for class org.biojava.nbio.structure.chem.DownloadChemCompProvider
- DownloadChemCompProvider(String) - Constructor for class org.biojava.nbio.structure.chem.DownloadChemCompProvider
- downloadClaFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- downloadComFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- downloadDesFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- downloadDomainDescriptionFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
- downloadDomainListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
- downloadDomallFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
- downloadFile() - Static method in class org.biojava.nbio.structure.chem.AllChemCompProvider
-
Downloads the components.cif.gz file from the wwPDB site.
- downloadFile(URL, File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
-
Download the content provided at URL url and store the result to a local file, using a temp file to cache the content in case something goes wrong in download.
- downloadFile(URL, File) - Method in class org.biojava.nbio.phosphosite.Dataset
- downloadFileFromRemote(URL, File) - Method in class org.biojava.nbio.structure.cath.CathInstallation
- downloadFileFromRemote(URL, File) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- downloadHieFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- downloadNodeListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
- downloadStructure(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Downloads an MMCIF file from the PDB to the local path
- downstream(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Return the adjacent location of specified length directly downstream of this location.
- dpeptide - org.biojava.nbio.structure.chem.PolymerType
-
polypeptide(D)
- dPeptideAminoTerminus - org.biojava.nbio.structure.chem.ResidueType
- dPeptideCarboxyTerminus - org.biojava.nbio.structure.chem.ResidueType
- dPeptideLinking - org.biojava.nbio.structure.chem.ResidueType
- drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that draws symmetry or inertia axes for a structure.
- drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script that draws symmetry or inertia axes for a structure.
- drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
- drawBoxes(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
draw high scoring fragments that are used for the initial alignment seed selection
- drawDistances(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
For each element in matrix, draw it as a colored square or pixel.
- drawIdx(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
- drawPairs(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
draw alternative alignments
- drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that draws an invisible polyhedron around a structure.
- drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script that draws an invisible polyhedron around a structure.
- drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
- drawScale(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
draw the Scale
- drawSequence(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
draw the Amino acid sequence
- dSaccharide - org.biojava.nbio.structure.chem.ResidueType
- dSaccharide14and14linking - org.biojava.nbio.structure.chem.ResidueType
- dSaccharide14and16linking - org.biojava.nbio.structure.chem.ResidueType
- DSSP_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
-
Secondary strucuture parsed from a DSSP output file
- DSSPParser - Class in org.biojava.nbio.structure.secstruc
-
Class to parse a DSSP file (output of the DSSP program), that contains the secondary structure assignment of a structure.
- DSSPParser() - Constructor for class org.biojava.nbio.structure.secstruc.DSSPParser
- dump() - Method in class org.biojava.nbio.survival.cox.CoxInfo
- dump(ArrayList<SurvivalInfo>, PrintStream, String) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
-
For each analysis this allows outputing of the data used in the calculations to a printstream/file.
- duplicateCA2(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Utility method for working with circular permutations.
- duplicationHint - Variable in class org.biojava.nbio.structure.align.ce.CECPParameters
- duplicationHint - Variable in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
- Dy - org.biojava.nbio.structure.Element
- DYNAMIC - org.biojava.nbio.alignment.template.GapPenalty.Type
E
- E - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
- E - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
- E - Static variable in class org.biojava.nbio.aaproperties.Constraints
- ECOD - org.biojava.nbio.structure.align.client.StructureName.Source
- ECOD_RE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
- ECOD_URL - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
- EcodDatabase - Interface in org.biojava.nbio.structure.ecod
-
General API for interacting with ECOD.
- EcodDomain - Class in org.biojava.nbio.structure.ecod
-
An EcodDomain contains all the information of the ECOD database: id, classification groups (from higher to lower in the tree: X,H,T,F), PDB code, chain, residue ranges and status (manual or automatic classification).
- EcodDomain() - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
-
Default constructor with all null properties
- EcodDomain(Long, String, Boolean, Integer, Integer, Integer, Integer, String, String, String, String, String, String, String, String, Long, Set<String>) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
- EcodDomain(Long, String, Boolean, Integer, Integer, Integer, Integer, String, String, String, String, String, String, String, String, String, Long, Set<String>) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
- EcodDomain(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
- EcodDomain(EcodDomain) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
- EcodFactory - Class in org.biojava.nbio.structure.ecod
-
Controls global
EcodDatabases
being used. - EcodInstallation - Class in org.biojava.nbio.structure.ecod
-
Provides access to the Evolutionary Classification of Protein Domains (ECOD).
- EcodInstallation() - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation
- EcodInstallation(String, String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation
-
Use EcodFactory to create instances.
- EcodInstallation.EcodParser - Class in org.biojava.nbio.structure.ecod
- EcodParser(BufferedReader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
- EcodParser(File) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
- EcodParser(Reader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
- EcodParser(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
- edit(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
- edit(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.edits.Edit
- Edit<C extends Compound> - Interface in org.biojava.nbio.core.sequence.edits
-
Interface for carrying out edit operations on a Sequence.
- Edit.AbstractEdit<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits
-
Abstract class which defines all edit operations as a call to discover what 5' and 3' ends of an editing Sequence should be joined together with a target Sequence.
- Edit.Delete<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits
-
Implementation which allows for the deletion of bases from a Sequence
- Edit.Insert<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits
-
Edit implementation which allows us to insert a base at any position in a Sequence.
- Edit.Substitute<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits
-
Allows for the substitution of bases into an existing Sequence.
- ef - Variable in class org.biojava.nbio.survival.cox.CoxInfo
- Efron - org.biojava.nbio.survival.cox.CoxMethod
- eig() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Eigenvalue Decomposition
- EigenvalueDecomposition - Class in org.biojava.nbio.structure.jama
-
Eigenvalues and eigenvectors of a real matrix.
- EigenvalueDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.EigenvalueDecomposition
-
Check for symmetry, then construct the eigenvalue decomposition Structure to access D and V.
- ELECTRON_CRYSTALLOGRAPHY - org.biojava.nbio.structure.ExperimentalTechnique
- ELECTRON_MICROSCOPY - org.biojava.nbio.structure.ExperimentalTechnique
- Element - Class in org.biojava.nbio.aaproperties.xml
-
One way to model the elements
- Element - Enum in org.biojava.nbio.structure
-
Element is an enumeration of the elements of the periodic table.
- Element() - Constructor for class org.biojava.nbio.aaproperties.xml.Element
- Element(String, String, int, List<Isotope>, double) - Constructor for class org.biojava.nbio.aaproperties.xml.Element
- ElementTable - Class in org.biojava.nbio.aaproperties.xml
- ElementTable() - Constructor for class org.biojava.nbio.aaproperties.xml.ElementTable
- ElementTable(List<Element>) - Constructor for class org.biojava.nbio.aaproperties.xml.ElementTable
- ElementType - Enum in org.biojava.nbio.structure
-
ElementType is an enumeration of the types of elements found in the periodic table.
- EMAIL - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- EmblId - Class in org.biojava.nbio.core.sequence.io.embl
-
This class contains the processed data of embl file Primary accession number Sequence version number Topology: 'circular' or 'linear' Molecule type Data class Taxonomic division Sequence length
- EmblId(String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblId
- EmblReader - Class in org.biojava.nbio.core.sequence.io.embl
-
This class should process the data of embl file
- EmblReader() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblReader
- EmblRecord - Class in org.biojava.nbio.core.sequence.io.embl
-
this class contains the parsed data of embl file
- EmblRecord() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblRecord
- EmblReference - Class in org.biojava.nbio.core.sequence.io.embl
-
This class contains the processed data of embl file that contains the referenceNumber, referenceComment, referencePosition referenceCrossReference, referenceGroup, referenceAuthor referenceTitle, referenceLocation
- EmblReference() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblReference
- EMPTY - Static variable in interface org.biojava.nbio.core.sequence.location.template.Location
-
Basic location which is set to the minimum and maximum bounds of
Integer
. - EMPTY_ANNOTATION - Static variable in interface org.biojava.nbio.ontology.utils.Annotation
-
A really useful empty and immutable annotation object.
- ENA - org.biojava.nbio.core.sequence.DataSource
- enableCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
- encodeFileURL(String) - Method in class org.biojava.nbio.survival.cox.CoxVariables
- end() - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Get the ending index.
- END_SEQUENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
- endIndex - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair
- ENDOFFILE - Static variable in class org.biojava.nbio.core.exceptions.Messages
- ENDS - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
- endsAfter(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Check if this location ends after other location ends.
- endsBefore(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Check if this location ends before other location ends.
- ENDSEND - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
- ensureClaInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- ensureComInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- ensureDesInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- ensureDomainDescriptionInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
- ensureDomainListInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
- ensureDomainsFileInstalled() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
Blocks until ECOD domains file has been downloaded and parsed.
- ensureDomallInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
- ensureHieInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- ensureNodeListInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
- entity_poly_type - Variable in enum org.biojava.nbio.structure.chem.PolymerType
- EntityFinder - Class in org.biojava.nbio.structure.io
-
Heuristical finding of Entities (called Compounds in legacy PDB format) in a given Structure.
- EntityFinder() - Constructor for class org.biojava.nbio.structure.io.EntityFinder
- EntityInfo - Class in org.biojava.nbio.structure
-
An object to contain the info from the PDB header for a Molecule.
- EntityInfo() - Constructor for class org.biojava.nbio.structure.EntityInfo
- EntityInfo(EntityInfo) - Constructor for class org.biojava.nbio.structure.EntityInfo
-
Constructs a new EntityInfo copying all data from the given one but not setting the Chains
- EntityType - Enum in org.biojava.nbio.structure
- entityTypeFromString(String) - Static method in enum org.biojava.nbio.structure.EntityType
-
Creates a new EntityType from a String value.
- ENTREZ_QUERY - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- entrySet() - Method in class org.biojava.nbio.core.util.SoftHashMap
- entrySet() - Method in class org.biojava.nbio.ontology.utils.SmallMap
- entrySet() - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
- entrySet() - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
-
Always returns the empty set
- entrySet() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
- EQR_COLOR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
- equal(boolean, boolean) - Static method in class org.biojava.nbio.core.util.Equals
- equal(int, int) - Static method in class org.biojava.nbio.core.util.Equals
- equal(long, long) - Static method in class org.biojava.nbio.core.util.Equals
- equal(Object, Object) - Static method in class org.biojava.nbio.core.util.Equals
-
Does not compare class types.
- equalLengthSequences(ProteinSequence[]) - Static method in class org.biojava.nbio.core.util.SequenceTools
-
A method to check whether an array of sequences contains at least two sequences having an equal length.
- equals(Object) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
- equals(Object) - Method in class org.biojava.nbio.core.search.io.Hit
-
Implements conceptual comparisons of search results.
- equals(Object) - Method in class org.biojava.nbio.core.search.io.Hsp
-
Experimental.
- equals(Object) - Method in class org.biojava.nbio.core.search.io.Result
-
Experimental.
- equals(Object) - Method in class org.biojava.nbio.core.sequence.AccessionID
- equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
- equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
- equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
- equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
- equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
- equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
- equals(Object) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
- equals(Object) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
- equals(Object) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
- equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
- equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
- equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
- equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
- equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
- equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
- equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
- equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
- equals(Object) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
- equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
- equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
- equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
- equals(Object) - Method in class org.biojava.nbio.data.sequence.FastaSequence
- equals(Object) - Method in class org.biojava.nbio.genome.parsers.gff.Location
- equals(Object) - Method in class org.biojava.nbio.ontology.Term.Impl
- equals(Object) - Method in interface org.biojava.nbio.ontology.Triple
-
Check to see if an object is an equivalent Triple.
- equals(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl
-
Two triples are equal if all their fields are identical.
- equals(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
- equals(Object) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
- equals(Object) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
- equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureAtom
- equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
- equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
- equals(Object) - Method in class org.biojava.nbio.ronn.Jronn.Range
- equals(Object) - Method in class org.biojava.nbio.ronn.ModelLoader.Model
- equals(Object) - Method in class org.biojava.nbio.structure.align.client.PdbPair
- equals(Object) - Method in class org.biojava.nbio.structure.align.client.StructureName
- equals(Object) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
A week equality metric.
- equals(Object) - Method in class org.biojava.nbio.structure.Author
- equals(Object) - Method in class org.biojava.nbio.structure.chem.ChemComp
- equals(Object) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor
- equals(Object) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
- equals(Object) - Method in class org.biojava.nbio.structure.contact.Pair
- equals(Object) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
- equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
- equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
- equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
- equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
- equals(Object) - Method in class org.biojava.nbio.structure.io.SSBondImpl
- equals(Object) - Method in class org.biojava.nbio.structure.PdbId
- equals(Object) - Method in class org.biojava.nbio.structure.ResidueNumber
- equals(Object) - Method in class org.biojava.nbio.structure.ResidueRange
- equals(Object) - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
- equals(Object) - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
Compares the fields sunID, category, classificationId, and name for equality
- equals(Object) - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
- equals(Object) - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
- equals(Object) - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
- equals(Object) - Method in class org.biojava.nbio.structure.Site
- equals(Object) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
- equals(Object) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
- equals(Object) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
- equals(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
- equals(GeneName) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
- equals(PDBHeader) - Method in class org.biojava.nbio.structure.PDBHeader
-
Compare two PDBHeader objects
- Equals - Class in org.biojava.nbio.core.util
-
A set of helper methods which return true if the two parameters are equal to each other.
- Equals() - Constructor for class org.biojava.nbio.core.util.Equals
- equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
- equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
- equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
- equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
- equalsIgnoreCase(Compound) - Method in interface org.biojava.nbio.core.sequence.template.Compound
- equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
- equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
- equalsPositional(Object) - Method in class org.biojava.nbio.structure.ResidueNumber
-
Check if the seqNum and insertion code are equivalent, ignoring the chain
- equalsToIgnoreEndline(String, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
-
Compares two strings in a case-sensitive manner for equality, line by line, ignoring any difference of end line delimiters contained within the 2 Strings.
- equalsToXml(String, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
-
This method is not implemented or used, never returns true and should probably be removed.
- EQUIVALENCE - Static variable in class org.biojava.nbio.ontology.OntoTools
- EQUIVALENT - org.biojava.nbio.structure.align.quaternary.QsRelation
-
All the Subunits of one Structure have an equivalent in the other Structure.
- EQUIVALENT - Static variable in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
flag if this position is equivalent
- EQUIVALENT_VERSIONS - Static variable in class org.biojava.nbio.structure.scop.BerkeleyScopInstallation
-
A map from SCOP version names which the Berkeley server offers as a download to an array of equivalent deprecated SCOP version names.
- Er - org.biojava.nbio.structure.Element
- error(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
- errorEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
- errorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Return the error probabilities from the specified FASTQ formatted sequence.
- errorProbabilities(Fastq, double[]) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.
- errorProbability(char) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
-
Convert the specified quality in ASCII format to an error probability.
- errorProbability(int) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
-
Calculate the error probability given the specified quality score.
- Es - org.biojava.nbio.structure.Element
- escape(String, boolean) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
- escapeChars - Static variable in class org.biojava.nbio.ontology.obo.OboFileParser
- Eu - org.biojava.nbio.structure.Element
- eval(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
- evalString(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
Execute a command String in the current Jmol panel.
- evalString(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
- evalString(String) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
- evaluate(Phylogeny, DistanceMatrix) - Static method in class org.biojava.nbio.phylo.DistanceTreeEvaluator
-
Evaluate the goodness of fit of a given tree to the original distance matrix.
- EXACT_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
- EXACT_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym
- execute(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative
-
This method uses iteratively CeSymm to calculate all symmetries in the input array of atoms and organize them in a multiple alignment of the repeats.
- executeCmd(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
- ExonComparator - Class in org.biojava.nbio.core.sequence
-
Sort Exon where it is a little confusing if exons should always be ordered left to right where a negative stranded gene should go the other direction.
- ExonComparator() - Constructor for class org.biojava.nbio.core.sequence.ExonComparator
- ExonSequence - Class in org.biojava.nbio.core.sequence
-
A gene contains a collection of Exon sequences
- ExonSequence(GeneSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.ExonSequence
-
Need a parent gene sequence and the bioBegin and bioEnd.
- expandNcsOps(Structure, Map<String, String>, Map<String, Matrix4d>) - Static method in class org.biojava.nbio.structure.xtal.CrystalBuilder
-
Apply the NCS operators in the given Structure adding new chains as needed.
- expandUserHome(String) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
-
Expands ~ in paths to the user's home directory.
- EXPECT - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- EXPECT_HIGH - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
- EXPECT_LOW - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
- ExperimentalTechnique - Enum in org.biojava.nbio.structure
-
An enum to represent the experimental technique of a PDB structure
- EXPERT - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
- ExpressionFigure - Class in org.biojava.nbio.survival.kaplanmeier.figure
- ExpressionFigure() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
- extended - org.biojava.nbio.structure.secstruc.SecStrucType
- extendFragments(Atom[], Atom[], JointFragments[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
- extendFragments(Atom[], Atom[], JointFragments, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
- extendHelix(int) - Method in class org.biojava.nbio.structure.symmetry.core.HelixExtender
- ExtinctionCoefficient_False - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
- ExtinctionCoefficient_True - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
- extractAFPChains(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
- extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
- extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
- extractSubunits(Structure, int, double, int) - Static method in class org.biojava.nbio.structure.cluster.SubunitExtractor
-
Extract the information of each protein Chain in a Structure and converts them into a List of Subunit.
F
- f(Double) - Method in class org.biojava.nbio.survival.cox.StrataInfo
- F - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
- F - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
- F - org.biojava.nbio.structure.Element
- F - Static variable in class org.biojava.nbio.aaproperties.Constraints
- F_UNCLASSIFIED - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
-
String for unclassified F-groups
- f1Dot2(float) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
- Family - org.biojava.nbio.structure.scop.ScopCategory
- FASTA - org.biojava.nbio.core.alignment.template.Profile.StringFormat
- FASTA - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
- FASTA_FORMAT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
- FastaAFPChainConverter - Class in org.biojava.nbio.structure.io
-
A collection of static utilities to convert between
AFPChains
andFastaSequences
. - FastaAFPChainConverter() - Constructor for class org.biojava.nbio.structure.io.FastaAFPChainConverter
- fastaFileToAfpChain(File, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Reads the file
fastaFile
, expecting exactly two sequences which give a pairwise alignment. - FastaGeneWriter - Class in org.biojava.nbio.core.sequence.io
-
A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.
- FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.FastaGeneWriter
- FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean, int) - Constructor for class org.biojava.nbio.core.sequence.io.FastaGeneWriter
- FastaHeaderFormatInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
- FastaReader<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta files
- FastaReader(File, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaReader
-
If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
- FastaReader(InputStream, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaReader
-
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.
- FastaReaderHelper - Class in org.biojava.nbio.core.sequence.io
- FastaReaderHelper() - Constructor for class org.biojava.nbio.core.sequence.io.FastaReaderHelper
- FastaSequence - Class in org.biojava.nbio.data.sequence
-
A FASTA formatted sequence.
- FastaSequence(String, String) - Constructor for class org.biojava.nbio.data.sequence.FastaSequence
-
Upon construction the any whitespace characters are removed from the sequence
- FastaSequenceParser - Class in org.biojava.nbio.core.sequence.io
-
Used to parse a stream of a fasta file to get the sequence
- FastaSequenceParser() - Constructor for class org.biojava.nbio.core.sequence.io.FastaSequenceParser
- fastaStringToAfpChain(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Returns an AFPChain corresponding to the alignment between
structure1
andstructure2
, which is given by the gapped protein sequencessequence1
andsequence2
. - FastaStructureParser - Class in org.biojava.nbio.structure.io
-
Reads a protein sequence from a fasta file and attempts to match it to a 3D structure.
- FastaStructureParser(File, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
- FastaStructureParser(InputStream, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
- FastaStructureParser(FastaReader<ProteinSequence, AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
- fastaToAfpChain(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
TODO Write comment
- fastaToAfpChain(Map<String, ProteinSequence>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment.
- fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>, AminoAcidCompound>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Provided only for convenience.
- fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Returns an AFPChain corresponding to the alignment between
structure1
andstructure2
, which is given by the gapped protein sequencessequence1
andsequence2
. - FastaWriter<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
The FastaWriter writes a collection of sequences to an outputStream.
- FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriter
-
Use default line length of 60
- FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriter
-
Set custom lineLength
- FastaWriterHelper - Class in org.biojava.nbio.core.sequence.io
-
The class that should be used to write out fasta file of a sequence collection
- FastaWriterHelper() - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriterHelper
- fastq(Fastq) - Method in interface org.biojava.nbio.genome.io.fastq.StreamListener
-
Notify this listener of a FASTQ formatted sequence.
- Fastq - Class in org.biojava.nbio.genome.io.fastq
-
FASTQ formatted sequence.
- FASTQ_ILLUMINA - org.biojava.nbio.genome.io.fastq.FastqVariant
-
Illumina FASTQ sequence format variant.
- FASTQ_SANGER - org.biojava.nbio.genome.io.fastq.FastqVariant
-
Sanger FASTQ sequence format variant.
- FASTQ_SOLEXA - org.biojava.nbio.genome.io.fastq.FastqVariant
-
Solexa FASTQ sequence format variant.
- FastqBuilder - Class in org.biojava.nbio.genome.io.fastq
-
Fluent builder API for creating FASTQ formatted sequences.
- FastqBuilder() - Constructor for class org.biojava.nbio.genome.io.fastq.FastqBuilder
-
Create a new FASTQ formatted sequence builder.
- FastqBuilder(Fastq) - Constructor for class org.biojava.nbio.genome.io.fastq.FastqBuilder
-
Create a new FASTQ formatted sequence builder configured from the specified FASTQ formatted sequence.
- FastqReader - Interface in org.biojava.nbio.genome.io.fastq
-
Reader for FASTQ formatted sequences.
- FastqTools - Class in org.biojava.nbio.genome.io.fastq
-
Utility methods for FASTQ formatted sequences.
- FastqVariant - Enum in org.biojava.nbio.genome.io.fastq
-
FASTQ sequence format variant.
- FastqWriter - Interface in org.biojava.nbio.genome.io.fastq
-
Writer for FASTQ formatted sequences.
- fatal(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
- fatalEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
- FatCat - Class in org.biojava.nbio.structure.align.fatcat
- FatCat() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCat
- FATCAT_BLOCK - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
- FATCAT_TEXT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
- FatCatAligner - Class in org.biojava.nbio.structure.align.fatcat.calc
-
A class that does calculations on an AFPChain
- FatCatAligner() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
- FatCatFlexible - Class in org.biojava.nbio.structure.align.fatcat
- FatCatFlexible() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
- FatCatParameters - Class in org.biojava.nbio.structure.align.fatcat.calc
- FatCatParameters() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
- FatCatRigid - Class in org.biojava.nbio.structure.align.fatcat
- FatCatRigid() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatRigid
- FatCatStartupParams() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
- FatCatUserArgumentProcessor - Class in org.biojava.nbio.structure.align.fatcat
- FatCatUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
- FatCatUserArgumentProcessor.FatCatStartupParams - Class in org.biojava.nbio.structure.align.fatcat
- FCAlignHelper - Class in org.biojava.nbio.structure.align.fatcat.calc
- FCAlignHelper(double[][], int, int, double, double) - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper
-
do an alignment given the provided matrix sij0
- fDot2(double) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
- Fe - org.biojava.nbio.structure.Element
- Feature - Class in org.biojava.nbio.genome.parsers.gff
-
A Feature corresponds to a single row in a GFF file.
- Feature(String, String, String, Location, Double, int, String) - Constructor for class org.biojava.nbio.genome.parsers.gff.Feature
-
Construct a new Feature from raw data (usually a GFF row).
- Feature(Feature) - Constructor for class org.biojava.nbio.genome.parsers.gff.Feature
-
Make a copy of the specified feature.
- FEATURE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
- FeatureDbReferenceInfo<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features
-
It is
DBReferenceInfo
which implementsFeatureInterface
. - FeatureDbReferenceInfo(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
- featureGlobalEnd - Variable in class org.biojava.nbio.core.sequence.location.InsdcParser
-
these variables are used to compute the global start and end of complex features
- featureGlobalStart - Variable in class org.biojava.nbio.core.sequence.location.InsdcParser
-
these variables are used to compute the global start and end of complex features
- FeatureHelper - Class in org.biojava.nbio.genome.parsers.gff
- FeatureHelper() - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureHelper
- FeatureI - Interface in org.biojava.nbio.genome.parsers.gff
-
A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.
- FeatureInterface<S extends AbstractSequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.features
-
Interface class to handle describing arbitrary features.
- FeatureList - Class in org.biojava.nbio.genome.parsers.gff
-
A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.
- FeatureList() - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Construct an empty list.
- FeatureList(Collection<FeatureI>) - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Construct a new list containing the same features as the specified list.
- FeatureRetriever<C extends Compound> - Interface in org.biojava.nbio.core.sequence.features
-
If a SequenceProxyReader implements this interface then that external source has a list features
- FeaturesKeyWordInterface - Interface in org.biojava.nbio.core.sequence.features
-
Models the keywords that are annotated for a protein sequence at Uniprot.
- FETCH_CURRENT - org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
-
Fetch the most recent version of the PDB entry.
- FETCH_FILES - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
-
Fetch missing files from the server.
- FETCH_IF_OUTDATED - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
-
Fetch missing files from the server, also fetch if file present but older than the server file.
- FETCH_OBSOLETE - org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
-
Fetch the obsolete entry from the PDB archives.
- FETCH_REMEDIATED - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
-
Fetch missing files from the server.
- fh2 - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
- FIBER_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique
- figureLineInfoLowerPercentX - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
- figureLineInfoLowerPercentY - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
- FILE - org.biojava.nbio.structure.align.client.StructureName.Source
- FileConvert - Class in org.biojava.nbio.structure.io
-
Methods to convert a structure object into different file formats.
- FileConvert(Structure) - Constructor for class org.biojava.nbio.structure.io.FileConvert
-
Constructs a FileConvert object.
- FileDownloadUtils - Class in org.biojava.nbio.core.util
- FileDownloadUtils() - Constructor for class org.biojava.nbio.core.util.FileDownloadUtils
- FileParsingParameters - Class in org.biojava.nbio.structure.io
-
A class that configures parameters that can be sent to the PDB file parsers
FileParsingParameters.setParseCAOnly(boolean)
- parse only the Atom records for C-alpha atomsFileParsingParameters.setParseSecStruc(boolean)
- a flag if the secondary structure information from the PDB file (author's assignment) should be parsed. - FileParsingParameters() - Constructor for class org.biojava.nbio.structure.io.FileParsingParameters
- FileProxyDNASequenceCreator - Class in org.biojava.nbio.core.sequence.io
-
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
- FileProxyDNASequenceCreator(File, CompoundSet<NucleotideCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator
-
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
- FileProxyProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io
-
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
- FileProxyProteinSequenceCreator(File, CompoundSet<AminoAcidCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator
-
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
- FileProxyRNASequenceCreator - Class in org.biojava.nbio.core.sequence.io
-
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
- FileProxyRNASequenceCreator(File, CompoundSet<NucleotideCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator
-
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
- FILESPLIT - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
- FILESPLIT - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
- fillAlignedAtomArrays(AFPChain, Atom[], Atom[], Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Fill the aligned Atom arrays with the equivalent residues in the afpChain.
- FILTER - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- filterByCathCode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return list of CATH descriptions whose CATH codes (e.g. 1.4.6.10) start with the query.
- filterByCathCode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
- filterByClassificationId(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Get all scop descriptions that start with a classification ID, e.g. b.1.18
- filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- filterByDescription(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return list of CATH descriptions whose descriptions (name field) starts with the query.
- filterByDescription(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
- filterByDescription(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Get all scop descriptions that start with a certain name. e.g.
- filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- filterByDomainName(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
search through SCOP and filter based on domain name
- filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
- filterByHierarchy(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase
-
Get a list of domains within a particular level of the hierarchy
- filterByHierarchy(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
Get a list of domains within a particular level of the hierarchy
- filterByNodeName(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return list of CATH domains whose node name (e.g.
- filterByNodeName(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
- filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
-
Takes as input an AFPChain where ca2 has been artificially duplicated.
- filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[], CECPParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
- filterLigands(List<Group>) - Static method in class org.biojava.nbio.structure.StructureTools
-
Removes all polymeric and solvent groups from a list of groups
- finalizeStructure() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
- findAtomLinkages(Group, Group, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
Find linkages between two groups within tolerance of bond length, from potential atoms.
- findAtomLinkages(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
Find linkages between two groups within tolerance of bond length, from potential atoms.
- findGroup(String, String) - Method in interface org.biojava.nbio.structure.Structure
-
Request a particular group from a structure.
- findGroup(String, String) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a particular group from a structure.
- findGroup(String, String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Request a particular group from a structure.
- findGroup(String, String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a particular group from a structure.
- findLinkage(Group, Group, String, String, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
Find a linkage between two groups within tolerance of bond length.
- findNearestAtomLinkage(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
Find a linkage between two groups within tolerance of bond length, from potential atoms.
- findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method performs a search for base pairs in the structure.
- findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This is an implementation for finding non-canonical base pairs when there may be missing or overhanging bases.
- findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
-
This is an alternative implementation of findPair() that looks for anything that would fit the criteria for a base-pair, useful for the context of tertiary structure of RNA.
- findPolyEntities(List<List<Chain>>) - Static method in class org.biojava.nbio.structure.io.EntityFinder
-
Utility method that employs some heuristics to find the
EntityInfo
s for the polymeric chains given in constructor. - findUnescaped(String, char) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
- findUnescaped(String, char, int, int) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
- findUnescaped(String, char, int, int, boolean) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
- finish() - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
- finish() - Method in interface org.biojava.nbio.structure.io.cif.CifFileConsumer
-
Ultimate setup which can include steps which require several categories to be available and integrate them into the final container.
- finish() - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- finish() - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl
- finish(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
- FIRST - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
- first_cut - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
- FIRST_QUERY_NUM - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
- FIRST25 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
- FIRST50 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
- FIRST75 - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
- fixMicroheterogenity(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
This sets all microheterogeneous groups (previously alternate location groups) as separate groups.
- flagLoading(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache
- flagLoadingFinished(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache
- FlatFileCache - Class in org.biojava.nbio.core.util
-
Provides a cache for storing multiple small files in memory.
- FlatQueryAnchored - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
- FlatQueryAnchoredNoIdentities - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
- flemingHarrington - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
- flipAlignment(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
-
Takes an XML representation of the alignment and flips the positions of name1 and name2
- flipChain(AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainFlipper
-
Flip the position of name1 and name2 (as well as all underlying data) in an AFPChain.
- floor(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
-
Return the largest key in the table <= k.
- FLUORESCENCE_TRANSFER - org.biojava.nbio.structure.ExperimentalTechnique
- flush() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
- flushCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
- Fm - org.biojava.nbio.structure.Element
- fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxCoefficient
- fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxInfo
- fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxVariables
- fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
- fmtpl(String, int) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
Pad left a string with spaces
- fmtpr(String, int) - Method in class org.biojava.nbio.survival.cox.CoxInfo
- Fold - org.biojava.nbio.structure.scop.ScopCategory
- FORCE_DOWNLOAD - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
-
For every file, force downloading from the server
- ForesterWrapper - Class in org.biojava.nbio.phylo
-
This class contains wrapper methods for communication between BioJava and forester (e.g, Data Structure conversion).
- FORMAT_ENTREZ_QUERY - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
- FORMAT_OBJECT - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
- FORMAT_PARAM - Static va