Index

A

A - Enum constant in enum class org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

 

A - Enum constant in enum class org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

 

A - Enum constant in enum class org.forester.evoinference.matrix.character.CharacterStateMatrix.NucleotideStates

 

A - Static variable in class org.biojava.nbio.aaproperties.Constraints

 

aa - Class in org.forester.applications

 

aa() - Constructor for class org.forester.applications.aa

 

AA - Enum constant in enum class org.forester.sequence.MolecularSequence.TYPE

 

AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil

Valid Amino acids

AA_REGEXP - Static variable in interface org.forester.sequence.MolecularSequence

 

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

 

aaa - Class in org.forester.applications

 

aaa() - Constructor for class org.forester.applications.aaa

 

AAindexFactory - Class in org.biojava.nbio.core.alignment.matrices

Factory class to get Providers for substitution matrices the are provided by the AAINDEX database.

AAindexFactory() - Constructor for class org.biojava.nbio.core.alignment.matrices.AAindexFactory

 

AAIndexFileParser - Class in org.biojava.nbio.core.alignment.matrices

 

AAIndexFileParser() - Constructor for class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser

 

AAIndexProvider - Interface in org.biojava.nbio.core.alignment.matrices

 

aaScore(char, char) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay

 

AboutDialog - Class in org.biojava.nbio.structure.align.gui

 

AboutDialog() - Constructor for class org.biojava.nbio.structure.align.gui.AboutDialog

 

abs(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix

 

abs(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix

 

ABS_MAX_COUNTS_DIFFERENCE - Enum constant in enum class org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField

 

ABSENT - Enum constant in enum class org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates

 

absolutePercentialRNAsuiteness - Variable in class org.biojava.nbio.structure.validation.Entry

 

absolutePercentileClashscore - Variable in class org.biojava.nbio.structure.validation.Entry

 

absolutePercentileDCCRfree - Variable in class org.biojava.nbio.structure.validation.Entry

 

absolutePercentilePercentRamaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry

 

absolutePercentilePercentRotaOutliers - Variable in class org.biojava.nbio.structure.validation.Entry

 

absolutePercentilePercentRSRZOutliers - Variable in class org.biojava.nbio.structure.validation.Entry

 

Absorbance_False - Enum constant in enum class org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

 

Absorbance_True - Enum constant in enum class 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.

AbstractBean - Class in org.biojava.nbio.structure.io.mmcif.model

a generic class that implements the toString method for a bean

AbstractBean() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AbstractBean

 

AbstractCompound - Class in org.biojava.nbio.core.sequence.template

The details of a Compound

AbstractCompound() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound

 

AbstractCompound(String) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound

 

AbstractCompoundSet<C extends Compound> - Class in org.biojava.nbio.core.sequence.template

 

AbstractCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

 

AbstractCompoundTranslator<F extends Compound,T extends Compound> - Class in org.biojava.nbio.core.sequence.template

 

AbstractCompoundTranslator(SequenceCreatorInterface<T>, CompoundSet<F>, CompoundSet<T>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

 

AbstractEdit(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

 

AbstractEdit(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

 

AbstractFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features

A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that feature

AbstractFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.AbstractFeature

A feature has a type and a source

AbstractLocation - Class in org.biojava.nbio.core.sequence.location.template

Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand

AbstractLocation() - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation

 

AbstractLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation

Default constructor

AbstractLocation(Point, Point, Strand, boolean, boolean, AccessionID, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation

Default constructor

AbstractMatrixAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template

Implements common code for an Aligner which builds a score matrix during computation.

AbstractMatrixAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner

Before running an alignment, data must be sent in via calls to AbstractMatrixAligner.setGapPenalty(GapPenalty) and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).

AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner

Prepares for an alignment.

AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner

Prepares for an alignment.

AbstractNucleotideCompoundSet<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.template

 

AbstractNucleotideCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet

 

AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template

Implements common code for an Aligner for a pair of Sequences.

AbstractPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner

Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).

AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner

Prepares for a pairwise global sequence alignment.

AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner

Prepares for a pairwise sequence alignment.

AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template

Implements common code for an Aligner for a pair of Profiles.

AbstractProfileProfileAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner

Before running a profile-profile alignment, data must be sent in via calls to AbstractProfileProfileAligner.setQuery(Profile), AbstractProfileProfileAligner.setTarget(Profile), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).

AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner

Prepares for a profile-profile alignment run concurrently.

AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner

Prepares for a profile-profile alignment run concurrently.

AbstractProfileProfileAligner(Profile<S, C>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner

Prepares for a profile-profile alignment run concurrently.

AbstractProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner

Prepares for a profile-profile alignment.

AbstractRenderer - Class in org.forester.development

 

AbstractRenderer() - Constructor for class org.forester.development.AbstractRenderer

 

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 Class in org.biojava.nbio.core.sequence.template

 

AbstractStructureAlignment - Class in org.biojava.nbio.structure.align

 

AbstractStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.AbstractStructureAlignment

 

AbstractTerm - Class in org.biojava.nbio.ontology

Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.

AbstractTerm() - Constructor for class org.biojava.nbio.ontology.AbstractTerm

 

AbstractUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce

Base class for a new structure alignment CLI.

AbstractUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

 

Ac - Enum constant in enum class org.biojava.nbio.structure.Element

 

Accent - Enum constant in enum class org.jcolorbrewer.ColorBrewer

 

AccesionedLocation - Interface in org.biojava.nbio.core.sequence.location.template

A location which is bound to an AccessionID.

Accession - Class in org.forester.phylogeny.data

 

Accession(String) - Constructor for class org.forester.phylogeny.data.Accession

 

Accession(String, String) - Constructor for class org.forester.phylogeny.data.Accession

 

Accession(String, String, String) - Constructor for class org.forester.phylogeny.data.Accession

 

Accession(String, Accession.Source) - Constructor for class org.forester.phylogeny.data.Accession

 

ACCESSION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

ACCESSION_COMMENT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

ACCESSION_SOURCE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

ACCESSION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

 

Accession.Source - Enum Class in org.forester.phylogeny.data

 

Accessioned - Interface in org.biojava.nbio.core.sequence.template

Indicates an entity is accessioned

AccessionID - Class in org.biojava.nbio.core.sequence

Used in Sequences as the unique indentifier.

AccessionID() - Constructor for class org.biojava.nbio.core.sequence.AccessionID

 

AccessionID(String) - Constructor for class org.biojava.nbio.core.sequence.AccessionID

 

AccessionID(String, DataSource) - Constructor for class org.biojava.nbio.core.sequence.AccessionID

 

AccessionID(String, DataSource, Integer, String) - Constructor for class org.biojava.nbio.core.sequence.AccessionID

 

AccessionParser - Class in org.forester.io.parsers.phyloxml.data

 

acen - Enum constant in enum class org.biojava.nbio.genome.parsers.cytoband.StainType

 

acentricOutliers - Variable in class org.biojava.nbio.structure.validation.Entry

 

ACETYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset

 

ACTINOID - Enum constant in enum class 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.DBResultTable

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener

Invoked when the user presses the stop button.

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel

The user selected one of the Combo boxes...

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.JPrintPanel

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyAlignmentLoadListener

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyDistMaxListener

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyExportListener

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyOpenPdbFileListener

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MySaveFileListener

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.ShowPDBIDListener

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.gui.RasmolCommandListener

Deprecated.

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel

 

actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryListener

 

actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.ArchaeopteryxE

 

actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.FontChooser

 

actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.MainFrame

Action performed.

actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.MainFrameApplication

 

actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.tools.PhyloInferenceDialog

 

actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.TreePanel

 

actionPerformed(ActionEvent) - Method in class org.forester.msa_compactor.Chart

 

actionPerformed(ActionEvent) - Method in class org.jcolorbrewer.ui.DivergingColorPalettePanel

 

actionPerformed(ActionEvent) - Method in class org.jcolorbrewer.ui.QualitativeColorPalettePanel

 

actionPerformed(ActionEvent) - Method in class org.jcolorbrewer.ui.SequentialColorPalettePanel

 

activate() - Method in class org.forester.archaeopteryx.tools.PhyloInferenceDialog

 

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

 

addAlignmentProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable

 

addAlignmentProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.FarmJob

 

addAligPosListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener

 

addAligPosListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener

 

addAll(Collection<AtomContact>) - Method in class org.biojava.nbio.structure.contact.AtomContactSet

 

addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains, SortedSet<BinaryDomainCombination>) - Static method in class org.forester.surfacing.SurfacingUtil

 

addAllDomainIdsToSet(GenomeWideCombinableDomains, SortedSet<String>) - Static method in class org.forester.surfacing.SurfacingUtil

 

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

 

addAnnotation(Annotation) - Method in class org.forester.phylogeny.data.Sequence

 

addAsChild(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny

Adds this Phylogeny to the list of child nodes of PhylogenyNode parent and sets the parent of this to parent.

addAsChild(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode

Adds PhylogenyNode n to the list of child nodes and sets the _parent of n to this.

addASPFamPredicted(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addAsSibling(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny

 

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 getContacts 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 getContacts 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

addAxis(Matrix4d, List<List<Integer>>, List<Integer>, Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Deprecated.

Use SymmetryAxes.addAxis(Matrix4d, int, SymmetryType) instead. Repeats and Superposition are now inferred automatically.

addBond(Bond) - Method in interface org.biojava.nbio.structure.Atom

Add a bond

addBond(Bond) - Method in class org.biojava.nbio.structure.AtomImpl

 

addBridge(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

Adds a Bridge to the residue.

addCDS(AccessionID, int, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

Add a Coding Sequence region with phase to the transcript sequence

addCell(String, String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet

Add data to a cell

addChain(Chain) - Method in class org.biojava.nbio.structure.Compound

Add new Chain to this Compound

addChain(Chain) - Method in interface org.biojava.nbio.structure.Structure

Add a new chain.

addChain(Chain) - Method in class org.biojava.nbio.structure.StructureImpl

Add a new chain.

addChain(Chain, int) - Method in interface org.biojava.nbio.structure.Structure

Add a new chain, if several models are available.

addChain(Chain, int) - Method in class org.biojava.nbio.structure.StructureImpl

Add a new chain, if several models are available.

addCharges(Structure) - Static method in class org.biojava.nbio.structure.io.ChargeAdder

Function to add the charges to a given structure.

addChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary

add a new component to the dictionary

addChildElement(XmlElement) - Method in class org.forester.io.parsers.phyloxml.XmlElement

 

addChildElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper

 

addColumn(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet

 

addColumns(ArrayList<String>, String) - Method in class org.biojava.nbio.survival.data.WorkSheet

Add columns to worksheet and set default value

addCombinableDomain(String) - Method in class org.forester.surfacing.BasicCombinableDomains

 

addCombinableDomain(String) - Method in interface org.forester.surfacing.CombinableDomains

To add a new combinable domain.

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

 

addCompound(Compound) - Method in interface org.biojava.nbio.structure.Structure

Add a Compound to this Structure

addCompound(Compound) - Method in class org.biojava.nbio.structure.StructureImpl

Add a Compound to this Structure

addCompounds(F, T...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

 

addCompoundsToList(List<T>, List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

 

addCompoundToLists(List<List<T>>, T) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

 

addConfidence(Confidence) - Method in class org.forester.phylogeny.data.BranchData

 

addContinuousVariable(String, Double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

 

addCrossReference(Accession) - Method in class org.forester.phylogeny.data.Sequence

 

addDBReference(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

 

addDistribution(Distribution) - Method in class org.forester.phylogeny.data.NodeData

 

addDomain(ProteinDomain) - Method in class org.forester.phylogeny.data.DomainArchitecture

 

addDomainIdToIgnore(String) - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

 

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.

addGainedCharacter(String) - Method in class org.forester.phylogeny.data.BinaryCharacters

 

addGene(AccessionID, int, int, Strand) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence

Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0.

addGeneIDGFF2GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper

Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequences

addGeneMarkGTFGeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper

 

addGFBuildMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

 

addGFFalseDiscoveryRate(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

 

addGFNewHampshire(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

 

addGFTreeID(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

 

addGlimmerGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper

 

addGmodGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper

Load GFF3 file using mRNA as the gene feature as not all GFF3 files are complete

addGroup(Group) - Method in interface org.biojava.nbio.structure.Chain

add a group to the list of ATOM record group of this chain.

addGroup(Group) - Method in class org.biojava.nbio.structure.ChainImpl

add a group to the list of ATOM record group of this chain.

addGSAccessionNumber(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addGSdbReference(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addGSDescription(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addGSLook(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addGSOrganismClassification(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addGSOrganismSpecies(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addHelix(Helix) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

 

addIindex(int) - Method in class org.biojava.nbio.structure.contact.GridCell

 

addIndex(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Add an attribute that will be used as index for queries

addIndexes(List<String>) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Add a list of attributes that will be used as indexes for queries

addInteraction(String, String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper

To test for interactions use two variables and create a third variable where the two are multiplied together.

addIntron(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addIntron(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence

Add an Intron Currently used to mark an IntronSequence as a feature

addIntronsUsingExons() - Method in class org.biojava.nbio.core.sequence.GeneSequence

Once everything has been added to the gene sequence where you might have added exon sequences only then you can infer the intron sequences and add them.

addJindex(int) - Method in class org.biojava.nbio.structure.contact.GridCell

 

addKeyDomainProtein(String) - Method in class org.forester.surfacing.BasicCombinableDomains

 

addKeyDomainProtein(String) - Method in interface org.forester.surfacing.CombinableDomains

 

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

 

addLength(Species, int) - Method in class org.forester.surfacing.DomainLengths

 

addLengths(List<Protein>) - Method in class org.forester.surfacing.DomainLengthsTable

 

addLigand(RCSBLigand) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigands

 

addLigandBinding(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addLostCharacter(String) - Method in class org.forester.phylogeny.data.BinaryCharacters

 

addMatrixListener(MatrixListener) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

 

addMatrixListener(MatrixListener) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

 

addMember(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

 

addMirror(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

 

addMMcifConsumer(MMcifConsumer) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser

Add a MMcifConsumer that listens to even being triggered by the parser and processes the data into a backend provided by the Consumer.

addMMcifConsumer(MMcifConsumer) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

 

addModel(List<Chain>) - Method in interface org.biojava.nbio.structure.Structure

Add a new model.

addModel(List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl

Add a new model.

addMolecularSeqsToTree(Phylogeny, Msa) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

addMultipleAlignment(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Add a new MultipleAlignment to the end of the ensemble and set its parent ensemble to this.

addMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

 

addNote(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Add notes about this sequence that will get exported for GFF3

addNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet

 

addOboFileEventListener(OboFileEventListener) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

 

addOneSystemProperty(String) - Method in class org.biojava.nbio.structure.align.gui.SystemInfo

 

addPairing(double, int, int) - Method in class org.forester.evoinference.distance.Sarray

 

addPairing(double, int, int) - Method in class org.forester.evoinference.distance.Sset

 

addPairing(int, int, int) - Method in class org.forester.evoinference.distance.Sarray

 

addPairing(int, int, int) - Method in class org.forester.evoinference.distance.Sset

 

addPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

 

addPhylogenyInNewTab(Phylogeny, Configuration, String, String) - Method in class org.forester.archaeopteryx.MainPanel

 

addPoint(Point3d, double) - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia

 

addPoint(Point3d, T) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox

 

addPolymer(RCSBPolymer) - Method in class org.biojava.nbio.structure.rcsb.RCSBDescription

 

addPosteriorProbability(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addPresentCharacter(String) - Method in class org.forester.phylogeny.data.BinaryCharacters

 

addProcess(String) - Method in class org.forester.archaeopteryx.tools.ProcessPool

 

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

addProperty(Property) - Method in class org.forester.phylogeny.data.PropertiesMap

 

addProteinDomain(Domain) - Method in class org.forester.protein.BasicProtein

 

addProteinDomain(Domain) - Method in interface org.forester.protein.Protein

 

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(Reference) - Method in class org.forester.phylogeny.data.NodeData

 

addResidue(SiftsResidue) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

 

addRotation(Rotation) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

 

addRow(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet

 

addRows(ArrayList<String>, String) - Method in class org.biojava.nbio.survival.data.WorkSheet

Add rows to the worksheet and fill in default value

addSecondaryStructure(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addSegment(SiftsSegment) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

 

addSeqResGroup(Group) - Method in class org.biojava.nbio.structure.ChainImpl

 

addSequence(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

Deprecated.

Use StockholmStructure.appendToSequence(String,String) instead

addSequence(Sequence) - Method in class org.forester.phylogeny.data.NodeData

 

addSequenceRelation(SequenceRelation) - Method in class org.forester.phylogeny.data.Sequence

 

addSSBond(Bond) - Method in interface org.biojava.nbio.structure.Structure

Add a single disulfide Bond to this structure

addSSBond(Bond) - Method in class org.biojava.nbio.structure.StructureImpl

Adds a single disulfide Bond to this structure

addStartCodonSequence(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

 

addStopCodonSequence(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

 

addStrataInfoHashMap(LinkedHashMap<String, StrataInfo>, String) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo

 

addStrings(String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

 

addSurfaceAccessibility(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addSynonym(Object) - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm

 

addSynonym(Object) - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

 

addSynonym(Object) - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl

 

addSynonym(Object) - Method in interface org.biojava.nbio.ontology.Term

Add a synonym for this term.

addSynonym(Object) - Method in class org.biojava.nbio.ontology.Term.Impl

 

addSynonym(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl

 

addTaxonomy(Taxonomy) - Method in class org.forester.phylogeny.data.NodeData

 

addToCache(String, File) - Static method in class org.biojava.nbio.core.util.FlatFileCache

 

addToGFComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation

 

addToRefAuthor(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference

 

addToRefTitle(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference

 

addTranscript(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence

Add a transcription sequence to a gene which describes a ProteinSequence

addTransformation(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

 

addTransMembrane(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

addUniqueSequenceList(UniqueSequenceList) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster

 

addUnknownDataTypeVariable(String, String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

 

addUri(Uri) - Method in class org.forester.phylogeny.data.Annotation

 

addUri(Uri) - Method in interface org.forester.phylogeny.data.MultipleUris

 

addUri(Uri) - Method in class org.forester.phylogeny.data.Sequence

 

addUri(Uri) - Method in class org.forester.phylogeny.data.Taxonomy

 

addValue(double) - Method in class org.forester.util.BasicDescriptiveStatistics

 

addValue(double) - Method in interface org.forester.util.DescriptiveStatistics

 

AdjactantDirectedBinaryDomainCombination - Class in org.forester.surfacing

 

AdjactantDirectedCombinableDomains - Class in org.forester.surfacing

 

AdjactantDirectedCombinableDomains(String, Species) - Constructor for class org.forester.surfacing.AdjactantDirectedCombinableDomains

 

AFFINE - Enum constant in enum class org.biojava.nbio.alignment.template.GapPenalty.Type

 

AFP - Class in org.biojava.nbio.structure.align.model

A class to represent a FATCAT AFP

AFP() - Constructor for class org.biojava.nbio.structure.align.model.AFP

 

afp2Res(AFPChain, int, int[], int) - Static method in class org.biojava.nbio.structure.align.AFPTwister

Set the list of equivalent residues in the two proteins given a list of AFPs WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain!

AFPAlignmentDisplay - Class in org.biojava.nbio.structure.align.util

 

AFPAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay

 

AFPCalculator - Class in org.biojava.nbio.structure.align.fatcat.calc

a class that performs calculations on AFPCHains

AFPCalculator() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator

 

AFPChain - Class in org.biojava.nbio.structure.align.model

A bean to contain the core of a structure alignment.

AFPChain() - Constructor for class org.biojava.nbio.structure.align.model.AFPChain

Deprecated.

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

 

AFPOptimizer - Class in org.biojava.nbio.structure.align.fatcat.calc

 

AFPOptimizer() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer

 

afpPairConn(int, int, FatCatParameters, AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer

//Key function: calculate the connectivity of AFP pairs //no compatibility criteria is executed //note: afp1 is previous to afp2 in terms of the position //this module must be optimized

AFPPostProcessor - Class in org.biojava.nbio.structure.align.fatcat.calc

does post processing after alignment chaingin

AFPPostProcessor() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor

 

AFPTwister - Class in org.biojava.nbio.structure.align

 

AFPTwister() - Constructor for class org.biojava.nbio.structure.align.AFPTwister

 

Ag - Enum constant in enum class org.biojava.nbio.structure.Element

 

AGGRESSIVE - Enum constant in enum class org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION

 

AgScore - Class in org.biojava.nbio.survival.cox.stats

 

AgScore() - Constructor for class org.biojava.nbio.survival.cox.stats.AgScore

 

Al - Enum constant in enum class 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(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_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 Class in org.biojava.nbio.core.alignment.template

Defines an alignment step in order to pass alignment information from an Aligner to a constructor.

Aligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template

Defines an algorithm which computes an alignment Profile from a list of Sequences.

AlignerHelper - Class in org.biojava.nbio.alignment.routines

Static utility to construct alignment routines from a common library of methods.

AlignerHelper() - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper

 

AlignerHelper.Anchor - Class in org.biojava.nbio.alignment.routines

Compounds in query and target sequences that must align

AlignerHelper.Anchor.QueryIndexComparator - Class in org.biojava.nbio.alignment.routines

 

AlignerHelper.Cut - Class in org.biojava.nbio.alignment.routines

Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.

AlignerHelper.Last - Enum Class in org.biojava.nbio.alignment.routines

Define a traceback pointer for the three edit operations: substitution (match/replacement of a query compound with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and insertion (addition of a target compound opening a gap in the query sequence).

AlignerHelper.Subproblem - Class in org.biojava.nbio.alignment.routines

Alignment subproblem.

alignFlexible(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat

 

ALIGNMENT_PANEL - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator

 

ALIGNMENT_VIEW - Enum constant in enum class 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.

AlignmentCalcDB - Class in org.biojava.nbio.structure.align.gui

 

AlignmentCalcDB(AlignmentGui, Structure, String, UserConfiguration, String, Boolean) - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentCalcDB

 

AlignmentCalculationRunnable - Interface in org.biojava.nbio.structure.align.gui

 

alignmentEnded() - Method in class org.biojava.nbio.structure.align.client.CountProgressListener

 

alignmentEnded() - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener

 

alignmentEnded() - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener

 

AlignmentGui - Class in org.biojava.nbio.structure.align.gui

A JFrame that allows to trigger a pairwise structure alignment, either from files in a directory, or after manual upload.

AlignmentGui() - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentGui

 

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 - Interface in org.biojava.nbio.structure.align.events

 

AlignmentProgressListener() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener

 

AlignmentResult - Class in org.biojava.nbio.structure.align.pairwise

A class to track the alignment results in a flat file

AlignmentResult() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlignmentResult

 

Alignments - Class in org.biojava.nbio.alignment

Static utility to easily run alignment routines.

ALIGNMENTS - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

 

ALIGNMENTS - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

 

Alignments.PairInProfileScorerType - Enum Class in org.biojava.nbio.alignment

List of implemented sequence pair in a profile scoring routines.

Alignments.PairwiseSequenceAlignerType - Enum Class in org.biojava.nbio.alignment

List of implemented pairwise sequence alignment routines.

Alignments.PairwiseSequenceScorerType - Enum Class in org.biojava.nbio.alignment

List of implemented pairwise sequence scoring routines.

Alignments.ProfileProfileAlignerType - Enum Class in org.biojava.nbio.alignment

List of implemented profile-profile alignment routines.

Alignments.RefinerType - Enum Class in org.biojava.nbio.alignment

List of implemented profile refinement routines.

alignmentStarted(String, String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener

 

alignmentStarted(String, String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener

 

alignmentStarted(String, String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener

 

AlignmentTextPanel - Class in org.biojava.nbio.structure.align.gui

 

AlignmentTextPanel() - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentTextPanel

 

AlignmentTools - Class in org.biojava.nbio.structure.align.util

Methods for analyzing and manipulating AFPChains and for other pairwise alignment utilities.

AlignmentTools() - Constructor for class org.biojava.nbio.structure.align.util.AlignmentTools

 

AlignmentTools.IdentityMap<K> - Class in org.biojava.nbio.structure.align.util

A Map<K,V> can be viewed as a function from K to V.

alignmentToSIF(Writer, AFPChain, Atom[], Atom[], String, String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Creates a simple interaction format (SIF) file for an alignment.

alignOptimal(Atom[], Atom[], Object, AFPChain[]) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

Finds the optimal alignment between two proteins allowing for a circular permutation (CP).

alignPair(String, String) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable

 

alignPair(String, String, String) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable

 

AligNPE - Class in org.biojava.nbio.structure.align.pairwise

 

AligNPE() - Constructor for class org.biojava.nbio.structure.align.pairwise.AligNPE

 

alignPermuted(Atom[], Atom[], Object, int) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

Aligns ca1 with ca2 permuted by cp residues.

alignRigid(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat

 

alignRigid(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat

 

AlignTools - Class in org.biojava.nbio.structure.align.helper

 

AlignTools() - Constructor for class org.biojava.nbio.structure.align.helper.AlignTools

 

AligPanel - Class in org.biojava.nbio.structure.align.gui.aligpanel

A JPanel that can display an AFPChain in a nice way and interact with Jmol.

AligPanel() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

 

AligPanelMouseMotionListener - Class in org.biojava.nbio.structure.align.gui.aligpanel

 

AligPanelMouseMotionListener(AligPanel) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener

 

AligUIManager - Class in org.biojava.nbio.structure.align.webstart

 

AligUIManager() - Constructor for class org.biojava.nbio.structure.align.webstart.AligUIManager

 

ALKALI_METAL - Enum constant in enum class org.biojava.nbio.structure.ElementType

 

ALKALINE_EARTH_METAL - Enum constant in enum class org.biojava.nbio.structure.ElementType

 

ALL - Enum constant in enum class org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION

 

ALL - Enum constant in enum class org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput

 

ALL - Enum constant in enum class org.forester.ws.wabi.TxSearch.RANKS

 

ALL - Enum constant in enum class org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS

 

ALL - Enum constant in enum class org.forester.ws.wabi.TxSearch.TAX_RANK

 

ALL_PFAMS_ENCOUNTERED_SUFFIX - Static variable in class org.forester.application.surfacing

 

ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX - Static variable in class org.forester.application.surfacing

 

ALL_PFAMS_GAINED_AS_DC_SUFFIX - Static variable in class org.forester.application.surfacing

 

ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX - Static variable in class org.forester.application.surfacing

 

ALL_PFAMS_LOST_AS_DC_SUFFIX - Static variable in class org.forester.application.surfacing

 

ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX - Static variable in class org.forester.application.surfacing

 

ALL_POLYMER_TYPES - Static variable in enum class org.biojava.nbio.structure.io.mmcif.chem.PolymerType

Convenience Set of all polymer types.

ALL_SEQUENCES - Enum constant in enum class org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection

 

AllChemCompProvider - Class in org.biojava.nbio.structure.io.mmcif

A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.

AllChemCompProvider() - Constructor for class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider

 

allComponents() - Static method in class org.biojava.nbio.protmod.Component

 

allComponents() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

 

allIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

 

allKeywords() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

 

allModifications() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

 

ALLOW_DDBJ_BLAST - Static variable in class org.forester.archaeopteryx.Constants

 

ALLOW_MULTIPLE_PARENTS_DEFAULT - Static variable in class org.forester.phylogeny.Phylogeny

 

allPdbccIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

 

allPsimodIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

 

allResidIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

 

ALN - Enum constant in enum class org.biojava.nbio.core.alignment.template.Profile.StringFormat

 

ALN - Enum constant in enum class org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat

 

ALPHABETICAL_KEY_ID - Enum constant in enum class org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder

 

AlreadyExistsException - Exception in org.biojava.nbio.ontology

Thrown to indicate that a term or triple can't be added to an ontology because it is already present.

AlreadyExistsException() - Constructor for exception org.biojava.nbio.ontology.AlreadyExistsException

 

AlreadyExistsException(String) - Constructor for exception org.biojava.nbio.ontology.AlreadyExistsException

 

ALT_ID - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

 

AltAligComparator - Class in org.biojava.nbio.structure.align.pairwise

a comparator to sort AlternativeAlignments based on their number of equivalent residues and RMSD.

AltAligComparator() - Constructor for class org.biojava.nbio.structure.align.pairwise.AltAligComparator

 

altcode - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

 

AlternativeAlignment - Class in org.biojava.nbio.structure.align.pairwise

Implements a class which handles one possible (alternative) solution.

AlternativeAlignment() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

 

AlternativeAlignmentFrame - Class in org.biojava.nbio.structure.gui.util

a frame showing the alternative alignments, which are the result of a structure superimposition

AlternativeAlignmentFrame(Structure, Structure) - Constructor for class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame

 

ALVEOLATA_COLOR - Static variable in class org.forester.util.TaxonomyColors

 

Am - Enum constant in enum class 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 two additional letters - XU

AMBIGUOUS_NUCLEOTIDE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil

Ambiguous nucleotide

AMIGO_LINK - Static variable in class org.forester.surfacing.SurfacingConstants

 

AMINO_ACID_MATCHER - Static variable in class org.biojava.nbio.structure.AtomPositionMap

Matches CA atoms of protein groups

AminoAcid - Interface in org.biojava.nbio.structure

A Group that represents an AminoAcid.

AMINOACID - Enum constant in enum class 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.

aminoAcidsCompounds(CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

 

AMOEBOZOA_COLOR - Static variable in class org.forester.util.TaxonomyColors

 

amount(Atom) - Static method in class org.biojava.nbio.structure.Calc

Gets the length of the vector (2-norm)

analyze(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm

Analyze the symmetries of the input Atom array using the DEFAULT parameters.

analyze(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm

Analyze the symmetries of the input Atom array using the provided parameters.

analyzeLevel(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm

Analyze a single level of symmetry.

AncestralTaxonomyInference - Class in org.forester.analysis

 

AncestralTaxonomyInference() - Constructor for class org.forester.analysis.AncestralTaxonomyInference

 

AncestralTaxonomyInferenceException - Exception in org.forester.analysis

 

AncestralTaxonomyInferenceException() - Constructor for exception org.forester.analysis.AncestralTaxonomyInferenceException

 

AncestralTaxonomyInferenceException(String) - Constructor for exception org.forester.analysis.AncestralTaxonomyInferenceException

 

AncestralTaxonomyInferrer - Class in org.forester.archaeopteryx.tools

 

AncestralTaxonomyInferrer(MainFrame, TreePanel, Phylogeny) - Constructor for class org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer

 

Anchor(int, int) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor

 

AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.routines

This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.

AnchoredPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner

Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).

AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner

Prepares for a pairwise global sequence alignment.

AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner

Prepares for a pairwise global sequence alignment.

anchors - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

 

angle(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Gets the angle between two vectors

ANGLE - Enum constant in enum class 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.

angleOutlier - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

 

AngleOutlier - Class in org.biojava.nbio.structure.validation

Java class for anonymous complex type.

AngleOutlier() - Constructor for class org.biojava.nbio.structure.validation.AngleOutlier

 

Annotatable - Interface in org.biojava.nbio.ontology.utils

Indicates that an object has an associated annotation.

Annotation - Class in org.forester.phylogeny.data

 

Annotation - Interface in org.biojava.nbio.ontology.utils

Arbitrary annotation associated with one or more objects.

Annotation() - Constructor for class org.forester.phylogeny.data.Annotation

 

Annotation(String) - Constructor for class org.forester.phylogeny.data.Annotation

 

Annotation(String, String) - Constructor for class org.forester.phylogeny.data.Annotation

 

ANNOTATION - Enum constant in enum class org.forester.phylogeny.data.Property.AppliesTo

 

ANNOTATION - Static variable in class org.forester.archaeopteryx.TreeColorSet

 

ANNOTATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

ANNOTATION_DESC - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

ANNOTATION_EVIDENCE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

ANNOTATION_REF_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

ANNOTATION_SOURCE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

ANNOTATION_TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

AnnotationParser - Class in org.forester.io.parsers.phyloxml.data

 

annotator - Class in org.forester.application

 

annotator() - Constructor for class org.forester.application.annotator

 

antiparallel - Enum constant in enum class 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

APACHE_FEATURES_VALIDATION_SCHEMA - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser

 

APACHE_FEATURES_VALIDATION_SCHEMA - Static variable in class org.forester.io.parsers.tol.TolParser

 

APACHE_FEATURES_VALIDATION_SCHEMA_FULL - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser

 

APACHE_FEATURES_VALIDATION_SCHEMA_FULL - Static variable in class org.forester.io.parsers.tol.TolParser

 

APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser

 

APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION - Static variable in class org.forester.io.parsers.tol.TolParser

 

apairs_from_idxlst(JointFragments) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

Set apairs according to a list of (i,j) tuples.

apairs_from_seed(int, int, int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

Set apairs according to a seed position.

ApliphaticIndex - Enum constant in enum class org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

 

App - Class in org.biojava.nbio.genome

Hello world!

App - Class in org.biojava.nbio.ontology

Hello world!

App() - Constructor for class org.biojava.nbio.genome.App

 

App() - Constructor for class org.biojava.nbio.ontology.App

 

append(T, Iterable<Fastq>) - Method in class org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriter

 

append(T, Iterable<Fastq>) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter

Append the specified FASTQ formatted sequences to the specified appendable.

append(T, Fastq...) - Method in class org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriter

 

append(T, Fastq...) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqWriter

Append the specified FASTQ formatted sequences to the specified appendable.

appendClose(Writer, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendElement(Writer, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendElement(Writer, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendElement(Writer, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendElement(Writer, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendElement(Writer, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendElement(Writer, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendElement(Writer, String, String, String, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendElement(Writer, String, String, String, String, String, String, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendOpen(Writer, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendOpen(Writer, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendOpen(Writer, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendOpen(Writer, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendOpen(Writer, String, String, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendOpen(Writer, String, String, String, String, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

 

appendQuality(String) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.

appendQuality(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this listener of a quality line.

appendSeparatorIfNotEmpty(StringBuffer, char) - Static method in class org.forester.util.ForesterUtil

 

appendSequence(String) - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.

appendSequence(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this parse listener of an additional sequence line.

appendToSequence(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure

 

appendValue(String) - Method in class org.forester.io.parsers.phyloxml.XmlElement

 

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

 

APTX_VISUALIZATION_REF - Static variable in class org.forester.phylogeny.data.NodeVisualData

 

AptxUtil - Class in org.forester.archaeopteryx

 

AptxUtil() - Constructor for class org.forester.archaeopteryx.AptxUtil

 

AptxUtil.GraphicsExportType - Enum Class in org.forester.archaeopteryx

 

APUSOZOA_COLOR - Static variable in class org.forester.util.TaxonomyColors

 

Ar - Enum constant in enum class org.biojava.nbio.structure.Element

 

ARACYC - Enum constant in enum class org.forester.go.GoXRef.Type

 

ARACYC_STR - Static variable in interface org.forester.go.GoXRef

 

ARCHAEA - Static variable in class org.forester.ws.seqdb.UniProtTaxonomy

 

ARCHAEA_COLOR - Static variable in class org.forester.util.TaxonomyColors

 

Archaeopteryx - Class in org.forester.archaeopteryx

 

Archaeopteryx() - Constructor for class org.forester.archaeopteryx.Archaeopteryx

 

ArchaeopteryxA - Class in org.forester.archaeopteryx

 

ArchaeopteryxA() - Constructor for class org.forester.archaeopteryx.ArchaeopteryxA

 

ArchaeopteryxE - Class in org.forester.archaeopteryx

 

ArchaeopteryxE() - Constructor for class org.forester.archaeopteryx.ArchaeopteryxE

 

Architecture - Enum constant in enum class 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.

arithmeticMean() - Method in class org.forester.util.BasicDescriptiveStatistics

 

arithmeticMean() - Method in interface org.forester.util.DescriptiveStatistics

 

arrayLeftDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Element-by-element left division, C = A.\B

arrayLeftDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Element-by-element left division in place, A = A.\B

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./B

arrayRightDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Element-by-element right division in place, A = A./B

arrayTimes(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Element-by-element multiplication, C = A.*B

arrayTimesEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Element-by-element multiplication in place, A = A.*B

ARTIFACTUAL - Enum constant in enum class org.biojava.nbio.protmod.ModificationOccurrenceType

 

As - Enum constant in enum class org.biojava.nbio.structure.Element

 

AS_INTERNAL_NODE_NAMES - Enum constant in enum class org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE

 

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(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.

AsciiHistogram - Class in org.forester.util

 

AsciiHistogram(DescriptiveStatistics) - Constructor for class org.forester.util.AsciiHistogram

 

AsciiHistogram(DescriptiveStatistics, String) - Constructor for class org.forester.util.AsciiHistogram

 

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.

asSequenceList() - Method in class org.forester.msa.BasicMsa

 

asSequenceList() - Method in interface org.forester.msa.Msa

 

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

 

AssignmentXMLSerializer - Class in org.biojava.nbio.structure.domain

 

AssignmentXMLSerializer() - Constructor for class org.biojava.nbio.structure.domain.AssignmentXMLSerializer

 

asSimpleText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

 

asSimpleText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

 

asSimpleText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

 

asSimpleText() - Method in class org.forester.go.BasicGoTerm

 

asSimpleText() - Method in class org.forester.phylogeny.data.Accession

 

asSimpleText() - Method in class org.forester.phylogeny.data.Annotation

 

asSimpleText() - Method in class org.forester.phylogeny.data.BinaryCharacters

 

asSimpleText() - Method in class org.forester.phylogeny.data.BranchColor

 

asSimpleText() - Method in class org.forester.phylogeny.data.BranchData

 

asSimpleText() - Method in class org.forester.phylogeny.data.BranchWidth

 

asSimpleText() - Method in class org.forester.phylogeny.data.Confidence

 

asSimpleText() - Method in class org.forester.phylogeny.data.Date

 

asSimpleText() - Method in class org.forester.phylogeny.data.Distribution

 

asSimpleText() - Method in class org.forester.phylogeny.data.DomainArchitecture

 

asSimpleText() - Method in class org.forester.phylogeny.data.Event

 

asSimpleText() - Method in class org.forester.phylogeny.data.Identifier

 

asSimpleText() - Method in class org.forester.phylogeny.data.NodeData

 

asSimpleText() - Method in class org.forester.phylogeny.data.NodeVisualData

 

asSimpleText() - Method in interface org.forester.phylogeny.data.PhylogenyData

 

asSimpleText() - Method in class org.forester.phylogeny.data.Point

 

asSimpleText() - Method in class org.forester.phylogeny.data.Polygon

 

asSimpleText() - Method in class org.forester.phylogeny.data.PropertiesMap

 

asSimpleText() - Method in class org.forester.phylogeny.data.Property

 

asSimpleText() - Method in class org.forester.phylogeny.data.ProteinDomain

 

asSimpleText() - Method in class org.forester.phylogeny.data.Reference

 

asSimpleText() - Method in class org.forester.phylogeny.data.Sequence

 

asSimpleText() - Method in class org.forester.phylogeny.data.SequenceRelation

 

asSimpleText() - Method in class org.forester.phylogeny.data.Taxonomy

 

asSimpleText() - Method in class org.forester.phylogeny.data.Uri

 

asString() - Method in interface org.forester.pccx.Coverage

 

asString() - Method in interface org.forester.pccx.CoverageCalculationOptions

 

asString() - Method in class org.forester.pccx.ExternalNodeBasedCoverage

 

asString() - Method in class org.forester.pccx.ExternalNodeBasedCoverageMethodOptions

 

asSummary() - Method in class org.forester.util.BasicDescriptiveStatistics

 

asSummary() - Method in interface org.forester.util.DescriptiveStatistics

 

asText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

 

asText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

 

asText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

 

asText() - Method in class org.forester.go.BasicGoTerm

 

asText() - Method in class org.forester.phylogeny.data.Accession

 

asText() - Method in class org.forester.phylogeny.data.Annotation

 

asText() - Method in class org.forester.phylogeny.data.BinaryCharacters

 

asText() - Method in class org.forester.phylogeny.data.BranchColor

 

asText() - Method in class org.forester.phylogeny.data.BranchData

 

asText() - Method in class org.forester.phylogeny.data.BranchWidth

 

asText() - Method in class org.forester.phylogeny.data.Confidence

 

asText() - Method in class org.forester.phylogeny.data.Date

 

asText() - Method in class org.forester.phylogeny.data.Distribution

 

asText() - Method in class org.forester.phylogeny.data.DomainArchitecture

 

asText() - Method in class org.forester.phylogeny.data.Event

 

asText() - Method in class org.forester.phylogeny.data.Identifier

 

asText() - Method in class org.forester.phylogeny.data.NodeData

 

asText() - Method in class org.forester.phylogeny.data.NodeVisualData

 

asText() - Method in interface org.forester.phylogeny.data.PhylogenyData

 

asText() - Method in class org.forester.phylogeny.data.Point

 

asText() - Method in class org.forester.phylogeny.data.Polygon

 

asText() - Method in class org.forester.phylogeny.data.PropertiesMap

 

asText() - Method in class org.forester.phylogeny.data.Property

 

asText() - Method in class org.forester.phylogeny.data.ProteinDomain

 

asText() - Method in class org.forester.phylogeny.data.Reference

 

asText() - Method in class org.forester.phylogeny.data.Sequence

 

asText() - Method in class org.forester.phylogeny.data.SequenceRelation

 

asText() - Method in class org.forester.phylogeny.data.Taxonomy

 

asText() - Method in class org.forester.phylogeny.data.Uri

 

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 Class in org.biojava.nbio.structure.scop

An ASTRAL sequence-identity cutoff with an identifier such as:

ASYMMETRIC - Enum constant in enum class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia.SymmetryClass

 

At - Enum constant in enum class org.biojava.nbio.structure.Element

 

atom - Variable in class org.biojava.nbio.structure.validation.Clash

 

atom - Variable in class org.biojava.nbio.structure.validation.SymmClash

 

Atom - Interface in org.biojava.nbio.structure

A simple interface for an Atom.

ATOM_CA_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.FileParsingParameters

The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.

ATOM_PLANE - Enum constant in enum class org.biojava.nbio.structure.BondType

 

atom0 - Variable in class org.biojava.nbio.structure.validation.AngleOutlier

 

atom0 - Variable in class org.biojava.nbio.structure.validation.BondOutlier

 

atom1 - Variable in class org.biojava.nbio.structure.validation.AngleOutlier

 

atom1 - Variable in class org.biojava.nbio.structure.validation.BondOutlier

 

atom2 - Variable in class org.biojava.nbio.structure.validation.AngleOutlier

 

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, boolean) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache

Deprecated.

isSplit parameter is ignored (4.0.0)

AtomCache(String, String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache

Creates an instance of an AtomCache that is pointed to the a particular path in the file system.

AtomCache(String, String, boolean) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache

Deprecated.

isSplit parameter is ignored (4.0.0)

AtomCache(UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache

Creates a new AtomCache object based on the provided UserConfiguration.

AtomContact - Class in org.biojava.nbio.structure.contact

A pair of atoms that are in contact

AtomContact(Pair<Atom>, double) - Constructor for class org.biojava.nbio.structure.contact.AtomContact

 

AtomContactSet - Class in org.biojava.nbio.structure.contact

A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations

AtomContactSet(double) - Constructor for class org.biojava.nbio.structure.contact.AtomContactSet

 

AtomIdentifier - Class in org.biojava.nbio.structure.contact

 

AtomIdentifier(int, String) - Constructor for class org.biojava.nbio.structure.contact.AtomIdentifier

 

AtomImpl - Class in org.biojava.nbio.structure

Implementation of an Atom of a PDB file.

AtomImpl() - Constructor for class org.biojava.nbio.structure.AtomImpl

 

AtomInfo - Class in org.biojava.nbio.structure.align.gui.jmol

This class uniquely describes an atom

AtomInfo() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AtomInfo

 

AtomInfoParser - Class in org.biojava.nbio.structure.align.gui.jmol

 

AtomInfoParser() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser

 

AtomIterator - Class in org.biojava.nbio.structure

an iterator over all atoms of a structure / group.

AtomIterator(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.

atomn - Enum constant in enum class org.biojava.nbio.structure.io.mmcif.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

 

atoms - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier

 

atoms - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier

 

AtomSite - Class in org.biojava.nbio.structure.io.mmcif.model

 

AtomSite() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AtomSite

 

AtomSites - Class in org.biojava.nbio.structure.io.mmcif.model

A class containing the _atom_sites data.

AtomSites() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AtomSites

 

atomsToPoints(Atom[]) - Static method in class org.biojava.nbio.structure.Calc

Convert an array of atoms into an array of vecmath points

ATTACHMENT - Enum constant in enum class org.biojava.nbio.protmod.ModificationCategory

 

attemptedValidationSteps - Variable in class org.biojava.nbio.structure.validation.Entry

 

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.

attributeEqualsValue(XmlElement, String, String) - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler

 

attributeEqualsValue(XmlElement, String, String) - Static method in class org.forester.io.parsers.tol.TolXmlHandler

 

attributes() - Method in class org.biojava.nbio.genome.parsers.gff.Feature

Get the string of key/value attributes.

attributeValues(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

Create a collection of the unique values for the specified key.

Au - Enum constant in enum class org.biojava.nbio.structure.Element

 

AU - Enum constant in enum class org.biojava.nbio.structure.xtal.TransformType

 

AuditAuthor - Class in org.biojava.nbio.structure.io.mmcif.model

 

AuditAuthor() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor

 

AugmentedResidueRange - Class in org.biojava.nbio.structure

Created by douglas on 1/23/15.

AugmentedResidueRange(String, 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

 

AUTH - Enum constant in enum class org.biojava.nbio.structure.PDBStatus.Status

 

AUTHDATE - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

 

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

 

AUTHORITY - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

 

AUTHORS_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

 

AUTO - Enum constant in enum class org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType

 

AutoSuggestProvider - Interface in org.biojava.nbio.structure.align.gui.autosuggest

A class that provides auto-completion suggestions for JAutoSuggest

AV - Enum constant in enum class org.biojava.nbio.phylo.TreeConstructorType

What does this stand for? (Aleix: Nov 2015)

available() - Method in class org.biojava.nbio.core.util.UncompressInputStream

 

available() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser

 

AverageHydropathyValue - Enum constant in enum class org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

 

avgoccu - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

 

AVGTM_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

 

Axis(Matrix4d, int, CESymmParameters.SymmetryType, int, int) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

 

AxisAligner - Class in org.biojava.nbio.structure.symmetry.core

 

AxisAligner() - Constructor for class org.biojava.nbio.structure.symmetry.core.AxisAligner

 

axisStroke - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

 

B

B - Enum constant in enum class org.biojava.nbio.structure.Element

 

Ba - Enum constant in enum class org.biojava.nbio.structure.Element

 

BACKGROUND - Static variable in class org.forester.archaeopteryx.TreeColorSet

 

BACKGROUND_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel

 

BACKGROUND_GRADIENT_BOTTOM - Static variable in class org.forester.archaeopteryx.TreeColorSet

 

BACTERIA - Static variable in class org.forester.ws.seqdb.UniProtTaxonomy

 

BACTERIA_COLOR - Static variable in class org.forester.util.TaxonomyColors

 

BALL_AND_STICK - Enum constant in enum class 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_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES - Static variable in class org.forester.application.surfacing

 

BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES - Static variable in class org.forester.application.surfacing

 

BASE_UNIPROT_URL - Static variable in class org.forester.ws.seqdb.SequenceDbWsTools

 

baseURL - Static variable in class org.biojava.nbio.structure.rcsb.RCSBUpdates

 

BASIC - Enum constant in enum class org.forester.protein.BinaryDomainCombination.DomainCombinationType

 

BASIC - Enum constant in enum class org.forester.surfacing.DomainSimilarityCalculator.Detailedness

 

BASIC_GO_TERM - Enum constant in enum class org.forester.go.OBOparser.ReturnType

 

BasicBinaryDomainCombination - Class in org.forester.surfacing

 

BasicCharacterStateMatrix<S> - Class in org.forester.evoinference.matrix.character

 

BasicCharacterStateMatrix(int, int) - Constructor for class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

 

BasicCharacterStateMatrix(int, int, S) - Constructor for class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

 

BasicCharacterStateMatrix(List<List<S>>) - Constructor for class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

 

BasicCharacterStateMatrix(S[][]) - Constructor for class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

 

BasicCombinableDomains - Class in org.forester.surfacing

 

BasicCombinableDomains(String, Species) - Constructor for class org.forester.surfacing.BasicCombinableDomains

 

BasicDescriptiveStatistics - Class in org.forester.util

 

BasicDescriptiveStatistics() - Constructor for class org.forester.util.BasicDescriptiveStatistics

 

BasicDescriptiveStatistics(String) - Constructor for class org.forester.util.BasicDescriptiveStatistics

 

BasicDomain - Class in org.forester.protein

 

BasicDomain(String) - Constructor for class org.forester.protein.BasicDomain

 

BasicDomain(String, int, int, short, short, double, double) - Constructor for class org.forester.protein.BasicDomain

 

BasicDomainSimilarityCalculator - Class in org.forester.surfacing

 

BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField, boolean, boolean, boolean) - Constructor for class org.forester.surfacing.BasicDomainSimilarityCalculator

 

BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField, boolean, boolean, boolean, boolean) - Constructor for class org.forester.surfacing.BasicDomainSimilarityCalculator

 

BasicExternalNodeBasedCoverageExtender - Class in org.forester.pccx

 

BasicExternalNodeBasedCoverageExtender() - Constructor for class org.forester.pccx.BasicExternalNodeBasedCoverageExtender

 

BasicGenomeWideCombinableDomains - Class in org.forester.surfacing

 

BasicGoRelationship - Class in org.forester.go

 

BasicGoRelationship(String) - Constructor for class org.forester.go.BasicGoRelationship

 

BasicGoRelationship(String, String) - Constructor for class org.forester.go.BasicGoRelationship

 

BasicGoRelationship(GoRelationship.Type, GoId) - Constructor for class org.forester.go.BasicGoRelationship

 

BasicGoSubset - Class in org.forester.go

 

BasicGoSubset(String) - Constructor for class org.forester.go.BasicGoSubset

 

BasicGoSubset(GoSubset.Type) - Constructor for class org.forester.go.BasicGoSubset

 

BasicGoTerm - Class in org.forester.go

 

BasicGoTerm(String, String, String, boolean) - Constructor for class org.forester.go.BasicGoTerm

 

BasicGoTerm(GoId, String, GoNameSpace, boolean) - Constructor for class org.forester.go.BasicGoTerm

 

BasicGoXRef - Class in org.forester.go

 

BasicGoXRef(String) - Constructor for class org.forester.go.BasicGoXRef

 

BasicGoXRef(GoXRef.Type, String) - Constructor for class org.forester.go.BasicGoXRef

 

BasicMsa - Class in org.forester.msa

 

BasicMsa(int, int, MolecularSequence.TYPE) - Constructor for class org.forester.msa.BasicMsa

 

BasicPhylogeniesWebserviceClient - Class in org.forester.archaeopteryx.webservices

 

BasicPhylogeniesWebserviceClient(String, String, String, String, WebservicesManager.WsPhylogenyFormat, PhylogenyMethods.PhylogenyNodeField, String, boolean, String, Object) - Constructor for class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient

 

BasicProtein - Class in org.forester.protein

 

BasicProtein(String, String, int) - Constructor for class org.forester.protein.BasicProtein

 

BasicSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence

Bare bones version of the Sequence object to be used sparingly.

BasicSequence - Class in org.forester.sequence

 

BasicSequence(String, char[], MolecularSequence.TYPE) - Constructor for class org.forester.sequence.BasicSequence

Only use if you know what you are doing!

BasicSequence(String, String, MolecularSequence.TYPE) - Constructor for class org.forester.sequence.BasicSequence

Only use if you know what you are doing!

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

 

BasicSpecies - Class in org.forester.species

 

BasicSpecies(String) - Constructor for class org.forester.species.BasicSpecies

 

BasicSymmetricalDistanceMatrix - Class in org.forester.evoinference.matrix.distance

 

BasicSymmetricalDistanceMatrix(int) - Constructor for class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

 

BasicTable<E> - Class in org.forester.util

 

BasicTable() - Constructor for class org.forester.util.BasicTable

 

BasicTableParser - Class in org.forester.util

 

BDC_PRESENT_NEXUS - Static variable in class org.forester.application.surfacing

 

Be - Enum constant in enum class org.biojava.nbio.structure.Element

 

BEGIN_CHARACTERS - Static variable in class org.forester.io.parsers.nexus.NexusConstants

 

BEGIN_DATA - Static variable in class org.forester.io.parsers.nexus.NexusConstants

 

BEGIN_TAXA - Static variable in class org.forester.io.parsers.nexus.NexusConstants

 

BEGIN_TREES - Static variable in class org.forester.io.parsers.nexus.NexusConstants

 

bend - Enum constant in enum class org.biojava.nbio.structure.secstruc.SecStrucType

 

BerkeleyScopInstallation - Class in org.biojava.nbio.structure.scop

SCOPe: The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop.berkeley.edu/).

BerkeleyScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.BerkeleyScopInstallation

 

bestTrace1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

 

bestTrace1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

 

bestTrace2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

 

bestTrace2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

 

bestTraces1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

 

bestTraces1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

 

bestTraces2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

 

bestTraces2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

 

bestTraceScore - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

 

bestTraceScore - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

 

bestTracesN - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

 

bestTracesN - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

 

bestTracesScores - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

 

bestTracesScores - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

 

BetaBridge - Class in org.biojava.nbio.structure.secstruc

Container that represents a beta Bridge between two residues.

BetaBridge(int, int, BridgeType) - Constructor for class org.biojava.nbio.structure.secstruc.BetaBridge

 

BETTER_PERFORMANCE_MORE_MEMORY - Enum constant in enum class org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior

use a built-in HashMap for faster access to memory, at the price of more memory consumption

BETWEEN_11 - Enum constant in enum class org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION

 

BETWEEN_12 - Enum constant in enum class org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION

 

BETWEEN_13 - Enum constant in enum class org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION

 

BETWEEN_22 - Enum constant in enum class org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION

 

BETWEEN_23 - Enum constant in enum class org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION

 

BETWEEN_33 - Enum constant in enum class org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION

 

Bi - Enum constant in enum class org.biojava.nbio.structure.Element

 

BINARY_CHARACTER - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

BINARY_CHARACTERS - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

BINARY_CHARACTERS_GAINED - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

BINARY_CHARACTERS_GAINED_COUNT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

BINARY_CHARACTERS_LOST - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

BINARY_CHARACTERS_LOST_COUNT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

BINARY_CHARACTERS_PRESENT - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

BINARY_CHARACTERS_PRESENT_COUNT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

BINARY_CHARACTERS_TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

BINARY_DOMAIN_COMBINATIONS - Static variable in class org.forester.archaeopteryx.TreeColorSet

 

BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO - Static variable in class org.forester.application.surfacing

 

BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH - Static variable in class org.forester.application.surfacing

 

BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED - Static variable in class org.forester.application.surfacing

 

BinaryCharacters - Class in org.forester.phylogeny.data

 

BinaryCharacters() - Constructor for class org.forester.phylogeny.data.BinaryCharacters

 

BinaryCharacters(SortedSet<String>, SortedSet<String>, SortedSet<String>, String) - Constructor for class org.forester.phylogeny.data.BinaryCharacters

 

BinaryCharacters(SortedSet<String>, SortedSet<String>, SortedSet<String>, String, int, int, int) - Constructor for class org.forester.phylogeny.data.BinaryCharacters

 

BinaryCharactersParser - Class in org.forester.io.parsers.phyloxml.data

 

BinaryDomainCombination - Interface in org.forester.protein

 

BinaryDomainCombination.DomainCombinationType - Enum Class in org.forester.protein

 

BinaryDomainCombination.OutputFormat - Enum Class in org.forester.protein

 

BindingDB_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

 

BIO - Enum constant in enum class org.biojava.nbio.structure.align.client.StructureName.Source

 

BIO_ASSEMBLY - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider

 

BIO_NAME_PATTERN - Static variable in class org.biojava.nbio.structure.BioAssemblyIdentifier

 

BioAssemblyIdentifier - Class in org.biojava.nbio.structure

 

BioAssemblyIdentifier(String) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier

 

BioAssemblyIdentifier(String, int) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier

 

BioAssemblyInfo - Class in org.biojava.nbio.structure.quaternary

Representation of a Biological Assembly annotation as provided by the PDB.

BioAssemblyInfo() - Constructor for class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

Empty constructor

BioAssemblyTools - Class in org.biojava.nbio.structure.quaternary

 

BioAssemblyTools() - Constructor for class org.biojava.nbio.structure.quaternary.BioAssemblyTools

 

bioEnd() - Method in class org.biojava.nbio.genome.parsers.gff.Location

Get end index, in biocoordinates.

BIOJAVA_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo

Secondary strucuture calculated and assigned by DSSP of BioJava

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

 

BIOLOGICAL_PROCESS - Enum constant in enum class org.forester.go.GoNameSpace.GoNamespaceType

 

BIOLOGICAL_PROCESS_STR - Static variable in class org.forester.go.GoNameSpace

 

BiologicalAssemblyBuilder - Class in org.biojava.nbio.structure.quaternary

Reconstructs the quaternary structure of a protein from an asymmetric unit

BiologicalAssemblyBuilder() - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder

 

BiologicalAssemblyTransformation - Class in org.biojava.nbio.structure.quaternary

The transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file.

BiologicalAssemblyTransformation() - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Default Constructor

BiologicalAssemblyTransformation(BiologicalAssemblyTransformation) - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Copy Constructor

bioStart() - Method in class org.biojava.nbio.genome.parsers.gff.Location

Get start index, in biocoordinates.

bioStrand() - Method in class org.biojava.nbio.genome.parsers.gff.Location

Get character representation of strand.

BioUnitDataProvider - Interface in org.biojava.nbio.structure.quaternary.io

Provides access to the data that is needed in order to rebuild the correct biological assembly of a protein.

BioUnitDataProviderFactory - Class in org.biojava.nbio.structure.quaternary.io

Factory to create BioUnitDataProvider instances.

BitArrayWorker(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.

Bk - Enum constant in enum class 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 - Class in org.forester.archaeopteryx.tools

 

Blast() - Constructor for class org.forester.archaeopteryx.tools.Blast

 

BLAST_PROGRAM - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

 

BlastAlignmentParameterEnum - Enum Class 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 Class in org.biojava.nbio.ws.alignment.qblast

Enum representing matrices supported by QBlast

blastn - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum

 

BlastOutputAlignmentFormatEnum - Enum Class in org.biojava.nbio.ws.alignment.qblast

Enum representing available output alignment types.

BlastOutputFormatEnum - Enum Class in org.biojava.nbio.ws.alignment.qblast

Enum representing available output formats.

BlastOutputParameterEnum - Enum Class in org.biojava.nbio.ws.alignment.qblast

Output parameters accepted by QBlast service.

blastp - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum

 

BlastProgramEnum - Enum Class 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 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum

 

BlastXMLParser - Class in org.biojava.nbio.core.search.io.blast

Re-designed by Paolo Pavan on the footprint of: org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis You may want to find my contacts on Github and LinkedIn for code info or discuss major changes.

BlastXMLParser() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastXMLParser

 

BlastXMLQuery - Class in org.biojava.nbio.genome.query

 

BlastXMLQuery(String) - Constructor for class org.biojava.nbio.genome.query.BlastXMLQuery

 

Block - Interface in org.biojava.nbio.structure.align.multiple

A Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in a sequential order.

BlockImpl - Class in org.biojava.nbio.structure.align.multiple

General implementation of a Block that supports any type of sequential alignment with gaps.

BlockImpl(BlockImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl

Copy constructor.

BlockImpl(BlockSet) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl

Constructor.

blockInfo(AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer

get the afp list and residue list for each block

BlockSet - Interface in org.biojava.nbio.structure.align.multiple

A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment.

BlockSetImpl - Class in org.biojava.nbio.structure.align.multiple

A general implementation of a BlockSet to store a flexible part of a multiple alignment.

BlockSetImpl(BlockSetImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl

Copy constructor.

BlockSetImpl(MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl

Constructor.

BLOSUM45 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum

 

BLOSUM50 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum

 

Blosum62 - Static variable in class org.biojava.nbio.ronn.RonnConstraint

 

BLOSUM62 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum

 

BLOSUM80 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum

 

BLOSUM90 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum

 

Blues - Enum constant in enum class org.jcolorbrewer.ColorBrewer

 

BMP - Enum constant in enum class org.forester.archaeopteryx.AptxUtil.GraphicsExportType

 

BOLD - Enum constant in enum class org.forester.phylogeny.data.NodeVisualData.FontType

 

BOLD_ITALIC - Enum constant in enum class org.forester.phylogeny.data.NodeVisualData.FontType

 

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

 

bondOutlier - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

 

BondOutlier - Class in org.biojava.nbio.structure.validation

Java class for anonymous complex type.

BondOutlier() - Constructor for class org.biojava.nbio.structure.validation.BondOutlier

 

BONDS_INITIAL_CAPACITY - Static variable in class org.biojava.nbio.structure.AtomImpl

The inital capacity of the bonds list.

BondType - Enum Class in org.biojava.nbio.structure

Work in progress - NOT final!

BootstrapResampler - Class in org.forester.evoinference.tools

 

BootstrapResampler() - Constructor for class org.forester.evoinference.tools.BootstrapResampler

 

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(Atom[]) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox

Constructs a BoundingBox by calculating maxs and mins of given array of atoms.

BoundingBox(BoundingBox) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox

 

BoundingBox(BoundingBox[]) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox

Given a set of bounding boxes returns a bounding box that bounds all of them.

bounds() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList

The union of all locations of all features in this list, mapped to the positive strand.

Br - Enum constant in enum class org.biojava.nbio.structure.Element

 

BRANCH - Static variable in class org.forester.archaeopteryx.TreeColorSet

 

BRANCH_LENGTH - Static variable in class org.forester.archaeopteryx.TreeColorSet

 

BRANCH_LENGTH - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

BRANCH_LENGTH_DEFAULT - Static variable in class org.forester.phylogeny.data.PhylogenyDataUtil

Value of -99.0 is used as default value.

BRANCH_WIDTH_DEFAULT_VALUE - Static variable in class org.forester.phylogeny.data.BranchWidth

 

BranchColor - Class in org.forester.phylogeny.data

 

BranchColor() - Constructor for class org.forester.phylogeny.data.BranchColor

 

BranchColor(Color) - Constructor for class org.forester.phylogeny.data.BranchColor

 

BranchCountingBasedScoringMethod - Class in org.forester.pccx

 

BranchCountingBasedScoringMethod() - Constructor for class org.forester.pccx.BranchCountingBasedScoringMethod

 

BranchData - Class in org.forester.phylogeny.data

 

BranchData() - Constructor for class org.forester.phylogeny.data.BranchData

 

BranchLengthBasedScoringMethod - Class in org.forester.pccx

 

BranchLengthBasedScoringMethod() - Constructor for class org.forester.pccx.BranchLengthBasedScoringMethod

 

BranchWidth - Class in org.forester.phylogeny.data

 

BranchWidth() - Constructor for class org.forester.phylogeny.data.BranchWidth

 

BranchWidth(double) - Constructor for class org.forester.phylogeny.data.BranchWidth

 

BranchWidthParser - Class in org.forester.io.parsers.phyloxml.data

 

BravaisLattice - Enum Class in org.biojava.nbio.structure.xtal

An enum to represent the 7 Bravais lattices

BrBG - Enum constant in enum class org.jcolorbrewer.ColorBrewer

 

Breslow - Enum constant in enum class org.biojava.nbio.survival.cox.CoxMethod

 

bridge - Enum constant in enum class org.biojava.nbio.structure.secstruc.SecStrucType

 

BridgeType - Enum Class in org.biojava.nbio.structure.secstruc

A bridge is formed by two non-overlapping stretches of three residues each (i-1,i,i+1) and (j-1,j,j+1), where i<j.

BROAD_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

 

BROAD_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym

 

BrowserOpener - Class in org.biojava.nbio.structure.align.webstart

 

BrowserOpener() - Constructor for class org.biojava.nbio.structure.align.webstart.BrowserOpener

 

BUFFER_ONLY - Enum constant in enum class org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON

 

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.

BuGn - Enum constant in enum class org.jcolorbrewer.ColorBrewer

 

build - Static variable in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry

 

build() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

The method to finish any calls to the builder with which returns a transcription engine.

build() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

 

build() - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder

Build and return a new FASTQ formatted sequence configured from the properties of this builder.

buildChooser() - Method in class org.jcolorbrewer.ui.DivergingColorPalettePanel

 

buildChooser() - Method in class org.jcolorbrewer.ui.QualitativeColorPalettePanel

 

buildChooser() - Method in class org.jcolorbrewer.ui.SequentialColorPalettePanel

 

builder() - Static method in class org.biojava.nbio.sequencing.io.fastq.Fastq

Create and return a new FastqBuilder.

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

 

bulkSolventB - Variable in class org.biojava.nbio.structure.validation.Entry

 

bulkSolventK - Variable in class org.biojava.nbio.structure.validation.Entry

 

BuPu - Enum constant in enum class org.jcolorbrewer.ColorBrewer

 

BY_ALGORITHM - Enum constant in enum class org.forester.rio.RIO.REROOTING

 

BYTES_PER_INT - Static variable in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

 

bytesRead - Variable in class org.biojava.nbio.ontology.obo.OboFileParser

 

C

c - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange

first allowed c-term

C - Enum constant in enum class org.biojava.nbio.aaproperties.CommandPrompt.PropertyName

 

C - Enum constant in enum class org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode

 

C - Enum constant in enum class org.biojava.nbio.structure.Element

 

C - Enum constant in enum class org.forester.evoinference.matrix.character.CharacterStateMatrix.NucleotideStates

 

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

C2RotationSolver - Class in org.biojava.nbio.structure.symmetry.core

 

C2RotationSolver(Subunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.C2RotationSolver

 

C3_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools

The atom name of the backbone C3' in RNA

C4_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools

The atom name of the backbone C4' in RNA

Ca - Enum constant in enum class org.biojava.nbio.structure.Element

 

CA_AND_SIDE_CHAIN_ANGLE_SCORING - Enum constant in enum class org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

 

CA_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools

The atom name of the backbone C-alpha atom.

CA_MIN_DIST - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc

min distance of two CA atoms if H-bonds are allowed to form

CA_SCORING - Enum constant in enum class org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

 

cache - Variable in class org.biojava.nbio.structure.align.client.FarmJobRunnable

 

cache(K, V) - Method in class org.biojava.nbio.structure.domain.SerializableCache

This will not cache null values.

CACHE_PROPERTY - Static variable in class org.biojava.nbio.core.util.InputStreamProvider

 

CachedRemoteScopInstallation - Class in org.biojava.nbio.structure.scop

An extension of the RemoteScopInstallation that caches some of the data locally.

CachedRemoteScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation

 

CachedRemoteScopInstallation(boolean) - Constructor for class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation

 

CacheFactory - Class in org.biojava.nbio.structure.align.util

provides a SoftHashMap singleton.

cacheFileName - Variable in class org.biojava.nbio.structure.domain.SerializableCache

 

CAConverter - Class in org.biojava.nbio.structure.io

Converts full atom representations to Calpha only ones.

CAConverter() - Constructor for class org.biojava.nbio.structure.io.CAConverter

 

calAfpRmsd(int, int[], int, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer

//return the rmsd of the residues from the segments that form the given AFP list //this value can be a measurement (1) for the connectivity of the AFPs

Calc - Class in org.biojava.nbio.structure

Utility operations on Atoms, AminoAcids, etc.

Calc() - Constructor for class org.biojava.nbio.structure.Calc

 

calc_rmsd(Atom[], Atom[], int, boolean) - 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.CECalculator

Deprecated.

Use CECalculator.calc_rmsd(Atom[],Atom[],int,boolean) instead

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.

calcBasicGapinessStatistics(Msa) - Static method in class org.forester.msa.MsaMethods

 

CalcBioAssemblySymmetry - Class in org.biojava.nbio.structure.symmetry.analysis

 

CalcBioAssemblySymmetry(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry

 

calcCenterOfRotation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner

 

calcColor(double, double, double, double, Color, Color, Color) - Static method in class org.forester.util.ForesterUtil

This calculates a color.

calcColor(double, double, double, Color, Color) - Static method in class org.forester.util.ForesterUtil

This calculates a color.

calcFractionalDissimilarities(Msa) - Static method in class org.forester.evoinference.distance.PairwiseDistanceCalculator

 

calcGappiness() - Method in class org.forester.msa.DeleteableMsa

 

calcGapRatio(Msa) - Static method in class org.forester.msa.MsaMethods

 

calcGapSumPerColumn(Msa, int) - Static method in class org.forester.msa.DeleteableMsa

 

calcGapSumPerColumn(Msa, int) - Static method in class org.forester.msa.MsaMethods

 

calcIdSimilarity(char[], char[], int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay

 

calcKimuraDistances(Msa) - Static method in class org.forester.evoinference.distance.PairwiseDistanceCalculator

 

calcKimuraDistances(Msa, double) - Static method in class org.forester.evoinference.distance.PairwiseDistanceCalculator

 

calcLength(List<ResidueRangeAndLength>) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength

Calculates the combined number of residues of the ResidueRanges in rrs.

calcNormalizedShannonsEntropy(int, Msa) - Static method in class org.forester.msa.MsaMethods

 

calcNormalizedShannonsEntropy(int, Msa, int) - Static method in class org.forester.msa.MsaMethods

 

calcNumberOfGaps(MolecularSequence) - Static method in class org.forester.msa.MsaMethods

 

calcNumberOfGapsInMsa(Msa) - Static method in class org.forester.msa.MsaMethods

 

calcNumberOfGapsStats(Msa) - Static method in class org.forester.msa.MsaMethods

 

calcPairwiseAlignments() - Method in class org.biojava.nbio.structure.symmetry.core.ClusterMerger

Aligns all pairs of input clusters, calculating their pairwise alignments

calcPoissonDistances(Msa) - Static method in class org.forester.evoinference.distance.PairwiseDistanceCalculator

 

calcQuatSymmetry(Subunits, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector

 

calcRotationAngleInDegrees(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Calculates the angle from centerPt to targetPt in degrees.

calcScale(int) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay

a value of 100 means that the whole sequence should be displayed in the current visible window a factor of 1 means that one amino acid shoud be drawn as big as possible

calcScores(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

calculates scores for this alignment ( %id )

calcScores(Subunits, Matrix4d, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer

Returns minimum, mean, and maximum RMSD and TM-Score for two superimposed sets of subunits TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)

calcSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain

 

calcTree() - Method in class org.forester.msa_compactor.MsaCompactor

 

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.

calculateBranchLengthStatistics(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

calculateColorFromString(String, boolean) - Static method in class org.forester.archaeopteryx.AptxUtil

 

calculateConfidenceStatistics(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

calculateCopyNumberDifferences(List<GenomeWideCombinableDomains>, SortedMap<Species, List<Protein>>, List<String>, List<String>, List<String>, int, Double, File, File, File, Map<String, List<GoId>>, Map<GoId, GoTerm>, File, File, File) - Static method in class org.forester.surfacing.DomainCountsDifferenceUtil

 

calculateCoverage(List<Phylogeny>, List<String>, boolean) - Method in class org.forester.pccx.CoverageCalculator

 

calculateCoverage(List<Phylogeny>, List<String>, CoverageCalculationOptions, boolean) - Method in interface org.forester.pccx.CoverageCalculationMethod

 

calculateCoverage(List<Phylogeny>, List<String>, CoverageCalculationOptions, boolean) - Method in class org.forester.pccx.ExternalNodeBasedCoverageMethod

 

calculateDepth() - Method in class org.forester.phylogeny.PhylogenyNode

 

calculateDescriptiveStatisticsForMeanValues(Set<DomainSimilarity>) - Static method in class org.forester.surfacing.SurfacingUtil

 

calculatedFragmentPairs(List<FragmentPair>) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener

 

calculateDistance(PhylogenyNode, PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Calculates the distance between PhylogenyNodes node1 and node2.

calculateDistanceToRoot() - Method in class org.forester.phylogeny.PhylogenyNode

 

calculateEffectiveLengthStatistics(Msa) - Static method in class org.forester.msa.MsaMethods

 

calculateIdentityRatio(int, int, Msa) - Static method in class org.forester.msa.MsaMethods

 

calculateIdentityRatio(Msa, int) - Static method in class org.forester.msa.MsaMethods

 

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

calculateLCA(PhylogenyNode, PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Returns the LCA of PhylogenyNodes node1 and node2.

calculateLCAonTreeWithIdsInPreOrder(PhylogenyNode, PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Returns the LCA of PhylogenyNodes node1 and node2.

calculateMaxBranchesToLeaf(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

calculateMaxDepth(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

calculateMaxDistanceToRoot(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

calculateMeanBasedStatistics() - Method in class org.forester.surfacing.DomainLengths

Returns descriptive statistics based on the arithmetic means for each species.

calculateMeanBasedStatisticsForAllSpecies() - Method in class org.forester.surfacing.DomainLengthsTable

 

calculateMeanBasedStatisticsForDomain(String) - Method in class org.forester.surfacing.DomainLengthsTable

 

calculateMeanBasedStatisticsForSpecies(Species) - Method in class org.forester.surfacing.DomainLengthsTable

 

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.

calculateNodeWithMaxDistanceToRoot(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

calculateNumberOfDescendantsPerNodeStatistics(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

calculateNumberOfExternalNodesWithoutTaxonomy(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

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

 

calculateOrthologTable(Phylogeny[], boolean) - Static method in class org.forester.rio.RIO

 

calculateOverlap(Domain, List<Boolean>) - Static method in class org.forester.util.ForesterUtil

 

calculateResidueDestributionPerColumn(Msa, int) - Static method in class org.forester.msa.MsaMethods

 

calculateScoreForExternalNode(SortedMap<PhylogenyNode, Double>, Phylogeny, PhylogenyNode, CoverageCalculationOptions) - Method in class org.forester.pccx.BranchCountingBasedScoringMethod

 

calculateScoreForExternalNode(SortedMap<PhylogenyNode, Double>, Phylogeny, PhylogenyNode, CoverageCalculationOptions) - Method in interface org.forester.pccx.ScoringMethodForExternalNode

This calculates the coverage score for one external node.

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.

calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

This returns a score between 0.0 (no binary domain combination in common) and 1.0 (all binary domain combinations in common) measuring the similarity between two genomes based on the number of shared binary domain combinations: t: sum of (distinct) binary domain combinations s: sum of shared (distinct) binary domain combinations 1 - ( ( t - s ) / t )

calculateSharedDomainsBasedGenomeSimilarityScore() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

This returns a score between 0.0 (no domains in common) and 1.0 (all domains in common) measuring the similarity between two genomes based on the number of shared domains: t: sum of (distinct) domains s: sum of shared (distinct) domains 1 - ( ( t - s ) / t )

calculateSimilarities(PairwiseDomainSimilarityCalculator, List<GenomeWideCombinableDomains>, boolean, boolean) - Method in class org.forester.surfacing.BasicDomainSimilarityCalculator

 

calculateSimilarities(PairwiseDomainSimilarityCalculator, List<GenomeWideCombinableDomains>, boolean, boolean) - Method in interface org.forester.surfacing.DomainSimilarityCalculator

 

calculateSimilarity(CombinableDomains, CombinableDomains) - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator

 

calculateSimilarity(CombinableDomains, CombinableDomains) - Method in class org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator

 

calculateSimilarity(CombinableDomains, CombinableDomains) - Method in interface org.forester.surfacing.PairwiseDomainSimilarityCalculator

 

calculateSimilarity(CombinableDomains, CombinableDomains) - Method in class org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator

 

calculateSubtreeHeight(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny

This calculates the height of the subtree emanating at n for rooted, tree-shaped phylogenies

calculateSuperpositionByIdx(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

 

calculateWaldTestInfo(CoxInfo) - Static method in class org.biojava.nbio.survival.cox.CoxR

 

calculateZScoreForSpecies(Species) - Method in class org.forester.surfacing.DomainLengths

Note.

calculator - Variable in class org.biojava.nbio.structure.align.ce.CeMain

 

call() - Method in class org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner

 

call() - Method in class org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer

 

call() - Method in class org.biojava.nbio.alignment.template.CallableProfileProfileAligner

 

call() - Method in class org.biojava.nbio.ronn.ORonn

 

call() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

 

call() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer

 

CallablePairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template

Implements a concurrency wrapper for a PairwiseSequenceAligner.

CallablePairwiseSequenceAligner(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner

Creates a pairwise sequence alignment task for simplified parallel execution.

CallablePairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template

Implements a concurrency wrapper for a PairwiseSequenceScorer.

CallablePairwiseSequenceScorer(PairwiseSequenceScorer<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer

Creates a pairwise sequence scoring task for simplified parallel execution.

CallableProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template

Implements a concurrency wrapper for a ProfileProfileAligner.

CallableProfileProfileAligner(ProfileProfileAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallableProfileProfileAligner

Creates a profile-profile alignment task for simplified parallel execution.

CallableStructureAlignment - Class in org.biojava.nbio.structure.align

 

CallableStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment

Default constructor.

CallableStructureAlignment(Atom[], Atom[], String, ConfigStrucAligParams) - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment

Constructor for all-to-all alignment calculation.

calNS(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva

 

calSigAll(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva

 

canComplement(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

Uses the Sequence's CompoundSet to decide if a compound can be assgined to ComplementCompound meaning it can complement

canDoMsa() - Method in class org.forester.archaeopteryx.tools.InferenceManager

 

CartesianProduct<T> - Class in org.biojava.nbio.structure.quaternary

A cartesian product between two lists A and B is the set of all ordered pairs of the elements of both sets.

CartesianProduct(List<T>, List<T>) - Constructor for class org.biojava.nbio.structure.quaternary.CartesianProduct

Class constructor specifying the two lists of a cartesian product.

CARTOON - Enum constant in enum class org.biojava.nbio.structure.gui.RenderStyle

 

CaseFreeAminoAcidCompoundSet - Class in org.biojava.nbio.aaproperties.xml

Set of proteinogenic amino acids.

CaseFreeAminoAcidCompoundSet() - Constructor for class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet

 

CaseInsensitiveCompound - Class in org.biojava.nbio.core.sequence.transcription

Attempts to wrap compounds so it is possible to view them in a case insensitive manner

CaseInsensitiveCompound(NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

 

CaseInsensitiveTriplet(NucleotideCompound, NucleotideCompound, NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet

 

CasePreservingProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io

A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.

CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

 

categorizeData(ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper

Take a collection of categorical data and convert it to numeric to be used in cox calculations

CATH - Enum constant in enum class 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 Class 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

ccp4Version - Variable in class org.biojava.nbio.structure.validation.Entry

 

Cd - Enum constant in enum class org.biojava.nbio.structure.Element

 

CDD_SEARCH - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

 

CDS - Static variable in class org.biojava.nbio.genome.util.ChromosomeMappingTools

 

CDSComparator - Class in org.biojava.nbio.core.sequence

 

CDSComparator() - Constructor for class org.biojava.nbio.core.sequence.CDSComparator

 

CDSSequence - Class in org.biojava.nbio.core.sequence

Represents a exon or coding sequence in a gene.

CDSSequence(TranscriptSequence, int, int, int) - Constructor for class org.biojava.nbio.core.sequence.CDSSequence

 

Ce - Enum constant in enum class 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

 

ceColumnNames - Static variable in class org.biojava.nbio.structure.align.gui.DBResultTable

 

CeCPMain - Class in org.biojava.nbio.structure.align.ce

A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.

CeCPMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain

 

CeCPMain.CPRange - Class in org.biojava.nbio.structure.align.ce

Tiny wrapper for the disallowed regions of an alignment.

CECPParameters - Class in org.biojava.nbio.structure.align.ce

Provides parameters to CeCPMain

CECPParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CECPParameters

 

CECPParameters.DuplicationHint - Enum Class in org.biojava.nbio.structure.align.ce

 

CeCPStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

 

CeCPUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce

 

CeCPUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor

 

CeCPUserArgumentProcessor.CeCPStartupParams - Class in org.biojava.nbio.structure.align.ce

 

ceil(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable

Return the smallest key in the table >= k.

Cell - Class in org.biojava.nbio.structure.io.mmcif.model

 

Cell() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Cell

 

CELLTRANSL - Enum constant in enum class org.biojava.nbio.structure.xtal.TransformType

 

CELLULAR_COMPONENT - Enum constant in enum class org.forester.go.GoNameSpace.GoNamespaceType

 

CELLULAR_COMPONENT_STR - Static variable in class org.forester.go.GoNameSpace

 

CELLULAR_ORGANISMS - Static variable in class org.forester.ws.seqdb.UniProtTaxonomy

 

CeMain - Class in org.biojava.nbio.structure.align.ce

The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.

CeMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeMain

 

censored - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

 

CensorStatus - Class in org.biojava.nbio.survival.kaplanmeier.figure

 

CensorStatus() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

 

CensorStatus(String, Double, String) - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

 

CensorStatusSelect - Interface in org.biojava.nbio.survival.kaplanmeier.figure

 

center(Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

 

centerAtoms(Atom[]) - Static method in class org.biojava.nbio.structure.Calc

Center the atoms at the Centroid.

centerAtoms(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc

Center the atoms at the Centroid, if the centroid is already know.

centerOfMass() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia

 

centerOfMass(Atom[]) - Static method in class org.biojava.nbio.structure.Calc

 

centricOutliers - Variable in class org.biojava.nbio.structure.validation.Entry

 

centroid(Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

 

CeParameters - Class in org.biojava.nbio.structure.align.ce

Contains the parameters that can be sent to CE

CeParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CeParameters

 

CeParameters.ScoringStrategy - Enum Class in org.biojava.nbio.structure.align.ce

 

CeSideChainMain - Class in org.biojava.nbio.structure.align.ce

 

CeSideChainMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainMain

 

CeSideChainUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce

 

CeSideChainUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor

 

CeStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

 

CeSymm - Class in org.biojava.nbio.structure.symmetry.internal

Identify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment.

CeSymmIterative - Class in org.biojava.nbio.structure.symmetry.internal

Iterative version of CeSymm that aims at identifying all symmetry axis of a structure.

CeSymmIterative(CESymmParameters) - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative

For the iterative algorithm to work properly the refinement and optimization options should be turned on, because the alignment has to be consistent at every recursive step.

CESymmParameters - Class in org.biojava.nbio.structure.symmetry.internal

Provides parameters to CeSymm.

CESymmParameters() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

 

CESymmParameters.OrderDetectorMethod - Enum Class in org.biojava.nbio.structure.symmetry.internal

 

CESymmParameters.RefineMethod - Enum Class in org.biojava.nbio.structure.symmetry.internal

 

CESymmParameters.SymmetryType - Enum Class in org.biojava.nbio.structure.symmetry.internal

The internal symmetry detection can be divided into two types: CLOSE: includes the circular and dihedral symmetries, and OPEN: includes the helical and protein repeats symmetries.

CeSymmResult - Class in org.biojava.nbio.structure.symmetry.internal

This Class stores all the relevant information of an internal symmetry result obtained with CeSymm.

CeSymmResult() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

 

CeUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce

process the arguments from command line

CeUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor

 

CeUserArgumentProcessor.CeStartupParams - Class in org.biojava.nbio.structure.align.ce

 

Cf - Enum constant in enum class org.biojava.nbio.structure.Element

 

chain - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

 

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

 

ChainClusterer - Class in org.biojava.nbio.structure.symmetry.core

Wraps a sequence clustering with structural information

ChainClusterer(List<SequenceAlignmentCluster>) - Constructor for class org.biojava.nbio.structure.symmetry.core.ChainClusterer

 

chainEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

 

chainId - Variable in class org.biojava.nbio.structure.align.client.StructureName

 

CHAINID_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier

URL parameter specifying a single chain to include; overridden by residues

ChainImpl - Class in org.biojava.nbio.structure

A Chain in a PDB file.

ChainImpl() - Constructor for class org.biojava.nbio.structure.ChainImpl

Constructs a ChainImpl object.

ChainSignature - Class in org.biojava.nbio.structure.symmetry.misc

 

ChainSignature(String, int, List<String>) - Constructor for class org.biojava.nbio.structure.symmetry.misc.ChainSignature

 

change(String) - Method in interface org.biojava.nbio.survival.data.ChangeValue

 

changeColumnHeader(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

 

characters(char[], int, int) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler

 

characters(char[], int, int) - Method in class org.forester.io.parsers.tol.TolXmlHandler

 

CharacterStateMatrix<S> - Interface in org.forester.evoinference.matrix.character

 

CharacterStateMatrix.BinaryStates - Enum Class in org.forester.evoinference.matrix.character

It is crucial that the order ABSENT, UNKNOWN, PRESENT not be changes since this determines the sort order.

CharacterStateMatrix.Format - Enum Class in org.forester.evoinference.matrix.character

 

CharacterStateMatrix.GainLossStates - Enum Class in org.forester.evoinference.matrix.character

 

CharacterStateMatrix.NucleotideStates - Enum Class in org.forester.evoinference.matrix.character

 

charAt(int) - Method in class org.biojava.nbio.survival.data.CompactCharSequence

 

CHARGE - Enum constant in enum class 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

 

CHARSTATELABELS - Static variable in class org.forester.io.parsers.nexus.NexusConstants

 

chart(int, boolean, boolean) - Method in class org.forester.msa_compactor.MsaCompactor

 

Chart - Class in org.forester.msa_compactor

 

check_fasta - Class in org.forester.application

 

check_fasta() - Constructor for class org.forester.application.check_fasta

 

checkDoFirstInstall() - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider

Checks if the chemical components already have been installed into the PDB directory.

checkFileExists(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

 

checkForOutputFileWriteability(File) - Static method in class org.forester.surfacing.SurfacingUtil

 

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.

checkWriteabilityForPairwiseComparisons(DomainSimilarity.PRINT_OPTION, String[][], String, File) - Static method in class org.forester.surfacing.SurfacingUtil

 

CHEM_COMP_CACHE_DIRECTORY - Static variable in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider

 

chem_comp_type - Variable in enum class org.biojava.nbio.structure.io.mmcif.chem.ResidueType

String value of the type

chemComp - Variable in class org.biojava.nbio.structure.HetatomImpl

 

ChemComp - Class in org.biojava.nbio.structure.io.mmcif.model

A definition for a Chemical Component, as maintained by the wwPDB.

ChemComp() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemComp

 

ChemCompAtom - Class in org.biojava.nbio.structure.io.mmcif.model

stores these fields: _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_residue_numbering _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_polymer_type _chem_comp_atom.pdbx_ref_id _chem_comp_atom.pdbx_component_id _chem_comp_atom.pdbx_ordinal

ChemCompAtom() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

 

ChemCompBond - Class in org.biojava.nbio.structure.io.mmcif.model

 

ChemCompBond() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

 

ChemCompConsumer - Class in org.biojava.nbio.structure.io.mmcif

 

ChemCompConsumer() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer

 

ChemCompDescriptor - Class in org.biojava.nbio.structure.io.mmcif.model

Container object for _pdbx_chem_comp_descriptor

ChemCompDescriptor() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

 

ChemCompGroupFactory - Class in org.biojava.nbio.structure.io.mmcif

 

ChemCompGroupFactory() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory

 

ChemCompProvider - Interface in org.biojava.nbio.structure.io.mmcif

Interface that is implemented by all classes that can provide ChemComp definitions.

ChemCompTools - Class in org.biojava.nbio.structure.io.mmcif.chem

Some tools for working with chemical compounds.

ChemCompTools() - Constructor for class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools

 

CHEMICAL_MODIFICATION - Enum constant in enum class org.biojava.nbio.protmod.ModificationCategory

 

ChemicalComponentDictionary - Class in org.biojava.nbio.structure.io.mmcif

A representation of the Chemical Component Dictionary.

ChemicalComponentDictionary() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary

 

children() - Method in class org.biojava.nbio.alignment.GuideTree.Node

 

chiSq(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

 

CHLOROPHYTA_COLOR - Static variable in class org.forester.util.TaxonomyColors

 

CHOANOFLAGELLIDA - Static variable in class org.forester.util.TaxonomyColors

 

chol() - Method in class org.biojava.nbio.structure.jama.Matrix

Cholesky Decomposition

Cholesky2 - Class in org.biojava.nbio.survival.cox.stats

 

Cholesky2() - Constructor for class org.biojava.nbio.survival.cox.stats.Cholesky2

 

CholeskyDecomposition - Class in org.biojava.nbio.structure.jama

Cholesky Decomposition.

CholeskyDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.CholeskyDecomposition

Cholesky algorithm for symmetric and positive definite matrix.

ChooseDirAction - Class in org.biojava.nbio.structure.align.gui

Ask the user to provide a directory containting PDB files.

ChooseDirAction(JTextField, UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.gui.ChooseDirAction

 

CHROMOSOME - Enum constant in enum class 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

 

cid - Variable in class org.biojava.nbio.structure.validation.Clash

 

CIF - Enum constant in enum class org.biojava.nbio.structure.StructureIO.StructureFiletype

 

CIFLabel - Annotation Interface in org.biojava.nbio.structure.io.mmcif.model

Annotation indicating that a specific field of a bean should be mapped to a different label

CIRCLE - Enum constant in enum class org.forester.phylogeny.data.NodeVisualData.NodeShape

 

CIRCULAR - Enum constant in enum class org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE

 

CIRCULAR_DNA - Static variable in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

 

circularLocation(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Converts a location which defines the outer bounds of a circular location and splits it into the required portions.

circularLocation(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools

Converts a location which defines the outer bounds of a circular location and splits it into the required portions.

Cl - Enum constant in enum class org.biojava.nbio.structure.Element

 

CLADE - Enum constant in enum class org.forester.phylogeny.data.Property.AppliesTo

 

CLADE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

CLADE - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

 

CLADE_DATE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

CLADE_DATE_DESC - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

CLADE_DATE_MAX - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

CLADE_DATE_MIN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

CLADE_DATE_UNIT - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

CLADE_DATE_VALUE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

CLADE_NAME - Enum constant in enum class org.forester.phylogeny.PhylogenyMethods.PhylogenyNodeField

 

claFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation

 

clash - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup

 

Clash - Class in org.biojava.nbio.structure.validation

Java class for anonymous complex type.

Clash() - Constructor for class org.biojava.nbio.structure.validation.Clash

 

clashmag - Variable in class org.biojava.nbio.structure.validation.Clash

 

clashmag - Variable in class org.biojava.nbio.structure.validation.SymmClash

 

clashscore - Variable in class org.biojava.nbio.structure.validation.Entry

 

Class - Enum constant in enum class org.biojava.nbio.structure.cath.CathCategory

 

Class - Enum constant in enum class org.biojava.nbio.structure.scop.ScopCategory

 

CLASS - Enum constant in enum class org.forester.ws.wabi.TxSearch.RANKS

 

CLASS - Enum constant in enum class org.forester.ws.wabi.TxSearch.TAX_RANK

 

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 class org.biojava.nbio.structure.align.gui.AlignmentCalcDB

 

cleanup() - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable

 

cleanup() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc

 

cleanup() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch

 

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

 

clear() - Method in class org.biojava.nbio.core.util.FlatFileCache

 

clear() - Method in class org.biojava.nbio.core.util.SoftHashMap

 

clear() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider

reset all suggestions

clear() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider

 

clear() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider

 

clear() - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache

Clear the cached scores.

clear() - Method in interface org.biojava.nbio.structure.align.multiple.Block

Clear scores and other properties which depend on the specific alignment.

clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

 

clear() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Clear scores and other properties which depend on the specific alignment.

clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

 

clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Clear scores and other properties which depend on the specific alignment.

clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Clear scores and other properties which depend on the specific alignment.

clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

 

clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

 

clear() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Clears all domains, requiring the file to be reparsed for subsequent accesses

clear() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl

 

clear() - Method in interface org.biojava.nbio.structure.gui.Selection

 

clear() - Method in class org.biojava.nbio.structure.gui.SelectionImpl

 

clear() - Method in interface org.biojava.nbio.structure.gui.StructureViewer

Clear the current display

clear() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper

Clears all finite endpoints

clear() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

 

clear() - Method in class org.biojava.nbio.survival.data.WorkSheet

See if we can free up memory

clear() - Method in class org.forester.datastructures.Queue

Removes all elements from this queue.

clearAlgorithms() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory

Removes all algorithms from the list

clearAtoms() - Method in interface org.biojava.nbio.structure.Group

Remove all atoms from this group.

clearAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl

remove all atoms

clearCache() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence

 

clearCache() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence

Nullifies cached arrays/objects.

clearCache() - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory

Force the in-memory cache to be reset.

clearCache() - Static method in class org.biojava.nbio.structure.PDBStatus

The status of PDB IDs are cached to reduce server overload.

clearConsumers() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser

Remove all consumers from the parser.

clearConsumers() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

 

clearExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

clear the supported file extensions

clearHashIdToNodeMap() - Method in class org.forester.phylogeny.Phylogeny

 

clearListeners() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable

 

clearListeners() - Method in class org.biojava.nbio.structure.align.FarmJob

 

clearListeners() - Method in class org.biojava.nbio.structure.align.StructurePairAligner

 

clearListeners() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay

 

clearListeners() - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener

 

ClinicalMetaDataOutcome - Class in org.biojava.nbio.survival.kaplanmeier.metadata

 

ClinicalMetaDataOutcome() - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome

 

CliTools - Class in org.biojava.nbio.structure.align.util

Utilities for autoconfiguring javabeans based on command line arguments.

clone() - Method in class org.biojava.nbio.structure.align.model.AFPChain

Creates and returns a copy of this object.

clone() - Method in interface org.biojava.nbio.structure.align.multiple.Block

Creates and returns an identical copy of this block.

clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

 

clone() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Creates and returns an identical copy of this blockset, including a deep copy of all constituent Blocks.

clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

 

clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Creates and returns an identical copy of this alignment, including a deep copy of all constituent BlockSets.

clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Creates and returns an identical copy of this ensemble, including a deep clone of all constituent alignments.

clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

 

clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

 

clone() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

 

clone() - Method in class org.biojava.nbio.structure.AminoAcidImpl

returns and identical copy of this Group object .

clone() - Method in class org.biojava.nbio.structure.asa.GroupAsa

 

clone() - Method in interface org.biojava.nbio.structure.Atom

Return an identical copy of this object .

clone() - Method in class org.biojava.nbio.structure.AtomImpl

returns and identical copy of this object .

clone() - Method in interface org.biojava.nbio.structure.Chain

returns an identical copy of this Chain.

clone() - Method in class org.biojava.nbio.structure.ChainImpl

Returns an identical copy of this Chain .

clone() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

 

clone() - Method in interface org.biojava.nbio.structure.Group

returns and identical copy of this Group object .

clone() - Method in class org.biojava.nbio.structure.GroupIterator

Creates and returns a copy of this object.

clone() - Method in class org.biojava.nbio.structure.HetatomImpl

returns and identical copy of this Group object .

clone() - Method in class org.biojava.nbio.structure.io.SSBondImpl

 

clone() - Method in class org.biojava.nbio.structure.jama.Matrix

Clone the Matrix object.

clone() - Method in class org.biojava.nbio.structure.NucleotideImpl

 

clone() - Method in class org.biojava.nbio.structure.scop.ScopDescription

 

clone() - Method in class org.biojava.nbio.structure.scop.ScopDomain

 

clone() - Method in class org.biojava.nbio.structure.secstruc.HBond

 

clone() - Method in interface org.biojava.nbio.structure.Structure

Return an identical copy of this Structure object

clone() - Method in class org.biojava.nbio.structure.StructureImpl

returns an identical copy of this structure .

clone() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster

 

clone() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList

 

clone() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

 

clone() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

 

clone() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

 

clone() - Method in class org.forester.archaeopteryx.webservices.WebservicesManager

 

clone() - Method in class org.forester.evoinference.distance.PairwiseDistanceCalculator

 

clone() - Method in class org.forester.msa.MsaInferrer

 

clone() - Method in class org.forester.msa.MsaMethods

 

clone() - Method in class org.forester.phylogeny.factories.ParserBasedPhylogenyFactory

 

clone() - Method in class org.forester.phylogeny.PhylogenyMethods

 

clone() - Method in class org.forester.ws.seqdb.EbiDbEntry

 

clone() - Method in class org.forester.ws.seqdb.UniProtEntry

 

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.

cloneCAArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools

Deprecated.

Use the better-named StructureTools.cloneAtomArray(Atom[]) instead

cloneDM(BasicSymmetricalDistanceMatrix) - Static method in class org.biojava.nbio.phylo.ForesterWrapper

Helper function to clone a forester symmetrical DistanceMatrix.

cloneGroups(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools

Clone a set of representative Atoms, but returns the parent groups

clonePoint() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

 

clonePoint() - Method in interface org.biojava.nbio.core.sequence.location.template.Point

Returns a copy of this point

clonePoint3dArray(Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

 

close() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

 

close() - Method in class org.biojava.nbio.core.sequence.io.FastaReader

 

close() - Method in class org.biojava.nbio.core.sequence.io.GenbankReader

 

close() - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

 

close() - Method in interface org.biojava.nbio.core.util.XMLWriter

Close this XMLWriter, and it's underlying stream.

close() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser

Method closes current sequence and it's necessary to invoke it before setting new current sequence.

close() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile

 

close(Closeable) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Closes any Object which implements the interface Closeable and sending any error to the logger but not forcing any explicit catching of stream errors.

CLOSED - Enum constant in enum class 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

ClustalOmega - Class in org.forester.msa

 

CLUSTALW - Enum constant in enum class org.biojava.nbio.core.alignment.template.Profile.StringFormat

 

CLUSTALW - Enum constant in enum class org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat

 

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

 

ClusterAltAligs - Class in org.biojava.nbio.structure.align

A class that clusters alternative alignments according to their similarity.

ClusterAltAligs() - Constructor for class org.biojava.nbio.structure.align.ClusterAltAligs

 

ClusterDomains - Class in org.biojava.nbio.structure.domain.pdp

 

ClusterDomains() - Constructor for class org.biojava.nbio.structure.domain.pdp.ClusterDomains

 

ClusterMerger - Class in org.biojava.nbio.structure.symmetry.core

Merges clusters based on their sequence identity.

ClusterMerger(List<SequenceAlignmentCluster>, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ClusterMerger

 

ClusterProteinChains - Class in org.biojava.nbio.structure.symmetry.core

Clusters the chains of one or two structures by sequence.

ClusterProteinChains(Structure, Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains

 

ClusterProteinChains(Structure, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains

 

Cm - Enum constant in enum class org.biojava.nbio.structure.Element

 

CMD - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

 

CNIDARIA_COLOR - Static variable in class org.forester.util.TaxonomyColors

 

Co - Enum constant in enum class org.biojava.nbio.structure.Element

 

CODE - Enum constant in enum class org.forester.sdi.SDIutil.TaxonomyComparisonBase

 

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

 

coefficientOfVariation() - Method in class org.forester.util.BasicDescriptiveStatistics

 

coefficientOfVariation() - Method in interface org.forester.util.DescriptiveStatistics

Computes the coefficient of variation.

coil - Enum constant in enum class org.biojava.nbio.structure.secstruc.SecStrucType

 

COLLAPSED - Static variable in class org.forester.archaeopteryx.TreeColorSet

 

collapseSubtreeStructure(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

collapseWhiteSpace(String) - Static method in class org.forester.util.ForesterUtil

 

collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates>, BinaryDomainCombination.DomainCombinationType, List<BinaryDomainCombination>, boolean) - Static method in class org.forester.surfacing.SurfacingUtil

 

collection2file(File, Collection<?>, String) - Static method in class org.forester.util.ForesterUtil

 

collection2writer(Writer, Collection<?>, String) - Static method in class org.forester.util.ForesterUtil

 

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

 

COLOR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

COLOR_BLUE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

COLOR_GREEN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

COLOR_RED - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

ColorBrewer - Enum Class in org.jcolorbrewer

The data values were extracted from the RColorBrewer R package.

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

 

colorChooser - Variable in class org.jcolorbrewer.ui.ColorPaletteChooserDialog

The style editor panel.

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

 

ColorPaletteChooserDialog - Class in org.jcolorbrewer.ui

A ColorPaletteChooserDialog shows a dialog window for selecting a color palette.

ColorPaletteChooserDialog() - Constructor for class org.jcolorbrewer.ui.ColorPaletteChooserDialog

Create a non-modal color chooser dialog to select a color.

ColorPaletteChooserDialog(Dialog) - Constructor for class org.jcolorbrewer.ui.ColorPaletteChooserDialog

Create a modal color chooser dialog to select a color.

ColorPaletteChooserDialog(Frame) - Constructor for class org.jcolorbrewer.ui.ColorPaletteChooserDialog

Create a modal color chooser dialog to select a color.

ColorPanelSelectionModel - Class in org.jcolorbrewer.ui

 

ColorPanelSelectionModel() - Constructor for class org.jcolorbrewer.ui.ColorPanelSelectionModel

 

ColorParser - Class in org.forester.io.parsers.phyloxml.data

 

colorToHex(Color) - Static method in class org.forester.util.ForesterUtil

 

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

 

CombinableDomains - Interface in org.forester.surfacing

 

CombinationGenerator - Class in org.biojava.nbio.structure.symmetry.utils

 

CombinationGenerator(int, int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator

 

COMBINATIONS - Enum constant in enum class org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring

 

COMBINATIONS_COUNT - Enum constant in enum class org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder

 

CombinationsBasedPairwiseDomainSimilarity - Class in org.forester.surfacing

 

CombinationsBasedPairwiseDomainSimilarity(int, int, int) - Constructor for class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity

 

CombinationsBasedPairwiseDomainSimilarityCalculator - Class in org.forester.surfacing

 

CombinationsBasedPairwiseDomainSimilarityCalculator() - Constructor for class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator

 

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.

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

 

CommandLineArguments - Class in org.forester.util

 

CommandLineArguments(String[]) - Constructor for class org.forester.util.CommandLineArguments

 

CommandProcessBuilder - Class in org.forester.util

 

CommandProcessBuilder() - Constructor for class org.forester.util.CommandProcessBuilder

 

CommandPrompt - Class in org.biojava.nbio.aaproperties

 

CommandPrompt() - Constructor for class org.biojava.nbio.aaproperties.CommandPrompt

 

CommandPrompt.PropertyName - Enum Class in org.biojava.nbio.aaproperties

 

COMMENT - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

 

COMMENT_CHAR - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

 

COMMENT_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

 

COMMON_NAME - Enum constant in enum class org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS

 

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

 

compare(Phylogeny, Phylogeny, boolean, boolean, boolean) - Static method in class org.forester.tools.SupportCount

 

compare(StringInt, StringInt) - Method in class org.forester.util.StringInt.DescendingIntComparator

 

compareTo(Point) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint

 

compareTo(Point) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

 

compareTo(FastaSequence) - Method in class org.biojava.nbio.data.sequence.FastaSequence

 

compareTo(Cytoband) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband

 

compareTo(GeneChromosomePosition) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

 

compareTo(GeneName) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName

 

compareTo(Synonym) - Method in class org.biojava.nbio.ontology.Synonym

 

compareTo(ProteinModification) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

 

compareTo(ModifiedCompound) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

 

compareTo(StructureGroup) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

 

compareTo(PdbPair) - Method in class org.biojava.nbio.structure.align.client.PdbPair

 

compareTo(StructureName) - Method in class org.biojava.nbio.structure.align.client.StructureName

Orders identifiers lexicographically by PDB ID and then full Identifier

compareTo(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterface

 

compareTo(Domain) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

 

compareTo(Segment) - Method in class org.biojava.nbio.structure.domain.pdp.Segment

 

compareTo(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp

 

compareTo(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber

 

compareTo(Site) - Method in class org.biojava.nbio.structure.Site

 

compareTo(ChainSignature) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

 

compareTo(SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo

 

compareTo(SurvivalInfoIndex) - Method in class org.biojava.nbio.survival.cox.SurvivalInfoIndex

 

compareTo(CensorStatus) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

 

compareTo(HmmerDomain) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain

 

compareTo(HmmerResult) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult

 

compareTo(OntologizerResult) - Method in class org.forester.go.etc.OntologizerResult

 

compareTo(GoId) - Method in class org.forester.go.GoId

 

compareTo(GoRelationship) - Method in class org.forester.go.BasicGoRelationship

 

compareTo(GoSubset) - Method in class org.forester.go.BasicGoSubset

 

compareTo(GoTerm) - Method in class org.forester.go.BasicGoTerm

Compares based on GO id.

compareTo(GoXRef) - Method in class org.forester.go.BasicGoXRef

 

compareTo(Mapping) - Method in class org.forester.go.PfamToGoMapping

 

compareTo(GapContribution) - Method in class org.forester.msa_compactor.GapContribution

 

compareTo(Accession) - Method in class org.forester.phylogeny.data.Accession

 

compareTo(Annotation) - Method in class org.forester.phylogeny.data.Annotation

 

compareTo(Confidence) - Method in class org.forester.phylogeny.data.Confidence

 

compareTo(Sequence) - Method in class org.forester.phylogeny.data.Sequence

 

compareTo(Taxonomy) - Method in class org.forester.phylogeny.data.Taxonomy

 

compareTo(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode

 

compareTo(BinaryDomainCombination) - Method in class org.forester.surfacing.BasicBinaryDomainCombination

 

compareTo(Domain) - Method in class org.forester.protein.BasicDomain

Basic domains are compared/sorted based upon their identifiers (case insensitive) and their numbers.

compareTo(Domain) - Method in class org.forester.surfacing.SimpleDomain

 

compareTo(ProteinId) - Method in class org.forester.protein.ProteinId

 

compareTo(Species) - Method in class org.forester.species.BasicSpecies

 

compareTo(DomainSimilarity) - Method in class org.forester.surfacing.DomainSimilarity

 

Comparison - Class in org.biojava.nbio.phylo

This class provides static methods for the calculation of the percentage of identity between two aligned sequences.

Comparison() - Constructor for class org.biojava.nbio.phylo.Comparison

 

ComplementCompound - Interface in org.biojava.nbio.core.sequence.template

 

ComplementSequenceView<C extends ComplementCompound> - Class in org.biojava.nbio.core.sequence.views

For a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlying base e.g.

ComplementSequenceView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.views.ComplementSequenceView

 

complete() - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener

Notify this listener the FASTQ formatted sequence is complete.

complete() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

 

completeCircularPasses(int, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e.

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.

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.

componentHidden(ComponentEvent) - Method in class org.forester.archaeopteryx.MainPanel

 

componentMoved(ComponentEvent) - Method in class org.forester.archaeopteryx.MainPanel

 

componentResized(ComponentEvent) - Method in class org.forester.archaeopteryx.MainPanel

 

COMPONENTS_FILE_LOCATION - Static variable in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider

 

componentShown(ComponentEvent) - Method in class org.forester.archaeopteryx.MainPanel

 

ComponentXMLConverter - Class in org.biojava.nbio.protmod.io

 

ComponentXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.ComponentXMLConverter

 

COMPOSITION_BASED_STATISTICS - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

 

Compound - Class in org.biojava.nbio.structure

An object to contain the info from the PDB header for a Molecule.

Compound - Interface in org.biojava.nbio.core.sequence.template

 

Compound() - Constructor for class org.biojava.nbio.structure.Compound

 

Compound(Compound) - Constructor for class org.biojava.nbio.structure.Compound

Constructs a new Compound copying all data from the given one but not setting the Chains

COMPOUND - Enum constant in enum class org.biojava.nbio.core.alignment.template.AlignedSequence.Step

 

CompoundFinder - Class in org.biojava.nbio.structure.io

Heuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure.

CompoundFinder(Structure) - Constructor for class org.biojava.nbio.structure.io.CompoundFinder

 

CompoundNotFoundException - Exception in org.biojava.nbio.core.exceptions

 

CompoundNotFoundException(String) - Constructor for exception org.biojava.nbio.core.exceptions.CompoundNotFoundException

 

compoundsEqual(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

 

compoundsEquivalent(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

 

computeMappingCostL() - Method in class org.forester.sdi.SDI

Computes the cost of mapping the gene tree gene_tree onto the species tree species_tree.

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

confadd - Class in org.forester.application

 

confadd() - Constructor for class org.forester.application.confadd

 

Confidence - Class in org.forester.phylogeny.data

 

Confidence() - Constructor for class org.forester.phylogeny.data.Confidence

 

Confidence(double, String) - Constructor for class org.forester.phylogeny.data.Confidence

 

Confidence(double, String, double) - Constructor for class org.forester.phylogeny.data.Confidence

 

CONFIDENCE - Static variable in class org.forester.archaeopteryx.TreeColorSet

 

CONFIDENCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

CONFIDENCE_DEFAULT - Static variable in class org.forester.phylogeny.data.ProteinDomain

 

CONFIDENCE_DEFAULT_VALUE - Static variable in class org.forester.phylogeny.data.Confidence

 

CONFIDENCE_SD_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

CONFIDENCE_TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

 

ConfidenceAssessor - Class in org.forester.tools

 

ConfidenceParser - Class in org.forester.io.parsers.phyloxml.data

 

ConfigPDBInstallPanel - Class in org.biojava.nbio.structure.align.gui

 

ConfigStrucAligParams - Interface in org.biojava.nbio.structure.align.ce

 

Configuration - Class in org.forester.archaeopteryx

 

Configuration() - Constructor for class org.forester.archaeopteryx.Configuration

 

Configuration(String, boolean, boolean, boolean) - Constructor for class org.forester.archaeopteryx.Configuration

 

Configuration.EXT_NODE_DATA_RETURN_ON - Enum Class in org.forester.archaeopteryx

 

Configuration.UI - Enum Class in org.forester.archaeopteryx

 

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.

CONSOLE - Enum constant in enum class org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON

 

CONSORTIUM_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

 

CONSTANT - Enum constant in enum class org.biojava.nbio.alignment.template.GapPenalty.Type

 

Constants - Class in org.forester.archaeopteryx

 

Constants() - Constructor for class org.forester.archaeopteryx.Constants

 

constrain(double) - Method in enum class org.biojava.nbio.sequencing.io.fastq.FastqVariant

Constrain the specified quality score in double precision to the minimum and maximum quality scores in int precision.

Constraints - Class in org.biojava.nbio.aaproperties

This class is used to support the implementation of properties stated in IPeptideProperties.

Constraints() - Constructor for class org.biojava.nbio.aaproperties.Constraints

 

constructWithCopy(double[][]) - Static method in class org.biojava.nbio.structure.jama.Matrix

Construct a matrix from a copy of a 2-D array.

contacts(Point3d[], Point3d[], double) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition

 

contains(String) - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

 

contains(String) - Method in interface org.forester.surfacing.GenomeWideCombinableDomains

 

contains(List<String>, boolean) - Method in class org.forester.protein.BasicProtein

 

contains(List<String>, boolean) - Method in interface org.forester.protein.Protein

If in_nc_order is set to true, this should return true only and only if the order in List 'domains' and this protein (as determined by the start positions of the domains of this proteins, _not_ by their index) are the same (interspersing, 'other', domains in this are ignored).

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

 

contains(Subunits) - Method in class org.biojava.nbio.structure.symmetry.core.Subunits

 

containsChainId(String, String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

 

containsCharacter(String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

 

containsCharacter(String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

 

containsIdentifier(String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

 

containsIdentifier(String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

 

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(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.ForesterWrapper

Convert a BioJava MultipleSequenceAlignment to a forester Msa.

convert(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor

Returns the converted sequence.

convert(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriter

 

convert(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.SangerFastqWriter

 

convert(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriter

 

convert(Fastq, FastqVariant) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.

convert_3code_1code(String) - Static method in class org.biojava.nbio.structure.StructureTools

Deprecated.

Use StructureTools.get1LetterCodeAmino(String) instead

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

 

convertAtomToAtomSite(Atom, int, String, String) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Converts an Atom object to an AtomSite object.

convertAtomToAtomSite(Atom, int, String, String, int) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Converts an Atom object to an AtomSite object.

convertChainToAtomSites(Chain, int, String, String) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Converts a Chain into a List of AtomSite objects

convertColor4f(Color) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter

 

convertColor4f(Color[]) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter

 

convertCrystalCellToCell(CrystalCell) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Converts a CrystalCell object to a Cell object.

Convertor - Class in org.biojava.nbio.aaproperties.profeat.convertor

 

Convertor() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convertor

 

convertPairsToXML(SortedSet<PdbPair>, String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter

 

convertProteinSequencetoFasta(ProteinSequence) - Static method in class org.biojava.nbio.ronn.Jronn

Utility method to convert a BioJava ProteinSequence object to the FastaSequence object used internally in JRonn.

convertSpaceGroupToSymmetry(SpaceGroup) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Converts a SpaceGroup object to a Symmetry object.

convertStreamToString(InputStream) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper

 

convertStreamToString(InputStream) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient

 

convertStructureToAtomSites(Structure) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

Converts a Structure into a List of AtomSite objects

convertTo(FastqVariant) - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq

Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.

convertXMLtoPairs(String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter

 

CONVEX - Enum constant in enum class org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE

 

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() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

 

copy() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

 

copy() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

 

copy() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

 

copy() - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

 

copy() - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

 

copy() - Method in class org.forester.go.BasicGoTerm

Makes a shallow copy.

copy() - Method in class org.forester.phylogeny.data.Accession

 

copy() - Method in class org.forester.phylogeny.data.Annotation

 

copy() - Method in class org.forester.phylogeny.data.BinaryCharacters

 

copy() - Method in class org.forester.phylogeny.data.BranchColor

 

copy() - Method in class org.forester.phylogeny.data.BranchData

 

copy() - Method in class org.forester.phylogeny.data.BranchWidth

 

copy() - Method in class org.forester.phylogeny.data.Confidence

 

copy() - Method in class org.forester.phylogeny.data.Date

 

copy() - Method in class org.forester.phylogeny.data.Distribution

 

copy() - Method in class org.forester.phylogeny.data.DomainArchitecture

 

copy() - Method in class org.forester.phylogeny.data.Event

 

copy() - Method in class org.forester.phylogeny.data.Identifier

 

copy() - Method in class org.forester.phylogeny.data.NodeData

 

copy() - Method in class org.forester.phylogeny.data.NodeVisualData

 

copy() - Method in interface org.forester.phylogeny.data.PhylogenyData

Creates a new PhylogenyData object with identical values as this PhylogenyData.

copy() - Method in class org.forester.phylogeny.data.Point

 

copy() - Method in class org.forester.phylogeny.data.Polygon

 

copy() - Method in class org.forester.phylogeny.data.PropertiesMap

 

copy() - Method in class org.forester.phylogeny.data.Property

 

copy() - Method in class org.forester.phylogeny.data.ProteinDomain

 

copy() - Method in class org.forester.phylogeny.data.Reference

 

copy() - Method in class org.forester.phylogeny.data.Sequence

Not a deep copy.

copy() - Method in class org.forester.phylogeny.data.SequenceRelation

 

copy() - Method in class org.forester.phylogeny.data.Taxonomy

 

copy() - Method in class org.forester.phylogeny.data.Uri

 

copy() - Method in class org.forester.phylogeny.Phylogeny

Returns a deep copy of this Phylogeny.

copy() - Method in class org.forester.ws.seqdb.UniProtTaxonomy

Creates deep copy for all fields, except lineage.

copy(File, File) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils

Copy the content of file src to dst TODO since java 1.7 this is provided in java.nio.file.Files

copy(InputStream, OutputStream) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Moves the bytes from input to output using a 4KB byte array.

copy(ArrayList<PhylogenyData>) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

Creates a deep copy of ArrayList of PhylogenyData objects.

copy(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny

Returns a deep copy of this Phylogeny.

copyFile(File, File) - Static method in class org.biojava.nbio.phosphosite.Dataset

 

copyFile(File, File) - Static method in class org.forester.util.ForesterUtil

 

copyNodeData() - Method in class org.forester.phylogeny.PhylogenyNode

Returns a new PhylogenyNode which has its data copied from this PhylogenyNode.

copyNodeDataShallow() - Method in class org.forester.phylogeny.PhylogenyNode

Returns a new PhylogenyNode which has the same data as this PhylogenyNode.

copySequence(MolecularSequence) - Static method in class org.forester.sequence.BasicSequence

 

copyShallow() - Method in class org.forester.phylogeny.Phylogeny

Returns a shallow copy of this Phylogeny.

copyShallow(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny

 

core_chars - Class in org.forester.applications

 

core_chars() - Constructor for class org.forester.applications.core_chars

 

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.

CORUM - Enum constant in enum class org.forester.go.GoXRef.Type

 

CORUM_STR - Static variable in interface org.forester.go.GoXRef

 

count(Phylogeny, Phylogeny[], boolean, boolean) - Static method in class org.forester.tools.SupportCount

 

count(Phylogeny, Phylogeny[], boolean, double, boolean) - Static method in class org.forester.tools.SupportCount

This counts the support of topology phylogeny by the topologies in phylogenies.

COUNT_DEFAULT - Static variable in class org.forester.phylogeny.data.BinaryCharacters

 

count_support - Class in org.forester.application

 

count_support() - Constructor for class org.forester.application.count_support

 

countAT(Sequence<NucleotideCompound>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Returns the count of AT in the given sequence

countCategories(List<GoTerm>, List<GoTerm>, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils

This is for counting the how many times each GO term in 'categories' is a (direct or indirect) super term of the GO terms in 'experiment_set'.

countCategoriesId(List<GoId>, List<GoId>, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils

 

countChars(String, char) - Static method in class org.forester.util.ForesterUtil

 

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

 

countNumberOfOneDescendantNodes(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

countNumberOfPolytomies(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

CountProgressListener - Class in org.biojava.nbio.structure.align.client

 

CountProgressListener() - Constructor for class org.biojava.nbio.structure.align.client.CountProgressListener

 

CountsBasedPairwiseDomainSimilarity - Class in org.forester.surfacing

 

CountsBasedPairwiseDomainSimilarity(short, short) - Constructor for class org.forester.surfacing.CountsBasedPairwiseDomainSimilarity

counts_difference: (counts for domain 1) minus (counts for domain 2).

COVALENT - Enum constant in enum class org.biojava.nbio.structure.BondType

 

Coverage - Interface in org.forester.pccx

 

CoverageCalculationMethod - Interface in org.forester.pccx

 

CoverageCalculationOptions - Interface in org.forester.pccx

 

CoverageCalculator - Class in org.forester.pccx

 

CoverageExtender - Interface in org.forester.pccx

 

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 Class in org.biojava.nbio.survival.cox

 

coxphfitSCleanup(CoxInfo, boolean, boolean, ArrayList<String>) - Method in class org.biojava.nbio.survival.cox.CoxR

 

CoxR - Class in org.biojava.nbio.survival.cox

This is a port of the R survival code used for doing Cox Regression.

CoxR() - Constructor for class org.biojava.nbio.survival.cox.CoxR

 

coxsafe(double) - Method in class org.biojava.nbio.survival.cox.CoxR

 

CoxScore - Class in org.biojava.nbio.survival.cox

 

CoxScore() - Constructor for class org.biojava.nbio.survival.cox.CoxScore

 

CoxVariables - Class in org.biojava.nbio.survival.cox

 

CoxVariables(String, String, String) - Constructor for class org.biojava.nbio.survival.cox.CoxVariables

 

CoxVariablesOverallModelFitComparator - Class in org.biojava.nbio.survival.cox.comparators

 

CoxVariablesOverallModelFitComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator

Variables are stored as a string representation of an ArrayList [META_GENE] or [trtg, META_GENE] add variables used in cox regression to an array and then do toString.

CoxVariablesVariableComparator - Class in org.biojava.nbio.survival.cox.comparators

 

CoxVariablesVariableComparator(String, String) - Constructor for class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator

 

cpFastaToAfpChain(File, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.

cpFastaToAfpChain(String, String, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

 

cpFastaToAfpChain(ProteinSequence, ProteinSequence, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.

cpPoint - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

The CP point, specified as a residue index

CPRange() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange

 

Cr - Enum constant in enum class 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

 

create(Object, Object) - Method in class org.forester.phylogeny.factories.ParserBasedPhylogenyFactory

 

create(Object, Object) - Method in interface org.forester.phylogeny.factories.PhylogenyFactory

This must create a Phylogeny from source (e.g.

create(Object, Object, String) - Method in class org.forester.phylogeny.factories.ParserBasedPhylogenyFactory

 

createAaSequence(String, String) - Static method in class org.forester.sequence.BasicSequence

 

createAFPChain(Atom[], Atom[], ResidueNumber[], ResidueNumber[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Fundamentally, an alignment is just a list of aligned residues in each protein.

createAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory

Create an instance of AngleOutlier

createApplication(Phylogeny) - Static method in class org.forester.archaeopteryx.Archaeopteryx

 

createApplication(Phylogeny[]) - Static method in class org.forester.archaeopteryx.Archaeopteryx

 

createApplication(Phylogeny[], String, String) - Static method in class org.forester.archaeopteryx.Archaeopteryx

 

createApplication(Phylogeny, Configuration, String) - Static method in class org.forester.archaeopteryx.Archaeopteryx

 

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

 

createBalancedPhylogeny(int, int) - Static method in class org.forester.development.DevelopmentTools

Creates a completely balanced rooted phylogeny with a given number of levels and children per node.

createBiologicalProcess() - Static method in class org.forester.go.GoNameSpace

 

createBlastHit() - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder

 

createBlastHsp() - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder

 

createBlastResult() - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder

 

createBondOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory

Create an instance of BondOutlier

createBufferedWriter(File) - Static method in class org.forester.util.ForesterUtil

 

createBufferedWriter(String) - Static method in class org.forester.util.ForesterUtil

 

createCellularComponent() - Static method in class org.forester.go.GoNameSpace

 

createClash() - Method in class org.biojava.nbio.structure.validation.ObjectFactory

Create an instance of Clash

createDefaultClients() - Static method in class org.forester.archaeopteryx.webservices.WebserviceUtil

 

createDnaSequence(String, String) - Static method in class org.forester.sequence.BasicSequence

 

createDNASequence(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Create and return a new DNASequence from the specified FASTQ formatted sequence.

createDNASequenceWithErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Create and return a new DNASequence with error probabilities from the specified FASTQ formatted sequence.

createDNASequenceWithQualityScores(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Create and return a new DNASequence with quality scores from the specified FASTQ formatted sequence.

createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence.

createDomainIdToGoIdMap(List<PfamToGoMapping>) - Static method in class org.forester.surfacing.SurfacingUtil

 

createDomainIdToSecondaryFeaturesMap(File) - Static method in class org.forester.surfacing.SurfacingUtil

 

createEasyWriter(File) - Static method in class org.forester.util.ForesterUtil

 

createEasyWriter(String) - Static method in class org.forester.util.ForesterUtil

 

createEntry() - Method in class org.biojava.nbio.structure.validation.ObjectFactory

Create an instance of Entry

createErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Create and return a new QuantityFeature from the error probabilities of the specified FASTQ formatted sequence.

createFileForWriting(String) - Static method in class org.forester.util.ForesterUtil

 

createFromNhxString(String) - Static method in class org.forester.phylogeny.data.Property

 

createGoIdToGoTermMap(List<GoTerm>) - Static method in class org.forester.go.GoUtils

 

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.

createInstance() - Static method in class org.forester.archaeopteryx.tools.ProcessPool

 

createInstance() - Static method in class org.forester.evoinference.distance.NeighborJoining

 

createInstance() - Static method in class org.forester.evoinference.distance.NeighborJoiningF

 

createInstance() - Static method in class org.forester.evoinference.distance.NeighborJoiningR

 

createInstance() - Static method in class org.forester.evoinference.parsimony.DolloParsimony

 

createInstance() - Static method in class org.forester.io.parsers.SymmetricalDistanceMatrixParser

 

createInstance() - Static method in class org.forester.msa.MsaMethods

 

createInstance(boolean, int) - Static method in class org.forester.evoinference.distance.NeighborJoining

 

createInstance(boolean, int) - Static method in class org.forester.evoinference.distance.NeighborJoiningF

 

createInstance(boolean, int) - Static method in class org.forester.evoinference.distance.NeighborJoiningR

 

createInstance(String) - Static method in class org.forester.msa.ClustalOmega

 

createInstance(String) - Static method in class org.forester.msa.Mafft

 

createInstance(String, String, Configuration) - Static method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

 

createInstance(List<Double>, DescriptiveStatistics, Configuration) - Static method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

 

createInstance(List<Protein>, boolean, Species) - Static method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

 

createInstance(List<Protein>, boolean, Species, Map<String, List<GoId>>, BinaryDomainCombination.DomainCombinationType, Map<String, DescriptiveStatistics>, Map<String, DescriptiveStatistics>) - Static method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

 

createInstance(List<Protein>, boolean, Species, BinaryDomainCombination.DomainCombinationType) - Static method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

 

createInstance(List<MolecularSequence>) - Static method in class org.forester.msa.BasicMsa

 

createInstance(List<MolecularSequence>) - Static method in class org.forester.msa.DeleteableMsa

 

createInstance(Configuration) - Static method in class org.forester.archaeopteryx.Options

 

createInstance(Configuration) - Static method in class org.forester.archaeopteryx.tools.InferenceManager

 

createInstance(Configuration) - Static method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

 

createInstance(Msa) - Static method in class org.forester.msa.DeleteableMsa

 

createInstance(Phylogeny) - Static method in class org.forester.surfacing.DomainParsimonyCalculator

 

createInstance(Phylogeny[], Configuration) - Static method in class org.forester.archaeopteryx.MainFrameApplication

 

createInstance(Phylogeny[], Configuration, String, File) - Static method in class org.forester.archaeopteryx.MainFrameApplication

 

createInstance(Phylogeny, List<GenomeWideCombinableDomains>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator

 

createInstance(Phylogeny, List<GenomeWideCombinableDomains>, Map<String, Set<String>>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator

 

createInstanceFromNhxString(String) - Static method in class org.forester.phylogeny.Phylogeny

 

createInstanceFromNhxString(String) - Static method in class org.forester.phylogeny.PhylogenyNode

 

createInstanceFromNhxString(String, NHXParser.TAXONOMY_EXTRACTION) - Static method in class org.forester.phylogeny.PhylogenyNode

 

createInstanceFromNhxString(String, NHXParser.TAXONOMY_EXTRACTION, boolean) - Static method in class org.forester.phylogeny.PhylogenyNode

 

createInstanceFromPlainText(List<String>) - Static method in class org.forester.ws.seqdb.UniProtEntry

 

createInstanceFromPlainTextForRefSeq(List<String>) - Static method in class org.forester.ws.seqdb.EbiDbEntry

 

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.

createMaskFormatter(String) - Static method in class org.forester.archaeopteryx.AptxUtil

 

createMatrixOfBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator

 

createMatrixOfDomainPresenceOrAbsence(List<GenomeWideCombinableDomains>, SortedSet<String>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator

 

createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains>, Map<String, String>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator

 

createMeanBasedStatisticsPerSpeciesTable() - Method in class org.forester.surfacing.DomainLengthsTable

 

createModelledSubgroup() - Method in class org.biojava.nbio.structure.validation.ObjectFactory

Create an instance of ModelledSubgroup

createMogAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory

Create an instance of MogAngleOutlier

createMogBondOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory

Create an instance of MogBondOutlier

createMolecularFunction() - Static method in class org.forester.go.GoNameSpace

 

createNameToExtNodeMap(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

 

createNjTreeBasedOnMatrixToFile(File, DistanceMatrix) - Static method in class org.forester.surfacing.SurfacingUtil

 

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

 

createPalette(ColorBrewer, Border) - Method in class org.jcolorbrewer.ui.DivergingColorPalettePanel

 

createPalette(ColorBrewer, Border) - Method in class org.jcolorbrewer.ui.QualitativeColorPalettePanel

 

createPalette(ColorBrewer, Border) - Method in class org.jcolorbrewer.ui.SequentialColorPalettePanel

 

createParametersAsString(boolean, double, double, int, boolean, File, BinaryDomainCombination.DomainCombinationType) - Static method in class org.forester.surfacing.SurfacingUtil

 

createParserDependingFileContents(File, boolean) - Static method in class org.forester.io.parsers.util.ParserUtils

 

createParserDependingOnFileType(File, boolean) - Static method in class org.forester.io.parsers.util.ParserUtils

 

createParserDependingOnUrlContents(URL, boolean) - Static method in class org.forester.io.parsers.util.ParserUtils

 

createPhylogenyWriter() - Static method in class org.forester.io.writers.PhylogenyWriter

 

createPhyloXmlParser() - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

 

createPhyloXmlParserXsdValidating() - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

 

createProgram() - Method in class org.biojava.nbio.structure.validation.ObjectFactory

Create an instance of Program

createPrograms() - Method in class org.biojava.nbio.structure.validation.ObjectFactory

Create an instance of Programs

createQualityScores(Fastq) - Static method in class org.biojava.nbio.sequencing.io.fastq.FastqTools

Create and return a new QualityFeature from the quality scores of the specified FASTQ formatted sequence.

createReader(Object) - Static method in class org.forester.io.parsers.util.ParserUtils

 

createResampledColumnPositions(int, int, long) - Static method in class org.forester.evoinference.tools.BootstrapResampler

 

createRnaSequence(String, String) - Static method in class org.forester.sequence.BasicSequence

 

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.

createSingleDuplicationEvent() - Static method in class org.forester.phylogeny.data.Event

 

createSingleSpeciationEvent() - Static method in class org.forester.phylogeny.data.Event

 

createSingleSpeciationOrDuplicationEvent() - Static method in class org.forester.phylogeny.data.Event

 

createSpecialFromScientificName(String) - Static method in class org.forester.ws.seqdb.UniProtTaxonomy

 

createSplitWriters(File, String, Map<Character, Writer>) - Static method in class org.forester.surfacing.SurfacingUtil

 

createSubSequence(Sequence<C>, int, int) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Creates a simple sub sequence view delimited by the given start and end.

createSymmClash() - Method in class org.biojava.nbio.structure.validation.ObjectFactory

Create an instance of SymmClash

createTaxCodeToIdMap(Phylogeny) - Static method in class org.forester.surfacing.SurfacingUtil

 

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

 

createUnassigned() - Static method in class org.forester.go.GoNameSpace

 

createUriForSeqWeb(PhylogenyNode, Configuration, TreePanel) - Static method in class org.forester.archaeopteryx.TreePanelUtil

 

createUrisForPdbWeb(PhylogenyNode, List<Accession>, Configuration, TreePanel) - Static method in class org.forester.archaeopteryx.TreePanelUtil

 

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.

createWwPDBValidationInformation() - Method in class org.biojava.nbio.structure.validation.ObjectFactory

Create an instance of WwPDBValidationInformation

CROSS_LINK_1 - Enum constant in enum class org.biojava.nbio.protmod.ModificationCategory

 

CROSS_LINK_2 - Enum constant in enum class org.biojava.nbio.protmod.ModificationCategory

 

CROSS_LINK_3 - Enum constant in enum class org.biojava.nbio.protmod.ModificationCategory

 

CROSS_LINK_4 - Enum constant in enum class org.biojava.nbio.protmod.ModificationCategory

 

CROSS_LINK_5 - Enum constant in enum class org.biojava.nbio.protmod.ModificationCategory

 

CROSS_LINK_6 - Enum constant in enum class org.biojava.nbio.protmod.ModificationCategory

 

CROSS_LINK_7 - Enum constant in enum class org.biojava.nbio.protmod.ModificationCategory

 

CROSS_LINK_8_OR_LARGE - Enum constant in enum class 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

 

CROSSPLATFORM - Enum constant in enum class org.forester.archaeopteryx.Configuration.UI

 

CrystalBuilder - Class in org.biojava.nbio.structure.xtal

A class containing methods to find interfaces in a given crystallographic Structure by reconstructing the crystal lattice through application of symmetry operators

CrystalBuilder(Structure) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder

 

CrystalCell - Class in org.biojava.nbio.structure.xtal

A crystal cell's parameters.

CrystalCell() - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell

 

CrystalCell(double, double, double, double, double, double) - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell

 

CrystalTransform - Class in org.biojava.nbio.structure.xtal

Representation of a transformation in a crystal: - a transformation id (each of the transformations in a space group, 0 to m) - a crystal translation The transformation matrix in crystal basis is stored, representing the basic transformation together with the crystal translation.

CrystalTransform(CrystalTransform) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform

Copy constructor

CrystalTransform(SpaceGroup) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform

Creates a new CrystalTransform representing the identity transform in cell (0,0,0)

CrystalTransform(SpaceGroup, int) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform

Represents the n-th transform

Cs - Enum constant in enum class org.biojava.nbio.structure.Element

 

CS_HSV - Static variable in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace

The HSV color space

CTD_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

 

CTENOPHORA_COLOR - Static variable in class org.forester.util.TaxonomyColors

 

Cu - Enum constant in enum class org.biojava.nbio.structure.Element

 

CUBIC - Enum constant in enum class org.biojava.nbio.structure.xtal.BravaisLattice

 

CURATED - Enum constant in enum class org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType

 

CURRENT - Enum constant in enum class org.biojava.nbio.structure.PDBStatus.Status

 

CURVED - Enum constant in enum class org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE

 

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

 

cyclicPeptide - Enum constant in enum class org.biojava.nbio.structure.io.mmcif.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