- A - Static variable in class org.biojava3.aaproperties.Constraints
-
- AA - Static variable in class org.biojava3.data.sequence.SequenceUtil
-
Valid Amino acids
- aa - Static variable in class org.biojava3.phylo.ResidueProperties
-
- aa2ExtinctionCoefficient - Static variable in class org.biojava3.aaproperties.Constraints
-
- aa2Hydrophathicity - Static variable in class org.biojava3.aaproperties.Constraints
-
- aa2MolecularWeight - Static variable in class org.biojava3.aaproperties.Constraints
-
- aa2PKa - Static variable in class org.biojava3.aaproperties.Constraints
-
- aa2Triplet - Static variable in class org.biojava3.phylo.ResidueProperties
-
- aa3Hash - Static variable in class org.biojava3.phylo.ResidueProperties
-
- aaIndex - Static variable in class org.biojava3.phylo.ResidueProperties
-
- AAindexFactory - Class in org.biojava3.alignment.aaindex
-
Factory class to get Providers for substitution matrices the are provided by the AAINDEX database.
- AAindexFactory() - Constructor for class org.biojava3.alignment.aaindex.AAindexFactory
-
- AAIndexFileParser - Class in org.biojava3.alignment.aaindex
-
- AAIndexFileParser() - Constructor for class org.biojava3.alignment.aaindex.AAIndexFileParser
-
- AAIndexProvider - Interface in org.biojava3.alignment.aaindex
-
- aaScore(char, char) - Static method in class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
-
- AboutDialog - Class in org.biojava.bio.structure.align.gui
-
- AboutDialog() - Constructor for class org.biojava.bio.structure.align.gui.AboutDialog
-
- AbstractBean - Class in org.biojava.bio.structure.io.mmcif.model
-
a generic class that implements the toString method for a bean
- AbstractBean() - Constructor for class org.biojava.bio.structure.io.mmcif.model.AbstractBean
-
- AbstractCompound - Class in org.biojava3.core.sequence.template
-
The details of a Compound
- AbstractCompound(String) - Constructor for class org.biojava3.core.sequence.template.AbstractCompound
-
- AbstractCompoundSet<C extends Compound> - Class in org.biojava3.core.sequence.template
-
- AbstractCompoundSet() - Constructor for class org.biojava3.core.sequence.template.AbstractCompoundSet
-
- AbstractCompoundTranslator<F extends Compound,T extends Compound> - Class in org.biojava3.core.sequence.template
-
- AbstractCompoundTranslator(SequenceCreatorInterface<T>, CompoundSet<F>, CompoundSet<T>) - Constructor for class org.biojava3.core.sequence.template.AbstractCompoundTranslator
-
- AbstractFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava3.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.biojava3.core.sequence.features.AbstractFeature
-
A feature has a type and a source
- AbstractLocation - Class in org.biojava3.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.biojava3.core.sequence.location.template.AbstractLocation
-
- AbstractLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava3.core.sequence.location.template.AbstractLocation
-
Default constructor
- AbstractLocation(Point, Point, Strand, boolean, boolean, AccessionID, List<Location>) - Constructor for class org.biojava3.core.sequence.location.template.AbstractLocation
-
Default constructor
- AbstractMatrixAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.template
-
Implements common code for an
Aligner which builds a score matrix during computation.
- AbstractMatrixAligner() - Constructor for class org.biojava3.alignment.template.AbstractMatrixAligner
-
- AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.template.AbstractMatrixAligner
-
Prepares for an alignment.
- AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava3.alignment.template.AbstractMatrixAligner
-
Prepares for an alignment.
- AbstractNucleotideCompoundSet<C extends NucleotideCompound> - Class in org.biojava3.core.sequence.template
-
- AbstractNucleotideCompoundSet() - Constructor for class org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet
-
- AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.template
-
- AbstractPairwiseSequenceAligner() - Constructor for class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
-
- AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
-
Prepares for a pairwise global sequence alignment.
- AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
-
Prepares for a pairwise sequence alignment.
- AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.template
-
- AbstractProfileProfileAligner() - Constructor for class org.biojava3.alignment.template.AbstractProfileProfileAligner
-
- AbstractProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.template.AbstractProfileProfileAligner
-
Prepares for a profile-profile alignment.
- AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.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.biojava3.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.biojava3.alignment.template.AbstractProfileProfileAligner
-
Prepares for a profile-profile alignment run concurrently.
- AbstractScorer - Class in org.biojava3.alignment.template
-
Implements common code for algorithms which compute a score.
- AbstractScorer() - Constructor for class org.biojava3.alignment.template.AbstractScorer
-
- AbstractSequence<C extends Compound> - Class in org.biojava3.core.sequence.template
-
The base class for DNA, RNA and Protein sequences.
- AbstractSequence() - Constructor for class org.biojava3.core.sequence.template.AbstractSequence
-
- AbstractSequence(String, CompoundSet<C>) - Constructor for class org.biojava3.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.biojava3.core.sequence.template.AbstractSequence
-
A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location
of the sequence data.
- AbstractSequence.AnnotationType - Enum in org.biojava3.core.sequence.template
-
- AbstractStructureAlignment - Class in org.biojava.bio.structure.align
-
- AbstractStructureAlignment() - Constructor for class org.biojava.bio.structure.align.AbstractStructureAlignment
-
- AbstractUserArgumentProcessor - Class in org.biojava.bio.structure.align.ce
-
- AbstractUserArgumentProcessor() - Constructor for class org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
-
- accept(PDBHeader) - Method in interface org.biojava.bio.structure.server.PDBFilter
-
return true if this PDBHeader is passing this filter.
- AccesionedLocation - Interface in org.biojava3.core.sequence.location.template
-
A location which is bound to an AccessionID.
- Accessioned - Interface in org.biojava3.core.sequence.template
-
Indicates an entity is accessioned
- AccessionID - Class in org.biojava3.core.sequence
-
Used in Sequences as the unique indentifier.
- AccessionID() - Constructor for class org.biojava3.core.sequence.AccessionID
-
- AccessionID(String) - Constructor for class org.biojava3.core.sequence.AccessionID
-
- AccessionID(String, DataSource) - Constructor for class org.biojava3.core.sequence.AccessionID
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.ChooseDirAction
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.DBResultTable
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
-
Invoked when the user presses the stop button.
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.JmolPanel
-
The user selected one of the Combo boxes...
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.RasmolCommandListener
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.JPrintPanel
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.MyAlignmentLoadListener
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.MyDistMaxListener
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.MyExportListener
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.MyOpenPdbFileListener
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.MySaveFileListener
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.ShowPDBIDListener
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.gui.RasmolCommandListener
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
-
- AD - Variable in class org.biojava.bio.structure.domain.pdp.CutValues
-
- adapter - Static variable in class org.biojava.bio.structure.gui.BiojavaJmol
-
- adapter - Static variable in class org.biojava3.structure.gui.JmolViewerImpl
-
- add(int, int, int, int) - Method in class org.biojava.bio.structure.align.helper.JointFragments
-
- add(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
-
add two atoms ( a + b).
- add(FeatureI) - Method in class org.biojava3.genome.parsers.gff.FeatureList
-
Add specified feature to the end of the list.
- add(Collection<FeatureI>) - Method in class org.biojava3.genome.parsers.gff.FeatureList
-
Add all features in the specified list or collection to this list.
- addAlgorithm(StructureAlignment) - Static method in class org.biojava.bio.structure.align.StructureAlignmentFactory
-
Adds a new StructureAlignment algorithm to the list.
- addAlignedSequence(S) - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
-
A sequence that has been aligned to other sequences will have inserts.
- addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
-
- addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
-
- addAlignmentProgressListener(AlignmentProgressListener) - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
-
- addAlignmentProgressListener(AlignmentProgressListener) - Method in class org.biojava.bio.structure.align.FarmJob
-
- addAligPosListener(AlignmentPositionListener) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
-
- addAltLoc(Group) - Method in interface org.biojava.bio.structure.Group
-
Add a group that is an alternate location for this group.
- addAltLoc(Group) - Method in class org.biojava.bio.structure.HetatomImpl
-
- addAnchors(AlignerHelper.Cut[], short[], boolean, int[]) - Static method in class org.biojava3.alignment.routines.AlignerHelper
-
- addAtom(Atom) - Method in interface org.biojava.bio.structure.Group
-
add an atom to this group.
- addAtom(Atom) - Method in class org.biojava.bio.structure.HetatomImpl
-
add an atom to this group.
- addAtomLinkage(StructureAtomLinkage) - Method in interface org.biojava3.protmod.structure.ModifiedCompound
-
Add a linkage.
- addAtomLinkage(StructureAtomLinkage) - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
-
- addAtomLinkages(Collection<StructureAtomLinkage>) - Method in interface org.biojava3.protmod.structure.ModifiedCompound
-
Add a collections of linkages.
- addAtomLinkages(Collection<StructureAtomLinkage>) - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
-
- addCDS(AccessionID, int, int, int) - Method in class org.biojava3.core.sequence.TranscriptSequence
-
Add a Coding Sequence region with phase to the transcript sequence
- addChain(Chain) - Method in class org.biojava.bio.structure.Compound
-
- addChain(Chain) - Method in interface org.biojava.bio.structure.Structure
-
add a new chain.
- addChain(Chain, int) - Method in interface org.biojava.bio.structure.Structure
-
add a new chain, if several models are available.
- addChain(Chain) - Method in class org.biojava.bio.structure.StructureImpl
-
add a new chain.
- addChain(Chain, int) - Method in class org.biojava.bio.structure.StructureImpl
-
add a new chain, if several models are available.
- addChemComp(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
-
add a new component to the dictionary
- addChildElement(Element, String) - Static method in class org.biojava3.core.util.XMLHelper
-
- addCompound(C, C, Iterable<C>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
-
- addCompound(C, C, C...) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
-
- addCompound(C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
-
- addCompounds(F, T...) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
-
- addCompoundsToList(List<T>, List<List<T>>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
-
- addCompoundToLists(List<List<T>>, T) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
-
- addEquivalent(C, C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
-
- addExon(AccessionID, int, int) - Method in class org.biojava3.core.sequence.GeneSequence
-
Add an ExonSequence mainly used to mark as a feature
- addExtension(String) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
-
- addExtension(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
-
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.bio.structure.io.StructureIOFile
-
add a known File extension.
- addFeature(int, int, FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava3.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.biojava3.core.sequence.template.AbstractSequence
-
Add a feature to this sequence.
- addGene(AccessionID, int, int, Strand) - Method in class org.biojava3.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.biojava3.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.biojava3.genome.GeneFeatureHelper
-
- addGlimmerGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava3.genome.GeneFeatureHelper
-
- addGmodGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava3.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.bio.structure.Chain
-
add a group to the list of ATOM record group of this chain.
- addGroup(Group) - Method in class org.biojava.bio.structure.ChainImpl
-
add a group to the list of ATOM record group of this chain.
- addIntron(AccessionID, int, int) - Method in class org.biojava3.core.sequence.GeneSequence
-
Add an Intron Currently used to mark an IntronSequence as a feature
- addIntronsUsingExons() - Method in class org.biojava3.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.
- addKeyword(String) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
-
Add a keyword associate with the PTM.
- addKeywords(Collection<String>) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
-
- addMatrixListener(MatrixListener) - Method in class org.biojava.bio.structure.align.ce.CECalculator
-
- addMMcifConsumer(MMcifConsumer) - Method in interface org.biojava.bio.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.bio.structure.io.mmcif.SimpleMMcifParser
-
- addModel(List<Chain>) - Method in interface org.biojava.bio.structure.Structure
-
add a new model.
- addModel(List<Chain>) - Method in class org.biojava.bio.structure.StructureImpl
-
add a new model.
- addNote(String) - Method in class org.biojava3.core.sequence.template.AbstractSequence
-
Add notes about this sequence that will get exported for GFF3
- addNucleotideCompound(String, String, String...) - Method in class org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet
-
- addOneSystemProperty(String) - Method in class org.biojava.bio.structure.align.gui.SystemInfo
-
- addPDBFilter(PDBFilter) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
Deprecated.
- addPDBFilter(PDBFilter) - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
-
Deprecated.
- addPDBFilter(PDBFilter) - Method in interface org.biojava.bio.structure.server.PDBInstallation
-
Deprecated.
add a filter for PDB files.
- addProgessListener(NJTreeProgressListener) - Method in class org.biojava3.phylo.TreeConstructor
-
- addProgressListener(AlignmentProgressListener) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
- addProperty(String, String) - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
-
Add a property and type to associate with this DBReferenceInfo
- addQuantity(Number) - Method in class org.biojava3.core.sequence.features.QuantityFeature
-
- addSSBond(SSBond) - Method in interface org.biojava.bio.structure.Structure
-
add a single SSBond to this structure
- addSSBond(SSBond) - Method in class org.biojava.bio.structure.StructureImpl
-
add a single SSBond to this structure
- addStartCodonSequence(AccessionID, int, int) - Method in class org.biojava3.core.sequence.TranscriptSequence
-
- addStopCodonSequence(AccessionID, int, int) - Method in class org.biojava3.core.sequence.TranscriptSequence
-
- addStrings(String, String...) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
-
- addStructureListener(StructureListener) - Method in class org.biojava.bio.structure.server.SimpleStructureServer
-
Deprecated.
- addStructureListener(StructureListener) - Method in class org.biojava.bio.structure.server.StructureFetcherRunnable
-
Deprecated.
- addStructureListener(StructureListener) - Method in interface org.biojava.bio.structure.server.StructureServer
-
Deprecated.
- addToCache(String, File) - Static method in class org.biojava3.core.util.FlatFileCache
-
- addTranscript(AccessionID, int, int) - Method in class org.biojava3.core.sequence.GeneSequence
-
Add a transcription sequence to a gene which describes a ProteinSequence
- AFP - Class in org.biojava.bio.structure.align.model
-
A class to represent a FATCAT AFP
- AFP() - Constructor for class org.biojava.bio.structure.align.model.AFP
-
- afp2Res(AFPChain, int, int[], int) - Static method in class org.biojava.bio.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.bio.structure.align.util
-
- AFPAlignmentDisplay() - Constructor for class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
-
- AFPCalculator - Class in org.biojava.bio.structure.align.fatcat.calc
-
a class that performs calculations on AFPCHains
- AFPCalculator() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.AFPCalculator
-
- AFPChain - Class in org.biojava.bio.structure.align.model
-
a bean to contain the core of an alignment
The FatCat aligner class is working on the AFPChain class.
- AFPChain() - Constructor for class org.biojava.bio.structure.align.model.AFPChain
-
- AFPChain(AFPChain) - Constructor for class org.biojava.bio.structure.align.model.AFPChain
-
Copy constructor
- AFPChainCoordManager - Class in org.biojava.bio.structure.align.gui.aligpanel
-
- AFPChainCoordManager() - Constructor for class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
-
- AFPChainer - Class in org.biojava.bio.structure.align.fatcat.calc
-
a class to chain AFPs to an alignment
- AFPChainer() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.AFPChainer
-
- AFPChainFlipper - Class in org.biojava.bio.structure.align.xml
-
- AFPChainFlipper() - Constructor for class org.biojava.bio.structure.align.xml.AFPChainFlipper
-
- AFPChainScorer - Class in org.biojava.bio.structure.align.util
-
- AFPChainScorer() - Constructor for class org.biojava.bio.structure.align.util.AFPChainScorer
-
- AfpChainWriter - Class in org.biojava.bio.structure.align.model
-
- AfpChainWriter() - Constructor for class org.biojava.bio.structure.align.model.AfpChainWriter
-
- AFPChainXMLConverter - Class in org.biojava.bio.structure.align.xml
-
- AFPChainXMLConverter() - Constructor for class org.biojava.bio.structure.align.xml.AFPChainXMLConverter
-
- AFPChainXMLParser - Class in org.biojava.bio.structure.align.xml
-
- AFPChainXMLParser() - Constructor for class org.biojava.bio.structure.align.xml.AFPChainXMLParser
-
- AFPOptimizer - Class in org.biojava.bio.structure.align.fatcat.calc
-
- AFPOptimizer() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer
-
- afpPairConn(int, int, FatCatParameters, AFPChain) - Static method in class org.biojava.bio.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.bio.structure.align.fatcat.calc
-
does post processing after alignment chaingin
- AFPPostProcessor() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.AFPPostProcessor
-
- AFPTwister - Class in org.biojava.bio.structure.align
-
- AFPTwister() - Constructor for class org.biojava.bio.structure.align.AFPTwister
-
- Ala - Static variable in class org.biojava3.phylo.ResidueProperties
-
- algorithmName - Static variable in class org.biojava.bio.structure.align.BioJavaStructureAlignment
-
- algorithmName - Static variable in class org.biojava.bio.structure.align.ce.CeCPMain
-
- algorithmName - Static variable in class org.biojava.bio.structure.align.ce.CeMain
-
- algorithmName - Static variable in class org.biojava.bio.structure.align.ce.CeSideChainMain
-
- algorithmName - Static variable in class org.biojava.bio.structure.align.fatcat.FatCatFlexible
-
- algorithmName - Static variable in class org.biojava.bio.structure.align.fatcat.FatCatRigid
-
- algorithmName - Static variable in class org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
-
- ALIGFACTOR - Static variable in class org.biojava.bio.structure.align.pairwise.Gotoh
-
- AligMatEl - Class in org.biojava.bio.structure.align.helper
-
- AligMatEl() - Constructor for class org.biojava.bio.structure.align.helper.AligMatEl
-
- align(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.AbstractStructureAlignment
-
- align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.AbstractStructureAlignment
-
- align(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.BioJavaStructureAlignment
-
- align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.BioJavaStructureAlignment
-
- align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.ce.CeCPMain
-
- align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.ce.CeMain
-
Align ca2 onto ca1.
- align(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CeMain
-
- align(Atom[], Atom[], boolean, FatCatParameters) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatAligner
-
- align(Atom[], Atom[], FatCatParameters, boolean) - Method in class org.biojava.bio.structure.align.fatcat.FatCat
-
- align(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.fatcat.FatCatFlexible
-
- align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.fatcat.FatCatFlexible
-
- align(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.fatcat.FatCatRigid
-
- align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.fatcat.FatCatRigid
-
- align(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
-
- align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
-
- align(Atom[], Atom[]) - Method in interface org.biojava.bio.structure.align.StructureAlignment
-
Run an alignment while specifying the atoms to be aligned.
- align(Atom[], Atom[], Object) - Method in interface org.biojava.bio.structure.align.StructureAlignment
-
run an alignment and also send a bean containing the parameters.
- align(Structure, Structure) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
Calculate the alignment between the two full structures with default parameters
- align(Structure, Structure, StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
Calculate the alignment between the two full structures with user provided parameters
- align(Structure, String, Structure, String) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
Align two chains from the structures.
- align(Structure, String, Structure, String, StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
Aligns two chains from the structures using user provided parameters.
- align(Atom[], Atom[], StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
calculate the protein structure superimposition, between two sets of atoms.
- align(Structure, List<Chain>) - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
-
- align(List<Group>, List<Group>) - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
-
aligns two chains of groups, where the first parent is representing the
list of amino acids as obtained from the SEQRES records, and the second parent
represents the groups obtained from the ATOM records (and containing the actual ATOM information).
- align() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
-
- align_NPE(Matrix, StrucAligParameters) - Static method in class org.biojava.bio.structure.align.pairwise.AligNPE
-
Align w/o penalizing endpags.
- Alignable - Interface in org.biojava.bio.structure.align.pairwise
-
- AlignedPosition - Class in org.biojava.bio.structure.gui.util
-
- AlignedPosition() - Constructor for class org.biojava.bio.structure.gui.util.AlignedPosition
-
- AlignedSequence<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
-
Defines a data structure for a
Sequence within an alignment.
- AlignedSequence.Step - Enum in org.biojava3.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.biojava3.alignment.template
-
Defines an algorithm which computes an alignment
Profile from a list of
Sequences.
- AlignerHelper - Class in org.biojava3.alignment.routines
-
Static utility to construct alignment routines from a common library of methods.
- AlignerHelper() - Constructor for class org.biojava3.alignment.routines.AlignerHelper
-
- AlignerHelper.Cut - Class in org.biojava3.alignment.routines
-
Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
- AlignerHelper.Cut(int, int[]) - Constructor for class org.biojava3.alignment.routines.AlignerHelper.Cut
-
- AlignerHelper.Last - Enum in org.biojava3.alignment.routines
-
Defines 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).
- alignFlexible(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.bio.structure.align.fatcat.FatCat
-
- ALIGNMENT_PANEL - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
-
- AlignmentCalc - Class in org.biojava.bio.structure.align.gui
-
A class that obtains two structures via DAS and aligns them
This is done in a separate thread.
- AlignmentCalc(AlignmentGui, Structure, Structure, String, String) - Constructor for class org.biojava.bio.structure.align.gui.AlignmentCalc
-
requests an alignment of pdb1 vs pdb 2.
- AlignmentCalc - Class in org.biojava.bio.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.bio.structure.gui.util.AlignmentCalc
-
requests an alignment of pdb1 vs pdb 2.
- AlignmentCalcDB - Class in org.biojava.bio.structure.align.gui
-
- AlignmentCalcDB(AlignmentGui, Structure, String, UserConfiguration, String) - Constructor for class org.biojava.bio.structure.align.gui.AlignmentCalcDB
-
- AlignmentCalculationRunnable - Interface in org.biojava.bio.structure.align.gui
-
- alignmentEnded() - Method in class org.biojava.bio.structure.align.client.CountProgressListener
-
- alignmentEnded() - Method in interface org.biojava.bio.structure.align.events.AlignmentProgressListener
-
- alignmentEnded() - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
-
- AlignmentGui - Class in org.biojava.bio.structure.align.gui
-
A JFrame that allows to trigger a pairwise structure alignment,
either from files in a directory,
or after manual upload.
- AlignmentGuiDemo - Class in demo
-
- AlignmentGuiDemo() - Constructor for class demo.AlignmentGuiDemo
-
- AlignmentPositionListener - Interface in org.biojava.bio.structure.gui.events
-
- AlignmentProgressListener - Interface in org.biojava.bio.structure.align.events
-
- AlignmentProgressListener - Class in org.biojava.bio.structure.align.pairwise
-
A class to listen to progress of the structure alignmnent calcualtions
- AlignmentProgressListener() - Constructor for class org.biojava.bio.structure.align.pairwise.AlignmentProgressListener
-
- AlignmentResult - Class in org.biojava.bio.structure.align.pairwise
-
A class to track the alignment results in a flat file
- AlignmentResult() - Constructor for class org.biojava.bio.structure.align.pairwise.AlignmentResult
-
- Alignments - Class in org.biojava3.alignment
-
Static utility to easily run alignment routines.
- Alignments.PairInProfileScorerType - Enum in org.biojava3.alignment
-
List of implemented sequence pair in a profile scoring routines.
- Alignments.PairwiseSequenceAlignerType - Enum in org.biojava3.alignment
-
List of implemented pairwise sequence alignment routines.
- Alignments.PairwiseSequenceScorerType - Enum in org.biojava3.alignment
-
List of implemented pairwise sequence scoring routines.
- Alignments.ProfileProfileAlignerType - Enum in org.biojava3.alignment
-
List of implemented profile-profile alignment routines.
- Alignments.RefinerType - Enum in org.biojava3.alignment
-
List of implemented profile refinement routines.
- alignmentStarted(String, String) - Method in class org.biojava.bio.structure.align.client.CountProgressListener
-
- alignmentStarted(String, String) - Method in interface org.biojava.bio.structure.align.events.AlignmentProgressListener
-
- alignmentStarted(String, String) - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
-
- AlignmentTextPanel - Class in org.biojava.bio.structure.align.gui
-
- AlignmentTextPanel() - Constructor for class org.biojava.bio.structure.align.gui.AlignmentTextPanel
-
- alignPair(String, String) - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
-
- AligNPE - Class in org.biojava.bio.structure.align.pairwise
-
- AligNPE() - Constructor for class org.biojava.bio.structure.align.pairwise.AligNPE
-
- alignRigid(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.fatcat.FatCat
-
- alignRigid(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.bio.structure.align.fatcat.FatCat
-
- alignSuperfamily() - Method in class demo.DemoSCOP
-
- AlignTools - Class in org.biojava.bio.structure.align.helper
-
- AlignTools() - Constructor for class org.biojava.bio.structure.align.helper.AlignTools
-
- AligPanel - Class in org.biojava.bio.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.bio.structure.align.gui.aligpanel.AligPanel
-
- AligPanelMouseMotionListener - Class in org.biojava.bio.structure.align.gui.aligpanel
-
- AligPanelMouseMotionListener(AligPanel) - Constructor for class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
-
- AligUIManager - Class in org.biojava.bio.structure.align.webstart
-
- AligUIManager() - Constructor for class org.biojava.bio.structure.align.webstart.AligUIManager
-
- aliphatic - Static variable in class org.biojava3.phylo.ResidueProperties
-
- ALL_POLYMER_TYPES - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
-
Convenience Set of all polymer types.
- AllChemCompProvider - Class in org.biojava.bio.structure.io.mmcif
-
A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.
- AllChemCompProvider() - Constructor for class org.biojava.bio.structure.io.mmcif.AllChemCompProvider
-
- allComponents() - Static method in class org.biojava3.protmod.Component
-
- allComponents() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
-
- allIds() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
-
- allKeywords() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
-
- allModifications() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
-
- allPdbccIds() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
-
- allPsimodIds() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
-
- allResidIds() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
-
- AltAligComparator - Class in org.biojava.bio.structure.align.pairwise
-
a comparator to sort AlternativeAlignments based on their number of equivalent residues
and RMSD.
- AltAligComparator() - Constructor for class org.biojava.bio.structure.align.pairwise.AltAligComparator
-
- AlternativeAlignment - Class in org.biojava.bio.structure.align.pairwise
-
Implements a class which handles one possible (alternative) solution.
- AlternativeAlignment() - Constructor for class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- AlternativeAlignmentFrame - Class in org.biojava.bio.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.bio.structure.gui.util.AlternativeAlignmentFrame
-
- AmbiguityDNACompoundSet - Class in org.biojava3.core.sequence.compound
-
- AmbiguityDNACompoundSet() - Constructor for class org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet
-
- AmbiguityRNACompoundSet - Class in org.biojava3.core.sequence.compound
-
- AmbiguityRNACompoundSet() - Constructor for class org.biojava3.core.sequence.compound.AmbiguityRNACompoundSet
-
- AMBIGUOUS_AA - Static variable in class org.biojava3.data.sequence.SequenceUtil
-
Same as AA pattern but with two additional letters - XU
- AMBIGUOUS_NUCLEOTIDE - Static variable in class org.biojava3.data.sequence.SequenceUtil
-
Ambiguous nucleotide
- AminoAcid - Interface in org.biojava.bio.structure
-
A
Group that represents an AminoAcid.
- AMINOACID - Static variable in class org.biojava.bio.structure.GroupType
-
the type for amino acids
- AminoAcidComposition - Class in org.biojava3.aaproperties.xml
-
- AminoAcidComposition() - Constructor for class org.biojava3.aaproperties.xml.AminoAcidComposition
-
- AminoAcidComposition(String, String, String, List<Name2Count>, List<Name2Count>) - Constructor for class org.biojava3.aaproperties.xml.AminoAcidComposition
-
- AminoAcidCompositionTable - Class in org.biojava3.aaproperties.xml
-
- AminoAcidCompositionTable() - Constructor for class org.biojava3.aaproperties.xml.AminoAcidCompositionTable
-
- AminoAcidCompositionTable(List<AminoAcidComposition>) - Constructor for class org.biojava3.aaproperties.xml.AminoAcidCompositionTable
-
- AminoAcidCompound - Class in org.biojava3.core.sequence.compound
-
Used to describe an Amino Acid.
- AminoAcidCompound(AminoAcidCompoundSet, String, String, String, Float) - Constructor for class org.biojava3.core.sequence.compound.AminoAcidCompound
-
- AminoAcidCompoundSet - Class in org.biojava3.core.sequence.compound
-
Set of proteinogenic amino acids.
- AminoAcidCompoundSet() - Constructor for class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
-
- AminoAcidImpl - Class in org.biojava.bio.structure
-
AminoAcid inherits most from Hetatom.
- AminoAcidImpl() - Constructor for class org.biojava.bio.structure.AminoAcidImpl
-
- aminoAcidsCompounds(CompoundSet<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
-
- amount(Atom) - Static method in class org.biojava.bio.structure.Calc
-
amount.
- AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.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.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
-
- AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
-
Prepares for a pairwise global sequence alignment.
- AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, int) - Constructor for class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
-
Prepares for a pairwise global sequence alignment.
- AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, int, int[]) - Constructor for class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
-
Prepares for a pairwise global sequence alignment.
- anchors - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
-
- angle(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
-
angle.
- angleCheckOk(FragmentPair, FragmentPair, float) - Method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
-
- apairs_from_idxlst(JointFragments) - Method in class org.biojava.bio.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.bio.structure.align.pairwise.AlternativeAlignment
-
Set apairs according to a seed position.
- App - Class in org.biojava3.genome
-
Hello world!
- App() - Constructor for class org.biojava3.genome.App
-
- App - Class in org.biojava3.phylo
-
Hello world!
- App() - Constructor for class org.biojava3.phylo.App
-
- applyFilters() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
Deprecated.
- applyValues() - Method in class org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
-
- approach_ap3(Atom[], Atom[], FragmentPair[], StrucAligParameters) - Method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
-
- Arg - Static variable in class org.biojava3.phylo.ResidueProperties
-
- aromatic - Static variable in class org.biojava3.phylo.ResidueProperties
-
- arrayLeftDivide(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Element-by-element left division, C = A.
- arrayLeftDivideEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Element-by-element left division in place, A = A.
- ArrayListProxySequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.loader
-
- ArrayListProxySequenceReader() - Constructor for class org.biojava3.core.sequence.loader.ArrayListProxySequenceReader
-
- ArrayListSequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.storage
-
Stores a Sequence as a collection of compounds in an ArrayList
- ArrayListSequenceReader() - Constructor for class org.biojava3.core.sequence.storage.ArrayListSequenceReader
-
- ArrayListSequenceReader(List<C>, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.ArrayListSequenceReader
-
- ArrayListSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.ArrayListSequenceReader
-
- arrayRightDivide(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Element-by-element right division, C = A.
- arrayRightDivideEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Element-by-element right division in place, A = A.
- arrayTimes(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Element-by-element multiplication, C = A.
- arrayTimesEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Element-by-element multiplication in place, A = A.
- Asn - Static variable in class org.biojava3.phylo.ResidueProperties
-
- Asp - Static variable in class org.biojava3.phylo.ResidueProperties
-
- assertLocation() - Method in class org.biojava3.core.sequence.location.InsdcLocations.BondLocation
-
- assertLocation() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
-
- assign(Structure) - Method in class org.biojava.bio.structure.secstruc.SecStruc
-
assigns the secondary structure to the groups in this Structure object
and set the results in the group properties.
- Atom - Interface in org.biojava.bio.structure
-
A simple interface for an Atom.
- ATOM_CA_THRESHOLD - Static variable in class org.biojava.bio.structure.io.PDBFileParser
-
the maximum number of atoms that will be parsed before the parser switches to a CA-only
representation of the PDB file.
- AtomCache - Class in org.biojava.bio.structure.align.util
-
A utility class that provides easy access to Structure objects.
- AtomCache() - Constructor for class org.biojava.bio.structure.align.util.AtomCache
-
Default AtomCache constructor.
- AtomCache(String, boolean) - Constructor for class org.biojava.bio.structure.align.util.AtomCache
-
Creates an instance of an AtomCache that is pointed to the a particular
path in the file system.
- AtomCache(UserConfiguration) - Constructor for class org.biojava.bio.structure.align.util.AtomCache
-
Creates a new AtomCache object based on the provided UserConfiguration.
- AtomImpl - Class in org.biojava.bio.structure
-
Implementation of an Atom of a PDB file.
- AtomImpl() - Constructor for class org.biojava.bio.structure.AtomImpl
-
- AtomInfo - Class in org.biojava.bio.structure.align.gui.jmol
-
This class uniquely describes an atom
- AtomInfo() - Constructor for class org.biojava.bio.structure.align.gui.jmol.AtomInfo
-
- AtomInfoParser - Class in org.biojava.bio.structure.align.gui.jmol
-
- AtomInfoParser() - Constructor for class org.biojava.bio.structure.align.gui.jmol.AtomInfoParser
-
- AtomIterator - Class in org.biojava.bio.structure
-
an iterator over all atoms of a structure / group.
- AtomIterator(Structure) - Constructor for class org.biojava.bio.structure.AtomIterator
-
Constructs an AtomIterator object.
- AtomIterator(Group) - Constructor for class org.biojava.bio.structure.AtomIterator
-
Constructs an AtomIterator object.
- ATOMRECORD - Static variable in interface org.biojava.bio.structure.AminoAcid
-
Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.
- atoms - Variable in class org.biojava.bio.structure.HetatomImpl
-
- AtomSite - Class in org.biojava.bio.structure.io.mmcif.model
-
- AtomSite() - Constructor for class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- attribute(String, String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
-
- attribute(String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
-
- attribute(String, String, String) - Method in interface org.biojava3.core.util.XMLWriter
-
Add an attribute to an element.
- attribute(String, String) - Method in interface org.biojava3.core.util.XMLWriter
-
Add an un-qualified attribute to an element.
- attributes() - Method in class org.biojava3.genome.parsers.gff.Feature
-
Get the string of key/value attributes.
- attributeValues(String) - Method in class org.biojava3.genome.parsers.gff.FeatureList
-
Create a collection of the unique values for the specified key.
- AuditAuthor - Class in org.biojava.bio.structure.io.mmcif.model
-
- AuditAuthor() - Constructor for class org.biojava.bio.structure.io.mmcif.model.AuditAuthor
-
- Author - Class in org.biojava.bio.structure
-
Describes author attributes for author information in a PDB file.
- Author() - Constructor for class org.biojava.bio.structure.Author
-
- available() - Method in class org.biojava3.core.util.UncompressInputStream
-
- C - Static variable in class org.biojava3.aaproperties.Constraints
-
- CA_AND_SIDE_CHAIN_ANGLE_SCORING - Static variable in class org.biojava.bio.structure.align.ce.CeParameters
-
- CA_MIN_DIST - Static variable in class org.biojava.bio.structure.secstruc.SecStruc
-
the minimal distance of two CA atoms if H-bonds are allowed to form.
- caAtomName - Static variable in class org.biojava.bio.structure.StructureTools
-
The Atom name of C-alpha atoms.
- CACHE_PROPERTY - Static variable in class org.biojava3.core.util.InputStreamProvider
-
- CacheFactory - Class in org.biojava.bio.structure.align.util
-
provides a SoftHashMap singleton.
- CAConverter - Class in org.biojava.bio.structure.io
-
Converts full atom representations to Calpha only ones.
- CAConverter() - Constructor for class org.biojava.bio.structure.io.CAConverter
-
- calAfpRmsd(int, int[], int, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.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.bio.structure
-
utility operations on Atoms, AminoAcids, etc.
- Calc() - Constructor for class org.biojava.bio.structure.Calc
-
- calc_rmsd(Atom[], Atom[], int, boolean, boolean) - Method in class org.biojava.bio.structure.align.ce.CECalculator
-
superimpose and get rmsd
- calcIdSimilarity(char[], char[], int) - Static method in class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
-
- calcScale(int) - Method in class org.biojava.bio.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.bio.structure.align.pairwise.AlternativeAlignment
-
calculates scores for this alignment ( %id )
- calcSimilarity() - Method in class org.biojava.bio.structure.align.model.AFPChain
-
- calculatedFragmentPairs(List<FragmentPair>) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentProgressListener
-
- calculateHBondEnergy(SecStrucGroup, SecStrucGroup) - Method in class org.biojava.bio.structure.secstruc.SecStruc
-
calculate HBond energy of two groups in cal/mol ...
- calculateIndirectAmbiguities() - Method in class org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet
-
Loops through all known nucelotides and attempts to find which are
equivalent to each other.
- calculateSuperpositionByIdx(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- calculator - Variable in class org.biojava.bio.structure.align.ce.CeMain
-
- call() - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
-
- call() - Method in class org.biojava3.alignment.template.CallablePairwiseSequenceAligner
-
- call() - Method in class org.biojava3.alignment.template.CallablePairwiseSequenceScorer
-
- call() - Method in class org.biojava3.alignment.template.CallableProfileProfileAligner
-
- call() - Method in class org.biojava3.ronn.ORonn
-
- CallablePairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.template
-
- CallablePairwiseSequenceAligner(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava3.alignment.template.CallablePairwiseSequenceAligner
-
Creates a pairwise sequence alignment task for simplified parallel execution.
- CallablePairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.template
-
- CallablePairwiseSequenceScorer(PairwiseSequenceScorer<S, C>) - Constructor for class org.biojava3.alignment.template.CallablePairwiseSequenceScorer
-
Creates a pairwise sequence scoring task for simplified parallel execution.
- CallableProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.template
-
- CallableProfileProfileAligner(ProfileProfileAligner<S, C>) - Constructor for class org.biojava3.alignment.template.CallableProfileProfileAligner
-
Creates a profile-profile alignment task for simplified parallel execution.
- CallableStructureAlignment - Class in org.biojava.bio.structure.align
-
- CallableStructureAlignment() - Constructor for class org.biojava.bio.structure.align.CallableStructureAlignment
-
- calNS(FatCatParameters, AFPChain) - Method in class org.biojava.bio.structure.align.fatcat.calc.SigEva
-
- calSigAll(FatCatParameters, AFPChain) - Method in class org.biojava.bio.structure.align.fatcat.calc.SigEva
-
- cancel() - Method in class org.biojava3.phylo.TreeConstructor
-
- canceled(Object) - Method in interface org.biojava3.phylo.NJTreeProgressListener
-
- canceled(Object) - Method in class org.biojava3.phylo.ProgessListenerStub
-
- canComplement(Sequence<C>) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
-
Uses the Sequence's CompoundSet to decide if a compound can
be assgined to ComplementCompound meaning it can complement
- CaseFreeAminoAcidCompoundSet - Class in org.biojava3.aaproperties.xml
-
Set of proteinogenic amino acids.
- CaseFreeAminoAcidCompoundSet() - Constructor for class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- CaseInsensitiveCompound - Class in org.biojava3.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.biojava3.core.sequence.transcription.CaseInsensitiveCompound
-
- cbAtomName - Static variable in class org.biojava.bio.structure.StructureTools
-
- CDSComparator - Class in org.biojava3.core.sequence
-
- CDSComparator() - Constructor for class org.biojava3.core.sequence.CDSComparator
-
- CDSSequence - Class in org.biojava3.core.sequence
-
Represents a exon or coding sequence in a gene.
- CDSSequence(TranscriptSequence, int, int, int) - Constructor for class org.biojava3.core.sequence.CDSSequence
-
- CECalculator - Class in org.biojava.bio.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.bio.structure.align.ce.CECalculator
-
- ceColumnNames - Static variable in class org.biojava.bio.structure.align.gui.DBResultTable
-
- CeCPMain - Class in org.biojava.bio.structure.align.ce
-
A wrapper for
CeMain which sets default parameters to be appropriate for finding
circular permutations
- CeCPMain() - Constructor for class org.biojava.bio.structure.align.ce.CeCPMain
-
- CeMain - Class in org.biojava.bio.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.bio.structure.align.ce.CeMain
-
- centerAtoms(Atom[]) - Static method in class org.biojava.bio.structure.Calc
-
Center the atoms at the Centroid.
- centerAtoms(Atom[], Atom) - Static method in class org.biojava.bio.structure.Calc
-
Center the atoms at the Centroid, if the centroid is already know.
- centerOfMass(Atom[]) - Static method in class org.biojava.bio.structure.Calc
-
- CeParameters - Class in org.biojava.bio.structure.align.ce
-
Contains the parameters that can be sent to CE
- CeParameters() - Constructor for class org.biojava.bio.structure.align.ce.CeParameters
-
- CeSideChainMain - Class in org.biojava.bio.structure.align.ce
-
- CeSideChainMain() - Constructor for class org.biojava.bio.structure.align.ce.CeSideChainMain
-
- CeSideChainUserArgumentProcessor - Class in org.biojava.bio.structure.align.ce
-
- CeSideChainUserArgumentProcessor() - Constructor for class org.biojava.bio.structure.align.ce.CeSideChainUserArgumentProcessor
-
- CeUserArgumentProcessor - Class in org.biojava.bio.structure.align.ce
-
process the arguments from command line
- CeUserArgumentProcessor() - Constructor for class org.biojava.bio.structure.align.ce.CeUserArgumentProcessor
-
- Chain - Interface in org.biojava.bio.structure
-
Defines the interface for a Chain.
- CHAIN_NR_SYMBOL - Static variable in class org.biojava.bio.structure.align.util.AtomCache
-
- CHAIN_SPLIT_SYMBOL - Static variable in class org.biojava.bio.structure.align.util.AtomCache
-
- ChainImpl - Class in org.biojava.bio.structure
-
A Chain in a PDB file.
- ChainImpl() - Constructor for class org.biojava.bio.structure.ChainImpl
-
Constructs a ChainImpl object.
- charged - Static variable in class org.biojava3.phylo.ResidueProperties
-
- checkDoFirstInstall() - Method in class org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider
-
checks if the chemical components already have been installed into the PDB directory.
- checkPath() - Static method in class org.biojava.bio.structure.io.mmcif.AllChemCompProvider
-
make sure all paths are initialized correctly
- checkPoint() - Method in class org.biojava3.ronn.Timer
-
- checkSequence(String) - Static method in class org.biojava3.aaproperties.Utils
-
Checks if the sequence contains invalid characters.
- checkSequence(String, Set<Character>) - Static method in class org.biojava3.aaproperties.Utils
-
Checks if the sequence contains invalid characters.
- checksum(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
-
Performs a simple CRC64 checksum on any given sequence.
- CheckTreeAccuracy - Class in org.biojava3.phylo
-
- CheckTreeAccuracy() - Constructor for class org.biojava3.phylo.CheckTreeAccuracy
-
- CHEM_COMP_CACHE_DIRECTORY - Static variable in class org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider
-
- chem_comp_type - Variable in enum org.biojava.bio.structure.io.mmcif.chem.ResidueType
-
String value of the type
- ChemComp - Class in org.biojava.bio.structure.io.mmcif.model
-
A definition for a Chemical Component, as maintained by the wwPDB.
- ChemComp() - Constructor for class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- ChemCompConsumer - Class in org.biojava.bio.structure.io.mmcif
-
- ChemCompConsumer() - Constructor for class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
-
- ChemCompDescriptor - Class in org.biojava.bio.structure.io.mmcif.model
-
Container object for _pdbx_chem_comp_descriptor
- ChemCompDescriptor() - Constructor for class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
-
- ChemCompDistribution - Class in demo
-
- ChemCompDistribution() - Constructor for class demo.ChemCompDistribution
-
- ChemCompGroupFactory - Class in org.biojava.bio.structure.io.mmcif
-
- ChemCompGroupFactory() - Constructor for class org.biojava.bio.structure.io.mmcif.ChemCompGroupFactory
-
- ChemCompProvider - Interface in org.biojava.bio.structure.io.mmcif
-
Interface that is implemented by all classes that can provide
ChemComp definitions.
- ChemCompTools - Class in org.biojava.bio.structure.io.mmcif.chem
-
Some tools for working with chemical compounds.
- ChemCompTools() - Constructor for class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
-
- ChemicalComponentDictionary - Class in org.biojava.bio.structure.io.mmcif
-
A representation of the Chemical Component Dictionary.
- ChemicalComponentDictionary() - Constructor for class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
-
- children() - Method in class org.biojava3.alignment.GuideTree.Node
-
- chol() - Method in class org.biojava.bio.structure.jama.Matrix
-
Cholesky Decomposition
- CholeskyDecomposition - Class in org.biojava.bio.structure.jama
-
Cholesky Decomposition.
- CholeskyDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.CholeskyDecomposition
-
Cholesky algorithm for symmetric and positive definite matrix.
- ChooseDirAction - Class in org.biojava.bio.structure.align.gui
-
Ask the user to provide a directory containting PDB files.
- ChooseDirAction(JTextField, UserConfiguration) - Constructor for class org.biojava.bio.structure.align.gui.ChooseDirAction
-
- ChromosomeSequence - Class in org.biojava3.core.sequence
-
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
- ChromosomeSequence() - Constructor for class org.biojava3.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.biojava3.core.sequence.ChromosomeSequence
-
String is king and assume DNA
- ChromosomeSequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.ChromosomeSequence
-
Fairly important constructor given the size of a ChromsomeSequence where the
ProxySequenceReader could load from disk via RandomAccessFile so that the sequence
doesn't need to be kept in memory.
- ChromosomeSequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.ChromosomeSequence
-
Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet
- ChromosomeSequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.ChromosomeSequence
-
Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet
- circularLocation(int, int, Strand, int) - Static method in class org.biojava3.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.biojava3.core.sequence.location.template.Location.Tools
-
Converts a location which defines the outer bounds of a circular
location and splits it into the required portions.
- claFileName - Static variable in class org.biojava.bio.structure.scop.ScopInstallation
-
- classEqual(Object, Object) - Static method in class org.biojava3.core.util.Equals
-
This method should be called before beginning any equals methods.
- ClasspathResource - Class in org.biojava3.core.sequence.io.util
-
This object represents a classpath resource on the local system.
- ClasspathResource(String) - Constructor for class org.biojava3.core.sequence.io.util.ClasspathResource
-
Basic constructor only allowing you to specify where to find the file.
- ClasspathResource(String, boolean) - Constructor for class org.biojava3.core.sequence.io.util.ClasspathResource
-
Advanced constructor which allows you to optionally pre-cache the
data
- ClasspathResource(String, boolean, boolean) - Constructor for class org.biojava3.core.sequence.io.util.ClasspathResource
-
Advanced constructor which lets you set the preCache variable and to
force the type of file we are decompressing.
- cleanSequence(String, Set<Character>) - Static method in class org.biojava3.aaproperties.Utils
-
Returns a new sequence with all invalid characters being replaced by '-'.
- cleanSequence(String) - Static method in class org.biojava3.data.sequence.SequenceUtil
-
Removes all whitespace chars in the sequence string
- cleanup() - Method in class org.biojava.bio.structure.align.gui.AlignmentCalc
-
- cleanup() - Method in class org.biojava.bio.structure.align.gui.AlignmentCalcDB
-
- cleanup() - Method in interface org.biojava.bio.structure.align.gui.AlignmentCalculationRunnable
-
- cleanUp() - Method in class org.biojava.bio.structure.align.gui.AlignmentGui
-
- cleanup(List<Domain>) - Static method in class org.biojava.bio.structure.domain.pdp.ShortSegmentRemover
-
- cleanup() - Method in class org.biojava.bio.structure.gui.util.AlignmentCalc
-
- clear() - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
-
Clears all finite endpoints
- clear() - Method in class org.biojava3.core.util.FlatFileCache
-
- clear() - Method in class org.biojava3.core.util.SoftHashMap
-
- clear() - Method in class org.biojava3.structure.gui.JmolViewerImpl
-
- clear() - Method in interface org.biojava3.structure.gui.Selection
-
- clear() - Method in class org.biojava3.structure.gui.SelectionImpl
-
- clear() - Method in interface org.biojava3.structure.gui.StructureViewer
-
Clear the current display
- clearAlgorithms() - Static method in class org.biojava.bio.structure.align.StructureAlignmentFactory
-
Removes all algorithms from the list
- clearAtoms() - Method in interface org.biojava.bio.structure.Group
-
Remove all atoms from this group.
- clearAtoms() - Method in class org.biojava.bio.structure.HetatomImpl
-
remove all atoms
- clearCache() - Static method in class org.biojava.bio.structure.PDBStatus
-
The status of PDB IDs are cached to reduce server overload.
- clearCache() - Method in class org.biojava3.alignment.SimpleAlignedSequence
-
- clearCache() - Method in interface org.biojava3.alignment.template.AlignedSequence
-
Nullifies cached arrays/objects.
- clearConsumers() - Method in interface org.biojava.bio.structure.io.mmcif.MMcifParser
-
Remove all consumers from the parser.
- clearConsumers() - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
-
- clearExtensions() - Method in class org.biojava.bio.structure.io.MMCIFFileReader
-
- clearExtensions() - Method in class org.biojava.bio.structure.io.PDBFileReader
-
clear the supported file extensions
- clearExtensions() - Method in interface org.biojava.bio.structure.io.StructureIOFile
-
clear all file extensions
- clearFilters() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
Deprecated.
- clearFilters() - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
-
Deprecated.
- clearFilters() - Method in interface org.biojava.bio.structure.server.PDBInstallation
-
Deprecated.
remove all filters, next time getAll is called, it will return all available PDBs
- clearListeners() - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
-
- clearListeners() - Method in class org.biojava.bio.structure.align.FarmJob
-
- clearListeners() - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
- clearListeners() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- clearListeners() - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
-
- clearListeners() - Method in class org.biojava.bio.structure.server.StructureFetcherRunnable
-
Deprecated.
- clearStructureListeners() - Method in class org.biojava.bio.structure.server.SimpleStructureServer
-
Deprecated.
- clearStructureListeners() - Method in interface org.biojava.bio.structure.server.StructureServer
-
Deprecated.
- CliTools - Class in org.biojava.bio.structure.align.util
-
Utilities for autoconfiguring javabeans based on command line arguments.
- clone() - Method in class org.biojava.bio.structure.align.model.AFPChain
-
Creates and returns a copy of this object.
- clone() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- clone() - Method in class org.biojava.bio.structure.AminoAcidImpl
-
returns and identical copy of this Group object .
- clone() - Method in interface org.biojava.bio.structure.Atom
-
returns and identical copy of this object .
- clone() - Method in class org.biojava.bio.structure.AtomImpl
-
returns and identical copy of this object .
- clone() - Method in interface org.biojava.bio.structure.Chain
-
returns an identical copy of this Chain.
- clone() - Method in class org.biojava.bio.structure.ChainImpl
-
Returns an identical copy of this Chain .
- clone() - Method in class org.biojava.bio.structure.Compound
-
- clone() - Method in interface org.biojava.bio.structure.Group
-
returns and identical copy of this Group object .
- clone() - Method in class org.biojava.bio.structure.GroupIterator
-
Creates and returns a copy of this object.
- clone() - Method in class org.biojava.bio.structure.HetatomImpl
-
returns and identical copy of this Group object .
- clone() - Method in class org.biojava.bio.structure.jama.Matrix
-
Clone the Matrix object.
- clone() - Method in class org.biojava.bio.structure.NucleotideImpl
-
- clone() - Method in class org.biojava.bio.structure.secstruc.HBond
-
- clone() - Method in class org.biojava.bio.structure.SSBond
-
- clone() - Method in interface org.biojava.bio.structure.Structure
-
returns an identical copy of this Structure object
- clone() - Method in class org.biojava.bio.structure.StructureImpl
-
returns an identical copy of this structure .
- cloneCAArray(Atom[]) - Static method in class org.biojava.bio.structure.StructureTools
-
Provides an equivalent copy of Atoms in a new array.
- cloneGroups(Atom[]) - Static method in class org.biojava.bio.structure.StructureTools
-
Clone a set of CA Atoms, but returns the parent groups
- clonePoint() - Method in class org.biojava3.core.sequence.location.SimplePoint
-
- clonePoint() - Method in interface org.biojava3.core.sequence.location.template.Point
-
Returns a copy of this point
- close() - Method in class org.biojava.bio.structure.align.util.SynchronizedOutFile
-
- close() - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead
-
- close(Closeable) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
-
Closes any Object which implements the interface
Closeable and
sending any error to the logger but not forcing any explicit catching of
stream errors.
- close() - Method in class org.biojava3.core.util.PrettyXMLWriter
-
- close() - Method in interface org.biojava3.core.util.XMLWriter
-
Close this XMLWriter, and it's underlying stream.
- closeTag(String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
-
- closeTag(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
-
- closeTag(String, String) - Method in interface org.biojava3.core.util.XMLWriter
-
Closes an element
- closeTag(String) - Method in interface org.biojava3.core.util.XMLWriter
-
Closes an un-qualified element.
- cluster(AlternativeAlignment[]) - Static method in class org.biojava.bio.structure.align.ClusterAltAligs
-
- cluster(AlternativeAlignment[], int) - Static method in class org.biojava.bio.structure.align.ClusterAltAligs
-
- cluster(List<Domain>, PDPDistanceMatrix) - Static method in class org.biojava.bio.structure.domain.pdp.ClusterDomains
-
- ClusterAltAligs - Class in org.biojava.bio.structure.align
-
A class that clusters alternative alignments according to their
similarity.
- ClusterAltAligs() - Constructor for class org.biojava.bio.structure.align.ClusterAltAligs
-
- ClusterDomains - Class in org.biojava.bio.structure.domain.pdp
-
- ClusterDomains() - Constructor for class org.biojava.bio.structure.domain.pdp.ClusterDomains
-
- CodonCompound - Class in org.biojava3.core.sequence.compound
-
Define a codon
- CodonCompound(NucleotideCompound, NucleotideCompound, NucleotideCompound, boolean) - Constructor for class org.biojava3.core.sequence.compound.CodonCompound
-
- codonHash - Static variable in class org.biojava3.phylo.ResidueProperties
-
- codonHash2 - Static variable in class org.biojava3.phylo.ResidueProperties
-
- codonTranslate(String) - Static method in class org.biojava3.phylo.ResidueProperties
-
- CollectionTools - Class in org.biojava.bio.structure.align.util
-
Utilities for working with collections.
- CollectionTools() - Constructor for class org.biojava.bio.structure.align.util.CollectionTools
-
- coloring - Variable in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
-
- ColorInterpolator - Interface in org.biojava.bio.structure.gui.util.color
-
- ColorUtils - Class in org.biojava.bio.structure.gui.util.color
-
- ColorUtils() - Constructor for class org.biojava.bio.structure.gui.util.color.ColorUtils
-
- colorWheel - Static variable in class org.biojava.bio.structure.gui.util.color.ColorUtils
-
- COMMAND_LINE_HELP - Static variable in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
-
- CommandPrompt - Class in org.biojava3.aaproperties
-
- CommandPrompt() - Constructor for class org.biojava3.aaproperties.CommandPrompt
-
- CommandPrompt.PropertyName - Enum in org.biojava3.aaproperties
-
- compare(int[], int[]) - Method in class org.biojava.bio.structure.align.helper.IdxComparator
-
- compare(AlternativeAlignment, AlternativeAlignment) - Method in class org.biojava.bio.structure.align.pairwise.AltAligComparator
-
- compare(Segment, Segment) - Method in class org.biojava.bio.structure.domain.pdp.SegmentComparator
-
- compare(CDSSequence, CDSSequence) - Method in class org.biojava3.core.sequence.CDSComparator
-
Used to sort two CDSSequences where Negative Strand makes it tough
- compare(ExonSequence, ExonSequence) - Method in class org.biojava3.core.sequence.ExonComparator
-
- compare(AbstractSequence<?>, AbstractSequence<?>) - Method in class org.biojava3.core.sequence.SequenceComparator
-
- compareTo(PdbPair) - Method in class org.biojava.bio.structure.align.client.PdbPair
-
- compareTo(StructureName) - Method in class org.biojava.bio.structure.align.client.StructureName
-
- compareTo(Domain) - Method in class org.biojava.bio.structure.domain.pdp.Domain
-
- compareTo(Segment) - Method in class org.biojava.bio.structure.domain.pdp.Segment
-
- compareTo(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- compareTo(Site) - Method in class org.biojava.bio.structure.Site
-
- compareTo(Point) - Method in class org.biojava3.core.sequence.location.FuzzyPoint
-
- compareTo(Point) - Method in class org.biojava3.core.sequence.location.SimplePoint
-
- compareTo(FastaSequence) - Method in class org.biojava3.data.sequence.FastaSequence
-
- compareTo(ProteinModification) - Method in class org.biojava3.protmod.ProteinModificationImpl
-
- compareTo(ModifiedCompound) - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
-
- compareTo(StructureGroup) - Method in class org.biojava3.protmod.structure.StructureGroup
-
- Comparison - Class in org.biojava3.phylo
-
- Comparison() - Constructor for class org.biojava3.phylo.Comparison
-
- ComplementCompound - Interface in org.biojava3.core.sequence.template
-
- ComplementSequenceView<C extends ComplementCompound> - Class in org.biojava3.core.sequence.views
-
For a given sequence this class will create a view over the top of it
and for every request the code will return the complement of the underlying
base e.g. base A will become base T
- ComplementSequenceView(Sequence<C>) - Constructor for class org.biojava3.core.sequence.views.ComplementSequenceView
-
- complete(Object) - Method in interface org.biojava3.phylo.NJTreeProgressListener
-
- complete(Object) - Method in class org.biojava3.phylo.ProgessListenerStub
-
- completeCircularPasses(int, int) - Static method in class org.biojava3.core.sequence.location.LocationHelper
-
Works in a similar way to modulateCircularLocation but returns
the number of complete passes over a Sequence length a circular
location makes i.e. if we have a sequence of length 10 and the
location 3..52 we make 4 complete passes through the genome to
go from position 3 to position 52.
- completeCircularPasses(int, int) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools
-
Works in a similar way to modulateCircularLocation but returns
the number of complete passes over a Sequence length a circular
location makes i.e. if we have a sequence of length 10 and the
location 3..52 we make 4 complete passes through the genome to
go from position 3 to position 52.
- Component - Class in org.biojava3.protmod
-
contains information about a certain Component.
- ComponentXMLConverter - Class in org.biojava3.protmod.io
-
- ComponentXMLConverter() - Constructor for class org.biojava3.protmod.io.ComponentXMLConverter
-
- Compound - Class in org.biojava.bio.structure
-
Created by IntelliJ IDEA.
- Compound() - Constructor for class org.biojava.bio.structure.Compound
-
- Compound - Interface in org.biojava3.core.sequence.template
-
- CompoundNotFoundError - Error in org.biojava3.core.exceptions
-
- CompoundNotFoundError(CharSequence) - Constructor for error org.biojava3.core.exceptions.CompoundNotFoundError
-
- compoundsEqual(C, C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
-
- compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
-
- compoundsEquivalent(C, C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
-
- compoundsEquivalent(C, C) - Method in interface org.biojava3.core.sequence.template.CompoundSet
-
- CompoundSet<C extends Compound> - Interface in org.biojava3.core.sequence.template
-
- compoundsPerDatatype() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Should return the maximum amount of compounds we can encode per int
- compoundsPerDatatype() - Method in class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
- compoundsPerDatatype() - Method in class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
-
- compoundToInt(NucleotideCompound) - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
-
- CompoundTranslator<F extends Compound,T extends Compound> - Interface in org.biojava3.core.sequence.template
-
- computeMolecularWeight(ElementTable) - Method in class org.biojava3.aaproperties.xml.AminoAcidCompositionTable
-
Computes and store the molecular weight of each amino acid by its symbol in aaSymbol2MolecularWeight.
- ConcurrencyTools - Class in org.biojava3.core.util
-
Static utility to easily share a thread pool for concurrent/parallel/lazy execution.
- cond() - Method in class org.biojava.bio.structure.jama.Matrix
-
Matrix condition (2 norm)
- cond() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
-
Two norm condition number
- ConfigPDBInstallPanel - Class in org.biojava.bio.structure.align.gui
-
- ConfigStrucAligParams - Interface in org.biojava.bio.structure.align.ce
-
- ConfigurationException - Exception in org.biojava.bio.structure.align.util
-
- ConfigurationException(String) - Constructor for exception org.biojava.bio.structure.align.util.ConfigurationException
-
Constructs a ConfigurationException object.
- ConfigurationException(Throwable) - Constructor for exception org.biojava.bio.structure.align.util.ConfigurationException
-
Constructs a ConfigurationException object.
- configureBean(Object, String[]) - Static method in class org.biojava.bio.structure.align.util.CliTools
-
Configure a JavaBean based on a set of command line arguments.
- configureParameters() - Method in class org.biojava.bio.structure.align.gui.AlignmentGui
-
- ConfigXMLHandler - Class in org.biojava.bio.structure.align.webstart
-
XML content handler for serialisation of RegistryConfiguration class
- ConfigXMLHandler() - Constructor for class org.biojava.bio.structure.align.webstart.ConfigXMLHandler
-
- consistentAccessions(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper
-
Scans a list of locations and returns true if all the given locations
are linked to the same sequence.
- Constraints - Class in org.biojava3.aaproperties
-
This class is used to support the implementation of properties stated in IPeptideProperties.
- Constraints() - Constructor for class org.biojava3.aaproperties.Constraints
-
- constructWithCopy(double[][]) - Static method in class org.biojava.bio.structure.jama.Matrix
-
Construct a matrix from a copy of a 2-D array.
- contains(Location) - Method in class org.biojava3.genome.parsers.gff.Location
-
Check if this location contains the other.
- containsKey(Object) - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
-
- containsValue(Object) - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
-
- ContinuousColorMapper - Interface in org.biojava.bio.structure.gui.util.color
-
Provides a mapping between real numbers and Colors.
- ContinuousColorMapperTransform - Class in org.biojava.bio.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.bio.structure.gui.util.color.ContinuousColorMapperTransform
-
Creates a transform.
- convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Charge
-
Class for the conversion of protein sequence into charge
- convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Hydrophobicity
-
Class for the conversion of protein sequence into hydrophobicity
- convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
-
Class for the conversion of protein sequence into normalized van der waals volume
- convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Polarity
-
Class for the conversion of protein sequence into polarity
- convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Polarizability
-
Class for the conversion of protein sequence into polarizability
- convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2SecondaryStructure
-
Class for the conversion of protein sequence into secondary structure
- convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2SolventAccessibility
-
Class for the conversion of protein sequence into solvent accessibility
- convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convertor
-
Returns the grouping of the amino acid character.
- convert(ProteinSequence) - Method in class org.biojava3.aaproperties.profeat.convertor.Convertor
-
Returns the converted sequence.
- Convert2Charge - Class in org.biojava3.aaproperties.profeat.convertor
-
- Convert2Charge() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2Charge
-
- Convert2Hydrophobicity - Class in org.biojava3.aaproperties.profeat.convertor
-
- Convert2Hydrophobicity() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2Hydrophobicity
-
- Convert2NormalizedVanDerWaalsVolume - Class in org.biojava3.aaproperties.profeat.convertor
-
- Convert2NormalizedVanDerWaalsVolume() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
-
- Convert2Polarity - Class in org.biojava3.aaproperties.profeat.convertor
-
- Convert2Polarity() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2Polarity
-
- Convert2Polarizability - Class in org.biojava3.aaproperties.profeat.convertor
-
- Convert2Polarizability() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2Polarizability
-
- Convert2SecondaryStructure - Class in org.biojava3.aaproperties.profeat.convertor
-
- Convert2SecondaryStructure() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2SecondaryStructure
-
- Convert2SolventAccessibility - Class in org.biojava3.aaproperties.profeat.convertor
-
- Convert2SolventAccessibility() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2SolventAccessibility
-
- convert_3code_1code(String) - Static method in class org.biojava.bio.structure.StructureTools
-
convert three character amino acid codes into single character
e.g. convert CYS to C
- convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CECalculator
-
copy data from this class into AFPChain container object.
- convertAtomsToSeq(Atom[]) - Static method in class org.biojava.bio.structure.StructureTools
-
- Convertor - Class in org.biojava3.aaproperties.profeat.convertor
-
- Convertor() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convertor
-
- convertPairsToXML(SortedSet<PdbPair>) - Static method in class org.biojava.bio.structure.align.xml.PdbPairXMLConverter
-
- convertStreamToString(InputStream) - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
-
- convertXMLtoPairs(String) - Static method in class org.biojava.bio.structure.align.xml.PdbPairXMLConverter
-
- CookBook - Class in demo
-
- CookBook() - Constructor for class demo.CookBook
-
- CoordManager - Class in org.biojava.bio.structure.gui.util
-
a class that manages the conversion of sequence coordinate system to
JPanel drawing coordinates
- CoordManager() - Constructor for class org.biojava.bio.structure.gui.util.CoordManager
-
- copy() - Method in class org.biojava.bio.structure.jama.Matrix
-
Make a deep copy of a matrix
- copy(InputStream, OutputStream) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
-
Moves the bytes from input to output using a 4KB byte array.
- copyMatrix(DistanceMatrix) - Static method in class org.biojava3.phylo.CheckTreeAccuracy
-
- countAT(Sequence<NucleotideCompound>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
-
Returns the count of AT in the given sequence
- countCompounds(C...) - Method in class org.biojava3.alignment.SimpleAlignedSequence
-
- countCompounds(C...) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
-
- countCompounds(C...) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
-
- countCompounds(C...) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
-
- countCompounds(C...) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
-
- countCompounds(C...) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
-
Counts the number of times a compound appears in this sequence store
- countCompounds(C...) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
-
- countCompounds(C...) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
-
Delegates to SequenceMixin#countCompounds(org.biojava3.core.sequence.template.Sequence, C[])
- countCompounds(C...) - Method in class org.biojava3.core.sequence.template.AbstractSequence
-
- countCompounds(C...) - Method in interface org.biojava3.core.sequence.template.Sequence
-
Returns the number of times we found a compound in the Sequence
- countCompounds(Sequence<C>, C...) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
-
For the given vargs of compounds this method counts the number of
times those compounds appear in the given sequence
- countCompounds(C...) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
-
- countGC(Sequence<NucleotideCompound>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
-
Returns the count of GC in the given sequence
- countMatchesInSequence(String, String) - Static method in class org.biojava3.data.sequence.FastaSequence
-
- CountProgressListener - Class in org.biojava.bio.structure.align.client
-
- CountProgressListener() - Constructor for class org.biojava.bio.structure.align.client.CountProgressListener
-
- CRC64Checksum - Class in org.biojava3.core.util
-
Utility class that calculates a CRC64 checksum on a stream of bytes.
- CRC64Checksum() - Constructor for class org.biojava3.core.util.CRC64Checksum
-
- createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.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.bio.structure.align.util.AFPAlignmentDisplay
-
- createGradients() - Static method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
-
- createImage(String, String, Object, int) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
-
- createImageIcon(String) - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
-
Returns an ImageIcon, or null if the path was invalid.
- createIterator(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
-
Creates a simple sequence iterator which moves through a sequence going
from 1 to the length of the Sequence.
- createMMcifInfoList(File[], File, File) - Method in class org.biojava.bio.structure.server.PrepareMMcifIndexFile
-
parses a set of PDB files and writes info into a file
the file is tab separated and has the following columns:
name length resolution depositionDate modificationDate technique title classification filename
binaryDirectory: a directory in which binary files containing the atoms will be places, to provide a speedup
This method needs to be run, before a DBSearch can be performed, since the files created by this method
are required for the DBSearch
- createOutput(String, String) - Method in class org.biojava3.aaproperties.xml.SchemaGenerator
-
- createPDBInfoList(File[], File, File) - Method in class org.biojava.bio.structure.server.PrepareIndexFile
-
parses a set of PDB files and writes info into a file
the file is tab separated and has the following columns:
name length resolution depositionDate modificationDate technique title classification filename
binaryDirectory: a directory in which binary files containing the atoms will be places, to provide a speedup
This method needs to be run, before a DBSearch can be performed, since the files created by this method
are required for the DBSearch
- createSequence(Sequence<F>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
-
- createSequence(Sequence<F>) - Method in interface org.biojava3.core.sequence.template.CompoundTranslator
-
- createSequence(Sequence<NucleotideCompound>, Frame) - Method in class org.biojava3.core.sequence.transcription.DNAToRNATranslator
-
- createSequence(Sequence<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.DNAToRNATranslator
-
- createSequences(Sequence<F>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
-
- createSequences(Sequence<F>) - Method in interface org.biojava3.core.sequence.template.CompoundTranslator
-
- createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava3.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.biojava3.core.sequence.transcription.RNAToAminoAcidTranslator
-
Performs the core conversion of RNA to Peptide.
- createSubSequence(Sequence<C>, int, int) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
-
Creates a simple sub sequence view delimited by the given start and end.
- createVirtualCBAtom(AminoAcid) - Static method in class org.biojava.bio.structure.Calc
-
creates a virtual C-beta atom. this might be needed when working with GLY
thanks to Peter Lackner for a python template of this method.
- crossChains() - Method in interface org.biojava3.protmod.structure.ModifiedCompound
-
- crossChains() - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
-
- CS_HSV - Static variable in class org.biojava.bio.structure.gui.util.color.HSVColorSpace
-
The HSV color space
- Cut - Class in org.biojava.bio.structure.domain.pdp
-
- Cut() - Constructor for class org.biojava.bio.structure.domain.pdp.Cut
-
- cut(Atom[], Domain, CutValues, int[][], PDPDistanceMatrix) - Method in class org.biojava.bio.structure.domain.pdp.Cut
-
- CUT_OFF_VALUE - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
-
- CUT_OFF_VALUE1 - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
-
- CUT_OFF_VALUE1M - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
-
- CUT_OFF_VALUE1S - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
-
- CUT_OFF_VALUE2 - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
-
- CutDomain - Class in org.biojava.bio.structure.domain.pdp
-
- CutDomain(Atom[], PDPDistanceMatrix) - Constructor for class org.biojava.bio.structure.domain.pdp.CutDomain
-
- cutDomain(Domain, CutSites, PDPDistanceMatrix) - Method in class org.biojava.bio.structure.domain.pdp.CutDomain
-
- CutSites - Class in org.biojava.bio.structure.domain.pdp
-
- CutSites() - Constructor for class org.biojava.bio.structure.domain.pdp.CutSites
-
- cutsPerSection - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
-
- CutValues - Class in org.biojava.bio.structure.domain.pdp
-
- CutValues() - Constructor for class org.biojava.bio.structure.domain.pdp.CutValues
-
- cyan - Static variable in class org.biojava.bio.structure.gui.util.color.ColorUtils
-
- Cys - Static variable in class org.biojava3.phylo.ResidueProperties
-
- D - Static variable in class org.biojava3.aaproperties.Constraints
-
- darker(Color, double) - Static method in class org.biojava.bio.structure.gui.util.color.ColorUtils
-
Make a color darker.
- DatabasePDBremark - Class in org.biojava.bio.structure.io.mmcif.model
-
- DatabasePDBremark() - Constructor for class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark
-
- DatabasePDBrev - Class in org.biojava.bio.structure.io.mmcif.model
-
- DatabasePDBrev() - Constructor for class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- DatabaseReferenceInterface - Interface in org.biojava3.core.sequence.features
-
If a SequenceProxyReader implements this interface then that external source
has a list of cross reference id(s)
- DataSource - Enum in org.biojava3.core.sequence
-
GenBank gi|gi-number|gb|accession|locus
ENA Data Library gi|gi-number|emb|accession|locus
DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus
NBRF PIR pir||entry
Protein Research Foundation prf||name
SWISS-PROT UNIPROT sp|accession|name
Brookhaven Protein Data Bank (1) pdb|entry|chain
Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE
Patents pat|country|number
GenInfo Backbone Id bbs|number
General database identifier gnl|database|identifier
NCBI Reference Sequence ref|accession|locus
Local Sequence identifier lcl|identifier
- dateFormat - Static variable in class org.biojava.bio.structure.server.FlatFileInstallation
-
Deprecated.
- DBL - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
-
- DBRef - Class in org.biojava.bio.structure
-
A class to represent database cross references.
- DBRef() - Constructor for class org.biojava.bio.structure.DBRef
-
- DBReferenceInfo - Class in org.biojava3.core.sequence.features
-
If you have a uniprot ID then it is possible to get a collection
of other id(s) that the protein is known by.
- DBReferenceInfo(String, String) - Constructor for class org.biojava3.core.sequence.features.DBReferenceInfo
-
The source database and id
- DBResultTable - Class in org.biojava.bio.structure.align.gui
-
- DBResultTable() - Constructor for class org.biojava.bio.structure.align.gui.DBResultTable
-
- DBSearchGUI - Class in org.biojava.bio.structure.align.gui
-
- DBSearchGUI() - Constructor for class org.biojava.bio.structure.align.gui.DBSearchGUI
-
- debug - Static variable in class org.biojava.bio.structure.align.fatcat.calc.AFPCalculator
-
- debug - Static variable in class org.biojava.bio.structure.align.fatcat.calc.AFPChainer
-
- debug - Static variable in class org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer
-
- debug - Static variable in class org.biojava.bio.structure.align.fatcat.calc.AFPPostProcessor
-
- debug - Static variable in class org.biojava.bio.structure.align.fatcat.calc.FatCatAligner
-
- debug - Static variable in class org.biojava.bio.structure.align.gui.DisplayAFP
-
- DEBUG - Static variable in class org.biojava3.core.util.SoftHashMap
-
- declareNamespace(String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
-
- declareNamespace(String, String) - Method in interface org.biojava3.core.util.XMLWriter
-
Hints that a namespace is going to be used in a sub-tree.
- decorateRna(boolean) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
-
Performs an optimisation where RNASequences are not translated into
their own objects but are views onto the base DNA sequence.
- deepCleanSequence(String) - Static method in class org.biojava3.data.sequence.SequenceUtil
-
Removes all special characters and digits as well as whitespace chars
from the sequence
- DEFAUL_CHAIN_FILE - Static variable in class org.biojava.bio.structure.server.FlatFileInstallation
-
Deprecated.
- DEFAULT_ALGORITHM_NAME - Static variable in class org.biojava.bio.structure.align.model.AFPChain
-
the default algorithm used in the RCSB PDB all vs. all database searches
- DEFAULT_BATCH_SIZE - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
-
- DEFAULT_CHAIN_ID - Static variable in class org.biojava.bio.structure.ChainImpl
-
The default chain identifier is an empty space.
- DEFAULT_CHAR_SIZE - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
-
size per character
- DEFAULT_CLUSTER_CUTOFF - Static variable in class org.biojava.bio.structure.align.ClusterAltAligs
-
- DEFAULT_CONNECTION_TIMEOUT - Static variable in class org.biojava.bio.structure.align.util.HTTPConnectionTools
-
- DEFAULT_DIR_SPLIT - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
-
- DEFAULT_DISORDER - Static variable in class org.biojava3.ronn.RonnConstraint
-
- DEFAULT_FRAGLEN - Static variable in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
-
- DEFAULT_INDEX_FILE - Static variable in class org.biojava.bio.structure.server.FlatFileInstallation
-
Deprecated.
- DEFAULT_JOB_TIME - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
-
- DEFAULT_LIMIT - Static variable in class org.biojava3.core.util.SoftHashMap
-
- DEFAULT_LINE_LENGTH - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
-
number of chars per line
- DEFAULT_LINE_SEPARATION - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
-
separation of line 1 and 2 in alignment
- DEFAULT_MAX_ITERATIONS - Static variable in class org.biojava.bio.structure.secstruc.BigSqrt
-
- DEFAULT_NR_ALIGNMENTS - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
-
- DEFAULT_NR_THREADS - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
-
- DEFAULT_ORDER - Static variable in class org.biojava3.ronn.RonnConstraint
-
- DEFAULT_PDB_FILE_SERVER - Static variable in class org.biojava.bio.structure.io.PDBFileReader
-
- DEFAULT_PDB_PATH - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
-
- DEFAULT_PDB_SERVER - Static variable in class org.biojava.bio.structure.PDBStatus
-
- DEFAULT_RANGE_PROBABILITY_THRESHOLD - Static variable in class org.biojava3.ronn.RonnConstraint
-
- DEFAULT_RESOLUTION - Static variable in class org.biojava.bio.structure.PDBHeader
-
- DEFAULT_RIGHT_SPACER - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
-
Space on the right side between sequence and legend.
- DEFAULT_SCALE - Static variable in class org.biojava.bio.structure.secstruc.BigSqrt
-
we take 3 aftercomma
- DEFAULT_SCORING_STRATEGY - Static variable in class org.biojava.bio.structure.align.ce.CeParameters
-
- DEFAULT_SCRIPT - Static variable in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
-
- DEFAULT_SERVER - Static variable in class org.biojava.bio.structure.scop.RemoteScopInstallation
-
- DEFAULT_SERVER_URL - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
-
- DEFAULT_VERSION - Static variable in class org.biojava.bio.structure.scop.ScopInstallation
-
- DEFAULT_X_RIGHT_BORDER - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- DEFAULT_X_SPACE - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
-
left boundary
- DEFAULT_X_START - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- DEFAULT_Y_BOTTOM - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- DEFAULT_Y_HEIGHT - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- DEFAULT_Y_SPACE - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
-
top boundary
- DEFAULT_Y_START - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- DEFAULT_Y_STEP - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
-
size of space between rows
- DEFAULT_Y_STEP - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- DefaultAAIndexProvider - Class in org.biojava3.alignment.aaindex
-
The default provider for AAINDEX loads substituion matrices from the AAINDEX file in the resources directory
- DefaultAAIndexProvider() - Constructor for class org.biojava3.alignment.aaindex.DefaultAAIndexProvider
-
- DefaultMatrixMapper - Class in org.biojava.bio.structure.gui.util.color
-
Color Mapper which mimics the default coloring of JMatrixPanel pixels.
- DefaultMatrixMapper(double, float) - Constructor for class org.biojava.bio.structure.gui.util.color.DefaultMatrixMapper
-
- defaultProperties - Static variable in class org.biojava.bio.structure.align.gui.SystemInfo
-
- degreesPerRadian - Static variable in class org.biojava.bio.structure.Calc
-
Degrees per radian.
- demo - package demo
-
- DemoAtomCache - Class in demo
-
Example of how to load PDB files using the AtomCache class.
- DemoAtomCache() - Constructor for class demo.DemoAtomCache
-
- DemoCE - Class in demo
-
Example of how to run a structure alignment using the CE algorithm.
- DemoCE() - Constructor for class demo.DemoCE
-
- DemoChangeChemCompProvider - Class in demo
-
This demo shows how to use an alternative ChemCompProvider.
- DemoChangeChemCompProvider() - Constructor for class demo.DemoChangeChemCompProvider
-
- DemoCommandLineStartup - Class in demo
-
- DemoCommandLineStartup() - Constructor for class demo.DemoCommandLineStartup
-
- DemoDomainsplit - Class in demo
-
- DemoDomainsplit() - Constructor for class demo.DemoDomainsplit
-
- DemoFATCAT - Class in demo
-
- DemoFATCAT() - Constructor for class demo.DemoFATCAT
-
- DemoLoadStructure - Class in demo
-
Example for how to load protein structures (from PDB files).
- DemoLoadStructure() - Constructor for class demo.DemoLoadStructure
-
- DemoMMCIFReader - Class in demo
-
An example of how to read MMcif files
- DemoMMCIFReader() - Constructor for class demo.DemoMMCIFReader
-
- DemoSCOP - Class in demo
-
A class demonstrating the use of the SCOP parsing tools
- DemoSCOP() - Constructor for class demo.DemoSCOP
-
- DemoSW3DAligner - Class in demo
-
- DemoSW3DAligner() - Constructor for class demo.DemoSW3DAligner
-
- description() - Method in enum org.biojava3.protmod.ModificationCategory
-
- deserialize(File) - Static method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
-
- desFileName - Static variable in class org.biojava.bio.structure.scop.ScopInstallation
-
- destroy() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
-
- destroy() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
-
- destroy() - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
-
- destroy() - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
-
- destroy() - Static method in class org.biojava3.core.util.FlatFileCache
-
- destroy() - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
-
- det() - Method in class org.biojava.bio.structure.jama.LUDecomposition
-
Determinant
- det() - Method in class org.biojava.bio.structure.jama.Matrix
-
Matrix determinant
- detectCicular(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper
-
Loops through the given list of locations and returns true if it looks
like they represent a circular location.
- detectEnd(List<Location>, boolean) - Static method in class org.biojava3.core.sequence.location.LocationHelper
-
This will attempt to find what the last point is and returns that
position.
- detectStart(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper
-
Assumes that the first element is the start & clones it
- detectStrand(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper
-
Loops through the given list of locations and returns the consensus
Strand class.
- diAA2Instability - Static variable in class org.biojava3.aaproperties.Constraints
-
- dialogAsk(String, String) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
-
- DIGIT - Static variable in class org.biojava3.data.sequence.SequenceUtil
-
A digit
- display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.ce.GuiWrapper
-
- display(AFPChain, Group[], Atom[], Atom[], List<Group>, List<Group>, List<Group>, List<Group>) - Static method in class org.biojava.bio.structure.align.gui.DisplayAFP
-
Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
- display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.gui.StructureAlignmentDisplay
-
Display the alignment
- DisplayAFP - Class in org.biojava.bio.structure.align.gui
-
A utility class for visualistion of structure alignments
- DisplayAFP() - Constructor for class org.biojava.bio.structure.align.gui.DisplayAFP
-
- distance(Location) - Method in class org.biojava3.genome.parsers.gff.Location
-
Return distance between this location and the other location.
- DistEn - Class in org.biojava.bio.structure.secstruc
-
- DistEn() - Constructor for class org.biojava.bio.structure.secstruc.DistEn
-
- DNA_ONLY - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
-
Convenience Set of polymer types classified as DNA.
- dnaCompounds(CompoundSet<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
-
- DNACompoundSet - Class in org.biojava3.core.sequence.compound
-
- DNACompoundSet() - Constructor for class org.biojava3.core.sequence.compound.DNACompoundSet
-
- dnaRnaTranslator(DNAToRNATranslator) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
-
- DNASequence - Class in org.biojava3.core.sequence
-
This is class should model the attributes associated with a DNA sequence
- DNASequence() - Constructor for class org.biojava3.core.sequence.DNASequence
-
Shouldn't be used but makes it bean happy
- DNASequence(String) - Constructor for class org.biojava3.core.sequence.DNASequence
-
String is king and create a sequence from DNA with default DNA compound set
- DNASequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.DNASequence
-
Create a sequence where the actual storage of the sequence data is somewhere else
- DNASequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.DNASequence
-
Create a sequence from a string with user defined compound set
- DNASequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.DNASequence
-
Create a sequence from a ProxySequencereader and user defined compound set
- DNASequence.DNAType - Enum in org.biojava3.core.sequence
-
The type of DNA sequence
- DNASequenceCreator - Class in org.biojava3.core.sequence.io
-
A helper class that allows different ways to read a string and create a DNA sequence.
- DNASequenceCreator(CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.io.DNASequenceCreator
-
- DNAToRNATranslator - Class in org.biojava3.core.sequence.transcription
-
Performs the first stage of transcription by going from DNA to RNA.
- DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound>, CompoundSet<NucleotideCompound>, CompoundSet<NucleotideCompound>, boolean) - Constructor for class org.biojava3.core.sequence.transcription.DNAToRNATranslator
-
- doChainAfp(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.fatcat.calc.AFPChainer
-
// Key function: chain (assembly) the AFPs
// a AFP (k) is defined as (i, j, k), with i and j are staring points
// AFP extension (eg.
- documentEnd() - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
-
- documentEnd() - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
-
called at end of document
- documentEnd() - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
-
- documentStart() - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
-
- documentStart() - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
-
called at start of document
- documentStart() - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
-
Start the parsing
- doesSequenceContainInvalidChar(String, Set<Character>) - Static method in class org.biojava3.aaproperties.Utils
-
Checks if given sequence contains invalid characters.
- Domain - Class in org.biojava.bio.structure.domain.pdp
-
- Domain() - Constructor for class org.biojava.bio.structure.domain.pdp.Domain
-
- doPOST(URL, String) - Static method in class org.biojava.bio.structure.align.util.HTTPConnectionTools
-
do a POST to a URL and return the response stream for further processing elsewhere.
- doPOST(URL, String, int) - Static method in class org.biojava.bio.structure.align.util.HTTPConnectionTools
-
do a POST to a URL and return the response stream for further processing elsewhere.
- doPrintConnections() - Method in class org.biojava.bio.structure.io.FileConvert
-
returns if the Connections should be added
default is true;
- DotPlotPanel - Class in org.biojava.bio.structure.align.gui
-
Displays the dot plot trace for an alignment.
- DotPlotPanel(AFPChain) - Constructor for class org.biojava.bio.structure.align.gui.DotPlotPanel
-
- DownloadChemCompProvider - Class in org.biojava.bio.structure.io.mmcif
-
This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.
- DownloadChemCompProvider() - Constructor for class org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider
-
- downloadCIF(String) - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
-
Deprecated.
- downloadFile() - Static method in class org.biojava.bio.structure.io.mmcif.AllChemCompProvider
-
Downloads the components.cif.gz file from the wwPDB site.
- downloadingStructures(String) - Method in class org.biojava.bio.structure.align.client.CountProgressListener
-
- downloadingStructures(String) - Method in interface org.biojava.bio.structure.align.events.AlignmentProgressListener
-
- downloadingStructures(String) - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
-
- downloadPDB(String) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
-
- downstream(int) - Method in class org.biojava3.genome.parsers.gff.Location
-
Return the adjacent location of specified length directly downstream of this location.
- drawBoxes(Graphics) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
draw high scoring fragments that are used for the initial alignment seed
selection
- drawDistances(Graphics) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
For each element in matrix, draw it as a colored square or pixel.
- drawIdx(Graphics2D, int) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- drawPairs(Graphics) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
draw alternative alignments
- drawScale(Graphics2D, int) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
draw the Scale
- drawSequence(Graphics2D, int) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
draw the Amino acid sequence
- F - Static variable in class org.biojava3.aaproperties.Constraints
-
- FarmJob - Class in org.biojava.bio.structure.align
-
A job as it can be run on the farm.
- FarmJob() - Constructor for class org.biojava.bio.structure.align.FarmJob
-
- FarmJobParameters - Class in org.biojava.bio.structure.align.client
-
- FarmJobParameters() - Constructor for class org.biojava.bio.structure.align.client.FarmJobParameters
-
- FarmJobRunnable - Class in org.biojava.bio.structure.align.client
-
Contains the single thread for a job that can run multiple alignments.
- FarmJobRunnable(FarmJobParameters) - Constructor for class org.biojava.bio.structure.align.client.FarmJobRunnable
-
- FastaGeneWriter - Class in org.biojava3.core.sequence.io
-
A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.
- FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean) - Constructor for class org.biojava3.core.sequence.io.FastaGeneWriter
-
- FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean, int) - Constructor for class org.biojava3.core.sequence.io.FastaGeneWriter
-
- FastaHeaderFormatInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava3.core.sequence.io.template
-
- FastaHeaderParserInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava3.core.sequence.io.template
-
- FastaReader<S extends Sequence<?>,C extends Compound> - Class in org.biojava3.core.sequence.io
-
Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the
primary class used to read Fasta files
- FastaReader(InputStream, FastaHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava3.core.sequence.io.FastaReader
-
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about
local file offsets for quick reads.
- FastaReader(File, FastaHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava3.core.sequence.io.FastaReader
-
If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about
the location of the file.
- FastaReaderHelper - Class in org.biojava3.core.sequence.io
-
- FastaReaderHelper() - Constructor for class org.biojava3.core.sequence.io.FastaReaderHelper
-
- FastaSequence - Class in org.biojava3.data.sequence
-
A FASTA formatted sequence.
- FastaSequence(String, String) - Constructor for class org.biojava3.data.sequence.FastaSequence
-
Upon construction the any whitespace characters are removed from the
sequence
- FastaSequenceParser - Class in org.biojava3.core.sequence.io
-
Used to parse a stream of a fasta file to get the sequence
- FastaSequenceParser() - Constructor for class org.biojava3.core.sequence.io.FastaSequenceParser
-
- FastaWriter<S extends Sequence<?>,C extends Compound> - Class in org.biojava3.core.sequence.io
-
The FastaWriter writes a collection of sequences to an outputStream.
- FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>) - Constructor for class org.biojava3.core.sequence.io.FastaWriter
-
Use default line length of 60
- FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava3.core.sequence.io.FastaWriter
-
Set custom lineLength
- FastaWriterHelper - Class in org.biojava3.core.sequence.io
-
The class that should be used to write out fasta file of a sequence collection
- FastaWriterHelper() - Constructor for class org.biojava3.core.sequence.io.FastaWriterHelper
-
- FatCat - Class in org.biojava.bio.structure.align.fatcat
-
- FatCat() - Constructor for class org.biojava.bio.structure.align.fatcat.FatCat
-
- FATCAT_BLOCK - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
-
- FATCAT_TEXT - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
-
- FatCatAligner - Class in org.biojava.bio.structure.align.fatcat.calc
-
A class that does calculations on an AFPChain
- FatCatAligner() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.FatCatAligner
-
- FatCatFlexible - Class in org.biojava.bio.structure.align.fatcat
-
- FatCatFlexible() - Constructor for class org.biojava.bio.structure.align.fatcat.FatCatFlexible
-
- FatCatParameters - Class in org.biojava.bio.structure.align.fatcat.calc
-
- FatCatParameters() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
-
- FatCatRigid - Class in org.biojava.bio.structure.align.fatcat
-
- FatCatRigid() - Constructor for class org.biojava.bio.structure.align.fatcat.FatCatRigid
-
- FatCatUserArgumentProcessor - Class in org.biojava.bio.structure.align.fatcat
-
- FatCatUserArgumentProcessor() - Constructor for class org.biojava.bio.structure.align.fatcat.FatCatUserArgumentProcessor
-
- fatColumnNames - Static variable in class org.biojava.bio.structure.align.gui.DBResultTable
-
- FCAlignHelper - Class in org.biojava.bio.structure.align.fatcat.calc
-
- FCAlignHelper(double[][], int, int, double, double) - Constructor for class org.biojava.bio.structure.align.fatcat.calc.FCAlignHelper
-
do an alignment given the provided matrix sij0
- Feature - Class in org.biojava3.genome.parsers.gff
-
A Feature corresponds to a single row in a GFF file.
- Feature(Feature) - Constructor for class org.biojava3.genome.parsers.gff.Feature
-
Make a copy of the specified feature.
- Feature(String, String, String, Location, Double, int, String) - Constructor for class org.biojava3.genome.parsers.gff.Feature
-
Construct a new Feature from raw data (usually a GFF row).
- FeatureHelper - Class in org.biojava3.genome.parsers.gff
-
- FeatureHelper() - Constructor for class org.biojava3.genome.parsers.gff.FeatureHelper
-
- FeatureI - Interface in org.biojava3.genome.parsers.gff
-
A feature on a sequence (for example, an exon or a gene), defined by a location
and a set of attributes encoded as key/value pairs.
- FeatureInterface<S extends AbstractSequence<C>,C extends Compound> - Interface in org.biojava3.core.sequence.features
-
Interface class to handle describing arbitrary features.
- FeatureList - Class in org.biojava3.genome.parsers.gff
-
A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.
- FeatureList() - Constructor for class org.biojava3.genome.parsers.gff.FeatureList
-
Construct an empty list.
- FeatureList(Collection<FeatureI>) - Constructor for class org.biojava3.genome.parsers.gff.FeatureList
-
Construct a new list containing the same features
as the specified list.
- FeaturesKeyWordInterface - Interface in org.biojava3.core.sequence.features
-
Models the keywords that are annotated for a protein sequence at Uniprot.
- FIELD_LINE - Static variable in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
-
- FileAccessError - Error in org.biojava3.core.exceptions
-
Thrown from SequenceFileProxyLoader if error opening file using RandomnAccessFile
- FileAccessError(String) - Constructor for error org.biojava3.core.exceptions.FileAccessError
-
- FileConvert - Class in org.biojava.bio.structure.io
-
Methods to convert a structure object into different file formats.
- FileConvert(Structure) - Constructor for class org.biojava.bio.structure.io.FileConvert
-
Constructs a FileConvert object.
- FileParsingParameters - Class in org.biojava.bio.structure.io
-
- FileParsingParameters() - Constructor for class org.biojava.bio.structure.io.FileParsingParameters
-
- FileProxyDNASequenceCreator - Class in org.biojava3.core.sequence.io
-
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream
the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
- FileProxyDNASequenceCreator(File, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.io.FileProxyDNASequenceCreator
-
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
- FileProxyProteinSequenceCreator - Class in org.biojava3.core.sequence.io
-
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream
the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
- FileProxyProteinSequenceCreator(File, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.io.FileProxyProteinSequenceCreator
-
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
- fileSeparator - Static variable in class org.biojava.bio.structure.io.SandboxStyleStructureProvider
-
- FILESPLIT - Static variable in class org.biojava.bio.structure.scop.ScopInstallation
-
- filterByClassificationId(String) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
-
- filterByClassificationId(String) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
-
Get all scop descriptions that start with a classifcation ID, e.g. b.1.18
- filterByClassificationId(String) - Method in class org.biojava.bio.structure.scop.ScopInstallation
-
- filterByDescription(String) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
-
- filterByDescription(String) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
-
Get all scop descriptions that start with a certain name. e.g.
- filterByDescription(String) - Method in class org.biojava.bio.structure.scop.ScopInstallation
-
- filterByDomainName(String) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
-
- filterByDomainName(String) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
-
search through SCOP and filter based on domain name
- filterByDomainName(String) - Method in class org.biojava.bio.structure.scop.ScopInstallation
-
- filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.ce.CeCPMain
-
Takes as input an AFPChain where ca2 has been artificially duplicated.
- findAtomLinkages(Group, Group, boolean, double) - Static method in class org.biojava3.protmod.structure.StructureUtil
-
Find linkages between two groups within tolerance of bond length,
from potential atoms.
- findAtomLinkages(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava3.protmod.structure.StructureUtil
-
Find linkages between two groups within tolerance of bond length,
from potential atoms.
- findBonds(Group, List<Group>) - Static method in class org.biojava.bio.structure.StructureTools
-
- findChain(String) - Method in interface org.biojava.bio.structure.Structure
-
request a particular chain from a structure.
- findChain(String, int) - Method in interface org.biojava.bio.structure.Structure
-
request a particular chain from a particular model
- findChain(String, int) - Method in class org.biojava.bio.structure.StructureImpl
-
- findChain(String) - Method in class org.biojava.bio.structure.StructureImpl
-
- findCommonParent(PhylogenyNode) - Method in class org.biojava3.phylo.CheckTreeAccuracy
-
- findGroup(String, String) - Method in interface org.biojava.bio.structure.Structure
-
request a particular group from a structure.
- findGroup(String, String, int) - Method in interface org.biojava.bio.structure.Structure
-
request a particular group from a structure.
- findGroup(String, String, int) - Method in class org.biojava.bio.structure.StructureImpl
-
- findGroup(String, String) - Method in class org.biojava.bio.structure.StructureImpl
-
- findLinkage(Group, Group, String, String, double) - Static method in class org.biojava3.protmod.structure.StructureUtil
-
Find a linkage between two groups within tolerance of bond length.
- findNearestAtomLinkage(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava3.protmod.structure.StructureUtil
-
Find a linkage between two groups within tolerance of bond length,
from potential atoms.
- finish(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- first_cut - Variable in class org.biojava.bio.structure.domain.pdp.CutValues
-
- FlatFileCache - Class in org.biojava3.core.util
-
Provides a cache for storing multiple small files in memory.
- FlatFileInstallation - Class in org.biojava.bio.structure.server
-
Deprecated.
- FlatFileInstallation(File) - Constructor for class org.biojava.bio.structure.server.FlatFileInstallation
-
Deprecated.
create a new FlatFile Installation and point it to the directory that contains all PDB files
- flipAlignment(String) - Static method in class org.biojava.bio.structure.align.xml.AFPChainXMLParser
-
Takes an XML representation of the alignment and flips the positions of name1 and name2
- flipChain(AFPChain) - Static method in class org.biojava.bio.structure.align.xml.AFPChainFlipper
-
Flip the position of name1 and name2 (as well as all underlying data) in an AFPChain.
- FourBitSequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.storage
-
Four bit encoding of the bit formats.
- FourBitSequenceReader(Sequence<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader
-
- FourBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader
-
- FourBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader
-
- FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader
-
- FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader
-
- FourBitSequenceReader.FourBitArrayWorker<C extends Compound> - Class in org.biojava3.core.sequence.storage
-
A four bit per compound implementation of the bit array worker code.
- FourBitSequenceReader.FourBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
- FourBitSequenceReader.FourBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
- FourBitSequenceReader.FourBitArrayWorker(Sequence<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
- FourBitSequenceReader.FourBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
- FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
-
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment
Profile.
- FractionalIdentityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava3.alignment.FractionalIdentityInProfileScorer
-
Creates a fractional identity scorer for an aligned pair of sequences in the given alignment profile.
- FractionalIdentityScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
-
Implements an algorithm which computes a score for a sequence alignment pair.
- FractionalIdentityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava3.alignment.FractionalIdentityScorer
-
Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
- FractionalIdentityScorer(SequencePair<S, C>) - Constructor for class org.biojava3.alignment.FractionalIdentityScorer
-
Creates a fractional identity scorer for an aligned pair of sequences.
- FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
-
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment
Profile.
- FractionalSimilarityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava3.alignment.FractionalSimilarityInProfileScorer
-
Creates a fractional similarity scorer for an aligned pair of sequences in the given alignment profile.
- FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
-
Implements an algorithm which computes a score for a sequence alignment pair.
- FractionalSimilarityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava3.alignment.FractionalSimilarityScorer
-
Creates a fractional similarity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
- FractionalSimilarityScorer(SequencePair<S, C>) - Constructor for class org.biojava3.alignment.FractionalSimilarityScorer
-
Creates a fractional similarity scorer for an aligned pair of sequences.
- frag_pairwise_compat(FragmentPair[], int, float, int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
-
Calculate the pairwise compatibility of fpairs.
- FragmentJoiner - Class in org.biojava.bio.structure.align.pairwise
-
Joins the initial Fragments together to larger Fragments
- FragmentJoiner() - Constructor for class org.biojava.bio.structure.align.pairwise.FragmentJoiner
-
- FragmentPair - Class in org.biojava.bio.structure.align.pairwise
-
a pair of fragments of two protein structures
- FragmentPair(int, int, int) - Constructor for class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- Frame - Enum in org.biojava3.core.sequence.transcription
-
Indicates a way of translating a sequence.
- frame() - Method in class org.biojava3.genome.parsers.gff.Feature
-
Get frame (aka phase).
- fromBio(int, int, char) - Static method in class org.biojava3.genome.parsers.gff.Location
-
Create location from "biocoordinates", as in GFF file.
- fromBioExt(int, int, char, int) - Static method in class org.biojava3.genome.parsers.gff.Location
-
Create a location from MAF file coordinates, which represent negative
strand locations as the distance from the end of the sequence.
- fromCIEXYZ(float[]) - Method in class org.biojava.bio.structure.gui.util.color.HSVColorSpace
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- fromRGB(float[]) - Method in class org.biojava.bio.structure.gui.util.color.HSVColorSpace
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- fromStartupParams(StartupParameters) - Static method in class org.biojava.bio.structure.align.util.UserConfiguration
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- fromString(String) - Static method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
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- fromString(String) - Static method in enum org.biojava.bio.structure.