- G - Static variable in class org.biojava.nbio.aaproperties.Constraints
-
- GAP_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- GAP_COVERAGE_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.EntityFinder
-
Gap coverage value (num gaps over length of sequence) for each chain of the match:
2 chains with more gap coverage than this value will not be considered part of the same entity
- GapArray - Class in org.biojava.nbio.structure.align.helper
-
- GapArray() - Constructor for class org.biojava.nbio.structure.align.helper.GapArray
-
- gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- gapPenalty - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- GapPenalty - Interface in org.biojava.nbio.alignment.template
-
Defines a data structure for the gap penalties used during a sequence alignment routine.
- GapPenalty.Type - Enum in org.biojava.nbio.alignment.template
-
Defines the possible types of gap penalties.
- GCStats - Class in org.biojava.nbio.genome.parsers.gff
-
- GCStats() - Constructor for class org.biojava.nbio.genome.parsers.gff.GCStats
-
- GENBANK_FORMAT - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
The name of this format
- GenbankHeaderFormatInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
-
- GenbankProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
-
- GenbankProxySequenceReader(String, String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- GenbankReader<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the
primary class used to read Genbank files
- GenbankReader(InputStream, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReader
-
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about
local file offsets for quick reads.
- GenbankReader(File, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReader
-
If you are going to use the FileProxyProteinSequenceCreator then you
need to use this constructor because we need details about
the location of the file.
- GenbankReaderHelper - Class in org.biojava.nbio.core.sequence.io
-
- GenbankReaderHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
-
- GenbankReference - Class in org.biojava.nbio.core.sequence.reference
-
For Genbank format file only.
- GenbankReference() - Constructor for class org.biojava.nbio.core.sequence.reference.GenbankReference
-
- GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
- GenbankSequenceParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- genbankSplitPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser
-
Decodes a split pattern.
- GenbankWriter<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
- GenbankWriter(OutputStream, Collection<S>, GenbankHeaderFormatInterface<S, C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriter
-
Use default line length of 60
- GenbankWriter(OutputStream, Collection<S>, GenbankHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriter
-
Set custom lineLength
- GenbankWriterHelper - Class in org.biojava.nbio.core.sequence.io
-
The class that should be used to write out genbank file of a sequence
collection
- GenbankWriterHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
-
- GeneChromosomePosition - Class in org.biojava.nbio.genome.parsers.genename
-
- GeneChromosomePosition() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- GeneChromosomePositionParser - Class in org.biojava.nbio.genome.parsers.genename
-
A parser that parses a file from the UCSC genome browser that contains mapping of gene name to chromosome positions
- GeneChromosomePositionParser() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
-
- GeneFeatureHelper - Class in org.biojava.nbio.genome
-
- GeneFeatureHelper() - Constructor for class org.biojava.nbio.genome.GeneFeatureHelper
-
- GeneIDGFF2Reader - Class in org.biojava.nbio.genome.parsers.gff
-
http://www.bioperl.org/wiki/GTF
Read and write FeatureLists as GFF/GTF formatted files.
- GeneIDGFF2Reader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
-
- GeneIDXMLReader - Class in org.biojava.nbio.genome.parsers.geneid
-
- GeneIDXMLReader(String) - Constructor for class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
-
- GeneMarkGTFReader - Class in org.biojava.nbio.genome.parsers.gff
-
http://www.bioperl.org/wiki/GTF
Read and write FeatureLists as GFF/GTF formatted files.
- GeneMarkGTFReader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
-
- GeneName - Class in org.biojava.nbio.genome.parsers.genename
-
A simple bean that contains gene name information as available from www.genenames.org
- GeneName() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneName
-
- GeneNamesParser - Class in org.biojava.nbio.genome.parsers.genename
-
Parses a file from the www.genenames.org website that contains a mapping of human gene names to other databases
- GeneNamesParser() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
-
- generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Returns what the value of a compound is in the backing bit storage i.e.
- generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
Returns a Map which encodes the contents of CompoundSet.
- generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
-
Returns a Map which encodes TCAG into positions 0,1,2,3.
- generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
- generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
Returns a List which reverse encodes the Compound, Integer map
- generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
-
Returns a List which encodes TCAG into positions 0,1,2,3.
- GenericFastaHeaderFormat<S extends AbstractSequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
We store the original header if the sequence is parsed from a fasta file and will use that exact
sequence if we write out the sequences to a fasta file.
- GenericFastaHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat
-
- GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
The default fasta header parser where some headers are well defined based on the source
database which allows us to set the source of the protein sequence and the identifier
that can be used in future implementations to load features from external sources
If the user has a custom header with local data then they can create their own implementation
of a FastaHeaderParserInterface
GenBank gi|gi-number|gb|accession|locus
ENA Data Library gi|gi-number|emb|accession|locus
DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus
NBRF PIR pir||entry
Protein Research Foundation prf||name
SWISS-PROT sp|accession|name
Brookhaven Protein Data Bank (1) pdb|entry|chain
Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE
PDB EBI PDB:1ECY_A mol:protein length:142 ECOTIN
Patents pat|country|number
GenInfo Backbone Id bbs|number
General database identifier gnl|database|identifier
NCBI Reference Sequence ref|accession|locus
Local Sequence identifier lcl|identifier
- GenericFastaHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser
-
- GenericGenbankHeaderFormat<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
- GenericGenbankHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
-
- GenericGenbankHeaderFormat(String) - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
-
- GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
- GenericGenbankHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
-
- GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
- GenericInsdcHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat
-
- GeneSequence - Class in org.biojava.nbio.core.sequence
-
- GeneSequence(ChromosomeSequence, int, int, Strand) - Constructor for class org.biojava.nbio.core.sequence.GeneSequence
-
A class that keeps track of the details of a GeneSequence which is difficult to properly model.
- get(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
-
Returns the window specified at the given index in offsets i.e. asking
for position 2 in a moving window sequence of size 3 will get you
the window starting at position 4.
- get(Object) - Method in class org.biojava.nbio.core.util.SoftHashMap
-
- get(Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap
-
- get(Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
-
- get(Object) - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
-
- get(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Gets the interface corresponding to given id.
- get(K) - Method in class org.biojava.nbio.structure.domain.SerializableCache
-
- get(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- get(int, int) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get a single element.
- get(int, int) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix
-
access a value at i,j
- get(int) - Method in class org.biojava.nbio.structure.math.SparseVector
-
get a value
- get(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
-
Return the value paired with given key; null if key is not in table.
- get(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
-
- get(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
-
- get1LetterCode(String) - Static method in class org.biojava.nbio.structure.StructureTools
-
Convert a three letter amino acid or nucleotide code into a single
character code.
- get1LetterCodeAmino(String) - Static method in class org.biojava.nbio.structure.StructureTools
-
Convert three character amino acid codes into single character e.g.
- getA() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getA() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getAAComposition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the composition of the 20 standard amino acid in the sequence.
- getAAComposition(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
- getAAComposition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getAACompositionChar(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
- getAACompositionString(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
- getAAIndexProvider() - Static method in class org.biojava.nbio.core.alignment.matrices.AAindexFactory
-
- getAboutMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getAbsoluteMinimumSequenceLength() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
If the shortest subunit sequence length is higher or equal the
minimumSequenceLengthFraction times the median subunit sequence length,
then the minimumSequenceLength is set to shortest subunit sequence
length, but not shorter than the absoluteMinimumSequenceLength.
- getAbsolutePercentialRNAsuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
-
- getAbsolutePercentileClashscore() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the absolutePercentileClashscore property.
- getAbsolutePercentileDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry
-
- getAbsolutePercentilePercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the absolutePercentilePercentRamaOutliers property.
- getAbsolutePercentilePercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the absolutePercentilePercentRotaOutliers property.
- getAbsolutePercentilePercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the absolutePercentilePercentRSRZOutliers property.
- getAbsorbance(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the absorbance (optical density) of sequence.
- getAbsorbance(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to returns the absorbance (optical density) of sequence.
- getAbsorbance(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getAbsorpt_coefficient_mu() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getAbsorpt_correction_T_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getAbsorpt_correction_T_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getAbsorpt_correction_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getAbsorpt_process_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getAcc() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getAccept1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getAccept2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getAcceptedAtomNames() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
By default the parser will read in all atoms (unless using the CAonly switch).
- getAccession() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Unsupoorted
- getAccession() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getAccession() - Method in interface org.biojava.nbio.core.sequence.template.Accessioned
-
Returns the AccessionID this location is currently bound with
- getAccession() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getAccessionNr() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getAccessionNumber() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getAccessionNumber() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The AC (Accession number) line lists the accession numbers associated with
the entry.
- getAccessions() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Pull uniprot accessions associated with this sequence
- getAccessions() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
-
Gets the protein accessions mapped from the Fasta file.
- getAccessions() - Method in class org.biojava.nbio.structure.rcsb.RCSBMacromolecule
-
- getAcentricOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the acentricOutliers property.
- getAdapter() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
- getAddress() - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
-
- getAfpAftIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpBefIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpChain() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
-
- getAFPChain() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- getAfpChain() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- getAFPChainFromServer(String, String, String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getAFPChainFromServer(String, String, String, String, Atom[], Atom[], int) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getAfpChainLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpChainList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpChainTwiBin() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpChainTwiList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpChainTwiNum() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getAfpDisCut0() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getAfpIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpSet() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Get the set of AFPs for this alignment.
- getAlgebraicFromMatrix(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
-
- getAlgorithm(String) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeCPMain
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeMain
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
-
- getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Returns the name of the multiple structure alignment algorithm that
created the MultipleAlignment objects.
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
-
- getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner
-
Get the name of this Algorithm.
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
-
- getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.StructureAlignment
-
Get the name of the Algorithm
- getAliases() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Pull uniprot protein aliases associated with this sequence
Provided for backwards compatibility now that we support both
gene and protein aliases via separate methods.
- getAligMap() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
- getAligMat() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getAligMat(int, int) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getAligMat() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getAlign(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
Extract the alignment output
eg
STWNTWACTWHLKQP--WSTILILA
111111111111 22222222
SQNNTYACSWKLKSWNNNSTILILG
Those position pairs labeled by 1 and 2 are equivalent positions, belongs to
two blocks 1 and 2.
- getAlign(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- getAlign_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getAlign_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getAlign_se1() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getAlign_se1() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getAlign_se2() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getAlign_se2() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getAlignedAtoms1(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- getAlignedAtoms2(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- getAlignedAtomsForSubunits1(int) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
- getAlignedAtomsForSubunits2(int) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
- getAlignedAtomsSubunit(int) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
- getAlignedAtomsSubunits() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
- getAlignedModel(Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
get an artificial List of chains containing the Atoms and groups.
- getAlignedResIndex(Group, Chain) - Method in class org.biojava.nbio.structure.EntityInfo
-
Given a Group g of Chain c (member of this EnityInfo) return the corresponding position in the
alignment of all member sequences (1-based numbering), i.e. the index (1-based) in the SEQRES sequence.
- getAlignedSequence(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getAlignedSequence(S) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getAlignedSequence(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
- getAlignedSequence(S) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
Searches for the given
Sequence within this alignment profile.
- getAlignedSequence(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
Uses bioIndex starting at 1 instead of 0
- getAlignedSequence(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
-
- getAlignedSequences() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getAlignedSequences(int...) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getAlignedSequences(S...) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getAlignedSequences() - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
- getAlignedSequences(int...) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
- getAlignedSequences(S...) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
- getAlignedSequences() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
Get the list of sequences
- getAlignedSequences() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
-
Returns a
List containing the individual
Sequences of this alignment.
- getAlignedStructure(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
-
- getAlignedStructure(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Get an artificial Structure containing a different model for every
input structure, so that the alignment result can be viewed in Jmol.
- getAlignedStructure(Structure, Structure) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
create an artifical Structure object that contains the two
structures superimposed onto each other.
- getAlignedStructure(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Get an artifical Structure containing both chains.
- getAlignedSubunits1() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
Return the aligned subunits of the first Subunit group, in the alignment
order.
- getAlignedSubunits2() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
Return the aligned subunits of the second Subunit group, in the alignment
order.
- getAlignedUserCollection(String) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Takes a protein sequence string with capital and lowercase letters and sets its
user collection to record which letters are uppercase (aligned) and which are lowercase (unaligned).
- getAlignment() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getAlignment() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
The alignment that specifies the residue equivalencies of the equivalent
Subunits.
- getAlignmentAtoms(Structure) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
Returns the atoms that are being used for the alignment.
- getAlignmentFromFasta() - Static method in class demo.DemoAlignmentFromFasta
-
- getAlignmentFromSequence() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getAlignmentFromSequence() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Returns the alignment.
- getAlignmentIndexAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getAlignmentIndexAt(int) - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Returns the column index within an alignment corresponding to the given index in the original
Sequence.
- getAlignmentMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getAlignmentNumber() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
- getAlignmentOption(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getAlignmentOption(BlastAlignmentParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Gets the value of specified parameter or null if it is not set.
- getAlignmentOption(String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties
-
Method that returns the value associated with the key given in parameter.
- getAlignmentOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Gets parameters, which are currently set
- getAlignmentOptions() - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties
-
Method to get all keys to the information stored in this object.
- getAlignmentOutputFormat() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
- getAlignmentPairsFromServer() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
-
talk to centralized server and fetch all alignments to run.
- getAlignmentPanelMenu(JFrame, ActionListener, AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
Create the menu for the Alignment Panel representation of
Structural Alignments.
- getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
Extracts the actual Blast report for given request id according to options provided in outputProperties
argument.
- getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService
-
Getting the actual alignment results from this instantiated service for a given ID with specific
formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object.
- getAlignments() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getAlignments() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
return the alternative alignments that can be found for the two
structures
- getAlignmentString() - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
-
- getAlignmentTextMenu(JFrame, ActionListener, AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
Create the menu for the Text representations of Structural Alignments.
- getAlignPairs() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
The file that contains a list of PDB pairs to be aligned
- getAlignPos(int[][]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper
-
record the aligned pairs in alignList[][0], alignList[][1];
return the number of aligned pairs
- getAlignRes() - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Returns the double List containing the aligned residues for each
structure.
- getAlignRes() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
-
- getAlignResCounts() - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Returns the number of non null positions (residues) of each structure in
the alignment Block.
- getAlignResCounts() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
-
- getAlignResCounts() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
-
Returns the number of non null positions (residues) of each structure in
the alignment Block Set.
- getAlignResCounts() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
-
- getAlignResCounts() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Returns the number of non null positions (residues) of each structure in
the alignment.
- getAlignResCounts() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- getAlignScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlignScoreUpdate() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAligSeq(Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
returns the AligSeq (0 or 1) for a point
returns -1 if not over an alig seq.
- getAligSeq(Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Returns the index of the structure, for a given point in the Panel.
- getAliLenth() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getAll() - Static method in class org.biojava.nbio.structure.rcsb.GetRepresentatives
-
Returns the current list of all PDB IDs.
- getAllAlgorithmNames() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
-
- getAllAlgorithms() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
-
- getAllAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Convert all atoms of the structure (all models) into an Atom array
- getAllAtomArray(Structure, int) - Static method in class org.biojava.nbio.structure.StructureTools
-
Convert all atoms of the structure (specified model) into an Atom array
- getAllAtomArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns and array of all atoms of the chain, including
Hydrogens (if present) and all HETATOMs.
- getAllAtoms() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
-
- getAllChains() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
-
- getAllColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get the list of column names including those that may be hidden
- getAllCompounds() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- getAllCompounds() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- getAllCompounds() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- getAllCompounds() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- getAllCompounds() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
-
- getAllCytobands(URL) - Method in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
-
- getAllCytobands(InputStream) - Method in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
-
- getAllDomains() - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase
-
Get all ECOD domains
- getAllDomains() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
Get all ECOD domains
- getAllFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
-
- getAllGroupsFromSubset(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Expand a set of atoms into all groups from the same structure.
- getAllGroupsFromSubset(Atom[], GroupType) - Static method in class org.biojava.nbio.structure.StructureTools
-
Expand a set of atoms into all groups from the same structure.
- getAllNonHAtomArray(Structure, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns and array of all non-Hydrogen atoms in the given Structure,
optionally including HET atoms or not.
- getAllNonHAtomArray(Structure, boolean, int) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns and array of all non-Hydrogen atoms in the given Structure,
optionally including HET atoms or not.
- getAllNonHAtomArray(Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns and array of all non-Hydrogen atoms in the given Chain,
optionally including HET atoms or not Waters are not included.
- getAllNonHCoordsArray(Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns and array of all non-Hydrogen atoms coordinates in the given Chain,
optionally including HET atoms or not Waters are not included.
- getAllowsChildren() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getAllOxidationStates() - Method in enum org.biojava.nbio.structure.Element
-
Returns a list of all oxidation states the element is found in.
- getAllPairsAlignments(List<S>, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method which computes a sequence alignment for all
Sequence pairs in the given
List.
- getAllPairsScorers(List<S>, Alignments.PairwiseSequenceScorerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method which sets up a sequence pair scorer for all
Sequence pairs in the given
List.
- getAllPairsScores(List<S>, Alignments.PairwiseSequenceScorerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method which computes a sequence pair score for all
Sequence pairs in the given
List.
- getAllPairsScores() - Method in class org.biojava.nbio.alignment.GuideTree
-
Returns a sequence pair score for all
Sequence pairs in the given
List.
- getAllPDBIDs() - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
-
Returns a list of all PDB IDs that are available in this installation
- getAllRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get all rows including those that may be hidden
- getAllSpaceGroups() - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser
-
- getAllViruses() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
-
Get the PDB IDs of all virus structures in the current PDB
- getAlnbeg1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlnbeg2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlnLength() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlnseq1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlnseq2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlnSequences() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
-
- getAlnsymb() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlpha() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
A letter that is assigned to this cluster in stoichiometry.
- getAlpha() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getAlpha() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getAlphabet() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
- getAlt_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getAltAligNumber() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
returns the sequential number of this alternative alignment
- getAltcode() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the altcode property.
- getAlternativeAligs() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- getAlternativeAligs() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- getAltLoc() - Method in interface org.biojava.nbio.structure.Atom
-
Get alternate Location.
- getAltLoc() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get alternate Location.
- getAltLoc1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getAltLoc2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getAltLocGroup(Character) - Method in interface org.biojava.nbio.structure.Group
-
Gets the alternate location group to this group that has the alt-loc character code passed.
- getAltLocGroup(Character) - Method in class org.biojava.nbio.structure.HetatomImpl
-
- getAltLocs() - Method in interface org.biojava.nbio.structure.Group
-
Get the list of alternate locations.
- getAltLocs() - Method in class org.biojava.nbio.structure.HetatomImpl
-
- getAltShortSymbol() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets the alternative international short name (as sometimes used in PDB),
e.g.
- getAmbiguity(NucleotideCompound...) - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
-
Calculates the best symbol for a collection of compounds.
- getAminoacid() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
-
- getAminoAcid() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getAminoAcid(String) - Static method in class org.biojava.nbio.structure.StandardAminoAcid
-
get a standard amino acid.
- getAminoAcidCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getAminoAcidCompoundSet() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
-
- getAminoAcidCompoundSet() - Static method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- getAminoAcidCompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- getAminoAcids(Chain) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
Get all amino acids in a chain.
- getAminoAcidSubstitutionMatrix(String) - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns a substitution matrix for
amino acids given by the name
name.
- getAminoOneLetter(String) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
-
- getAminoThreeLetter(Character) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
-
- getAminoType() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Returns the name of the AA, in single letter code.
- getAminoType() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Returns the name of the AA, in single letter code.
- getAnchors() - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
-
Returns the list of anchors.
- getAngle() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
The rotation angle
- getAngle(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Calculate the rotation angle for a structure
- getAngle(Matrix) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Calculate the rotation angle for a given matrix
- getAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
Returns the pitch angle of the helix
- getAngle(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
Returns the magnitude of the angle between the first and second
blocks of afpChain, measured in degrees.
- getAngle_alpha() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getAngle_alpha_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getAngle_beta() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getAngle_beta_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getAngle_gamma() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getAngle_gamma_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getAngleDiff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the angleOutlier property.
- getAngleThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getAniso_B11() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getAniso_B12() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getAniso_B13() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getAniso_B22() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getAniso_B23() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getAniso_B33() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getAnnotation() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
-
- getAnnotation() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- getAnnotation() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
-
- getAnnotation() - Method in class org.biojava.nbio.ontology.Term.Impl
-
- getAnnotation() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getAnnotation() - Method in interface org.biojava.nbio.ontology.utils.Annotatable
-
Should return the associated annotation object.
- getAnnotationType() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getApliphaticIndex(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the apliphatic index of sequence.
- getApliphaticIndex(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the apliphatic index of sequence.
- getApliphaticIndex(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getApprovedName() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getApprovedSymbol() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getArchitectureId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getArchitectureName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getArray() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Access the internal two-dimensional array.
- getArrayCopy() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Copy the internal two-dimensional array.
- getAsaC() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
Returns the ASA of the residue in the complexed state
- getAsaU() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
Returns the ASA of the residue in the uncomplexed state
- getAsList() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns this Sequence store as a List
- getAsList() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getAsList() - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Returns the Sequence as a List of compounds
- getAsList() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getAssembly_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
-
- getAssemblyHeader() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The AH (Assembly Header) line provides column headings for the assembly information.
- getAssemblyId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getAssemblyInformation() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The AS (Assembly Information) lines provide information on the composition of
a TPA or TSA sequence.
- getAssignment() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
-
- getAssignments() - Method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer
-
- getAsym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getAsym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getAsym_id_list() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
-
- getAsymmetryParameter(double) - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
- getAtcc() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getAtom(String) - Method in interface org.biojava.nbio.structure.Group
-
Get an atom given its PDB name.
- getAtom(int) - Method in interface org.biojava.nbio.structure.Group
-
Get at atom by position.
- getAtom(String) - Method in class org.biojava.nbio.structure.HetatomImpl
-
Get an atom given its PDB name.
- getAtom(int) - Method in class org.biojava.nbio.structure.HetatomImpl
-
Get at atom by position.
- getAtom() - Method in class org.biojava.nbio.structure.validation.Clash
-
Gets the value of the atom property.
- getAtom() - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Gets the value of the atom property.
- getAtom0() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the atom0 property.
- getAtom0() - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Gets the value of the atom0 property.
- getAtom1() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
-
- getAtom1() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the atom1 property.
- getAtom1() - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Gets the value of the atom1 property.
- getAtom2() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
-
- getAtom2() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the atom2 property.
- getAtom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getAtom_id_1() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getAtom_id_2() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getAtomA() - Method in interface org.biojava.nbio.structure.Bond
-
Gets atom 'A' of this bond.
- getAtomA() - Method in class org.biojava.nbio.structure.BondImpl
-
Gets atom 'A' of this bond.
- getAtomArray(Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
-
- getAtomArray(Atom[], List<Group>) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
Returns the first atom for each group
- getAtomArray(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns an array of the requested Atoms from the Structure object.
- getAtomArray(Chain, String[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns an array of the requested Atoms from the Chain object.
- getAtomArrayAllModels(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns an array of the requested Atoms from the Structure object.
- getAtomArrays() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
-
- getAtomArrays() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Returns the array of Atoms for each structure from its parent Ensemble.
- getAtomArrays() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Get an array of representative atoms for each structure (CA atoms for
proteins).
- getAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
-
- getAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- getAtomAsaCs() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
- getAtomAsaUs() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
- getAtomB() - Method in interface org.biojava.nbio.structure.Bond
-
Gets atom 'B' of this bond.
- getAtomB() - Method in class org.biojava.nbio.structure.BondImpl
-
Gets atom 'B' of this bond.
- getAtomCAArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns an Atom array of the C-alpha atoms.
- getAtomCAArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Return an Atom array of the C-alpha atoms.
- getAtomCache() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getAtomCache() - Static method in class org.biojava.nbio.structure.StructureIO
-
- getAtomCaThreshold() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
The maximum number of atoms that will be parsed before the parser switches to a CA-only
representation of the PDB file.
- getAtomContacts() - Method in class org.biojava.nbio.structure.contact.Grid
-
Returns all contacts, i.e. all atoms that are within the cutoff distance.
- getAtomContacts() - Method in class org.biojava.nbio.structure.contact.GroupContact
-
- getAtomCoordinateBounds(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
-
- getAtomDistance(Atom, Atom) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
- getAtomForAligPos(AFPChain, int, int, Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
Return the atom at alignment position aligPos. at the present only works with block 0
- getAtomForSequencePosition(MultipleAlignment, List<Integer>, int, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Returns the Atom of the specified structure that is aligned in the
sequence alignment position specified.
- getAtomGroup(int) - Method in interface org.biojava.nbio.structure.Chain
-
Return the Group at given position,
from within Groups with observed density in the chain, i.e.
- getAtomGroup(int) - Method in class org.biojava.nbio.structure.ChainImpl
-
Return the Group at given position,
from within Groups with observed density in the chain, i.e.
- getAtomGroups() - Method in interface org.biojava.nbio.structure.Chain
-
Return all Groups with observed density in the chain, i.e.
- getAtomGroups(GroupType) - Method in interface org.biojava.nbio.structure.Chain
-
- getAtomGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl
-
- getAtomGroups() - Method in class org.biojava.nbio.structure.ChainImpl
-
Return all Groups with observed density in the chain, i.e.
- getAtomicMass() - Method in enum org.biojava.nbio.structure.Element
-
Returns the atomic mass for this Element.
- getAtomicNumber() - Method in enum org.biojava.nbio.structure.Element
-
Returns the atomic number of this Element.
- getAtomLength() - Method in interface org.biojava.nbio.structure.Chain
-
Returns the number of Groups with observed density in the chain, i.e.
- getAtomLength() - Method in class org.biojava.nbio.structure.ChainImpl
-
Returns the number of Groups with observed density in the chain, i.e.
- getAtomLigands() - Method in interface org.biojava.nbio.structure.Chain
-
- getAtomLigands() - Method in class org.biojava.nbio.structure.ChainImpl
-
Gets all groups that are not polymer groups and that are not solvent groups.
- getAtomLinkages() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
- getAtomLinkages() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- getAtomName() - Method in class org.biojava.nbio.protmod.structure.StructureAtom
-
- getAtomName() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- getAtomNames(Group) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
- getAtoms(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns the CA atoms for the provided name.
- getAtoms(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getAtoms() - Method in interface org.biojava.nbio.structure.Group
-
Get list of atoms.
- getAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl
-
Get list of atoms.
- getAtoms() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getAtoms() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
- getAtoms() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the atoms property.
- getAtoms() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the atoms property.
- getAtomsCAInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns the set of intra-chain contacts for the given chain for C-alpha
atoms (including non-standard aminoacids appearing as HETATM groups),
i.e. the contact map.
- getAtomSequence() - Method in interface org.biojava.nbio.structure.Chain
-
Returns the sequence of amino acids as it has been provided in the ATOM records.
- getAtomSequence() - Method in class org.biojava.nbio.structure.ChainImpl
-
Returns the sequence of amino acids as it has been provided in the ATOM records.
- getAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getAtomsForGroup(Group) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get a list of atoms for a group.
- getAtomsInContact(Chain, String[], double) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns the set of intra-chain contacts for the given chain for given
atom names, i.e. the contact map.
- getAtomsInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns the set of intra-chain contacts for the given chain for all non-H
atoms of non-hetatoms, i.e. the contact map.
- getAtomsInContact(Chain, Chain, String[], double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns the set of inter-chain contacts between the two given chains for
the given atom names.
- getAtomsInContact(Chain, Chain, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns the set of inter-chain contacts between the two given chains for
all non-H atoms.
- getAtomSiteHeader() - Static method in class org.biojava.nbio.structure.io.FileConvert
-
- getAtomType1() - Method in class org.biojava.nbio.structure.io.mmcif.chem.MetalBondDistance
-
- getAtomType2() - Method in class org.biojava.nbio.structure.io.mmcif.chem.MetalBondDistance
-
- getAttemptedValidationSteps() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the attemptedValidationSteps property.
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
Return the attribute of the grouping
- getAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
Get value of specified attribute key.
- getAttribute(String) - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
-
Get the attribute value for this key.
- getAttributeOld(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
- getAttributes() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
- getAttributes() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
-
- getAuBoundingBox(int) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox
-
Get the AU BoundingBox for the given cell index (cellIdx=0 would be original AU)
The AU BoundingBox is the BoundingBox that bounds all chains belonging to the AU
- getAuth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getAuth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getAuth_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getAuth_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getAuth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getAuth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getAuth_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getAuth_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getAuth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getAuth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getAuth_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getAuth_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getAuthorList() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the list of Authors of the JournalArticle
- getAuthors() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getAuthors() - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference
-
The authors are a list of Inventors that retrieved from the Reference section.
- getAuthors() - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
-
- getAuthors() - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface
-
Get the authors that retrieved from Reference section.
- getAuthors() - Method in class org.biojava.nbio.structure.PDBHeader
-
Return the names of the authors as listed in the AUTHORS section of a PDB file.
- getAutoSuggestProvider() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
-
- getAverageResidueDistances(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
The average residue distance Matrix contains the average distance from
each residue to all other residues aligned with it.
- getAverageResidueDistances(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
The average residue distance Matrix contains the average distance from
each residue to all other residues aligned with it.
- getAverageScore() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
Returns the average similarity score between all pairs of members in the cluster
- getAvgHydropathy(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the average hydropathy value of sequence.
- getAvgHydropathy(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the average hydropathy value of sequence.
- getAvgHydropathy(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getAvgoccu() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the avgoccu property.
- getAvgTMScore(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
-
Calculates the average TMScore of all the possible pairwise structure
comparisons of the given alignment.
- getAvgTMScore(List<Atom[]>, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
-
Calculates the average TMScore all the possible pairwise structure
comparisons of the given a set of superimposed Atoms and the original
structure lengths.
- getAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
- getAxisAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
Returns the AxisAngle of the helix transformation
- getAxisAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getAxisAngle(int, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
-
- getAxisAngle(int, AxisAngle4f) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
-
- getAxisAngle(int, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
-
- getAxisAngle4d() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Returns the rotation axis and angle in a single javax.vecmath.AxisAngle4d object
- getAxisEnds(Atom[]) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Find a segment of the axis that covers the specified set of atoms.
- getAxisFoldType(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Given a transformId returns the type of axis of rotation: 1 (no rotation), 2, 3, 4 or 6 -fold
and for improper rotations: -1, -2, -3, -4 and -6
- getAxisTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getAxisTypes() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getB() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getB() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getB_iso_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getB_iso_mean() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getB_iso_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getB_iso_or_equiv() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getB_iso_or_equiv_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getBackboneAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Return an Atom array of the main chain atoms: CA, C, N, O Any group that
contains those atoms will be included, be it a standard aminoacid or not
- getBackingSequence() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
-
Access the sequence which backs this window
- getBadRmsd() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getBase() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- getBaseIdentifier() - Method in class org.biojava.nbio.structure.align.client.StructureName
-
StructureName wraps another StructureIdentifier.
- getBegin() - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
- getBeta() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getBeta() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getBinaryOperators() - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver
-
Returns a list of operators for this assembly.
- getBioAssemblies() - Method in class org.biojava.nbio.structure.PDBHeader
-
Return the map of biological assemblies.
- getBioBegin() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getBioEnd() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getBioEnd() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getBioEnd() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView
-
1-indexed, inclusive.
- getBiol_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getBiologicalAssemblies(String, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns all biological assemblies for given PDB id.
- getBiologicalAssemblies(String, boolean) - Static method in class org.biojava.nbio.structure.StructureIO
-
Returns all biological assemblies for the given PDB id.
- getBiologicalAssemblies(String) - Static method in class org.biojava.nbio.structure.StructureIO
-
- getBiologicalAssembly(String, int, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the
assembly from the biounit annotations found in
Structure.getPDBHeader()
Note, the number of available biological unit files
varies.
- getBiologicalAssembly(String, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns the default biological unit (bioassemblyId=1, known in PDB as pdb1.gz).
- getBiologicalAssembly(String, boolean) - Static method in class org.biojava.nbio.structure.StructureIO
-
Returns the first biological assembly that is available for the given PDB id.
- getBiologicalAssembly(String) - Static method in class org.biojava.nbio.structure.StructureIO
-
Returns the first biological assembly that is available for the given PDB id,
using multiModel=
For more documentation on quaternary structures see:
http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies
- getBiologicalAssembly(String, int, boolean) - Static method in class org.biojava.nbio.structure.StructureIO
-
Returns the biological assembly for the given PDB id and bioassembly identifier.
- getBiologicalAssembly(String, int) - Static method in class org.biojava.nbio.structure.StructureIO
-
Returns the biological assembly for the given PDB id and bioassembly identifier,
using multiModel=
- getBiologicalMoleculeBounds(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
-
- getBiologicalMoleculeCentroid(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
-
Returns the centroid of the biological molecule.
- getBiologicalMoleculeMaximumExtend(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
-
Returns the maximum extend of the biological molecule in the x, y, or z direction.
- getBiologicalUnit() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getBioSequences() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
-
used to retrieve sequences from the structure
- getBioSequences(boolean, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
-
This function tolerates mixed case letters, and allows for forcing the output biosequence type (PFAM/RFAM).
- getBioSequences(boolean) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
-
Because some database files have incorrectly small letters (e.g.
- getBioStart() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getBioStart() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView
-
1-indexed, inclusive.
- getBioUnitTransformationList(PdbxStructAssembly, List<PdbxStructAssemblyGen>, List<PdbxStructOperList>) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
-
Returns a list of transformation matrices for the generation of a macromolecular
assembly for the specified assembly Id.
- getBJSequence() - Method in interface org.biojava.nbio.structure.Chain
-
Converts the SEQRES groups of a Chain to a Biojava Sequence object.
- getBJSequence() - Method in class org.biojava.nbio.structure.ChainImpl
-
Converts the SEQRES groups of a Chain to a Biojava Sequence object.
- getBlastAdvancedOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getBlastDatabase() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getBlastExpect() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getBlastFromPosition() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getBlastGapCosts() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Returns the actual string for the GAPCOSTS parameter which is used to build the URL
- getBlastGapCreation() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Returns the value for the GAP_CREATION parameter (first half of GAPCOSTS parameter)
- getBlastGapExtension() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Returns the value for the gap extension parameter (second half of GAPCOSTS parameter)
- getBlastMatrix() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Returns the value of the specified substitution matrix
- getBlastProgram() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getBlastToPosition() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getBlastWordSize() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Returns the value of the WORD_SIZE parameter used for this blast run
- getBlock(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Returns the Block with the specified index of the MultipleAlignment.
- getBlock(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- getBlock2Afp() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockForSequencePosition(MultipleAlignment, List<Integer>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Returns the block number of a specified position in the sequence
alignment, given the mapping from structure to function.
- getBlockGap() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockNrForAlignPos(AFPChain, int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
get the block number for an aligned position
- getBlockNum() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The number of blocks in the alignment
- getBlockNumClu() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockNumIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockNumSpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockResList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
tracks the residues of the initial blocks (before optimization)
- getBlockResSize() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockRotationMatrix() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlocks() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
-
Returns the List of alignment Blocks of the BlockSet.
- getBlocks() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
-
- getBlocks() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Convenience method to get a List of all Blocks from all BlockSets.
- getBlocks() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- getBlockScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockSequenceAlignment(MultipleAlignment, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Calculate the sequence alignment Strings for the alignment Blocks in an
alignment.
- getBlockSequenceAlignment(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Calculate the sequence alignment Strings for the alignment Blocks in an
alignment.
- getBlockSet() - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Returns the parent BlockSet of the Block.
- getBlockSet() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
-
- getBlockSet(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Returns the BlockSet with the specified index of the MultipleAlignment.
- getBlockSet(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- getBlockSets() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Returns the BlockSet List of the multiple structure alignment.
- getBlockSets() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- getBlockShiftVector() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockSize() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlosum100() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 100 matrix by Henikoff & Henikoff
- getBlosum30() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 30 matrix by Henikoff & Henikoff
- getBlosum35() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 35 matrix by Henikoff & Henikoff
- getBlosum40() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 40 matrix by Henikoff & Henikoff
- getBlosum45() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 45 matrix by Henikoff & Henikoff
- getBlosum50() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 50 matrix by Henikoff & Henikoff
- getBlosum55() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 55 matrix by Henikoff & Henikoff
- getBlosum60() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 60 matrix by Henikoff & Henikoff
- getBlosum62() - Static method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
-
- getBlosum62() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 62 matrix by Henikoff & Henikoff
- getBlosum65() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 65 matrix by Henikoff & Henikoff
- getBlosum70() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 70 matrix by Henikoff & Henikoff
- getBlosum75() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 75 matrix by Henikoff & Henikoff
- getBlosum80() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 80 matrix by Henikoff & Henikoff
- getBlosum85() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 85 matrix by Henikoff & Henikoff
- getBlosum90() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Blosum 90 matrix by Henikoff & Henikoff
- getBondOrder() - Method in interface org.biojava.nbio.structure.Bond
-
Gets the bond order of this bond.
- getBondOrder() - Method in class org.biojava.nbio.structure.BondImpl
-
Gets the bond order of this bond.
- getBondOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the bondOutlier property.
- getBonds() - Method in interface org.biojava.nbio.structure.Atom
-
Get all
Bonds this atom is part of.
- getBonds() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get all
Bonds this atom is part of.
- getBonds() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getBottom() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getBravLattice() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getBridge1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getBridge2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getBsa() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
Returns the BSA value for this group, i.e. the difference between ASA uncomplexed and ASA complexed
- getBsaToAsaRatio() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
Returns the bsa/asa(uncomplexed) ratio, i.e. the ratio of burial of a residue upon complexation
- getBtype() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getBuckle(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the buckle in degrees for the given base pair
- getBufferedReader() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource
-
Returns the reader representation of this classpath resource
- getBuildMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getBulkSolventB() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the bulkSolventB property.
- getBulkSolventK() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the bulkSolventK property.
- getByCategory(ModificationCategory) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getByCategory(CathCategory) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return list of CATH descriptions for node representatives at a CATH category (e.g.
- getByCategory(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getByCategory(ScopCategory) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Get all records of a particular classification.
- getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getByChainId(String, String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
-
- getByComponent(Component, Component...) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
Get ProteinModifications that involves one or more components.
- getById(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getByKeyword(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getByLabel(String) - Static method in enum org.biojava.nbio.protmod.ModificationCategory
-
- getByLabel(String) - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType
-
- getByLargestContacts() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
- getByLargestContactsNotLowestAngle() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
- getByLowestAngle() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
- getByName(String) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique
-
Returns the ExpTechnique given an experimental technique name as used in the PDB,
e.g.
- getByName(String) - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice
-
- getByOccurrenceType(ModificationOccurrenceType) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getByPdbccId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getByPsimodId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getByResidId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getBytesRead() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
-
Keep track of bytesread via ReadLine to account for CR-LF in the stream.
- getByUniProtId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
-
- getC() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Get C atom.
- getC() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Get C atom.
- getC() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getC() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getC2Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getC3Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getC4Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getCA() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Get CA atom.
- getCA() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Get CA atom.
- getCa1() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- getCa1() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- getCa1() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- getCa1Length() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getCa2() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- getCa2() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- getCa2Length() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getCache() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- getCacheFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getCacheFilePath() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getCacheFilePath() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getCacheLocation() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getCacheLocation() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
Get the location of the cache directory (usually set to the PDB_CACHE_DIR
property).
- getCacheLocation() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getCachePath() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns the path that contains the caching file for utility data, such as domain definitions.
- getCalculationTime() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getCalculationTime() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Returns the running time of the structure alignment calculation, in
milliseconds.
- getCalculationTime() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
-
- getCalculationTime() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getCalphaCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getCartn_transf_matrix11() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_transf_matrix12() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_transf_matrix13() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_transf_matrix21() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_transf_matrix22() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_transf_matrix23() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_transf_matrix31() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_transf_matrix32() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_transf_matrix33() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_transf_vector1() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_transf_vector2() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_transf_vector3() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_transform_axes() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getCartn_x() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getCartn_x_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getCartn_y() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getCartn_y_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getCartn_z() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getCartn_z_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getCategories() - Method in class demo.DemoSCOP
-
Get various categories
- getCategory() - Method in class org.biojava.nbio.ontology.Synonym
-
- getCategory() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getCategory() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getCategory() - Method in class org.biojava.nbio.structure.cath.CathNode
-
- getCategory() - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- getCATH() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getCathDatabase() - Static method in class org.biojava.nbio.structure.cath.CathFactory
-
Returns the default (singleton) CathDatabase.
- getCathDatabase(String) - Static method in class org.biojava.nbio.structure.cath.CathFactory
-
Returns a CATH database of the specified version.
- getCathDownloadUrl() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getCathNode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return the CathNode for a node ID.
- getCathNode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getCathVersion() - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return the CATH release version.
- getCathVersion() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getCB() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Get CB atom.
- getCB() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Get CB atom.
- getCCP4Version() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the ccp4Version property.
- getCdsEnd() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getCDSExonRanges(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Extracts the exon boundaries in CDS coordinates.
- getCDSLength(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Get the length of the CDS in nucleotides.
- getCDSLengthForward(List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Get the length of the coding sequence
- getCDSLengthReverse(List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Get the length of the coding sequence
- getCDSPosForChromosomeCoordinate(int, GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
I have a genomic coordinate, where is it on the mRNA
- getCDSPosForward(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene
living on the forward DNA strand.
- getCDSPosReverse(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene
living on the reverse DNA strand.
- getCDSRegions(List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Extracts the exons boundaries in CDS coordinates corresponding to the forward DNA strand.
- getCDSSequences() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Get the CDS sequences that have been added to the TranscriptSequences
- getCdsStart() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getCECalculator() - Method in class org.biojava.nbio.structure.align.ce.CeMain
-
- getCell() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getCell(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get cell value
- getCell_setting() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- getCellColor() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- getCellColor() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- getCellDouble(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getCellIndices(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
Get the index of a unit cell to which the query point belongs.
- getCellLine() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getCellTranslation(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getCellTranslations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getCellularLocation() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getCenter(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils
-
Get the centroid for the set of atoms starting from position pos, length fragmentLenght
- getCenter1() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getCenter2() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getCenterOfMass() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
- getCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getCenterVector(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
-
Returns the Vector that needs to be applied to shift a set of atoms to
the Centroid.
- getCenterVector(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Returns the Vector that needs to be applied to shift a set of atoms to
the Centroid, if the centroid is already known
- getCentricOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the centricOutliers property.
- getCentroid(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
-
Returns the centroid of the set of atoms.
- getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getChain() - Method in interface org.biojava.nbio.structure.Group
-
Returns the parent Chain of the Group.
- getChain() - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- getChain() - Method in class org.biojava.nbio.structure.HetatomImpl
-
Returns the parent Chain of the Group.
- getChain(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a Chain (polymeric, non-polymeric or water) based on
the 'internal' chain id (asymId) for the first model
- getChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a Chain (polymeric, non-polymeric or water) based on
the 'internal' chain id (asymId) for the given model index
- getChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Retrieve a Chain (polymeric, non-polymeric or water) based on
the 'internal' chain id (asymId) for the given model index
- getChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
Retrieve a Chain (polymeric, non-polymeric or water) based on
the 'internal' chain id (asymId) for the first model
- getChain() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the chain property.
- getChain1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getChain1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
-
- getChain2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getChainBoundingBox(int, int) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox
-
Get the chain BoundingBox for the given cell index (cellIdx=0 would be original AU)
and chain index
- getChainByIndex(int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a chain by its index within the Structure .
- getChainByIndex(int, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a chain by its indices within the Structure and model.
- getChainByIndex(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Retrieve a chain by its index within the Structure .
- getChainByIndex(int, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Retrieve a chain by its indices within the Structure and model.
- getChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure
-
- getChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
- getChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a chain by its public id (author id) for the given model index.
- getChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a chain by its public id (author id) for the first model.
- getChainId() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- getChainId() - Method in class org.biojava.nbio.structure.align.client.StructureName
-
Gets the chain ID, for structures where it is unique and well-defined.
- getChainId() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- getChainID() - Method in interface org.biojava.nbio.structure.Chain
-
- getChainID() - Method in class org.biojava.nbio.structure.ChainImpl
-
Gets the 'private' asymId of this chain.
- getChainId() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
-
- getChainId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getChainId() - Method in interface org.biojava.nbio.structure.Group
-
Utility method for returning the chainId of the Group or null if no
Chain has been set.
- getChainId() - Method in class org.biojava.nbio.structure.HetatomImpl
-
Utility method for returning the chainId of the Group or null if no
Chain has been set.
- getChainId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getChainId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getChainId() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Returns the chain identifier (asym id) that this transformation should be applied to.
- getChainId1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getChainID1() - Method in class org.biojava.nbio.structure.io.SSBondImpl
-
- getChainID1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getChainId2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getChainID2() - Method in class org.biojava.nbio.structure.io.SSBondImpl
-
- getChainID2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getChainIds() - Method in class org.biojava.nbio.structure.EntityInfo
-
Return the list of member chain ids (asym ids) that are described by this EntityInfo,
only unique chain IDs are contained in the list.
- getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
This method is provisional and should only be used for coloring Subunits.
- getChainIds() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- getChainIdsInEntry(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
-
- getChainIdToIndexMap() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
-
- getChainLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getChainName() - Method in class org.biojava.nbio.structure.DBRef
-
The name of the corresponding chain.
- getChainName() - Method in class org.biojava.nbio.structure.ResidueNumber
-
- getChainName() - Method in class org.biojava.nbio.structure.ResidueRange
-
- getChainRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getChains() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
- getChains() - Method in class org.biojava.nbio.structure.EntityInfo
-
Get the list of chains that are part of this EntityInfo.
- getChains() - Method in class org.biojava.nbio.structure.Model
-
Get all chains: polymeric, non-polymeric and water
- getChains() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getChains() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
- getChains() - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve all chains for the first model.
- getChains(int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve all chains of a model.
- getChains(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Retrieve all chains of a model.
- getChains() - Method in class org.biojava.nbio.structure.StructureImpl
-
Retrieve all chains for the first model.
- getCharge() - Method in interface org.biojava.nbio.structure.Atom
-
Get the charge of this atom
- getCharge() - Method in class org.biojava.nbio.structure.AtomImpl
-
- getCharge() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getChargeOfAminoAcid(char) - Static method in class org.biojava.nbio.aaproperties.AminoAcidProperties
-
Returns the charge of amino acid.
- getChargesOfAminoAcids(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
Returns the array of charges of each amino acid in a protein.
- getChemComp() - Method in interface org.biojava.nbio.structure.Group
-
Get the chemical component that closer describes this group.
- getChemComp() - Method in class org.biojava.nbio.structure.HetatomImpl
-
- getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider
-
Returns a new instance of a chemical component definition.
- getChemComp(String) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
-
- getChemComp(String) - Method in interface org.biojava.nbio.structure.io.mmcif.ChemCompProvider
-
Returns a new instance of a chemical component definition.
- getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
- getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
-
Loads the definitions for this
ChemComp from a local file and instantiates a new object.
- getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider
-
- getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider
-
- getChemCompProvider() - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
-
- getChild1() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getChild1() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Returns the first child node of this node.
- getChild2() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getChild2() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Returns the second child node of this node.
- getChildAt(int) - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getChildCount() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getChildren() - Method in class org.biojava.nbio.structure.scop.ScopNode
-
- getChildrenFeatures() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
Get the children features
- getChildrenFeatures() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getChildrenFeatures() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Get the features contained by this feature
- getChiSquare() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getChrLoc() - Method in class org.biojava.nbio.phosphosite.Site
-
- getChromosomalRangesForCDS(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Extracts the boundaries of the coding regions in chromosomal coordinates
- getChromosome() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- getChromosome() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getChromosome() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getChromosomeMappings() - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
-
- getChromosomeMappings(InputStream) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
-
- getChromosomeNumber() - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
-
- getChromosomePosForCDScoordinate(int, GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Maps the position of a CDS nucleotide back to the genome
- getChromosomeSequenceFromDNASequence(LinkedHashMap<String, DNASequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
-
- getChromPosForward(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Get the CDS position mapped onto the chromosome position
- getChromPosReverse(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Get the CDS position mapped on the chromosome position
- getCid() - Method in class org.biojava.nbio.structure.validation.Clash
-
Gets the value of the cid property.
- getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
Returns the radius of a circumscribed sphere, that goes
through all vertices
- getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
Returns the radius of a circumscribed sphere, that goes
through all vertices
- getCirumscribedRadius() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
-
- getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
Returns the radius of a circumscribed sphere, that goes
through all vertices
- getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
Returns the radius of a circumscribed sphere (length of diagonal of
rectangular prism/2, that goes through at least four vertices
- getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
Returns the radius of a circumscribed sphere, that goes
through all vertices
- getClaFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getClan() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getClash() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the clash property.
- getClashmag() - Method in class org.biojava.nbio.structure.validation.Clash
-
Gets the value of the clashmag property.
- getClashmag() - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Gets the value of the clashmag property.
- getClashscore() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the clashscore property.
- getClassId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getClassId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getClassification() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getClassificationId(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getClassificationId() - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- getClassificationId(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
Return a portion of the classificationID corresponding to the specified
category (class, fold, superfamily, family).
- getClassificationId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getClaURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
-
- getCloseMenuItem(JFrame) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getCluster() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
get the number of the cluster this alignment belongs to
- getCluster() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getCluster() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getClustererMethod() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
- getClustererMethod() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Method to cluster subunits.
- getClusterIds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getClusters(double) - Method in class org.biojava.nbio.core.util.SingleLinkageClusterer
-
Get the clusters by cutting the dendrogram at given cutoff
- getClusters() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Calculate the interface clusters for this StructureInterfaceList
using a contact overlap score to measure the similarity of interfaces.
- getClusters(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Calculate the interface clusters for this StructureInterfaceList
using a contact overlap score to measure the similarity of interfaces.
- getClusters() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
- getClustersNcs() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Get the interface clusters for this StructureInterfaceList grouped by NCS-equivalence.
- getClusterValue() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getCode() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getCodingSequence() - Method in class org.biojava.nbio.core.sequence.CDSSequence
-
A CDS sequence if negative stranded needs to be reverse complement
to represent the actual coding sequence.
- getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
-
Returns the compound set of codons
- getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava.nbio.core.sequence.transcription.Table
-
- getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
-
Returns a list of codons where the source and target compounds
are the same as those given by the parameters.
- getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava.nbio.core.sequence.transcription.Table
-
- getCoeff() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getCoefficient(String) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getCoefficientsList() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getCoefficientText(boolean, String, String, String, String) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getCohortName() - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
- getCol() - Method in class org.biojava.nbio.structure.align.helper.IndexPair
-
- getColor() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- getColor() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
-
- getColor(double) - Method in interface org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper
-
- getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform
-
Return the color corresponding to submapper.getColor(transform(value)).
- getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
-
- getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- getColor(int) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
-
- getColorPalette() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
Return the color pattelete of the AlignmentJmol instance.
- getCols() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getCols() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getCols() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getColumn(AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getColumn(C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
-
- getColumn(C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
-
- getColumnDimension() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get column dimension.
- getColumnIndex(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getColumnLookup() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getColumnPackedCopy() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Make a one-dimensional column packed copy of the internal array.
- getColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get the list of column names.
- getComFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getComment() - Static method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getComment() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getComments() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getComments(int) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getComments(int) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getComments(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Get comments about a SCOP domain by its sunid
- getComments(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getCommentsFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getCommentsXML(List<String>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getCommon_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getCommonValence() - Method in enum org.biojava.nbio.structure.Element
-
Returns the common valence for this Element.
- getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- getComparator(int) - Method in class org.biojava.nbio.structure.align.gui.MyTableRowSorter
-
- getComplement() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
-
- getComplement() - Method in class org.biojava.nbio.core.sequence.DNASequence
-
Returns a Sequence which will complement every base
- getComplement() - Method in class org.biojava.nbio.core.sequence.RNASequence
-
Get the complement view of the RNA sequence
- getComplement() - Method in interface org.biojava.nbio.core.sequence.template.ComplementCompound
-
- getComplexSignature() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
-
- getComplexStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
-
- getComponent(int) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Make a Stoichiometry object that corresponds to a single component.
- getComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getComponents() - Method in interface org.biojava.nbio.protmod.ModificationCondition
-
- getComponents() - Method in class org.biojava.nbio.protmod.ModificationConditionImpl
-
}
- getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
Returns the composition of the specific grouping for the given attribute.
- getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getComposition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
An adaptor method which returns the composition of the specific grouping for the given attribute.
- getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getComposition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getComposition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getComposition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getComposition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getComposition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getComposition(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Does a linear scan over the given Sequence and records the number of
times each base appears.
- getCompositionId() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- getCompositionId(String) - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getCompoundAt(int, int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getCompoundAt(S, int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getCompoundAt(int, int) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
Returns the
Compound at row of given sequence and column of alignment index.
- getCompoundAt(S, int) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
Returns the
Compound at row of given sequence and column of alignment index.
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Returns the compound at the specified biological index
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns the compound at the specified biological index
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Always returns the compound given at construction
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getCompoundAt(int) - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Returns the Compound at the given biological index
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.views.ReversedSequenceView
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- getCompoundById(int) - Method in interface org.biojava.nbio.structure.Structure
-
- getCompoundById(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a particular entity by its entity id (mol id in legacy PDB format)
- getCompoundCountsAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getCompoundCountsAt(int, List<C>) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getCompoundCountsAt(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
- getCompoundCountsAt(int, List<C>) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
Returns the number of each
Compound in the given column only for compounds in the given list.
- getCompoundForString(String) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- getCompoundForString(String) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- getCompoundForString(String) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- getCompoundForString(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- getCompoundForString(String) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
-
Return null if not recognised.
- getCompoundInQueryAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
-
- getCompoundInQueryAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
-
Returns the
Compound in query sequence at given column index in alignment.
- getCompoundInTargetAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
-
- getCompoundInTargetAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
-
Returns the
Compound in target sequence at given column index in alignment.
- getCompounds(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
-
For a given position into the windowed view this will return those
compounds we can see in the window. i.e. in the sequence AGGCCT requesting
index 1 returns AGG and requesting index 2 return CCT.
- getCompoundsAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getCompoundsAt(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
- getCompoundsAt(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
Get a list of compounds at a sequence position
- getCompoundsAt(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
-
- getCompoundSet() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getCompoundSet() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getCompoundSet() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getCompoundSet() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getCompoundSet() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
-
- getCompoundSet() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getCompoundSet() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getCompoundSet() - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
- getCompoundSet() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
-
Returns the
CompoundSet on which the matrix is defined.
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
-
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
Get the Compounds defined in the first sequence
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Returns the compound set backing this store
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns the compound set backing this store
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Returns the compound set given at construction
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getCompoundSet() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
-
- getCompoundSet() - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Gets the compound set used to back this Sequence
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getCompoundsOfQuery() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getCompoundsOfQuery() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getCompoundsOfQuery() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getCompoundsOfTarget() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getCompoundsOfTarget() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getCompoundsOfTarget() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getCompoundsToIndexLookup() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Returns a map which converts from compound to an integer representation
- getCompoundType() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getCompoundWeightsAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getCompoundWeightsAt(int, List<C>) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getCompoundWeightsAt(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
- getCompoundWeightsAt(int, List<C>) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
Returns the fraction of each
Compound in the given column only for compounds in the given list.
- getComputationTime() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getComputationTime() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getComputationTime() - Method in interface org.biojava.nbio.alignment.template.Aligner
-
Returns the computation time needed for an alignment computed in nanoseconds.
- getComURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
-
- getCondition() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getCondition() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getConfig() - Method in class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
-
- getConn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getConn_type_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getConnectedFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getConnectedTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getConsAnnotation() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
-
- getConstituents() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
-
- getConstructedSequence() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
Con(structed) sequences in the CON data classes represent complete
chromosomes, genomes and other long sequences constructed from segment entries.
- getContact(Atom, Atom) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
-
Returns the corresponding AtomContact or null if no contact exists between the 2 given atoms
- getContact(Group, Group) - Method in class org.biojava.nbio.structure.contact.GroupContactSet
-
Returns the corresponding GroupContact or null if no contact exists between the 2 given groups
- getContactOverlapScore(StructureInterface, boolean) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Calculates the contact overlap score between this StructureInterface and
the given one.
- getContacts() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getContacts() - Method in class org.biojava.nbio.structure.contact.Grid
-
- getContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getContacts() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getContactsToOtherCell(GridCell) - Method in class org.biojava.nbio.structure.contact.GridCell
-
Calculates all distances of atoms between this cell and the given cell returning those that are
within the given cutoff as a list of Contacts containing the indices of the pair and the calculated distance.
- getContactsWithinCell() - Method in class org.biojava.nbio.structure.contact.GridCell
-
Calculates all distances of atoms within this cell returning those that are within the given cutoff
as a list of Contacts containing the indices of the pair and the calculated distance.
- getContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
-
Returns the list of contacts from this set that are within the given distance.
- getContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.GroupContact
-
Returns the list of atom contacts in this GroupContact that are within the given distance.
- getContig() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
-
- getContinuousVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getConvergenceSteps() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- getCoordManager() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- getCoordManager() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
-
- getCoordpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getCoords() - Method in interface org.biojava.nbio.structure.Atom
-
Get the coordinates.
- getCoords() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get the coordinates.
- getCoordsAsPoint3d() - Method in interface org.biojava.nbio.structure.Atom
-
Get the coordinates.
- getCoordsAsPoint3d() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get the coordinates.
- getCopy() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
-
- getCopyWorkSheet(WorkSheet) - Static method in class org.biojava.nbio.survival.data.WorkSheet
-
Create a copy of a worksheet.
- getCopyWorkSheetSelectedRows(WorkSheet, ArrayList<String>) - Static method in class org.biojava.nbio.survival.data.WorkSheet
-
Create a copy of a worksheet.
- getCoreElectronCount() - Method in enum org.biojava.nbio.structure.Element
-
Returns the number of core electrons for this Element.
- getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Returns the number of aligned positions (columns) without gaps in the
Block.
- getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
-
- getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
-
Returns the number of aligned residues (columns) without gaps in the
alignment: the sum of all Block core lengths.
- getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
-
- getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Returns the number of aligned residues (columns) without gaps in the
alignment: the sum of all BlockSet core lengths.
- getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- getCoreOntology() - Static method in class org.biojava.nbio.ontology.OntoTools
-
Get the Ontology that defines our core "central dogma".
- getCorePositions(Block) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Calculate a List of alignment indicies that correspond to the core of a
Block, which means that all structures have a residue in that positon.
- getCoreResidues(double, double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Returns the residues belonging to the interface core, defined as those residues at
the interface (BSA>0) and for which the BSA/ASA ratio is above the given bsaToAsaCutoff
- getCorrelation_coeff_Fo_to_Fc() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getCorrelation_coeff_Fo_to_Fc_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getCount() - Method in class org.biojava.nbio.aaproperties.xml.Name2Count
-
- getCovalentRadius() - Method in enum org.biojava.nbio.structure.Element
-
Returns the covalent radius of this Element.
- getCoverage() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getCoverage() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Returns the coverage, as a fraction between 0 and 1, of this
AlignedSequence with respect to the original sequence.
- getCoverage1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Get the coverage of protein 1 with the alignment
- getCoverage2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Get the coverage of protein 2 with the alignment
- getCoverages() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Returns the coverage of the alignment for each structure in the
alignment as a fraction between 0.0 and 1.0.
- getCoverages() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- getCovered() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getCoxInfo(String) - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
- getCoxInfoHashMap() - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
- getCPPoint() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
- getCreate_co() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getCreatedDate() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The DT line shows when an entry first appeared in the database
- getCreator() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
-
- getCrystalCell() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Return the crystal cell
- getCrystalIds() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Returns a pair of identifiers for each of the 2 member molecules that
identify them uniquely in the crystal:
<molecule id (asym unit id)>+<operator id>+<crystal translation>
- getCrystallographicInfo() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getCrystallographicInfo() - Method in interface org.biojava.nbio.structure.Structure
-
Get crystallographic information for this structure
- getCrystallographicInfo() - Method in class org.biojava.nbio.structure.StructureImpl
-
Gets crystallographic information for this structure
- getCrystals_number() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getCrystalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
- getCurrent(String) - Static method in class org.biojava.nbio.structure.PDBStatus
-
Gets the current version of a PDB ID.
- getCurrentChain() - Method in class org.biojava.nbio.structure.AtomIterator
-
Get the chain that contains the current atom.
- getCurrentChain() - Method in class org.biojava.nbio.structure.GroupIterator
-
Get the current Chain.
- getCurrentModel() - Method in class org.biojava.nbio.structure.AtomIterator
-
Get the model number of the model containing the current atom.
- getCurrentModel() - Method in class org.biojava.nbio.structure.GroupIterator
-
Get the model number of the current model.
- getCurrentPDBIds() - Static method in class org.biojava.nbio.structure.PDBStatus
-
Returns a list of current PDB IDs
- getCurrentPDBIds() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
-
get the list of current PDB IDs
- getCurrentSequencePosition() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
- getCustomChain1() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getCustomFile1() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getCut_sites() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
-
- getCutoff() - Method in class org.biojava.nbio.structure.contact.Grid
-
- getCuts(int, AlignerHelper.Subproblem, int[], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
- getCutsPerSection() - Method in class org.biojava.nbio.alignment.routines.GuanUberbacher
-
Returns the number of cuts added to each section during each pass.
- getD() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition
-
Return the block diagonal eigenvalue matrix
- getData() - Method in class org.biojava.nbio.structure.scop.server.ListStringWrapper
-
- getData() - Method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper
-
- getData() - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
-
- getData_content_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxAuditRevisionHistory
-
- getDataAnisotropy() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the dataAnisotropy property.
- getDatabase() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
-
- getDatabase() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
-
- getDatabase() - Method in class org.biojava.nbio.structure.DBRef
-
The database of the db-ref.
- getDatabaseCrossReference() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The DR (Database Cross-reference) line cross-references other databases which
contain information related to the entry in which the DR line appears.
- getDatabaseReferences() - Method in interface org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface
-
- getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
The Uniprot mappings to other database identifiers for this sequence
- getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getDataClass() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
-
- getDataColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getDataCompleteness() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the dataCompleteness property.
- getDataRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get the list of row names
- getDataSource() - Method in class org.biojava.nbio.core.sequence.AccessionID
-
- getDataSource() - Method in class org.biojava.nbio.core.sequence.location.InsdcParser
-
- getDataSource() - Method in class org.biojava.nbio.core.sequence.TaxonomyID
-
- getDataVariables() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getDate() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getDate() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- getDate_original() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- getDb_align_beg() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getDb_align_end() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getDb_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getDb_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getDb_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getDbAccession() - Method in class org.biojava.nbio.structure.DBRef
-
Sequence database accession code.
- getDbComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getDbFile() - Method in class org.biojava.nbio.core.search.io.Result
-
- getDbIdCode() - Method in class org.biojava.nbio.structure.DBRef
-
Sequence database identification code.
- getDbReferences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getDBRefs() - Method in interface org.biojava.nbio.structure.Structure
-
Get the list of database references
- getDBRefs() - Method in class org.biojava.nbio.structure.StructureImpl
-
Get the list of database references
- getDBResultMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getDBSearch() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
-
- getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
-
- getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
-
- getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
-
- getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
-
- getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
-
- getDBSearchParameters() - Static method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getDbSearchResult(AFPChain) - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
-
- getDbSeqBegin() - Method in class org.biojava.nbio.structure.DBRef
-
Initial sequence number of the
database seqment.
- getDbSeqEnd() - Method in class org.biojava.nbio.structure.DBRef
-
Ending sequence position of the database segment.
- getDbxrefList(String, int, int) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
-
- getDCCR() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the dccr property.
- getDCCRefinementProgram() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the dccRefinementProgram property.
- getDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the dccRfree property.
- getDcl() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getdCutoff() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
-
The maximum allowed distance between the centroids of two equivalent
Subunits, in A.
- getDefault() - Static method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
Default instance to use when Transcribing from DNA -> RNA ->
Protein.
- getDefaultConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
-
- getDefaultFactory() - Static method in class org.biojava.nbio.ontology.OntoTools
-
- getDefaultFrame() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
-
- getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script to set the default orientation for a structure
- getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script to set the default orientation for a structure
- getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getDefaultParameters() - Static method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getDefaultText() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
-
- getDefinition() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getDefinitions() - Method in class org.biojava.nbio.structure.io.mmcif.MetalBondConsumer
-
- getDegreeFreedom() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getDelta() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getDendrogram() - Method in class org.biojava.nbio.core.util.SingleLinkageClusterer
-
Get the full dendrogram (size n-1) result of the hierarchical clustering
- getDensityCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getDepDate() - Method in class org.biojava.nbio.structure.PDBHeader
-
Return the deposition date of the structure in the PDB.
- getDeposit_site() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus
-
- getDesc() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getDescription() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getDescription() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
-
- getDescription() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
-
Returns the description of this matrix.
- getDescription() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getDescription() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
- getDescription() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getDescription() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Get the description that can be used to describe the feature
- getDescription() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- getDescription() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getDescription() - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- getDescription() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- getDescription() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getDescription() - Method in class org.biojava.nbio.genome.io.fastq.Fastq
-
Return the description of this FASTQ formatted sequence.
- getDescription() - Method in class org.biojava.nbio.genome.io.fastq.FastqBuilder
-
Return the description for this FASTQ formatted sequence builder.
- getDescription() - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
-
Return the description of this FASTQ sequence format variant.
- getDescription() - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- getDescription() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
-
- getDescription() - Method in interface org.biojava.nbio.ontology.Ontology
-
Return a human-readable description of this ontology, or the empty
string if none is available
- getDescription() - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- getDescription() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- getDescription() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
-
- getDescription() - Method in interface org.biojava.nbio.ontology.Term
-
Return a human-readable description of this term, or the empty string if
none is available.
- getDescription() - Method in class org.biojava.nbio.ontology.Term.Impl
-
- getDescription() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getDescription() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getDescription() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getDescription() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
return a description of this compound
- getDescription() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- getDescription() - Method in class org.biojava.nbio.structure.cath.CathNode
-
- getDescription() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getDescription() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getDescription() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getDescription() - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- getDescription() - Method in class org.biojava.nbio.structure.Site
-
gets the REMARK 800 description of the site
- getDescription() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
-
- getDescription() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
-
- getDescription2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Get a textual description for the protein 2 of the alignment.
- getDescriptionByCathId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return CATH description for CATH domain ID.
- getDescriptionByCathId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDescriptionByNodeId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return CATH description for node representative by node ID.
- getDescriptionByNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDescriptionNumber() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
- getDescriptor() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- getDescriptors() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getDesFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getDesURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
-
- getDetails() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getDetails() - Method in interface org.biojava.nbio.structure.SeqMisMatch
-
- getDetails() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
-
- getDf() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
-
- getDiagonalAtK(Atom[], int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils
-
Get distances along diagonal k from coordinate array coords.
- getDiagonalDistance() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getDiagonalDistance2() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getDictionary() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
-
- getDimension() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getDimension() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getDimension() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getDimensions() - Method in class org.biojava.nbio.structure.contact.BoundingBox
-
Returns the dimensions of this bounding box.
- getDir(String, boolean) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Gets the directory in which the file for a given MMCIF file would live,
creating it if necessary.
- getDirection() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getDiscreteColumnValues(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get back a list of unique values in the column
- getDiscreteRowValues(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get back a list of unique values in the row
- getDiscreteValues() - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
-
- getDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
Get the distance cutoff used during AFP chain connectivity checks
- getDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- getDisFilter() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getDisorder(FastaSequence) - Static method in class org.biojava.nbio.ronn.Jronn
-
Calculates the disordered regions of the sequence.
- getDisorder(List<FastaSequence>) - Static method in class org.biojava.nbio.ronn.Jronn
-
Calculates the disordered regions of the sequence for many sequences in the input.
- getDisorder(String) - Static method in class org.biojava.nbio.ronn.Jronn
-
Calculates the disordered regions of the protein sequence.
- getDisorderScores(FastaSequence) - Static method in class org.biojava.nbio.ronn.Jronn
-
Calculates the probability value for each residue in the protein sequence,
telling the probability that the residue belongs to disordered region.
- getDisorderScores(ProteinSequence) - Static method in class org.biojava.nbio.ronn.Jronn
-
Calculates the probability value for each residue in the protein sequence,
telling the probability that the residue belongs to disordered region.
- getDisorderScores(List<FastaSequence>) - Static method in class org.biojava.nbio.ronn.Jronn
-
Calculates the probability of disorder scores for each residue in the sequence for
many sequences in the input.
- getDisSmooth() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getDist() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- getDist() - Method in class org.biojava.nbio.structure.validation.Clash
-
Gets the value of the dist property.
- getDist() - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Gets the value of the dist property.
- getDist1() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getDist1() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getDist2() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getDist2() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getDisTable1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getDisTable2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getDistance() - Method in class org.biojava.nbio.alignment.template.AbstractScorer
-
- getDistance(double) - Method in class org.biojava.nbio.alignment.template.AbstractScorer
-
- getDistance() - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns score as a distance between 0.0 and 1.0.
- getDistance(double) - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns score as a distance between 0.0 and scale.
- getDistance() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
-
- getDistance(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
calculate distance between two atoms.
- getDistance() - Method in class org.biojava.nbio.structure.contact.AtomContact
-
- getDistance() - Method in class org.biojava.nbio.structure.contact.Contact
-
- getDistanceCutoff() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- getDistanceCutoff() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getDistanceFast(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Will calculate the square of distances between two atoms.
- getDistanceIncrement() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getDistanceMatrices() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
Returns a List of internal Distance Matrices,
one for each structure in the alignment.
- getDistanceMatrices() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
-
- getDistanceMatrices() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- getDistanceMatrix() - Method in class org.biojava.nbio.alignment.GuideTree
-
Returns the distance matrix used to construct this guide tree.
- getDistanceMatrix() - Method in interface org.biojava.nbio.alignment.template.HierarchicalClusterer
-
Returns the distance matrix used in clustering.
- getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils
-
Matrix of all distances between two sets of Atoms.
- getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
A matrix with ca1length rows and ca2length columns.
- getDistanceMatrix() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Returns the List containing the interatomic distance Matrix of each
structure.
- getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
-
- getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
The distance matrix this alignment is based on
- GetDistanceMatrix - Class in org.biojava.nbio.structure.domain.pdp
-
- GetDistanceMatrix() - Constructor for class org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix
-
- getDistanceMatrix(Atom[]) - Method in class org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix
-
A set of Calpha atoms that are representing the protein
- getDistanceToParent() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getDistanceToParent() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Returns the difference in height of this node and it's parent node.
- getDistMat() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
return the difference of distance matrix between the two structures
- getDistribution(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
Computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getDistributionPosition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
An adaptor method which computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getDistributionPosition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getDkMatrix(Atom[], Atom[], int, double[], double[], int, int) - Method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
- getDkMatrix(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
- getDNACodingSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Get the stitched together CDS sequences then maps to the cDNA
- getDNACodingSequences() - Method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
-
- getDnaCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getDNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet
-
- getDNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.DNACompoundSet
-
- getDNAOneLetter(String) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
-
- getDNARNAHybridCompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet
-
- getDnaRnaTranslator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getDnaToRna() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- getDNATwoLetter(Character) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
-
- getDNAType() - Method in class org.biojava.nbio.core.sequence.DNASequence
-
- getDoi() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the value of DOI field.
- getDomain(String, AtomCache) - Method in interface org.biojava.nbio.structure.domain.PDPProvider
-
Get the structure for a particular PDP domain
- getDomain(String, AtomCache) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider
-
Get the structure for a particular PDP domain
- getDomainByCathId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return CATH domain for CATH domain ID.
- getDomainByCathId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getDomainByScopID(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
- getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getDomainCounter() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getDomainDescriptionFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDomainId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getDomainId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getDomainId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getDomainListFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDomainName() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getDomainNames(String) - Method in interface org.biojava.nbio.structure.domain.DomainProvider
-
Get a list of constituent domain identifiers
- getDomainNames(String) - Method in class org.biojava.nbio.structure.domain.PDBDomainProvider
-
Gets a list of domain representatives for a given PDB ID.
- getDomainNames(String) - Method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
-
- getDomainProvider() - Static method in class org.biojava.nbio.structure.domain.DomainProviderFactory
-
- getDomainRangesFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getDomainRangesXML(SortedSet<String>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getDomains() - Method in class org.biojava.nbio.structure.domain.pdp.CutDomain
-
- getDomains() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
-
- getDomains() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getDomainsById(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase
-
Get a particular ECOD domain by the domain ID (e.g.
- getDomainsById(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
Get a particular ECOD domain by the domain ID (e.g.
- getDomainsByNodeId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return all CATH domains for a particular CATH node.
- getDomainsByNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDomainsForPdb(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return all CATH domains for a PDB ID.
- getDomainsForPdb(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDomainsForPdb(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase
-
Get a list of all ECOD domains for a particular PDB ID
- getDomainsForPdb(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
public EcodInstallation(String cacheLocation) {
this( cacheLocation, DEFAULT_VERSION );
}
/**
Get a list of all ECOD domains for a particular PDB ID
- getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getDomainsForPDB(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Get a list of ScopDomains that have been assigned to a PDB ID
- getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getDomainsFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getDomainsXML(SortedSet<Domain>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getDomallFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDonor1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getDonor2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getDoublePivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
-
Return pivot permutation vector as a one-dimensional double array
- getDuplicationHint() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- getDuplicationHint() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
-
- getDVar() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getEcNums() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getEcodDatabase() - Static method in class org.biojava.nbio.structure.ecod.EcodFactory
-
Returns the (singleton) database for the current default version
- getEcodDatabase(String) - Static method in class org.biojava.nbio.structure.ecod.EcodFactory
-
- getEditorList() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the list of editors of the JournalArticle
- getEDSR() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the edsr property.
- getEDSResolution() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the edsResolution property.
- getEDSResolutionLow() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the edsResolutionLow property.
- getElement() - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
-
- getElement(String) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
-
- getElement() - Method in interface org.biojava.nbio.structure.Atom
-
Get element of the atom, e.g.
- getElement() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get element of the atom, e.g.
- getElement1() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
-
- getElement2() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
-
- getElementaryAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Return the operator for all elementary axes of symmetry of the structure, that is,
the axes stored in the List as unique and from which all the symmetry
axes are constructed.
- getElementaryAxesObjects() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Return all elementary axes of symmetry of the structure, that is,
the axes stored in the List as unique and from which all the symmetry
axes are constructed.
- getElementaryAxis(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getElementFromHillIndex(int) - Static method in enum org.biojava.nbio.structure.Element
-
Returns the Element that corresponds to the specified Hill Order.
- getElementList() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- getElementType() - Method in enum org.biojava.nbio.structure.Element
-
Returns the Element Type for this Element.
- getElipsisRadii() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
The effective value of this distance for a certain body is known as its
radius of / gyration with respect to the given axis.
- getEmail() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
Get the email for QBlast.
- getEmblId() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The ID (IDentification) line
The tokens represent:
1.
- getEmblReference() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The Reference (RN, RC, RP, RX, RG, RA, RT, RL) Lines
These lines comprise the literature citations within the database.
- getEmbTrees() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getEmptyChemComp() - Static method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
Creates a new instance of the dummy empty ChemComp.
- getEmptySequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
Returns an empty sequence with the given compound set of the editing
sequence
- getEnd() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getEnd() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Returns the
Point within an alignment of the last element of the original
Sequence.
- getEnd() - Method in interface org.biojava.nbio.core.alignment.template.ProfileView
-
Returns the column index of the viewed
Profile corresponding to the final element in this view
- getEnd() - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
- getEnd(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute
-
Must use this rather than the no-args getEnd as this can return
-1 and the length of a sub is dependent on the length of the
Sequence; we cannot assume 1:1 mapping between characters in a
String and the number of compounds we will have to insert.
- getEnd() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getEnd() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
End of the location
- getEnd() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- getEnd() - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
- getEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- getEnd() - Method in class org.biojava.nbio.structure.ResidueRange
-
- getEndLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
- getEndLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
- getEnergy() - Method in class org.biojava.nbio.structure.secstruc.HBond
-
- getEngineered() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getEnrichment(ProteinSequence, AminoAcidCompound) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the composition of specified amino acid in the sequence.
- getEnrichment(String, PeptideProperties.SingleLetterAACode) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the composition of specified amino acid in the sequence.
- getEnrichment(String, char) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the composition of specified amino acid in the sequence.
- getEnrichment(String, String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the composition of specified amino acid in the sequence.
- getEnrichment(ProteinSequence, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getEnsemble() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Returns the parent Ensemble of the MultipleAlignment.
- getEnsemble() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- getEnsemblGeneId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getEnt() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the ent property.
- getEntities() - Method in class org.biojava.nbio.structure.io.sifts.SiftsXMLParser
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPoly
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getEntityById(int) - Method in interface org.biojava.nbio.structure.Structure
-
Request a particular entity by its entity id (mol id in legacy PDB format)
- getEntityById(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a particular entity by its entity id (mol id in legacy PDB format)
- getEntityId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- getEntityInfo() - Method in interface org.biojava.nbio.structure.Chain
-
Returns the EntityInfo for this chain.
- getEntityInfo() - Method in class org.biojava.nbio.structure.ChainImpl
-
Returns the EntityInfo for this chain.
- getEntityInfos() - Method in interface org.biojava.nbio.structure.Structure
-
Get all the EntityInfo for this Structure.
- getEntityInfos() - Method in class org.biojava.nbio.structure.StructureImpl
-
Get all the EntityInfo for this Structure.
- getEntityType() - Method in interface org.biojava.nbio.structure.Chain
-
Returns the EntityType of this chain.
- getEntityType() - Method in class org.biojava.nbio.structure.ChainImpl
-
- getEntityType() - Method in enum org.biojava.nbio.structure.EntityType
-
Returns the type of the Entity as a String
- getEntry() - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
-
Gets the value of the entry property.
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus
-
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
-
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- getEnumValuesAsString(Class<T>) - Static method in class org.biojava.nbio.structure.align.util.CliTools
-
Constructs a comma-separated list of values for an enum.
- getEnzClass() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getEqr() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
returns the number of euqivalent residues in this alignment
- getEQRAlignmentPos(AFPChain) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
- getEquivalent() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
- getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- getEquivalentCompounds(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- getEquivalentCompounds(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
-
- getEvalCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getEvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getEvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getEvalueThreshold() - Method in class org.biojava.nbio.core.search.io.SearchIO
-
- getEvCode() - Method in class org.biojava.nbio.structure.Site
-
gets the REMARK 800 EVIDENCE CODE for the site.
- getExampleUnitCell() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
-
- getExitMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getExonCount() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getExonEnds() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getExonSequences() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Get the exons as an ArrayList
- getExonStarts() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getExpectedExecutionTime() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
-
- getExperimentalTechniques() - Method in class org.biojava.nbio.structure.PDBHeader
-
Return the Set of ExperimentalTechniques, usually the set is of size 1 except for hybrid
experimental techniques when the Set will contain 2 or more values
- getExportPDBMenuItem(AbstractAlignmentJmol) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getExpression_system_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getExpressionSystem() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemAtccNumber() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemCell() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemCellLine() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemCellularLocation() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemGene() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemOrgan() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemOrganelle() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemOtherDetails() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemPlasmid() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemStrain() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemTaxId() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemTissue() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemVariant() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemVector() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExpressionSystemVectorType() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getExtensionPenalty() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
-
Returns the negative of the extension penalty passed to the constructor.
- getExtensionPenalty() - Method in interface org.biojava.nbio.alignment.template.GapPenalty
-
Returns penalty given when an already open gap elongates by a single element
- getExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- getExtensions() - Method in interface org.biojava.nbio.structure.io.StructureIOFile
-
Returns a list of extensions supported by this class
- getExtensions() - Method in enum org.biojava.nbio.structure.StructureIO.StructureFiletype
-
- getExtinctionCoefficient(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the extinction coefficient of sequence.
- getExtinctionCoefficient(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the extinction coefficient of sequence.
- getExtinctionCoefficient(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getFailedLines() - Method in class org.biojava.nbio.structure.scop.Astral
-
Gets a map describing lines read in the file that weren't understood.
- getFalseDiscoveryRate() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getFamilyId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getFarmJob() - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
-
- getFatCatAligner() - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
-
- getFeatureHeader() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The FH (Feature Header) lines are present only to improve readability of
an entry when it is printed or displayed on a terminal screen.
- getFeatureRetriever() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getFeatures() - Method in interface org.biojava.nbio.core.sequence.features.FeatureRetriever
-
- getFeatures(String) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getFeatures() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getFeatures() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- getFeatures(String, int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Return features at a sequence position by type
- getFeatures(int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Return features at a sequence position
- getFeatures() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getFeaturesByType(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getFeaturesKeyWord() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getFeatureTable() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The FT (Feature Table) lines provide a mechanism for the annotation of the
sequence data.
- getFetchBehavior() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Get the behavior for fetching files from the server
- getFetchBehavior() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getFetchBehavior() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Get the behavior for fetching files from the server
- getFGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getFGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getFieldNames(Field[]) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
-
Gets the mmCIF record name for each field.
- getFields(Class<?>) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
-
Gets all fields for a particular class, filtering fields annotated
with
@IgnoreField.
- getFile() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
- getFile1() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getFile2() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getFileAnnotation() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
-
- getFileExtension(File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
-
- getFileExtensions() - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
-
- getFileExtensions() - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
-
- getFileExtensions() - Method in interface org.biojava.nbio.core.search.io.ResultFactory
-
returns a list of file extensions associated to this ResultFactory
- getFileFormat() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getFileFormatSelect() - Static method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
-
- getFilename(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Converts a PDB ID into a filename with the proper extension
- getFilename(String) - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
-
- getFilename(String) - Method in class org.biojava.nbio.structure.io.MMTFFileReader
-
- getFilename(String) - Method in class org.biojava.nbio.structure.io.PDBFileReader
-
- getFileName() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
-
- getFileName() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
-
- getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.mmcif.MetalBondConsumer
-
- getFileParsingParameters() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
-
- getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
- getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.PDBFileParser
-
- getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
-
- getFileParsingParameters() - Method in interface org.biojava.nbio.structure.io.StructureProvider
-
Get the parameters that should be used for file parsing
- getFileParsingParams() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getFilePath1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
-
- getFilePrefix(File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
-
- getFinalIndex(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Calculates and returns the last position of the specified structure in
the alignment that is not null.
- getFinalIndex(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
-
- getFinalResidue(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Calculates and returns the last residue of the specified structure in the
alignment that is not null.
- getFinalResidue(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
-
- getFirst(String) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
- getFirst() - Method in class org.biojava.nbio.structure.AtomPositionMap
-
- getFirst() - Method in class org.biojava.nbio.structure.contact.Pair
-
- getFirstAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getFirstGroupAsa(ResidueNumber) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Gets the GroupAsa for the corresponding residue number of first chain
- getFirstGroupAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Gets a map of ResidueNumbers to GroupAsas for all groups of first chain.
- getFirstRepeat() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
Get the index of the first repeat used by this axis
- getFirstRepeats(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Get the first repeat index of each axis of a specified level.
- getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
Should return the 5-prime end of the given Sequence according to
the edit.
- getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
-
- getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Insert
-
- getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute
-
- getFlippableSidechain() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the flippableSidechain property.
- getFocusAfpList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getFocusAfpn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getFocusRes1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getFocusRes2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getFocusResn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getFoFcCorrelation() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the foFcCorrelation property.
- getFold() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getFold() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getFoldId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getFolds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getFoldType() - Method in enum org.biojava.nbio.structure.xtal.TransformType
-
- getFormat() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getFormat() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getFormatedSequence(int) - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
Format sequence per width letter in one string.
- getFormattedFasta() - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
- getFormula() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getFormula() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getFormula() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getFormula() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getFormula_weight() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getFormula_weight() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getForwardFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
-
Returns all frames in the forward orientation
- getFract_transf_matrix11() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getFract_transf_matrix12() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getFract_transf_matrix13() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getFract_transf_matrix21() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getFract_transf_matrix22() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getFract_transf_matrix23() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getFract_transf_matrix31() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getFract_transf_matrix32() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getFract_transf_matrix33() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getFract_transf_vector1() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getFract_transf_vector2() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getFract_transf_vector3() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSites
-
- getFragCompat() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getFragLen() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getFragLen() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- getFragLen() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getFragLenSq() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getFragment(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils
-
Get a continue subset of Atoms based by the starting position and the length
- getFragment() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getFragmentFromIdxList(Atom[], int[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils
-
Get a subset of Atoms based by their positions
- getFragmentId() - Method in class org.biojava.nbio.structure.cath.CathFragment
-
- getFragmentLength() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getFragmentMiniDistance() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getFragmentNoClone(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils
-
Get a continue subset of Atoms based by the starting position and the length
does not clone the original atoms.
- getFragmentPairs() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
get the results of step 1 - the FragmentPairs used for seeding the
alignment
- getFragmentPairs() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- getFragmentPairs() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- getFragmentsByPdbId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
- getFragmentsByPdbId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getFragScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getFrame() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
-
- getFrame() - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
-
- getFrom() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
-
- getFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getFromCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
-
- getFromFtp() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
-
- getFromHeteroAtomId(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromHeteroAtomId(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromHeteroAtomIds(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromHeteroAtomIds(List<String>) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromHeteroAtomIds(String...) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromPdbId(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromPdbId(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromPdbIds(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromPdbIds(List<String>) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromPdbIds(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromPdbIds(String...) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFullAtomSequence(List<Group>, Map<Integer, Integer>, boolean) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
-
Returns the full sequence of the Atom records of a parent
with X instead of HETATMSs.
- getFullMatrix() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Returns a matrix that describes both rotation and translation.
- getGagPolyproteins() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
-
get all PDB IDs of gag-polyproteins
- getGamma() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getGamma() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getGapCreate() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getGapExtCol() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getGapExtCol() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getGapExtend() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getGapExtend() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getGapExtend() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- getGapExtension() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getGapExtension() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- getGapExtension() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- getGapExtension() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getGapExtRow() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getGapExtRow() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getGapLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getGapOpen() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getGapOpen() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- getGapOpen() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- getGapOpen() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getGapOpen() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- getGapOpen() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getGapOpenCol() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getGapOpenCol() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getGapOpenRow() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getGapOpenRow() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getGapPenalty() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Returns the gap penalties.
- getGaps() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
return the number of gaps in this alignment
- getGatheringThreshs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
Not always 2.
- getGC() - Method in class org.biojava.nbio.core.sequence.RNASequence
-
- getGCCount() - Method in class org.biojava.nbio.core.sequence.DNASequence
-
Get the GC count in the DNA Sequence
- getGCGChecksum(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Calculates GCG checksum for entire list of sequences
- getGCGChecksum(S) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Calculates GCG checksum for a given sequence
- getGCGHeader(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Assembles a GCG file header
- getGCGType(CompoundSet<C>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Determines GCG type
- getGCStats(Collection<DNASequence>) - Static method in class org.biojava.nbio.genome.parsers.gff.GCStats
-
- getGCStatsString(Collection<String>) - Static method in class org.biojava.nbio.genome.parsers.gff.GCStats
-
- getGenbankDirectoryCache() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
Local directory cache of Genbank that can be downloaded
- getGene(String) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Get the gene based on accession.
- getGene() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getGene_src_common_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_dev_stage() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_genus() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_species() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_strain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_tissue() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_tissue_fraction() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGeneAliases() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Pull uniprot gene aliases associated with this sequence
- getGenebankId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getGeneName() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Get the gene name associated with this sequence.
- getGeneName() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getGeneNames() - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
-
- getGeneNames(InputStream) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
-
Get a list of GeneNames from an input stream.
- getGenes() - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
- getGeneSequences() - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key.
- getGeneSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
-
- getGeneSet() - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
- getGeneSymb() - Method in class org.biojava.nbio.phosphosite.Site
-
- getGenus() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
Returns a transformation matrix transform polyhedra for Cn structures.
- getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
Returns a transformation matrix transform polyhedra for Cn structures.
- getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
Returns the geometric center of polyhedron.
- getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
Returns the geometric center of polyhedron.
- getGonnet250() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns PAM 250 matrix by Gonnet, Cohen & Benner
- getGradientMapper(int, double, double) - Static method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
Constructs a gradientMapper to draw one of the pre-defined gradients
For example,
GradientMapper.getGradientMapper(GradientMapper.RAINBOW_GRADIENT, 0, 10)
- getGroup() - Method in class org.biojava.nbio.phosphosite.Site
-
- getGroup() - Method in class org.biojava.nbio.protmod.structure.StructureAtom
-
- getGroup() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
- getGroup() - Method in interface org.biojava.nbio.structure.Atom
-
Return the parent Group of the Atom.
- getGroup() - Method in class org.biojava.nbio.structure.AtomImpl
-
Return the parent Group of the Atom.
- getGroup() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
-
- getGroup_PDB() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getGroupAsas() - Method in class org.biojava.nbio.structure.asa.AsaCalculator
-
Calculates ASA for all atoms and return them as a GroupAsa
array (one element per residue in structure) containing ASAs per residue
and per atom.
- getGroupByPDB(ResidueNumber) - Method in interface org.biojava.nbio.structure.Chain
-
Get a group by its PDB residue numbering.
- getGroupByPDB(ResidueNumber) - Method in class org.biojava.nbio.structure.ChainImpl
-
Get a group by its PDB residue numbering.
- getGroupByPDBResidueNumber(Structure, ResidueNumber) - Static method in class org.biojava.nbio.structure.StructureTools
-
Get a group represented by a ResidueNumber.
- getGroupCategories(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getGroupCategories(String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
-
- getGroupContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getGroupDistancesWithinShell(Structure, Atom, Set<ResidueNumber>, double, boolean, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Finds Groups in structure that contain at least one Atom that is
within radius Angstroms of centroid.
- getGroupFromChemCompDictionary(String) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
Returns the groupings of the attribute
- getGroups() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
- getGroups(boolean) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
- getGroups() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- getGroups(boolean) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- getGroups() - Method in class org.biojava.nbio.structure.Site
-
- getGroups(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
Returns the List of Groups of the corresponding representative Atom
array.
- getGroups() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
Get the name of the groups that are being plotted in the figure
- getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in interface org.biojava.nbio.structure.Chain
-
Get all groups that are located between two PDB residue numbers.
- getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in interface org.biojava.nbio.structure.Chain
-
Get all groups that are located between two PDB residue numbers.
- getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in class org.biojava.nbio.structure.ChainImpl
-
- getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.ChainImpl
-
Get all groups that are located between two PDB residue numbers.
- getGroupsWithinShell(Structure, Atom, Set<ResidueNumber>, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
- getGroupsWithinShell(Structure, Group, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns a Set of Groups in a structure within the distance specified of a
given group.
- getGroupTable() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
-
- getH() - Method in class org.biojava.nbio.structure.jama.QRDecomposition
-
Return the Householder vectors
- getHazardRatio() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getHazardRatioHiCI() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getHazardRatioLoCI() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getHeader() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getHeader(S) - Method in class org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat
-
- getHeader(S) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
-
- getHeader(S) - Method in interface org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface
-
- getHeader(S) - Method in interface org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface
-
- getHeader() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- getHeaderParser() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- getHeaderVars() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getHeight() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
- getHeight() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
Returns the radius of a sphere, that is tangent to each
of the octahedron's edges
- getHelix(int) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
- getHelixLayers() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getHelixLayers() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getHelixRmsdThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getHelixRmsdToRiseRatio() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getHelpMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getHetero() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- getHetero() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getHgncId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getHGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getHGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getHieFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getHieURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
-
- getHigherOrderRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- getHillOrder() - Method in enum org.biojava.nbio.structure.Element
-
Returns the Hill Order of this Element.
- getHitAccession() - Method in class org.biojava.nbio.core.search.io.Hit
-
- getHitCounter() - Method in class org.biojava.nbio.core.search.io.Result
-
- getHitDef() - Method in class org.biojava.nbio.core.search.io.Hit
-
- getHitId() - Method in class org.biojava.nbio.core.search.io.Hit
-
- getHitLen() - Method in class org.biojava.nbio.core.search.io.Hit
-
- getHitNum() - Method in class org.biojava.nbio.core.search.io.Hit
-
- getHitSequence() - Method in class org.biojava.nbio.core.search.io.Hit
-
returns the reference to the original and whole sequence hit in the database.
- getHitsQueryDef(double) - Method in class org.biojava.nbio.genome.query.BlastXMLQuery
-
- getHmmAcc() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getHmmDesc() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getHmmFrom() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getHmmName() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getHmmTo() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getHomologyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getHost_org_common_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getHost_org_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getHost_org_genus() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getHost_org_species() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getHost_org_strain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getHRText() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getHSDMTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Calculate a phylogenetic tree of the MultipleAlignment using
dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for
distantly related proteins, structure-derived) and the Neighbor Joining
algorithm from forester.
- getHspAlignLen() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspBitScore() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspEvalue() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspGaps() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspHitFrame() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspHitFrom() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspHitTo() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspHseq() - Method in class org.biojava.nbio.core.search.io.Hsp
-
HSP aligned hit sequence string
- getHspIdentity() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspIdentityString() - Method in class org.biojava.nbio.core.search.io.Hsp
-
Identity string representing correspondence between aligned residues
- getHspNum() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspPositive() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspQseq() - Method in class org.biojava.nbio.core.search.io.Hsp
-
HSP aligned query sequence string
- getHspQueryFrame() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspQueryFrom() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspQueryTo() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHspScore() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getHSVColorSpace() - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
-
- getI() - Method in class org.biojava.nbio.structure.contact.Contact
-
- getIAtoms() - Method in class org.biojava.nbio.structure.contact.Grid
-
- getIclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- getIcode() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the icode property.
- getiCode1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getiCode2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getIcon(ActionListener, String) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getID() - Method in class org.biojava.nbio.core.sequence.AccessionID
-
- getId() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
-
- getId() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
-
- getID() - Method in class org.biojava.nbio.core.sequence.TaxonomyID
-
- getId() - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
Gets the value of id
- getId() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getId() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getId() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getId() - Method in interface org.biojava.nbio.structure.Chain
-
Get the 'private' asymId (internal chain IDs in mmCif) for this chain.
- getId() - Method in class org.biojava.nbio.structure.ChainImpl
-
Get the 'private' asymId (internal chain IDs in mmCif) for this chain.
- getId() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getId() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
- getId() - Method in class org.biojava.nbio.structure.DBRef
-
Get the ID used by Hibernate.
- getId() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- getId() - Method in class org.biojava.nbio.structure.EntityInfo
-
get the ID used by Hibernate
- getId() - Method in class org.biojava.nbio.structure.HetatomImpl
-
the Hibernate database ID
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getId() - Method in class org.biojava.nbio.structure.PDBHeader
-
Get the ID used by Hibernate.
- getId() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
-
The identifier for this Biological Assembly, from 1 to n
- getId() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Returns the identifier for this biological assembly transformation.
- getId() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getId() - Method in class org.biojava.nbio.structure.rcsb.RCSBTaxonomy
-
- getId() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
-
- getId() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement
-
Returns the ID of this element.
- getId() - Method in interface org.biojava.nbio.structure.Structure
-
Get the ID used by Hibernate
- getId() - Method in class org.biojava.nbio.structure.StructureImpl
-
get the ID used by Hibernate
- getId() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
-
- getId() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets the standard numeric identifier for the space group.
- getId() - Method in enum org.biojava.nbio.structure.xtal.TransformType
-
- getId() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getId() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
-
Request id (RID) as received from QBlast server
- getIdbnsBegin() - Method in class org.biojava.nbio.structure.DBRef
-
Insertion code of initial residue of the segment, if PDB is the
reference.
- getIdbnsEnd() - Method in class org.biojava.nbio.structure.DBRef
-
Insertion code of the ending
residue of the segment, if PDB is
the reference.
- getIdCode() - Method in class org.biojava.nbio.structure.DBRef
-
get the idCode for this entry
- getIdCode() - Method in class org.biojava.nbio.structure.PDBHeader
-
The PDB code for this protein structure.
- getIdenticalSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getIdentification() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getIdentifiedModifiedCompound() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- getIdentifier() - Method in class org.biojava.nbio.core.sequence.AccessionID
-
- getIdentifier() - Method in class org.biojava.nbio.structure.align.client.StructureName
-
Get the original form of the identifier
- getIdentifier() - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier
-
- getIdentifier() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getIdentifier() - Method in class org.biojava.nbio.structure.cluster.Subunit
-
The standard identifier of the Subunit.
- getIdentifier() - Method in class org.biojava.nbio.structure.domain.PDPDomain
-
- getIdentifier() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getIdentifier() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- getIdentifier() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- getIdentifier() - Method in class org.biojava.nbio.structure.PassthroughIdentifier
-
- getIdentifier() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getIdentifier() - Method in interface org.biojava.nbio.structure.Structure
-
Get a string representing this structure's contents.
- getIdentifier() - Method in interface org.biojava.nbio.structure.StructureIdentifier
-
Get the String form of this identifier.
- getIdentifier() - Method in class org.biojava.nbio.structure.StructureImpl
-
Get a string representing this structure's contents.
- getIdentifier() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
-
Get the String form of this identifier.
- getIdentifier() - Method in class org.biojava.nbio.structure.URLIdentifier
-
- getIdentity() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
- getIdentity() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The percent of residues that are sequence-identical in the alignment.
- getIDFormat(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Creates format String for accession IDs
- getIdx1() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
the positions of the structure equivalent positions in atom set 1
- getIdx1() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
get the identical position in the alignment
- getIdx2() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
the positions of the structure equivalent atoms in atom set 2
- getIdx2() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
get the identical position in the alignment
- getIdxlist() - Method in class org.biojava.nbio.structure.align.helper.JointFragments
-
- getImagEigenvalues() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition
-
Return the imaginary parts of the eigenvalues
- getImat() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getInChI() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getInChIKey() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getIndex(TreeNode) - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getIndex() - Method in class org.biojava.nbio.structure.align.helper.GapArray
-
- getIndex() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getIndex() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement
-
Returns the index of the SSE for its type.
- getIndex() - Method in class org.biojava.nbio.survival.data.HeaderInfo
-
- getIndexColumnName() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getIndexInQueryAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
-
- getIndexInQueryAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
-
Returns the query index corresponding to a given alignment column.
- getIndexInQueryForTargetAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
-
- getIndexInQueryForTargetAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
-
Returns the query index corresponding to a given target index.
- getIndexInTargetAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
-
- getIndexInTargetAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
-
Returns the target index corresponding to a given alignment column.
- getIndexInTargetForQueryAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
-
- getIndexInTargetForQueryAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
-
Returns the target index corresponding to a given query index.
- getIndexOf(C) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getIndexOf(C) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
Searches for the given
Compound within this alignment profile.
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns the first occurrence of the given compound in this store; performs
a linear search
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Returns 1 if the given compound is equal to the one given during
construction; otherwise will return -1.
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getIndexOf(C) - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Scans through the Sequence looking for the first occurrence of the given
compound
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
-
- getIndexOf(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- getIndexOfComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getIndexOfComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getIndexPair() - Method in class org.biojava.nbio.structure.contact.Contact
-
- getIndexToCompoundsLookup() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Returns a list of compounds the index position of which is used
to translate from the byte representation into a compound.
- getIndicesAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getIndicesAt(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
Returns the indices in the original
Sequences corresponding to the given column.
- getIndicesContacts() - Method in class org.biojava.nbio.structure.contact.Grid
-
Returns all contacts, i.e. all atoms that are within the cutoff distance, as simple Contact objects containing the atom indices pairs and the distance.
- getInertiaTensor() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
- getInitialK() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getInitials() - Method in class org.biojava.nbio.structure.Author
-
- getInputStream() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource
-
Returns the InputStream instance of this classpath resource
- getInputStream(String) - Static method in class org.biojava.nbio.core.util.FlatFileCache
-
- getInputStream(String) - Method in class org.biojava.nbio.core.util.InputStreamProvider
-
Get an InputStream for given file path.
- getInputStream(URL) - Method in class org.biojava.nbio.core.util.InputStreamProvider
-
- getInputStream(File) - Method in class org.biojava.nbio.core.util.InputStreamProvider
-
Get an InputStream for the file.
- getInputStream(URL, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
-
Connect to server and return result as an InputStream.
- getInputStream(URL) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
-
Connect to a URL and return result as an InputStream.
- getInputStream(URL, boolean, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
-
Open a URL and return an InputStream to it
if acceptGzipEncoding == true, use GZIPEncoding to
compress communication.
- getInputStream(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Load or download the specified structure and return it as an InputStream
for direct parsing.
- getInputStreamToAAindexFile() - Method in class org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider
-
- getInsCode() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- getInsCode() - Method in class org.biojava.nbio.structure.ResidueNumber
-
- getInsCode() - Method in interface org.biojava.nbio.structure.SeqMisMatch
-
- getInsCode() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
-
- getInsCode1() - Method in class org.biojava.nbio.structure.io.SSBondImpl
-
- getInsCode2() - Method in class org.biojava.nbio.structure.io.SSBondImpl
-
- getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
Returns the radius of an inscribed sphere, that is tangent to each
of the icosahedron's faces
- getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
Returns the radius of an inscribed sphere, that is tangent to each
of the octahedron's faces
- getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
Returns the radius of an inscribed sphere, that is tangent to each
of the icosahedron's faces
- getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
Returns the radius of an inscribed sphere, that is tangent to each
of the tetrahedrons's faces
- getInsertBegin() - Method in class org.biojava.nbio.structure.DBRef
-
Initial insertion code of the PDB sequence segment.
- getInsertEnd() - Method in class org.biojava.nbio.structure.DBRef
-
Ending insertion code of the PDB sequence segment.
- getInstabilityIndex(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the instability index of sequence.
- getInstabilityIndex(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the instability index of sequence.
- getInstabilityIndex(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getInstalledDomainDescription() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getInstalledDomainList() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getInstalledDomall() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getInstalledNodeList() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getInstance() - Static method in class org.biojava.nbio.core.sequence.io.IUPACParser
-
- getInstance() - Static method in class org.biojava.nbio.structure.align.gui.AlignmentGui
-
- getInstance() - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
-
- getInstance(int) - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
-
- getInstance() - Static method in class org.biojava.nbio.structure.gui.util.ScopInstallationInstance
-
- getInstance(QuatSymmetryResults) - Static method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
Returns an instance of AxisAligner for differnt type of QuatSymmetryResults (factory method)
- getInstance() - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
-
- getInstance(AxisAligner, String) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns an instance of a JmolSymmetryScriptGenerator, based on the symmetry of a structure (factory method)
- getInstanceNoVisibilityChange() - Static method in class org.biojava.nbio.structure.align.gui.AlignmentGui
-
- getInstanceNoVisibilityChange() - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
-
- getInstanceNoVisibilityChange() - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
-
- getInstantaneousOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that sets a specific orientation instantaneously
- getInt_Tables_number() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- getIntegerOntology() - Static method in class org.biojava.nbio.ontology.OntoTools
-
Get the Ontology that defines integers.
- getInteractingRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
-
- getInterfacingResidues(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Returns the residues belonging to the interface, i.e. the residues
at the surface with BSA>0
- getIntermediate(Color, Color, int, int) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
-
- getInternalChainID() - Method in interface org.biojava.nbio.structure.Chain
-
- getInternalChainID() - Method in class org.biojava.nbio.structure.ChainImpl
-
- getInterpolator() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- getIntersection(DistanceBox<T>) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
-
- getIntronSequences() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Get the introns as an ArrayList
- getInverse() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.RNASequence
-
Get the inverse view of the sequence.
- getInverse() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getInverse() - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Does the right thing to get the inverse of the current
Sequence.
- getInverse() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getIoTime() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getIoTime() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Returns the io time for this object, in milliseconds.
- getIoTime() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
-
- getIoTime() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getIoverSigma() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the ioverSigma property.
- getIsoelectricPoint(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the isoelectric point of sequence.
- getIsoelectricPoint(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
- getIsoelectricPoint(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the isoelectric point of sequence.
- getIsoelectricPoint(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
- getIsoelectricPoint(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getIsoelectricPoint(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getIsotope(String) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
-
- getIsotopeList() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- getIsotopes() - Method in class org.biojava.nbio.aaproperties.xml.Element
-
- getIterationNumber() - Method in class org.biojava.nbio.core.search.io.Result
-
- getJ() - Method in class org.biojava.nbio.structure.contact.Contact
-
- getJAtoms() - Method in class org.biojava.nbio.structure.contact.Grid
-
- getJclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- getJmolColor(Color4f) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
- getJmolColorScript(Map<Color4f, List<String>>) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
- getJmolLigandScript() - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
- getJmolPanel() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
Return the jmolPanel instance of the AlignmentJmol.
- getJmolPoint(Tuple3d) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
- getJmolScript(Atom[]) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Returns a Jmol script which will display the axis of rotation.
- getJmolScript(Atom[], int) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Returns a Jmol script which will display the axis of rotation.
- getJmolScript4Block(AFPChain, Atom[], Atom[], int) - Static method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- getJmolString(MultipleAlignment, List<Atom[]>, ColorBrewer, boolean) - Static method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
-
Generate a Jmol command String that colors the aligned residues of every
structure.
- getJmolString(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- getJoinRMSCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getJournal() - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference
-
The journal usually contains the Publication Number, Publication Date and Assignee
- getJournal() - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
-
- getJournal() - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface
-
Get the journal that retrieved from Reference section.
- getJournalArticle() - Method in class org.biojava.nbio.structure.PDBHeader
-
Get the associated publication as defined by the JRNL records in a PDB
file.
- getJournalArticle() - Method in interface org.biojava.nbio.structure.Structure
-
Get the associated publication as defined by the JRNL records in a PDB
file.
- getJournalArticle() - Method in class org.biojava.nbio.structure.StructureImpl
-
get the associated publication as defined by the JRNL records in a PDB
file.
- getJournalName() - Method in class org.biojava.nbio.structure.JournalArticle
-
- getJSpecViewProperty(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- getKappa() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getKey() - Method in class org.biojava.nbio.ontology.utils.KeyedWeakReference
-
- getKeyword() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The KW (KeyWord) lines provide information which can be used to generate
cross-reference indexes of the sequence entries based on functional,
structural, or other categories deemed important.
- getKeywords() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getKeyWords() - Method in interface org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface
-
- getKeyWords() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getKeyWords() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- getKeyWords() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Pull UniProt key words which is a mixed bag of words associated with this sequence
- getKeywords() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getKeywords() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getKimuraTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Calculate a phylogenetic tree of the MultipleAlignment using Kimura
distances and the Neighbor Joining algorithm from forester.
- getKMFigureInfo() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getL() - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition
-
Return triangular factor.
- getL() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
-
Return lower triangular factor
- getLabel_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getLabel_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getLabel_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getLabel_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getLabel_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getLabel_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getLabel_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getLabel_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getLabel_entity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getLabel_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getLabel_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getLabelOfAtomOnComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getLabelOfAtomOnComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getLargestSubunit() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getLast(String) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
- getLast() - Method in class org.biojava.nbio.structure.AtomPositionMap
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getLastIndexOf(C) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
Searches for the given
Compound within this alignment profile.
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns the last occurrence of the given compound in this store; performs
a linear search
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Returns the length of the Sequence if the given compound was equal to
the one given during construction.
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getLastIndexOf(C) - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Scans through the Sequence looking for the last occurrence of the given
compound
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
-
- getLastIndexOf(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- getLastUpdatedDate() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The DT (DaTe) line shows when an entry was last updated in the database.
- getLayerLines() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getLcmp() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getLcmp() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getLeft() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getLegend(String) - Static method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
provide the coordinates for where to draw the legend for line X and if it is chain 1 or 2
- getLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Provide the coordinates for where to draw the legend for
line X given the structure index.
- getLength() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getLength() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getLength() - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
Returns the number of columns in the alignment profile.
- getLength() - Method in class org.biojava.nbio.core.sequence.CDSSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.ExonSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.IntronSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getLength() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getLength() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
The sequence length
- getLength() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getLength() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
Returns the length of the outer bounds of this location
- getLength() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
Get the length of the MSA where it is assumed that
all sequence position
- getLength() - Method in class org.biojava.nbio.core.sequence.StartCodonSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.StopCodonSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getLength() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
- getLength() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns the length of the sequence
- getLength() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getLength() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Returns the length given during construction
- getLength() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getLength() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
-
Returns the number of columns in the alignment profile.
- getLength() - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Returns the length of the Sequence
- getLength() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getLength() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
-
Returns the size of the windowed sequence which is the length by the
window size.
- getLength() - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
- getLength() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getLength(int, int, String) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
Calculates the number of residues of the specified chain in a given range, inclusive.
- getLength(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
Calculates the number of atoms between two ResidueNumbers, inclusive.
- getLength() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the total number of base pairs that were found, used after the call to analyze().
- getLength() - Method in interface org.biojava.nbio.structure.Bond
-
Gets the distance between the two atoms of this bond.
- getLength() - Method in class org.biojava.nbio.structure.BondImpl
-
Gets the distance between the two atoms of this bond.
- getLength() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getLength() - Method in class org.biojava.nbio.structure.cath.CathFragment
-
- getLength() - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- getLength() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getLength() - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
-
- getLength() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement
-
Return the length (number of residues) in the SSE.
- getLength() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
Returns the radius of a circumscribed sphere, that goes
through all vertices
- getLength1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getLength2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getLength_a() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getLength_a_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getLength_b() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getLength_b_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getLength_c() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getLength_c_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getLengthDirectional(int, int, String) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
Calculates the number of residues of the specified chain in a given range.
- getLengthDirectional(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
Calculates the number of atoms between two ResidueNumbers, inclusive.
- getLevel() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
- getLfrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getLigands() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getLigands() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigands
-
- getLigandsByProximity(Collection<Group>, Atom[], double) - Static method in class org.biojava.nbio.structure.StructureTools
-
Finds all ligand groups from the target which fall within the cutoff distance
of some atom from the query set.
- getLigRSRnbrMean() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the ligRSRnbrMean property.
- getLigRSRnbrStdev() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the ligRSRnbrStdev property.
- getLigRSRnumnbrs() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the ligRSRnumnbrs property.
- getLigRSRZ() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the ligRSRZ property.
- getLikeSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getLinearPredictor() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getLineLength() - Method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter
-
- getLineLength() - Method in class org.biojava.nbio.core.sequence.io.FastaWriter
-
- getLineLength() - Method in class org.biojava.nbio.core.sequence.io.GenbankWriter
-
- getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
- getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getLineLoops() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
-
- getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
- getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
- getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
- getLinkages() - Method in interface org.biojava.nbio.protmod.ModificationCondition
-
- getLinkages() - Method in class org.biojava.nbio.protmod.ModificationConditionImpl
-
}
- getList() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource
-
Returns this resource as a list of Strings
- getList(BufferedReader) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Returns the contents of a buffered reader as a list of strings
- getList(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
- getList(File) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
- getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer
-
- getLoadMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getLocalDir() - Method in class org.biojava.nbio.phosphosite.Dataset
-
- getLocalFile(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Searches for previously downloaded files
- getLocalFileName(String) - Static method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
-
Returns the file name that contains the definition for this
ChemComp
- getLocalFiles() - Method in class org.biojava.nbio.phosphosite.Dataset
-
- getLocalTimeLimit() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getLocalTimeStart() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getLocation() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getLocationInAlignment() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getLocationInAlignment() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
- getLocations() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
- getLocations() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getLocations() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
The location(s) of this feature where the location should contain a reference to parent and sequence etc.
- getLocus() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- getLogLevel() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
-
- getLogScale(double) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get the log scale of this worksheet where a zero value will be set to .1
as Log(0) is undefined
- getLogScale(double, double) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get the log scale of this worksheet
- getLongName() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getLongName() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- getLongName() - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- getLongName() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- getLongName() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getLower() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getLowerBound() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getLowerLimit() - Method in class org.biojava.nbio.structure.io.mmcif.chem.MetalBondDistance
-
- getLs_d_res_high() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_d_res_low() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_matrix_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_number_parameters() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_number_reflns_all() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_number_reflns_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_number_reflns_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_number_reflns_R_work() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_number_restraints() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_percent_reflns_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_percent_reflns_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_all() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_R_free_error() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_R_free_error_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_R_work() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_redundancy_reflns_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_wR_factor_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_wR_factor_R_work() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLto() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getM() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getMacromolecularSize() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
-
Returns the macromolecular size of this biological assembly, i.e.
- getMajor_revision() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxAuditRevisionHistory
-
- getManual() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getMappingSequence() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
-
- getMapProperty() - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
-
- getMapSeqToStruct() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
-
- getMass() - Method in class org.biojava.nbio.aaproperties.xml.Element
-
- getMass() - Method in class org.biojava.nbio.aaproperties.xml.Isotope
-
- getMatches(File, double) - Static method in class org.biojava.nbio.genome.homology.BlastHomologyHits
-
- getMatchingAtomRes(Chain, List<Chain>, boolean) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
-
- getMatMatrix() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
Caution: this matrix is overwriten with very different data at several
points in the alignment algorithm.
- getMatMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
Caution: this matrix is overwriten with very different data at several
points in the alignment algorithm.
- getMatrices() - Method in class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser
-
- getMatrix(String) - Method in interface org.biojava.nbio.core.alignment.matrices.AAIndexProvider
-
- getMatrix(String) - Method in class org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider
-
- getMatrix() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getMatrix() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
-
- getMatrix() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
-
Returns entire matrix.
- getMatrix() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- getMatrix() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- getMatrix() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix(int, int, int, int) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get a submatrix.
- getMatrix(int[], int[]) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get a submatrix.
- getMatrix(int, int, int[]) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get a submatrix.
- getMatrix(int[], int, int) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get a submatrix.
- getMatrix11() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix11() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getMatrix12() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix12() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getMatrix13() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix13() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getMatrix21() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix21() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getMatrix22() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix22() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getMatrix23() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix23() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getMatrix31() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix31() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getMatrix32() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix32() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getMatrix33() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix33() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getMatrixAsString() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getMatrixAsString() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
-
- getMatrixAsString() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
-
Returns this matrix as a formatted String with
Compound labels along the axes.
- getMatrixFromAAINDEX(String) - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns any matrix from the AAINDEX database file
- getMatrixFromAlgebraic(String) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getMatrixPanel() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- getMatTransform() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
- getMax() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getMax() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
-
- getMax(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Scans through a list of locations to find the Location with the
highest end
- getMax(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
-
Scans through a list of locations to find the Location with the
highest end
- getMaxAtoms() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
The maximum numbers of atoms to load in a protein structure (prevents memory overflows)
- getMaxDimension() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
Gets the maximum dimension of the unit cell.
- getMaxExtension() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns the maximum extension (length) of structure
- getMaxExtension() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
Returns the maximum extension (length) of structure
- getMaxGap() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getMaxGapFrag() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getMaxGapSize() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
the Max gap size parameter G . default is 30, which was
described to obtained empirically in the CE paper.
- getMaxGapSize() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
CE specific parameter: set the Max gap size parameter G (during AFP extension).
- getMaximumCovalentValence() - Method in enum org.biojava.nbio.structure.Element
-
Returns the maximum valence for this Element.
- getMaximumExtend(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
-
Returns the maximum extend of the structure in the x, y, or z direction.
- getMaximumLocalCombinations() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getMaximumSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
-
- getMaximumValence() - Method in enum org.biojava.nbio.structure.Element
-
Returns the maximum valence for this Element.
- getMaxIter() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getMaxNrIterationsForOptimization() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Get the maximum nr of times the (slow) optimiziation of alignment should iterate.
- getMaxNrSuggestions() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
-
Get the maximun nr of suggestions
- getMaxNrSuggestions() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
-
- getMaxNrSuggestions() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
-
- getMaxOptRMSD() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)
- getMaxOptRMSD() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
(jCE specific): maximum RMSD that shall be calculated for the alignment.
- getMaxOrientationAngle() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
-
The maximum orientation angle between two equivalent Subunits, in
radians.
- getMaxPenalty() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getMaxPropeller() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.
- getMaxPropeller() - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
-
This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.
- getMaxrefine() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getMaxRmsd() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters
-
The maximum allowed RMSD of the alignment, in A.
- getMaxRmsd() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getMaxRmsd() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- getMaxRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getMaxScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
-
- getMaxScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
-
- getMaxScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getMaxScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
-
- getMaxScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getMaxScore() - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns maximum possible score.
- getMaxShear() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This method returns the maximum shear between bases used as criteria for the characterization of two bases as being paired.
- getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- getMaxSingleCompoundStringLength() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
-
Returns the maximum size of a compound String this set holds
- getMaxStagger() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This method returns the maximum stagger between bases used as criteria for the characterization of two bases as being paired.
- getMaxStagger() - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
-
This method returns the maximum stagger between bases used as criteria for the characterization of two bases as being paired.
- getMaxStretch() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This method returns the maximum stretch between bases used as criteria for the characterization of two bases as being paired.
- getMaxSymmOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getMaxTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getMaxTra() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
get the maximum number of Twists that are allowed...
- getMaxTra() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- getMaxTra() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
get the maximum nr of Twists that are allowed...
- getMaxValue() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getMaxValue() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
-
- getMaxValue() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
-
Returns the maximum value in this matrix.
- getMCScore(MultipleAlignment, double, double, double) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
-
Calculates the MC score, specific for the MultipleAlignment algorithm.
- getMean() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the mean property.
- getMean() - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Gets the value of the mean property.
- getMean() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the mean property.
- getMean() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the mean property.
- getMean() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getMeanExtension() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
Returns the mean extension (length) of structure
- getMembers() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
- getMembership() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getMessage() - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
-
- getMetaDataColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getMetaDataColumnsHashMap() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getMetaDataFilter() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getMetaDataRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getMetaDataRowsHashMap() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getMetalBondDefinitions() - Static method in class org.biojava.nbio.structure.io.mmcif.MetalBondParser
-
- getMethod() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
-
- getMethod() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getMethod() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getMethod_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getMethod_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
Returns the radius of a sphere, that is tangent to each
of the icosahedron's edges
- getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
Returns the radius of a sphere, that is tangent to each
of the octahedron's edges
- getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
Returns the radius of a sphere, that is tangent to each
of the tetrahedron's edges
- getMin() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getMin() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
-
- getMin(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Scans through a list of locations to find the Location with the
lowest start
- getMin(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
-
Scans through a list of locations to find the Location with the
lowest start
- getMinAlignedStructures() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- getMinBlockLen() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- getMinCoreLength() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getMinCPLength() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- getMinCPLength() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
-
- getMindiff() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the mindiff property.
- getMindiff() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the mindiff property.
- getMinDistance() - Method in class org.biojava.nbio.structure.contact.GroupContact
-
- getMinimumHelixAngle() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getMinimumHelixRise() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getMinimumSequenceLength() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Get the minimum number of residues of a subunits to be considered in the
clusters.
- getMinimumSequenceLengthFraction() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
If the shortest subunit sequence length is higher or equal the
minimumSequenceLengthFraction times the median subunit sequence length,
then the minimumSequenceLength is set to shortest subunit sequence
length, but not shorter than the absoluteMinimumSequenceLength.
- getMinimumSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
-
- getMinimumValence() - Method in enum org.biojava.nbio.structure.Element
-
Returns the minimum valence for this Element.
- getMinLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getMinLen() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getMinLen() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- getMinMax(double[]) - Method in class org.biojava.nbio.structure.contact.BoundingBox
-
Returns an array of size 2 with min and max values of given double array
- getMinor_revision() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxAuditRevisionHistory
-
- getMinRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getMinScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
-
- getMinScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
-
- getMinScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getMinScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
-
- getMinScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getMinScore() - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns minimum possible score.
- getMinTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getMinValue() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getMinValue() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
-
- getMinValue() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
-
Returns the minimum value in this matrix.
- getMirrors() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getMisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getMisLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getMismatchCount() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getMisScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getMMcifConsumer() - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
-
- getMod_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- getModDate() - Method in class org.biojava.nbio.structure.PDBHeader
-
Return the latest modification date of the structure.
- getModel(int) - Method in class org.biojava.nbio.ronn.ModelLoader
-
- getModel(int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve all Chains belonging to a model .
- getModel(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Retrieve all Chains belonging to a model .
- getModel() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the model property.
- getModel_Cartn_x() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getModel_Cartn_y() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getModel_Cartn_z() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getModelledSubgroup() - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
-
Gets the value of the modelledSubgroup property.
- getModelNumber() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
This method is provisional and should only be used for coloring Subunits.
- getModelVariables() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
-
- getModelVariables() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
-
- getModification() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
- getModification() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- getModType() - Method in class org.biojava.nbio.phosphosite.Site
-
- getMogAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the mogAngleOutlier property.
- getMogBondOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the mogBondOutlier property.
- getMogulIgnore() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the mogulIgnore property.
- getMolecularWeight(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the molecular weight of sequence.
- getMolecularWeight(ProteinSequence, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the molecular weight of sequence.
- getMolecularWeight(ProteinSequence, File, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the molecular weight of sequence.
- getMolecularWeight(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the molecular weight of sequence.
- getMolecularWeight(String, File, File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the molecular weight of sequence.
- getMolecularWeight(String, File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the molecular weight of sequence.
- getMolecularWeight(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getMolecularWeight(ProteinSequence, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getMolecularWeight(ProteinSequence, File, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getMolecularWeight(Character) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
-
- getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- getMolecularWeight() - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the molecular weight of sequence.
- getMolecularWeightBasedOnXML(String, AminoAcidCompositionTable) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method that returns the molecular weight of sequence.
- getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getMolecule() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getMoleculeIds() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Return the pair of identifiers identifying each of the 2 molecules of this interface
in the asymmetry unit (usually the chain identifier if this interface is between 2 chains)
- getMolecules() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getMoleculeType() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
-
Molecule type this represents the type of molecule as stored
- getMolId() - Method in class org.biojava.nbio.structure.EntityInfo
-
Return the molecule identifier, called entity_id in mmCIF dictionary.
- getMomentsOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getMon_nstd_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getMon_nstd_parent_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getMTranspose() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getMultiBlockJmolString(MultipleAlignment, List<Atom[]>, ColorBrewer, boolean) - Static method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
-
Colors every Block of the structures with a different color, following
the palette.
- getMultipleAlignment() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
-
- getMultipleAlignment() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
-
- getMultipleAlignment() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
-
Returns the parent MultipleAlignment of the BlockSet.
- getMultipleAlignment() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
-
- getMultipleAlignment(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Returns the MultipleAlignments at the specified index
in the ensemble.
- getMultipleAlignment(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
-
- getMultipleAlignment() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
The multiple alignment is calculated from the equivalent residues in the
SubunitCluster.
- getMultipleAlignment() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
- getMultipleAlignmentMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getMultipleAlignments() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Returns the List of MultipleAlignments in the ensemble.
- getMultipleAlignments() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
-
- getMultipleSequenceAlignment(List<S>, Object...) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method which computes a multiple sequence alignment for the given
List of
Sequences.
- getMultipleStructureAligner() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
-
- getMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getMutation() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getN() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Get N atom.
- getN() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Get N atom.
- getNaive_imat() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getNaiveVariance() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getName() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- getName() - Method in class org.biojava.nbio.aaproperties.xml.Element
-
- getName() - Method in class org.biojava.nbio.aaproperties.xml.Isotope
-
- getName() - Method in class org.biojava.nbio.aaproperties.xml.Name2Count
-
- getName() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getName() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Returns the name of this node.
- getName() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getName() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
-
- getName() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
-
Returns the name (short description) of this matrix.
- getName() - Method in class org.biojava.nbio.core.sequence.features.Qualifier
-
- getName() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
-
- getName() - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- getName() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
-
- getName() - Method in interface org.biojava.nbio.ontology.Ontology
-
Return the name of this ontology
- getName() - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- getName() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- getName() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
-
- getName() - Method in class org.biojava.nbio.ontology.Synonym
-
- getName() - Method in interface org.biojava.nbio.ontology.Term
-
Return the name of this term.
- getName() - Method in class org.biojava.nbio.ontology.Term.Impl
-
- getName() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getName() - Method in interface org.biojava.nbio.structure.Atom
-
Get atom name, e.g.
- getName() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get atom name, e.g.
- getName() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getName() - Method in interface org.biojava.nbio.structure.Chain
-
Get the 'public' authId (chain ID in PDB file)
- getName() - Method in class org.biojava.nbio.structure.ChainImpl
-
Get the 'public' authId (chain ID in PDB file)
- getName() - Method in class org.biojava.nbio.structure.cluster.Subunit
-
The Name of a Subunit is a free-text field, user defined.
- getName() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique
-
- getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
-
- getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getName() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getName() - Method in class org.biojava.nbio.structure.rcsb.RCSBMacromolecule
-
- getName() - Method in class org.biojava.nbio.structure.rcsb.RCSBTaxonomy
-
- getName() - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- getName() - Method in interface org.biojava.nbio.structure.Structure
-
Get biological name of Structure.
- getName() - Method in class org.biojava.nbio.structure.StructureImpl
-
Get biological name of Structure.
- getName() - Method in class org.biojava.nbio.structure.validation.Program
-
Gets the value of the name property.
- getName() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
-
- getName() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getName() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getName1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getName1() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
-
- getName1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getName1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getName2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getName2() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
-
- getName2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getName2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getNames() - Method in class org.biojava.nbio.structure.gui.util.SelectMultiplePanel
-
- getNames() - Method in class org.biojava.nbio.structure.scop.Astral
-
- getnAtom() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getnAtom() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getNatomsEDS() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the natomsEDS property.
- getNaturalPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getNavMap() - Method in class org.biojava.nbio.structure.AtomPositionMap
-
- getNcbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- getNcens() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getNclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- getNcsAsArray(Matrix4d[]) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get a list of length N*16 of a list of Matrix4d*N.
- getNcsAsMatrix4d(double[][]) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get a list of N 4*4 matrices from a single list of doubles of length 16*N.
- getNcsOperators() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Get the NCS operators.
- getNcuts() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
-
- getNdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getNdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getNdead() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getNdom() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getNearestAtRisk(double) - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
Selection of number of risk will depend on the precision and rounding of
time in the survival table.
- getNearestTime(double) - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
Need to find the actual time for the nearest time represented as a
percentage Would be used to then look up the number at risk at that
particular time
- getNeighbors(Point3d) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
-
- getNeighborsWithCache(Point3d) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
-
- getNestedValue(NestedValue, String, int) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
-
- getNetCharge(ProteinSequence, boolean, double) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the net charge of sequence at pH 7.
- getNetCharge(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
- getNetCharge(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
- getNetCharge(String, boolean, double) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the net charge of sequence at pH 7.
- getNetCharge(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
- getNetCharge(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
- getNetCharge(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getNetCharge(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getNetCharge(ProteinSequence, boolean, double) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getNeutronsNum() - Method in class org.biojava.nbio.aaproperties.xml.Isotope
-
- getNevent() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getNewDocument() - Static method in class org.biojava.nbio.core.util.XMLHelper
-
- getNewickString(Phylogeny, boolean) - Static method in class org.biojava.nbio.phylo.ForesterWrapper
-
Convert a Phylogenetic tree to its Newick representation, so that it can
be exported to an external application.
- getNext() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
-
- getNMRStructures() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
-
get list of all current NMR structures
- getNodeId() - Method in class org.biojava.nbio.structure.cath.CathNode
-
- getNodeListFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getNoiseCutoffs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
Not always 2.
- getNonenantpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getNonPolyChain(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a non-polymeric Chain based on the 'internal' chain
id (asymId) for the first model
- getNonPolyChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a non-polymeric Chain based on the 'internal' chain
id (asymId) for the given model index
- getNonPolyChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getNonPolyChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getNonPolyChains() - Method in class org.biojava.nbio.structure.Model
-
- getNonPolyChains() - Method in interface org.biojava.nbio.structure.Structure
-
Return all non-polymeric chains for the first model
- getNonPolyChains(int) - Method in interface org.biojava.nbio.structure.Structure
-
Return all non-polymeric chains for the given model index.
- getNonPolyChains() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getNonPolyChains(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getNonPolyChainsByPDB(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve all non-polymeric Chains corresponding to the given 'public' chain
name (authId) for the first model.
- getNonPolyChainsByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve all non-polymeric Chains corresponding to the 'public' chain
name (authId) and the given model index.
- getNonPolyChainsByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getNonPolyChainsByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getNormAlignScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getNotesList() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getNotObserved() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getNrAlignments() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getNrAtoms(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Count how many Atoms are contained within a Structure object.
- getNrBioAssemblies() - Method in class org.biojava.nbio.structure.PDBHeader
-
Get the number of biological assemblies available in the PDB header
- getNrCPU() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getNreported() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getNrEQR() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Get the number of structurally equivalent residues
- getNrGroups(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Count how many groups are contained within a structure object.
- getNrisk() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getNrThreads() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- getNseg() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- getnStart() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getNStart() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
Returns the number of starts if this rotation represents a helical rotation
- getNstd_chirality() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPoly
-
- getNstd_linkage() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPoly
-
- getNstd_monomer() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPoly
-
- getNuc4_2() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Nuc 4.2 matrix by Lowe
Only the first nucleotide sequence to align can contain ambiguous nucleotides
- getNuc4_4() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns Nuc 4.4 matrix by Lowe
Both of the nucleotide sequences to align can contain ambiguous nucleotides
- getNucleicChains(boolean) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method reports all the nucleic acid chains and has an option to remove duplicates if you
are considering an analysis of only unique DNA or RNA helices in the Structure.
- getNucleotides() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
-
- getNullValue() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
-
- getNum() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- getNum() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- getNumAtomContacts() - Method in class org.biojava.nbio.structure.contact.GroupContact
-
- getNumberCoefficients() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getNumberDiscreteValues() - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
-
- getNumberOfInvalidChar(String, Set<Character>, boolean) - Static method in class org.biojava.nbio.aaproperties.Utils
-
Return the number of invalid characters in sequence.
- getNumberVariables() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getNumBonds() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean
-
- getNumBondsInGroup(List<Atom>) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Find the number of bonds in a group
- getNumericalBondOrder() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
Converts this ChemCompBond's value_order attribute into an int using the
conversion:
SING -> 1
DOUB -> 2
TRIP -> 3
QUAD -> 4
Any other values will return -1.
- getNumericRepresentation() - Method in enum org.biojava.nbio.core.sequence.Strand
-
- getNumFreeReflections() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the numFreeReflections property.
- getNumGapPositions() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getNumGapPositions() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Returns number of gap positions (gap openings and extensions) in the sequence.
- getNumGaps() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getNumGaps() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Returns number of gaps (gap openings) in the sequence.
- getNumGroups(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Count the total number of groups in the structure
- getNumHReduce() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the numHReduce property.
- getNumHReduce() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the numHReduce property.
- getNumIdenticals() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
-
- getNumIdenticals() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
-
Returns the number of indices for which both the query and target sequences have an identical
Compound.
- getNumIindices() - Method in class org.biojava.nbio.structure.contact.GridCell
-
- getNumJindices() - Method in class org.biojava.nbio.structure.contact.GridCell
-
- getNumLeft() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
-
- getNumLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getNumMillerIndices() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the numMillerIndices property.
- getNumobs() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the numobs property.
- getNumobs() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the numobs property.
- getNumOperators() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets the number of symmetry operators corresponding to this SpaceGroup (counting
the identity operator)
- getNumRepeats() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
Return the symmetry order determined by the order detector if the
symmetry is significant.
- getNumRepeats() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Get the number of repeats.
- getNumRes() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getNumSequences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getNumSimilars() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
-
- getNumSimilars() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
-
Returns the number of indices for which both the query and target sequences have a similar
Compound.
- getO() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Get O atom.
- getO() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Get O atom.
- getO3Prime() - Method in class org.biojava.nbio.structure.NucleotideImpl
-
Returns the O3' atom if present, otherwise null
- getO5Prime() - Method in class org.biojava.nbio.structure.NucleotideImpl
-
Returns the O5' atom if present, otherwise null
- getObject() - Method in interface org.biojava.nbio.ontology.Triple
-
Return the object term of this triple.
- getObject() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getOboFileEventListener() - Method in class org.biojava.nbio.ontology.obo.OboFileParser
-
- getObs() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the obs property.
- getObs() - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Gets the value of the obs property.
- getObsoleteBehavior() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns how this instance deals with obsolete entries.
- getObsoleteBehavior() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getObsoleteBehavior() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Returns how this instance deals with obsolete entries.
- getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Location of obsolete files within the directory, as an array of paths.
- getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
-
- getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.MMTFFileReader
-
- getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader
-
- getObsval() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the obsval property.
- getObsval() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the obsval property.
- getOccupancy() - Method in interface org.biojava.nbio.structure.Atom
-
Get occupancy.
- getOccupancy() - Method in class org.biojava.nbio.structure.AtomImpl
-
- getOccupancy() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getOccupancy_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getOccupancy_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOccupancy_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOccurrenceType() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getOccurrenceType() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getOffset() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getOligomeric_count() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- getOligomeric_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- getOmega() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getOmimId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getOne() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getOne() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
-
- getOne() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getOne_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getOneLetterCode(ChemComp, ChemicalComponentDictionary) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
-
- getOneLetterCode(ChemComp) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
-
- getOnelineFasta() - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
- getOntology() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
-
- getOntology() - Method in interface org.biojava.nbio.ontology.OntologyTerm
-
Get the remote ontology referenced by this term
- getOntology() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- getOntology() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
-
- getOntology() - Method in interface org.biojava.nbio.ontology.Term
-
Return the ontology in which this term exists.
- getOntology() - Method in class org.biojava.nbio.ontology.Term.Impl
-
- getOntology() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getOpening(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the opening in degrees for the given base pair
- getOpenPDBMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getOpenPenalty() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
-
Returns the negative of the opening penalty passed to the constructor.
- getOpenPenalty() - Method in interface org.biojava.nbio.alignment.template.GapPenalty
-
Returns penalty given when a deletion or insertion gap first opens
- getOper_expression() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
-
- getOperator() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
Get the transformation operator for this axis as an homogeneous matrix
- getOps() - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- getOps() - Method in interface org.biojava.nbio.ontology.Ontology
-
Return the associated OntologyOps.
- getOps() - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- getOptAln() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Tracks the Atom positions in the optimal alignment.
- getOptAlnAsList(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Retrieves the optimum alignment from an AFPChain and returns it as a
java collection.
- getOptimization() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getOptimizationSteps() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getOptLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The length of each block
- getOptLength() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getOptRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getOrbits() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getOrbits() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getOrbits() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getOrder() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
-
- getOrder(List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
-
- getOrder() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- getOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
Get the order of this axis (closed symm) or the number of repeats
(open symm)
- getOrder() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getOrderDetectorMethod() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getOrderedPairs() - Method in class org.biojava.nbio.structure.quaternary.CartesianProduct
-
Generates the list of ordered pair between two sets.
- getOrdinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxAuditRevisionHistory
-
- getOrgan() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getOrGanelle() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The OG (OrGanelle) linetype indicates the sub-cellular location of non-nuclear
sequences.
- getOrganelle() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getOrganism() - Method in class org.biojava.nbio.phosphosite.Site
-
- getOrganism_common_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- getOrganism_scientific() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- getOrganismClassification() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The OC (Organism Classification) lines contain the taxonomic classification
Of the source organism
- getOrganismCommon() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getOrganismName() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Get the organism name assigned to this sequence
- getOrganismScientific() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getOrganismSpecies() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The OS (Organism Species) line specifies the preferred scientific name of
the organism which was the source of the stored sequence.
- getOrganismTaxId() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getOrientation() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that sets a specific orientation
- getOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
- getOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns the number of orientations available for this structure
- getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
-
- getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
-
- getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
-
- getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
- getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getOrientationMatrix() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
The orientation Matrix is a 3x3 Matrix with a column for each principal
axis.
- getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns the name of a specific orientation
- getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
-
Returns the name of a specific orientation
- getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
-
Returns the name of a specific orientation
- getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns the name of a specific orientation
- getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getOrientationWithZoom(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that sets a specific orientation and zoom
to draw either axes or polyhedron
- getOrientationWithZoom(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script that sets a specific orientation and zoom
to draw either axes or polyhedron
- getOrientationWithZoom(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getOrigGroup() - Method in interface org.biojava.nbio.structure.SeqMisMatch
-
- getOrigGroup() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
-
- getOriginalCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getOriginalHeader() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getOriginalMetaData(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getOriginalSequence() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getOriginalSequence() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Returns the original
Sequence before alignment.
- getOriginalSequences() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getOriginalSequences() - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
Returns a
List containing the original
Sequences used for alignment.
- getORmsdThr() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Get the Original RMSD threshold from which the alignment optimization is started
- getOrthologousSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getOther(Atom) - Method in interface org.biojava.nbio.structure.Bond
-
A utility method to get the other atom in a bond, given one of its atoms.
- getOther(Atom) - Method in class org.biojava.nbio.structure.BondImpl
-
A utility method to get the other atom in a bond, given one of its atoms.
- getOutFile() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- getOutFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getOutFile() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getOutFileLocation() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- getOutputFormat() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
- getOutputOption(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
- getOutputOption(BlastOutputParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
Gets the value of specified parameter or null if it is not set
- getOutputOption(String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties
-
Method that returns the value associated with the key given in parameter.
- getOutputOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
Gets output parameters, which are currently set
- getOutputOptions() - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties
-
Method to get all keys to the information stored in this object.
- getOverall_FOM_free_R_set() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOverall_FOM_work_R_set() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOverall_SU_B() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOverall_SU_ML() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOverall_SU_R_Cruickshank_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOverall_SU_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOverallModelFitPvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getOverlapCount() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getOverlapCount() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Returns the maximum number of elements contributed to a column of an alignment by this
Sequence.
- getOverlapLength(HmmerResult) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
Get the overlap between two HmmerResult objects
- getOwab() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the owab property.
- getOxidationState() - Method in enum org.biojava.nbio.structure.Element
-
Returns a typical oxidation state for this Element.
- getP() - Method in class org.biojava.nbio.structure.NucleotideImpl
-
Returns the P atom if present, otherwise null
- getP1() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getP2() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getPair() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getPair() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getPair() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceAligner
-
Returns sequence alignment pair.
- getPair() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileAligner
-
Returns alignment profile pair.
- getPair() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- getPair() - Method in class org.biojava.nbio.structure.contact.AtomContact
-
- getPair() - Method in class org.biojava.nbio.structure.contact.GroupContact
-
- getPairingNames() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the names of the pairs in terms of A, G, T/U, and C for each base pair group in the
list.
- getPairingParameters() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method reports all the pair parameters, in the order of:
buckle, propeller, opening (in degrees), shear, stagger, stretch (in Å).
- getPairInProfileScorer() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getPairInProfileScorer() - Method in interface org.biojava.nbio.alignment.template.RescoreRefiner
-
Returns class type of pairwise scoring subroutine.
- getPairs() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
-
- getPairSequence() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the primary strand's sequence where parameters were found.
- getPairwiseAligner(S, S, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method which constructs a pairwise sequence aligner.
- getPairwiseAlignment(S, S, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method which computes a sequence alignment for the given
Sequence pair.
- getPairwiseAlignmentMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getPairwiseStructureAligner() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
-
- getPAM250() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper
-
Returns PAM 250 matrix by Dayhoff
- getPanelPos(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
get the position of the sequence position on the Panel
- getPanelPos(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Get the X position on the Panel of a particular sequence position.
- getPanelPos(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
-
- getPara(int, int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
-
- getParameters() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
-
- getParameters() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeMain
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
-
- getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
-
- getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
-
- getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
-
- getParameters() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
-
- getParameters() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner
-
Return the parameters of this algorithm instance.
- getParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
-
- getParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
-
- getParameters() - Method in interface org.biojava.nbio.structure.align.StructureAlignment
-
Return the paramers for this algorithm.
- getParameters() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
-
- getParams() - Method in class org.biojava.nbio.structure.align.FarmJob
-
- getParams() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
get the parameters.
- getParams() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
- getParent() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getParent() - Method in interface org.biojava.nbio.structure.Chain
-
- getParent() - Method in class org.biojava.nbio.structure.ChainImpl
-
- getParent() - Method in class org.biojava.nbio.structure.DBRef
-
Get the structure object that this DBRef relates to.
- getParent(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
Get the parent of a component.
- getParentChains() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Finds the parent chains by looking up the references of first atom of each side of this interface
- getParentChromosomeSequence() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
The parent ChromosomeSequence which contains the actual DNA sequence data
- getParentCompounds() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Finds the parent compounds by looking up the references of first atom of each side of this interface
- getParentFeature() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
Get the parent Feature
- getParentFeature() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getParentFeature() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Get the parent feature
- getParentId() - Method in class org.biojava.nbio.structure.cath.CathNode
-
- getParentSequence() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getParentSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode
-
- getPartner() - Method in class org.biojava.nbio.structure.secstruc.HBond
-
- getPartner1() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
-
- getPartner2() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
-
- getPath() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getPath() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- getPath() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getPath() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Get the path that is used to cache PDB files.
- getPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Returns the path value.
- getPathSize() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getPathSize() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getPaulingElectronegativity() - Method in enum org.biojava.nbio.structure.Element
-
Returns the Pauling electronegativity for this Element.
- getPdb1() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getPdb1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getPdb2() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getPdb2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getPdb_format_compatible() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus
-
- getPdb_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdb_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdb_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdbAln() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
used temporarily during XML serialization to track the PDB positions of the alignmnet
- getPdbccId() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getPdbccId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getPdbccIds() - Method in class org.biojava.nbio.protmod.Component
-
- getPdbccName() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getPdbccName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getPdbChainIdClusters() - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
-
- getPdbChainIdClusters(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
-
- getPDBCharacter(boolean, char, char, boolean, char) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Creates formatted String for a single character of PDB output
- getPDBCode() - Method in interface org.biojava.nbio.structure.Structure
-
Get PDB code of structure.
- getPDBCode() - Method in class org.biojava.nbio.structure.StructureImpl
-
Get PDB code of structure.
- getPDBCode1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getPDBCode2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getPDBConservation(boolean, char, char, boolean) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Creates formatted String for displaying conservation in PDB output
- getPDBDirField() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
-
- getPdbEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getPdbFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getPdbFilePath() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getPdbFilePath() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getPdbGroup() - Method in interface org.biojava.nbio.structure.SeqMisMatch
-
- getPdbGroup() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
-
- getPDBHeader() - Method in interface org.biojava.nbio.structure.Structure
-
Return the header information for this PDB file
- getPDBHeader() - Method in class org.biojava.nbio.structure.StructureImpl
-
Return the header information for this PDB file
- getPdbId() - Method in class org.biojava.nbio.structure.align.client.StructureName
-
Get the PDB ID for this name, if any.
- getPdbId() - Method in class org.biojava.nbio.structure.domain.PDPDomain
-
- getPdbId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getPdbId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getPdbId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getPdbId() - Method in class org.biojava.nbio.structure.rcsb.RCSBDescription
-
- getPdbId() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigands
-
- getPdbId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getPdbId() - Method in interface org.biojava.nbio.structure.Structure
-
- getPdbId() - Method in class org.biojava.nbio.structure.StructureImpl
-
Deprecated.
- getPdbId() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
-
- getPdbIdAndChain() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
Returns a string of the form PDBID.CHAIN.
- getPdbInfo(Atom) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools
-
get jmol style info:
jmol style: [MET]508:A.CA/1 #3918
insertion code: [ASP]1^A:A.CA/1 #2
- getPdbInfo(Atom, boolean) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools
-
- getPDBLegend() - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Creates formatted String for displaying conservation legend in PDB output
- getPDBName() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- getPDBName() - Method in interface org.biojava.nbio.structure.Group
-
Get the PDB 3-letter name for this group.
- getPDBName() - Method in class org.biojava.nbio.structure.HetatomImpl
-
Returns the PDBName.
- getPDBNameOfPotentialAtomsOnComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getPDBNameOfPotentialAtomsOnComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getPdbPairs(String, int, String) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getPDBResidueNumber() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- getPdbResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getPDBresnum(int, AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
Return a list of pdb Strings corresponding to the aligned positions of the molecule.
- getPDBresnum(int, MultipleAlignment, Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
-
Utility method used in the
MultipleAlignmentJmol Frame,
when the aligned residues of a structure in the alignment have
to be selected for formatting them (coloring and style).
- getPdbResNum() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getPdbResNum() - Method in interface org.biojava.nbio.structure.SeqMisMatch
-
- getPdbResNum() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
-
- getPDBresnum1() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- getPDBresnum2() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- getPDBRevisionNumber() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the pdbRevisionNumber property.
- getPDBserial() - Method in interface org.biojava.nbio.structure.Atom
-
Get PDB atom number.
- getPDBserial() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get PDB atom number.
- getPdbSerial() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
-
- getPdbStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getPDBUploadPanel() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- getPdbx_align() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_align_begin() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getPdbx_alt_source_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_alt_source_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_ambiguous_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_aromatic_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_aromatic_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getPdbx_atcc() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_auth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
-
- getPdbx_auth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
-
- getPdbx_auth_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getPdbx_auth_seq_align_beg() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_auth_seq_align_end() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_auth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
-
- getPdbx_auth_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getPdbx_beg_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_beg_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_blank_PDB_chainid_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- getPdbx_CASP_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- getPdbx_cell() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_cell_line() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_cellular_location() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_component_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_component_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_component_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_data_cutoff_high_absF() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_data_cutoff_high_rms_absF() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_data_cutoff_low_absF() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_db_accession() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getPdbx_db_accession() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_db_align_beg_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_db_align_end_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_description() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getPdbx_description() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_descriptor() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- getPdbx_diffrn_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_dist_value() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ec() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getPdbx_end_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_end_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_evidence_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
-
- getPdbx_formal_charge() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getPdbx_formal_charge() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_fragment() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getPdbx_fragment() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_full_space_group_name_H_M() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- getPdbx_gene_src_atcc() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_cell() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_cell_line() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_cellular_location() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_fragment() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_gene() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_ncbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_organ() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_organelle() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_plasmid() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_plasmid_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_scientific_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_variant() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_atcc() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_cell() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_cell_line() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_cellular_location() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_culture_collection() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_gene() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_ncbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_organ() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_organelle() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_scientific_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_strain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_tissue() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_tissue_fraction() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_variant() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_vector() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_vector_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_ideal_coordinates_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_ideal_coordinates_missing_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_initial_date() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_isotropic_thermal_model() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_keywords() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
-
- getPdbx_leaving_atom_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_leaving_atom_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_leaving_atom_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ls_cross_valid_method() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_ls_sigma_F() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_ls_sigma_I() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_method_to_determine_struct() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_model_Cartn_x_ideal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_model_Cartn_y_ideal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_model_Cartn_z_ideal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_model_coordinates_db_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_model_coordinates_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_model_coordinates_missing_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_model_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- getPdbx_model_type_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- getPdbx_modified() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- getPdbx_modified_date() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_mutation() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getPdbx_ncbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_num_res() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getPdbx_num_residues() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSite
-
- getPdbx_number_of_molecules() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
-
- getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getPdbx_organ() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_organelle() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_organism_scientific() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_overall_ESU_R() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_ESU_R_Free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_phase_error() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_SU_R_Blow_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_SU_R_free_Blow_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_SU_R_free_Cruickshank_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_PDB_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_PDB_id_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_pdb_id_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getPdbx_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getPdbx_pdb_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getPdbx_PDB_model_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getPdbx_pdb_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getPdbx_plasmid_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_plasmid_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_polymer_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_processing_site() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_ptnr1_label_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr1_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr1_standard_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr2_label_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr2_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr3_label_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr3_label_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr3_label_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr3_label_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr3_label_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr3_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_R_Free_selection_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_ref_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_refine_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_release_status() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_replaced_by() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_replaces() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_residue_numbering() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_secretion() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_seq_align_beg_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_seq_align_end_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_seq_db_accession_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getPdbx_seq_db_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getPdbx_seq_db_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getPdbx_seq_one_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPoly
-
- getPdbx_seq_one_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getPdbx_seq_one_letter_code_can() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPoly
-
- getPdbx_seq_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_solvent_ion_probe_radii() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_solvent_shrinkage_radii() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_solvent_vdw_probe_radii() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_src_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_src_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_starting_model() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_stereo_config() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_stereo_config() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getPdbx_stereochem_target_val_spec_case() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_stereochemistry_target_values() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPoly
-
- getPdbx_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_subcomponent_list() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_synonyms() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_target_identifier() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPoly
-
- getPdbx_TLS_residual_ADP_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_unique_axis() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getPdbx_value_order() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_variant() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbxStructAssemblies() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
-
- getPdbxStructAssemblyGens() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
-
- getPdbxStructOperLists() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
-
- getPDPDomain(String) - Method in interface org.biojava.nbio.structure.domain.PDPProvider
-
Get a StructureIdentifier representing the specified PDP domain.
- getPDPDomain(String) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider
-
Get a StructureIdentifier representing the specified PDP domain.
- getPDPDomainNamesForPDB(String) - Method in interface org.biojava.nbio.structure.domain.PDPProvider
-
Get a list of all PDP domains for a given PDB entry
- getPDPDomainNamesForPDB(String) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider
-
Get a list of all PDP domains for a given PDB entry
- getPdpprovider() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getPercentage() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
-
- getPercentageIdentity() - Method in class org.biojava.nbio.core.search.io.Hsp
-
- getPercentageOfIdentity(boolean) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
-
Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.
- getPercentageOfIdentity(boolean) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
-
Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.
- getPercentFreeReflections() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the percentFreeReflections property.
- getPercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the percentRamaOutliers property.
- getPercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the percentRotaOutliers property.
- getPercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the percentRSRZOutliers property.
- getPercId() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- getPeriod() - Method in enum org.biojava.nbio.structure.Element
-
Returns the period in the periodic table of this Element.
- getPermutation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getPermutation(int) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
-
- getPermutation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getPermutationSize() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getPfamAccession() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getPhase() - Method in class org.biojava.nbio.core.sequence.CDSSequence
-
- getPhase() - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos
-
- getPhi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc
-
Calculate the phi angle.
- getPhi() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getPhi() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the phi property.
- getPivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
-
Return pivot permutation vector
- getPlasmid_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPlasmid_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPmid() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the value of PMID field.
- getPointGroup() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- getPolarityOfAminoAcid(char) - Static method in class org.biojava.nbio.aaproperties.AminoAcidProperties
-
There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
- getPolarityOfAminoAcids(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
Returns the array of polarity values of each amino acid in a protein sequence.
- getPolyChain(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a polymeric Chain based on the 'internal' chain
id (asymId) for the first model
See
Structure.getPolyChainByPDB(String) for a similar
method using the chain name (authId).
- getPolyChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
- getPolyChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPolyChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPolyChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a polymeric Chain based on the 'public' chain
name (authId) for the first model
See
Structure.getPolyChain(String) for a similar
method using the chain id (asymId).
- getPolyChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a polymeric Chain based on the 'public' chain
name (authId) for the given model index.
- getPolyChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPolyChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPolyChains() - Method in class org.biojava.nbio.structure.Model
-
- getPolyChains() - Method in interface org.biojava.nbio.structure.Structure
-
Return all polymeric chains for the first model
- getPolyChains(int) - Method in interface org.biojava.nbio.structure.Structure
-
Return all polymeric chains for the given model index.
- getPolyChains() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPolyChains(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPolygonVertices(int, double, Point3d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
Returns the vertices of an n-fold polygon of given radius and center
- getPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getPolymers() - Method in class org.biojava.nbio.structure.rcsb.RCSBDescription
-
- getPolymerType() - Method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType
-
Gets the associated PolymerType, which are less specific
- getPolymerType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPos() - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos
-
- getPos(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
- getPos1() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getPos1() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
- getPos2() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getPos2() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
- getPosition() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
-
- getPosition() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
-
- getPosition() - Method in interface org.biojava.nbio.core.sequence.location.template.Point
-
Returns the position held by this object
- getPosition(ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
Gets the 0-based index of residueNumber to the matched atoms
- getPositionInQueue(String, String, String, String) - Method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getPositionInQueue(String, String, String, String, int) - Method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getPredicate() - Method in interface org.biojava.nbio.ontology.Triple
-
Return a Term which defines the type of relationship between the subject and object terms.
- getPredicate() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getPredominantGroupType() - Method in interface org.biojava.nbio.structure.Chain
-
Get the predominant
GroupType for a given Chain, following these
rules: if the ratio of number of residues of a certain
GroupType to total non-water residues is above the threshold
, then that
GroupType is
returned if there is no
GroupType that is above the
threshold then the
GroupType with most members is chosen, logging
it
See also
ChemComp.getPolymerType() and
ChemComp.getResidueType() which follow the PDB chemical component
dictionary and provide a much more accurate description of groups and
their linking.
- getPredominantGroupType() - Method in class org.biojava.nbio.structure.ChainImpl
-
- getPredominantGroupType(Chain) - Static method in class org.biojava.nbio.structure.StructureTools
-
- getPreferredHeight() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
Y coordinate size
- getPreferredHeight() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Y coordinate size
- getPreferredSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
-
- getPreferredWidth() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
X coordinate size
- getPreferredWidth() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
X coordinate size
- getPreviousIDs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getPreviousNames() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getPreviousSymbols() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getPrimaryAccession() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
-
- getPrimitiveMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getPrincipalAxes() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
The principal axes of intertia
- getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getPrincipalAxisIndex() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- getPrincipalMomentsOfInertia() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
- getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getPrintMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getProbability() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The probability (FATCAT) or Z-score (CE) of the alignment.
- getProcess_site() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus
-
- getProfile() - Method in class org.biojava.nbio.alignment.FractionalIdentityInProfileScorer
-
- getProfile() - Method in class org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer
-
- getProfile() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getProfile() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getProfile() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getProfile() - Method in interface org.biojava.nbio.alignment.template.Aligner
-
Returns the alignment
Profile produced by this alignment algorithm.
- getProfile() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Returns the profile stored at this node.
- getProfile() - Method in interface org.biojava.nbio.alignment.template.PairInProfileScorer
-
Returns the
Profile from which the aligned pair originated.
- getProfileFuture() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getProfileFuture() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Returns the profile future stored at this node, but does not force the calculation, yet.
- getProfileProfileAligner() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getProfileProfileAligner() - Method in interface org.biojava.nbio.alignment.template.PartitionRefiner
-
Returns class type of profile-profile alignment subroutine.
- getProfileProfileAligner() - Method in interface org.biojava.nbio.alignment.template.RescoreRefiner
-
Returns class type of profile-profile alignment subroutine.
- getProgram() - Method in class org.biojava.nbio.core.search.io.Result
-
- getProgram() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- getProgram() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- getProgram() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- getProgram() - Method in class org.biojava.nbio.structure.validation.Programs
-
Gets the value of the program property.
- getProgram_version() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- getProgram_version() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- getProgram_version() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- getPrograms() - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
-
Gets the value of the programs property.
- getProgramSpecificParameter(String) - Method in class org.biojava.nbio.core.search.io.Result
-
- getProgramSpecificParametersList() - Method in class org.biojava.nbio.core.search.io.Result
-
- getProgressiveAlignment(GuideTree<S, C>, Alignments.ProfileProfileAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method to run the profile-profile alignments of a progressive multiple sequence alignment concurrently.
- getProjectedDistance(Atom) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Get the distance from a point to the axis of rotation
- getProjectedPoint(Atom) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Projects a given point onto the axis of rotation
- getProjectIdentifier() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
- getPropeller(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the propeller ("propeller-twist") in degrees for the given base pair
- getProperties() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
-
Get the properties
- getProperties() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
-
Implement this to return the Map delegate.
- getProperties() - Method in class org.biojava.nbio.ontology.utils.SmallAnnotation
-
- getProperties() - Method in interface org.biojava.nbio.structure.Group
-
return properties.
- getProperties() - Method in class org.biojava.nbio.structure.HetatomImpl
-
return properties.
- getProperties() - Method in class org.biojava.nbio.structure.validation.Program
-
Gets the value of the properties property.
- getProperty(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
-
- getProperty(Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation
-
Retrieve the value of a property by key.
- getProperty(String) - Method in interface org.biojava.nbio.structure.Group
-
get a single property .
- getProperty(String) - Method in class org.biojava.nbio.structure.HetatomImpl
-
get a single property .
- getProtein() - Method in class org.biojava.nbio.phosphosite.Site
-
- getProteinAliases() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Pull uniprot protein aliases associated with this sequence
- getProteinCDSSequences() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Return a list of protein sequences based on each CDS sequence
where the phase shift between two CDS sequences is assigned to the
CDS sequence that starts the triplet.
- getProteinSequence() - Method in class org.biojava.nbio.core.sequence.RNASequence
-
Get the ProteinSequence from the RNA sequence
- getProteinSequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.RNASequence
-
Get the ProteinSequene from the RNA sequence with user defined
transcription engine
- getProteinSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Get the protein sequence
- getProteinSequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Get the protein sequence with user defined TranscriptEngine
- getProteinSequence() - Method in class org.biojava.nbio.structure.cluster.Subunit
-
Get the protein sequence of the Subunit.
- getProteinSequenceCreator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getProteinSequenceForStructure(Structure, Map<Integer, Group>) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher
-
Generates a ProteinSequence corresponding to the sequence of struct,
and maintains a mapping from the sequence back to the original groups.
- getProteinSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
-
- getProteinSequences() - Method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
-
- getProteinSequenceString() - Method in class org.biojava.nbio.structure.cluster.Subunit
-
Get the protein sequence of the Subunit as String.
- getProxySequenceReader() - Method in interface org.biojava.nbio.core.sequence.location.template.AccesionedLocation
-
Return the proxy reader used to get sequence for this location.
- getProxySequenceReader() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getPsi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc
-
Calculate the psi angle.
- getPsi() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getPsi() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the psi property.
- getPsimodId() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getPsimodId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getPsimodName() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getPsimodName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getPtnr1_auth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_auth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_auth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_label_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_label_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_label_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_label_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_symmetry() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_auth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_auth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_auth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_label_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_label_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_label_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_label_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_symmetry() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPublicationDate() - Method in class org.biojava.nbio.structure.JournalArticle
-
- getPublisher() - Method in class org.biojava.nbio.structure.JournalArticle
-
- getPvalue() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getPvalue() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
-
- getPvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getPx() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getQ() - Method in class org.biojava.nbio.structure.jama.QRDecomposition
-
Generate and return the (economy-sized) orthogonal factor
- getQualifiers() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
- getQualifiers() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getQualifiers() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Get the qualifiers for this feature
- getQualities() - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
-
- getQualities(int, int) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
-
- getQuality() - Method in class org.biojava.nbio.genome.io.fastq.Fastq
-
Return the quality scores for this FASTQ formatted sequence.
- getQualityAt(int) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
-
- getQuantities() - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature
-
- getQuat4d(int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
-
- getQuat4d(int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
-
- getQuaternarySymmetry(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
Given a symmetry result, it calculates the overall global symmetry,
factoring out the alignment and detection steps of
QuatSymmetryDetector algorithm.
- getQuery() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
-
- getQuery() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
-
- getQuery() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
-
- getQuery() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getQuery() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getQuery() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceScorer
-
Returns the first sequence of the pair.
- getQuery() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileScorer
-
Returns the first profile of the pair.
- getQuery() - Method in class org.biojava.nbio.core.alignment.SimpleProfilePair
-
- getQuery() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
-
- getQuery() - Method in interface org.biojava.nbio.core.alignment.template.ProfilePair
-
Returns the first
Profile of the pair.
- getQuery() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
-
- getQueryDef() - Method in class org.biojava.nbio.core.search.io.Result
-
- getQueryEndIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
-
- getQueryID() - Method in class org.biojava.nbio.core.search.io.Result
-
- getQueryIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
-
- getQueryIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
-
- getQueryLength() - Method in class org.biojava.nbio.core.search.io.Result
-
- getQuerySequence() - Method in class org.biojava.nbio.core.search.io.Result
-
returns the reference to the original and whole sequence used to query the database.
- getQueryStartIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
-
- getR() - Method in class org.biojava.nbio.structure.jama.QRDecomposition
-
Return the upper triangular factor
- getRadius(Atom) - Static method in class org.biojava.nbio.structure.asa.AsaCalculator
-
Gets the van der Waals radius of the given atom following the values defined by
Chothia (1976) J.Mol.Biol.105,1-14
NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates"
slightly the heavy atoms to account for Hydrogens.
- getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
Returns the radius for drawing polyhedra
- getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
Returns the radius for drawing the minor rotation axis in the xy-plane
- getRadiusOfGyration() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
- getRama() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the rama property.
- getRandomDataColumns(int) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getRandomDataColumns(int, ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getRandomSeed() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- getRandomSleepTime() - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getRandomUsername() - Static method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
-
- getRange() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
Get the range of this domain, in PDB residue numbers (mmCif's
_pdbx_poly_seq_scheme.pdb_seq_num and pdb_ins_code).
- getRange() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement
-
Returns the residue range of this SSE.
- getRanges() - Method in class org.biojava.nbio.structure.AtomPositionMap
-
Returns a list of
ResidueRanges corresponding to this entire AtomPositionMap.
- getRanges() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getRanges() - Method in interface org.biojava.nbio.structure.Structure
-
- getRanges() - Method in class org.biojava.nbio.structure.StructureImpl
-
Deprecated.
- getRealEigenvalues() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition
-
Return the real parts of the eigenvalues
- getRealEnd() - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
-
- getRealStart() - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
-
- getReason() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
Return a String describing the reasons for the CE-Symm final decision in
this particular result.
- getRecordAdditionalAttachments() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- getRecordType() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Allows to distinguish between amino acids that are provided
as ATOM records and a SEQRES records.
- getRecordType() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Allows to distinguish between amino acids that are provided
as ATOM records and a SEQRES records.
- getRecordUnidentifiableCompounds() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- getRecvd_initial_deposition_date() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus
-
- getReducedStructure(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
-
Reduce a structure to a single-atom representation (e.g.
- getReducedStructure(Structure, String) - Static method in class org.biojava.nbio.structure.StructureTools
-
- getRef() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the value of REF field.
- getRef_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getRefAuthor() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- getRefChainId() - Method in class org.biojava.nbio.structure.EntityInfo
-
Return the ref chain id value.
- getRefComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getReference() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
-
- getReference() - Method in class org.biojava.nbio.core.search.io.Result
-
- getReferenceAuthor() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
-
The RA (Reference Author) lines list the authors of the paper (or other
work) cited.
- getReferenceComment() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
-
The RC (Reference Comment) linetype is an optional linetype which appears if
The reference has a comment.
- getReferenceCrossReference() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
-
The RX (reference cross-reference) linetype is
an optional linetype which appears if
one or more contiguous base spans of the
presented sequence can be attributed
to the reference in question.
- getReferenceFrames() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
- getReferenceGroup() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
-
The RG (Reference Group) lines list the working groups/consortia that
produced the record.
- getReferenceLocation() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
-
The RL (Reference Location) line contains the conventional citation
information for the reference.
- getReferenceNumber() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
-
The RN (Reference Number) line gives a unique number to each reference
Citation within an entry.
- getReferencePosition() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
-
The RP (Reference Position) linetype is
an optional linetype which appears if
one or more contiguous base spans of
the presented sequence can be attributed
to the reference in question.
- getReferences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getReferences() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getReferenceTitle() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
-
The RT (Reference Title) lines give the title of the paper (or other work) as
exactly as is possible given the limitations of computer character sets.
- getRefinedScoreThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getRefineMethod() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getRefLocation() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- getRefmacVersion() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the refmacVersion property.
- getRefMedline() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- getRefn() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the value of REFN field.
- getRefRMSD(MultipleAlignment, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
-
/** Calculates the average RMSD from all structures to a reference s
tructure, given a set of superimposed atoms.
- getRefRMSD(List<Atom[]>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
-
Calculates the average RMSD from all structures to a reference s
tructure, given a set of superimposed atoms.
- getRefseqIds() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getRefTitle() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- getRefTMScore(MultipleAlignment, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
-
Calculates the average TMScore from all structures to a reference
structure, given a set of superimposed atoms.
- getRefTMScore(List<Atom[]>, List<Integer>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
-
Calculates the average TMScore from all structures to a reference
structure, given a set of superimposed atoms.
- getRegistryInfo() - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- getRelation() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
The quaternary structure relation
QsRelation between the two
groups of Subunits.
- getRelativeAsaC() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
Returns the relative (complexed) ASA, i.e. the ASA of the residue
with respect to its ASA in an extended tri-peptide conformation (GLY-x-GLY)
- getRelativeAsaU() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
Returns the relative (uncomplexed) ASA, i.e. the ASA of the residue
with respect to its ASA in an extended tri-peptide conformation (GLY-x-GLY)
- getRelativePercentileClashscore() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the relativePercentileClashscore property.
- getRelativePercentileDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry
-
- getRelativePercentilePercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the relativePercentilePercentRamaOutliers property.
- getRelativePercentilePercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the relativePercentilePercentRotaOutliers property.
- getRelativePercentilePercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the relativePercentilePercentRSRZOutliers property.
- getRelativePercentileRNAsuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
-
- getRelDate() - Method in class org.biojava.nbio.structure.PDBHeader
-
Return the release date of the structure in the PDB.
- getRelevantSubLocations() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
Returns the normalised list of sub locations i.e. only those locations
which do not have a sub location.
- getRelevantSubLocations() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
An extension to
Location.getSubLocations() which returns sub-locations
of sub-locations; this will continue until it runs out of those locations.
- getRelevantSubSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getRelevantSubSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
Will return a SequenceReader object which offers a view of all resolved
locations i.e. those locations which are not complex and define the
true Sequence represented
- getRemoteBlastInfo() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
A simple method to check the availability of the QBlast service.
- getRemoteTerm() - Method in interface org.biojava.nbio.ontology.RemoteTerm
-
Return the imported term
- getRemoteTerm() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
-
- getRemoteTerms() - Method in interface org.biojava.nbio.ontology.OntologyOps
-
Get the set of all remote terms.
- getRepeatRelation(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Get the indices of participating repeats in Cauchy two-line form.
- getRepeatRelation(SymmetryAxes.Axis) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getRepeatRelation(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getRepeatsCyclicForm(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Get the indices of participating repeats in cyclic form.
- getRepeatsCyclicForm(SymmetryAxes.Axis) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getRepeatsCyclicForm(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getRepeatsCyclicForm(SymmetryAxes.Axis, List<?>) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getRepeatsCyclicForm(List<List<Integer>>, List<?>) - Static method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
- getRepeatsID() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
Return the symmetric repeats as structure identifiers, if the result is
symmetric and it was refined, return null otherwise.
- getRepeatTransform(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Return the transformation that needs to be applied to a
repeat in order to superimpose onto repeat 0.
- getRepeatTransform(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Return the transformation that needs to be applied to
repeat x in order to superimpose onto repeat y.
- getRepeatUnitCenters() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
-
- getRepeatUnitIndices() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
-
- getRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
-
- getRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getReplaced(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
if ChemComp is replacing another one, get the old version
otherwise return the same ChemComp again.
- getReplaced(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
- getReplacement(String, boolean, boolean) - Static method in class org.biojava.nbio.structure.PDBStatus
-
Gets the PDB which superseded oldPdbId.
- getReplacer(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
if ChemComp is replaced by another one, get the newer version
otherwise return the same ChemComp again.
- getReplacer(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
- getReplaces() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- getReplaces(String, boolean) - Static method in class org.biojava.nbio.structure.PDBStatus
-
Get the ID of the protein which was made obsolete by newPdbId.
- getRepresentative() - Method in class org.biojava.nbio.structure.cath.CathNode
-
- getRepresentative() - Method in class org.biojava.nbio.structure.EntityInfo
-
Get the representative Chain for this EntityInfo.
- getRepresentative() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- getRepresentativeAtomArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools
-
Gets a representative atom for each group that is part of the chain
backbone.
- getRepresentativeAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Gets a representative atom for each group that is part of the chain
backbone.
- getRepresentativeAtoms(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns the representative atoms for the provided name.
- getRepresentativeAtoms(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getRepresentativeAtoms() - Method in class org.biojava.nbio.structure.cluster.Subunit
-
Get all the representative Atoms of the Subunit.
- getRepresentativeAtoms(Structure) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
Returns the representative Atom Array of the first model, if the
structure is NMR, or the Array for each model, if it is a biological
assembly with multiple models.
- getRepresentativeAtomsInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns the set of intra-chain contacts for the given chain for C-alpha
or C3' atoms (including non-standard aminoacids appearing as HETATM
groups), i.e. the contact map.
- getRepresentativeAtomsOnly(List<Chain>) - Static method in class org.biojava.nbio.structure.io.CAConverter
-
Convert a List of chain objects to another List of chains, containing Representative atoms only.
- getRepresentativeAtomsOnly(Chain) - Static method in class org.biojava.nbio.structure.io.CAConverter
-
Convert a Chain to a new Chain containing C-alpha atoms only.
- getRepresentativeChain(String, String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
-
- getRepresentativeDomains() - Method in interface org.biojava.nbio.structure.domain.DomainProvider
-
Get the full list of representative domains for the PDB.
- getRepresentativeDomains() - Method in class org.biojava.nbio.structure.domain.PDBDomainProvider
-
Gets a list of all domain representatives
- getRepresentativeDomains() - Method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
-
- getRepresentatives(String, int) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- GetRepresentatives - Class in org.biojava.nbio.structure.rcsb
-
TODO Move this to Representatives.
- GetRepresentatives() - Constructor for class org.biojava.nbio.structure.rcsb.GetRepresentatives
-
- getRepresentatives(int) - Static method in class org.biojava.nbio.structure.rcsb.GetRepresentatives
-
Returns a representative set of PDB protein chains at the specified sequence
identity cutoff.
- getRepresentatives(Astral.AstralSet) - Static method in class org.biojava.nbio.structure.scop.Astral
-
Get a list of representatives' names for the specified ASTRAL cutoff.
- getRepresentatives(String) - Static method in class org.biojava.nbio.structure.scop.Astral
-
Get a list of representatives' names for the specified ASTRAL cutoff.
- getRepresentatives(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
-
- getResidId() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getResidId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getResidName() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getResidName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getResidual() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getResidualVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getResidue() - Method in class org.biojava.nbio.phosphosite.Site
-
- getResidue(int) - Method in class org.biojava.nbio.structure.AugmentedResidueRange
-
Returns the ResidueNumber that is at position positionInRange in this ResidueRange.
- getResidue(int, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange
-
Returns the ResidueNumber that is at position positionInRange in
this ResidueRange.
- getResidueName() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- getResidueNumber() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- getResidueNumber() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- getResidueNumber() - Method in interface org.biojava.nbio.structure.Group
-
returns a dynamically created ResidueNumber for the group - this
contains the chainId, resNum and insCode of the group.
- getResidueNumber() - Method in class org.biojava.nbio.structure.HetatomImpl
-
returns a dynamically created ResidueNumber for the group - this
contains the chainId, resNum and insCode of the group.
- getResidueRanges() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getResidueRanges() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getResidueRanges() - Method in interface org.biojava.nbio.structure.Structure
-
- getResidueRanges() - Method in class org.biojava.nbio.structure.StructureImpl
-
Deprecated.
- getResidueRanges() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
-
- getResidues() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
-
For each residue in the fasta file, return the ResidueNumber in the
corresponding structure.
- getResidues() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- getResidueType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getResidueTypeFromString(String) - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType
-
Get ResidueType by chem_comp_type
- getResidueTypes() - Method in enum org.biojava.nbio.structure.GroupType
-
Get a set of ResidueTypes loosely equivalent to this GroupType.
- getResname() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the resname property.
- getResName1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getResName2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getResNames() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getResnum() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the resnum property.
- getResnum1() - Method in class org.biojava.nbio.structure.io.SSBondImpl
-
- getResnum2() - Method in class org.biojava.nbio.structure.io.SSBondImpl
-
- getResolution() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getResolution() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getResolver() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
-
- getResourceManager(String) - Static method in class org.biojava.nbio.structure.align.util.ResourceManager
-
- getResScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getResSeq1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getResSeq2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getRestypesNotcheckedForBondAngleGeometry() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the restypesNotcheckedForBondAngleGeometry property.
- getResultFile() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getRev_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
-
- getReverse() - Method in class org.biojava.nbio.core.sequence.DNASequence
-
Returns a Sequence which runs in the current reverse order
- getReverse() - Method in enum org.biojava.nbio.core.sequence.Strand
-
- getReverse() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getReverseComplement() - Method in class org.biojava.nbio.core.sequence.DNASequence
-
- getReverseComplement() - Method in class org.biojava.nbio.core.sequence.RNASequence
-
Get reverse complement view of the sequence
- getReverseFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
-
Returns all frames which are in the reverse orientation
- getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getRevision_date() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxAuditRevisionHistory
-
- getRevisionRecords() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getRfree() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getRibosomes() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
-
- getRight() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getRimResidues(double, double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Returns the residues belonging to the interface rim, defined as those residues at
the interface (BSA>0) and for which the BSA/ASA ratio is below the given bsaToAsaCutoff
- getRise(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the rise for the given base pair, relative to the one before it.
- getRise() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getRms() - Method in class org.biojava.nbio.structure.align.helper.JointFragments
-
- getRMS(Atom[], Atom[], JointFragments) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
-
get the RMS of the JointFragments pair frag
- getRms() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getRmsd() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getRMSD(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
-
Calculates the RMSD of all-to-all structure comparisons (distances) of
the given MultipleAlignment.
- getRMSD(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
-
Calculates the RMSD of all-to-all structure comparisons (distances),
given a set of superimposed atoms.
- getRmsd() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- getRmsd() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
The RMSD between the equivalent residues of the equivalent Subunits after
superposition of the Subunit groups.
- getRmsd(Point3d[], Point3d[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition
-
Calculate the RMSD between two arrays of equivalent points that are not
superposed.
- getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP
-
- getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQuat
-
- getRmsd(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
-
- getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionSVD
-
- getRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getRmsdAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions
-
- getRmsdCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getRmsdCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
The cutoff to be used during AFP detection
- getRmsdCut() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- getRmsdIntra() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getRMSDMatrix(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Calculate the RMSD matrix of a MultipleAlignment, that is, entry (i,j) of
the matrix contains the RMSD between structures i and j.
- getRmsdThr() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
RMSD Threshold
- getRMSDThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Structure similarity threshold (measured with RMSD) to consider for the
structural subunit clustering.
- getRmsdThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getRmsdThrJoin() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
RMSD threshold for joining of AFPs
- getRnaAminoAcidTranslator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getRnaCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getRNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet
-
- getRNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.RNACompoundSet
-
- getRNASequence() - Method in class org.biojava.nbio.core.sequence.DNASequence
-
Return the RNASequence equivalent of the DNASequence using default Transcription Engine.
- getRNASequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.DNASequence
-
Allow a user to pass in a rules engine to do the DNA to RNA translation
- getRNASequence(Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence
-
Allows the user to pass in the Frame shift.
- getRNASequence(TranscriptionEngine, Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence
-
- getRnaSequenceCreator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getRnaSuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
-
- getRnaToDna() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- getRndSeed() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getRobustStdError() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getRoll(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the roll for the given base pair, relative to the one before it.
- getRoot() - Method in class org.biojava.nbio.alignment.GuideTree
-
Returns the root
GuideTree.Node which corresponds to the full multiple sequence alignment.
- getRoot() - Method in interface org.biojava.nbio.alignment.template.HierarchicalClusterer
-
Returns the root node of the tree resulting from this clustering algorithm.
- getRootURL() - Method in class org.biojava.nbio.structure.scop.ScopMirror
-
Get the URL for the root download directory, or null if none is set.
- getRot() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getRota() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the rota property.
- getRotatedAtoms(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay
-
New structures are downloaded if they were not cached in the alignment
and they are entirely transformed here with the superposition information
in the Multiple Alignment.
- getRotation(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- getRotationAxis() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Get a unit vector along the rotation axis
- getRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
Get the transformation operator as a rotation axis.
- getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getRotationJAMA(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices
-
Convert a transformation matrix into a JAMA rotation matrix.
- getRotationMatrix() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
Gets the rotation matrix from the last call to
calc_rmsd.
- getRotationMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
Gets the rotation matrix from the last call to
calc_rmsd.
- getRotationMatrix() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1
- getRotationMatrix() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Get the rotation matrix corresponding to this axis
- getRotationMatrix(double) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Get the rotation matrix corresponding to a rotation about this axis
- getRotationMatrix(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices
-
Convert a transformation matrix into a rotation matrix.
- getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getRotationPos() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Get a position on the rotation axis.
- getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getRotAxisAndAngle(Matrix3d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Given a rotation matrix calculates the rotation axis and angle for it.
- getRotAxisAngle(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getRotAxisType(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Given a transformation matrix containing a rotation returns the type of rotation:
1 for identity, 2 for 2-fold rotation, 3 for 3-fold rotation, 4 for 4-fold rotation,
6 for 6-fold rotation,
-1 for inversions, -2 for mirror planes, -3 for 3-fold improper rotation,
-4 for 4-fold improper rotation and -6 for 6-fold improper rotation
- getRotMax(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- getRow(AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getRow(C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
-
- getRow(C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
-
- getRow() - Method in class org.biojava.nbio.structure.align.helper.IndexPair
-
- getRowDimension() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get row dimension.
- getRowHeader() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getRowIndex(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getRowLookup() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getRowPackedCopy() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Make a one-dimensional row packed copy of the internal array.
- getRows() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getRows() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getRows() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get the list of row names.
- getRscc() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the rscc property.
- getRscore() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getRscoreLogrankTestpvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getRsr() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the rsr property.
- getRsrz() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the rsrz property.
- getRwork() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getS() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Return the diagonal matrix of singular values
- getSaid() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the said property.
- getSaturation() - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
-
- getSaveAlignmentMenuItem(AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getSaveOutputDir() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getScale() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getScale() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- getScale() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
- getScale() - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- getScaleableMatrixPanel(Matrix) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
-
- getScalevalue() - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
-
- getScid() - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Gets the value of the scid property.
- getSCOP() - Method in class org.biojava.nbio.structure.gui.util.ScopInstallationInstance
-
- getSCOP() - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
Get the current default instance for the default version
- getSCOP(boolean) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
- getSCOP(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
requests a particular version of SCOP.
- getSCOP(String, boolean) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
Gets an instance of the specified scop version.
- getScopDescription() - Method in class org.biojava.nbio.structure.scop.server.ScopDescriptions
-
- getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getScopDescriptionBySunid(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Return the SCOP description for a node in the hierarchy by its "sunid" id.
- getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getScopDescriptionFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopDescriptionsXML(List<ScopDescription>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopDescriptionXML(ScopDescription) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopDomain() - Method in class org.biojava.nbio.structure.scop.server.ScopDomains
-
- getScopDomainFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getScopDomainsBySunid(Integer) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Get a SCOP domain by its sunid
- getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getScopDomainsXML(List<ScopDomain>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopDomainXML(ScopDomain) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScope() - Method in class org.biojava.nbio.ontology.Synonym
-
- getScopId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getScopNode(int) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getScopNode(int) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getScopNode(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Access a particular ScopNode.
- getScopNode(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getScopNode() - Method in class org.biojava.nbio.structure.scop.server.ScopNodes
-
- getScopNodeFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopNodesXML(List<ScopNode>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopNodeXML(ScopNode) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopSelectPanel() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- getScopVersion() - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getScopVersion() - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getScopVersion() - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Returns the SCOP version
- getScopVersion() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
-
- getScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
-
- getScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
-
- getScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getScore() - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns score resulting from algorithm.
- getScore() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getScore(String) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
-
- getScore(String) - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache
-
Get the value for a particular score.
- getScore() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getScore() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
the alignment score
- getScore() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getScore() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- getScore() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
-
- getScore() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getScore() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getScoreLogrankTest() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getScoreLogrankTestpvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getScoreMatrix() - Method in class org.biojava.nbio.alignment.GuideTree
-
Returns the similarity matrix used to construct this guide tree.
- getScoreMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getScoreMatrix() - Method in interface org.biojava.nbio.alignment.template.MatrixAligner
-
Returns the entire score matrix built during alignment.
- getScoreMatrixAsString() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getScoreMatrixAsString() - Method in interface org.biojava.nbio.alignment.template.MatrixAligner
-
Returns a depiction of the score matrix as a
String.
- getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getScores(File) - Method in class org.biojava.nbio.ronn.ORonnModel
-
- getScores() - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
-
- getScores() - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache
-
Get a collection of all scores that have been set.
- getScores() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getScores() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
Returns QuatSymmetryScores averaged over all rotations
(except the first rotation, which is the unit operation E)
- getScores() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getScores() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getScores() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
Returns QuatSymmetryScores averaged over all rotations
(except the first rotation, which is the unit operation E)
- getScoringStrategy() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getScoringStrategy() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- getScrewTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Get the component of translation parallel to the axis of rotation
- getSearchFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
An input file to be used for the DB search
- getSearchMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getSecond() - Method in class org.biojava.nbio.structure.contact.Pair
-
- getSecondAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getSecondGroupAsa(ResidueNumber) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Gets the GroupAsa for the corresponding residue number of second chain
- getSecondGroupAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Gets a map of ResidueNumbers to GroupAsas for all groups of second chain.
- getSecretion() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getSecStrucElements(Structure) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools
-
Obtain the List of secondary structure elements (SecStrucElement) of a
Structure.
- getSecStrucElements(List<Group>) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools
-
Obtain the List of secondary structure elements (SecStrucElement) of a
List of Groups (assumed to be sequential, this is, connected in the
original Structure).
- getSecStrucInfo(Structure) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools
-
Obtain the List of secondary structure information (SecStrucInfo) of a
Structure.
- getSecStructType(Group) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get the secondary structure as defined by DSSP.
- getSecStructTypeFromDsspIndex(int) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Set the DSSP type based on a numerical index.
- getSeedFragmentLength() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getSeedRmsdCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getSegId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- getSegmentAtPos(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- getSegmentId() - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- getSegments() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSegments() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- getSegments() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- getSelectedAlignmentPos() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- getSelectedAlignmentPos() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- getSelection() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- getSelection() - Method in interface org.biojava.nbio.structure.gui.Selection
-
- getSelection() - Method in class org.biojava.nbio.structure.gui.SelectionImpl
-
- getSelection() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
-
- getSelectPDBPanel() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- getSelfAlignment() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
- getSeparatorSequence() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
-
- getSeq() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the seq property.
- getSeq_align_beg() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getSeq_align_end() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getSeq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getSeq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getSeq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
-
- getSeqBegin() - Method in class org.biojava.nbio.structure.DBRef
-
Initial sequence number of the PDB sequence segment.
- getSeqEnd() - Method in class org.biojava.nbio.structure.DBRef
-
Ending sequence number of the PDB sequence segment.
- getSeqIdRange() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
Get the range of this domain, in 1-based residue indices (mmCif's
_pdbx_poly_seq_scheme.seq_id)
Note that
EcodDomain.getRange() is used when constructing the domain.
- getSeqMisMatches() - Method in interface org.biojava.nbio.structure.Chain
-
Gets annotated sequence mismatches for this chain.
- getSeqMisMatches() - Method in class org.biojava.nbio.structure.ChainImpl
-
- getSeqNum() - Method in class org.biojava.nbio.structure.ResidueNumber
-
- getSeqNum() - Method in interface org.biojava.nbio.structure.SeqMisMatch
-
- getSeqNum() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
-
- getSeqPos(int, Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
Convert from a X position in the JPanel to alignment position
- getSeqPos(int, Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Convert from an X position in the JPanel to the position
in the sequence alignment.
- getSeqPos(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
-
start counting at 0...
- getSeqresEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getSeqResGroup(int) - Method in interface org.biojava.nbio.structure.Chain
-
Return the Group at given position,
from within groups in the SEQRES records of the chain, i.e.
- getSeqResGroup(int) - Method in class org.biojava.nbio.structure.ChainImpl
-
Return the Group at given position,
from within groups in the SEQRES records of the chain, i.e.
- getSeqResGroups(GroupType) - Method in interface org.biojava.nbio.structure.Chain
-
- getSeqResGroups() - Method in interface org.biojava.nbio.structure.Chain
-
Returns a list of all groups in SEQRES records of the chain, i.e.
- getSeqResGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl
-
- getSeqResGroups() - Method in class org.biojava.nbio.structure.ChainImpl
-
Returns a list of all groups in SEQRES records of the chain, i.e.
- getSeqResLength() - Method in interface org.biojava.nbio.structure.Chain
-
Returns the number of groups in the SEQRES records of the chain, i.e.
- getSeqResLength() - Method in class org.biojava.nbio.structure.ChainImpl
-
Returns the number of groups in the SEQRES records of the chain, i.e.
- getSeqResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getSeqResOneLetterSeq() - Method in class org.biojava.nbio.structure.ChainImpl
-
Get the one letter sequence so that Sequence is guaranteed to
be the same length as seqResGroups.
- getSeqResSequence() - Method in interface org.biojava.nbio.structure.Chain
-
Returns the PDB SEQRES sequence as a one-letter sequence string.
- getSeqResSequence() - Method in class org.biojava.nbio.structure.ChainImpl
-
Returns the PDB SEQRES sequence as a one-letter sequence string.
- getSeqresStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
-
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
-
- getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
-
Assumes all compounds were uppercase
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
-
- getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
-
- getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
-
- getSequence() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The Sequence Data Line
- getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.FastaSequenceParser
-
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator
-
Even though we are passing in the sequence we really only care about the length of the sequence and the offset
index in the fasta file.
- getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator
-
Should be able to extend the same concept to a remote URL call or database connection.
- getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator
-
Not sure of use case and currently not supported
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator
-
Even though we are passing in the sequence we really only care about the length of the sequence and the offset
index in the fasta file.
- getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator
-
Should be able to extend the same concept to a remote URL call or database connection.
- getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator
-
Not sure of use case and currently not supported
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator
-
Even though we are passing in the sequence we really only care about the length of the sequence and the offset
index in the fasta file.
- getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator
-
Should be able to extend the same concept to a remote URL call or database connection.
- getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator
-
Not sure of use case and currently not supported
- getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
-
- getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
-
- getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
-
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
-
- getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
-
- getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
-
- getSequence(String, long) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
-
- getSequence(ProxySequenceReader<C>, long) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
-
- getSequence(List<C>) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
-
- getSequence(BufferedReader, int) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceParserInterface
-
- getSequence() - Method in class org.biojava.nbio.core.sequence.location.SequenceLocation
-
- getSequence() - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
Gets the value of sequence
- getSequence() - Method in class org.biojava.nbio.genome.io.fastq.Fastq
-
Return the sequence for this FASTQ formatted sequence.
- getSequence(String, int, int) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitFacade
-
Extract a sequence from a chromosome, using chromosomal coordinates
- getSequence() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSequence() - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- getSequence5PrimeTo3Prime() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Try to give method clarity where you want a DNASequence coding in the 5' to 3' direction
Returns the DNASequence representative of the 5' and 3' reading based on strand
- getSequenceAlignment(MultipleAlignment, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Calculate the sequence alignment Strings for the whole alignment.
- getSequenceAlignment(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Calculate the sequence alignment Strings for the whole alignment.
- getSequenceAsString() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns the sequence as a String
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getSequenceAsString(List<C>, CompoundSet<C>, Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
- getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
- getSequenceAsString() - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Returns the String representation of the Sequence
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.ReversedSequenceView
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- getSequenceCollection() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
-
- getSequenceCoverageThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
The minimum coverage of the sequence alignment between two subunits to be
clustered together.
- getSequenceDescription() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The DE (Description) lines contain general descriptive information about the
sequence stored.
- getSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSequenceFromAlignment() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getSequenceFromAlignment() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Returns the sequence positions at each alignment index
- getSequenceFromString(String) - Method in class org.biojava.nbio.core.util.SequenceTools
-
- getSequenceHeader() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
The SQ (SeQuence header) line marks the beginning of the sequence data and
Gives a summary of its content.
- getSequenceHeader() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSequenceHeader() - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- getSequenceHeaderParser() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getSequenceIdentityThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Sequence identity threshold to consider for the subunits clustering.
- getSequenceIndexAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getSequenceIndexAt(int) - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Returns the index in the original
Sequence corresponding to the given index within an alignment.
- getSequenceLength() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
-
Sequence length The last item on the ID line is the length of the
sequence (the total number of bases in the sequence).
- getSequenceNames() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
- getSequences() - Method in class org.biojava.nbio.alignment.GuideTree
-
Returns the
Sequences which make up the leaves of this tree.
- getSequences() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
-
- getSequences() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
-
Gets the protein sequences read from the Fasta file.
- getSequenceScore() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Provide place holder for a metric that indicate a score associated with the sequence
- getSequenceUsage() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
-
- getSequenceVersion() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
-
return the sequence version
- getSeqWeight() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Should sequence conservation be considered as part of the alignment?
- getSerialversionuid() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getSerNum() - Method in class org.biojava.nbio.structure.io.SSBondImpl
-
- getServer() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getServer() - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider
-
- getServer() - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getServerName() - Static method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Return the String with the PDB server name, including the leading protocol
String (http:// or ftp://).
- getSG_entry() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus
-
- getShear(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the shear in Å for the given base pair
- getShift() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
Gets the shift from the last call to
calc_rmsd.
- getShift() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
Gets the shift from the last call to
calc_rmsd.
- getShift() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
returns the shift vector that has to be applied on structure to to shift on structure one
- getShift(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
Return the shift for the given base pair, relative to the one before it.
- getShorName() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- getShortDescription() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
- getShortDescription() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getShortDescription() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Get the short description that can be used to describe the feature
- getShortName() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getShortName() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
-
- getShortName() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- getShortName() - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- getShortName() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- getShortName() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getShortName() - Method in enum org.biojava.nbio.structure.xtal.TransformType
-
- getShortSymbol() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets the international short name (as used in PDB),
e.g.
- getShowDBresult() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getShowPDBMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getSiftsMapping(String) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
-
- getSimCount() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getSimilarity() - Method in class org.biojava.nbio.alignment.template.AbstractScorer
-
- getSimilarity(double) - Method in class org.biojava.nbio.alignment.template.AbstractScorer
-
- getSimilarity() - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns score as a similarity between 0.0 and 1.0.
- getSimilarity(double) - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns score as a similarity between 0.0 and scale.
- getSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Returns the similarity score for the alignment.
- getSingularValues() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Return the one-dimensional array of singular values
- getSite_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getSiteID() - Method in class org.biojava.nbio.structure.Site
-
- getSites() - Method in interface org.biojava.nbio.structure.Structure
-
- getSites() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getSize() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getSize() - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
Returns the number of rows in this profile.
- getSize() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
Get the number of sequences in the MSA
- getSize() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
-
Returns the number of rows in this profile.
- getSize() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- getSlide(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the slide for the given base pair, relative to the one before it.
- getSmiles() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getSOILD() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSolvent_model_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getSolvent_model_param_bsol() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getSolvent_model_param_ksol() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getSortVariable() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
-
- getSortVariable() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
-
- getSource() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
The feature source
- getSource() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getSource() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
The source of the feature.
- getSource() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Added support for the source of this sequence for GFF3 export
If a sub sequence doesn't have source then check for parent source
- getSource() - Method in class org.biojava.nbio.structure.align.client.StructureName
-
- getSource() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSourceSeed() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getSourceStructure() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getSpace_group_name_H_M() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- getSpace_group_name_Hall() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- getSpaceGroup() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Get the SpaceGroup
- getSpaceGroup(int) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser
-
Gets the space group for the given standard identifier.
- getSpaceGroup(String) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser
-
Get the space group for the given international short name, using
the PDB format, e.g.
- getSpaceGroupAsString(SpaceGroup) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get the string representation of a space group.
- getSparse() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getSpecies() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getSpeciesId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getSphereCount() - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
-
- getSphereCount() - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
-
- getSplitDirPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Location of split files within the directory, as an array of paths.
- getSplitDirPath() - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
-
- getSplitDirPath() - Method in class org.biojava.nbio.structure.io.MMTFFileReader
-
- getSplitDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader
-
- getSplitpat1() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getSplitpat2() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getSqFrom() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getSqTo() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getSrc_method() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getSsBondListFromBondList(List<Bond>) - Static method in class org.biojava.nbio.structure.io.SSBondImpl
-
- getSSBonds() - Method in interface org.biojava.nbio.structure.Structure
-
Get the list of disulfide Bonds as they have been defined in the PDB files
- getSSBonds() - Method in class org.biojava.nbio.structure.StructureImpl
-
Get the list of disulfide Bonds as they have been defined in the PDB files
- getSSEThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getStagger(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the stagger in Å for the given base pair
- getStainTypeFromString(String) - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType
-
- getStandardDeviation() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getStart() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getStart() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Returns the
Point within an alignment of the first element of the original
Sequence.
- getStart() - Method in interface org.biojava.nbio.core.alignment.template.ProfileView
-
Returns the column index of the viewed
Profile corresponding to the first element in this view
- getStart() - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
- getStart() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getStart() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
Start of the location
- getStart() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- getStart() - Method in class org.biojava.nbio.structure.cath.CathFragment
-
- getStart() - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- getStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- getStart() - Method in class org.biojava.nbio.structure.ResidueRange
-
- getStart_construct_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getStartCodonSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
- getStartIndex(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Calculates and returns the first position of the specified structure in
the alignment that is not null.
- getStartIndex(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
-
- getStartPage() - Method in class org.biojava.nbio.structure.JournalArticle
-
- getStartResidue(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Calculates and returns the first residue of the specified structure in
the alignment that is not null.
- getStartResidue(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
-
- getStartTimestamp() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
-
- getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
-
StartupParameters is a bean to store all the possible
command line parameters.
- getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
-
- getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
-
- getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
-
- getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
-
- getStatus() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getStatus() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- getStatus(String) - Static method in class org.biojava.nbio.structure.PDBStatus
-
Get the status of the PDB in question.
- getStatus(String[]) - Static method in class org.biojava.nbio.structure.PDBStatus
-
Get the status of the a collection of PDBs in question in a single query.
- getStatus() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getStatus() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getStatus_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus
-
- getStatus_code_cs() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus
-
- getStatus_code_mr() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus
-
- getStatus_code_sf() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus
-
- getStatusListener() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
- getStderr() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getStdError() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getStdev() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the stdev property.
- getStdev() - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Gets the value of the stdev property.
- getStdev() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the stdev property.
- getStdev() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the stdev property.
- getStdlow() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getStepParameters() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method reports all the base-pair step parameters, in the order of:
tilt, roll, twist (in degrees), shift, slide, rise (in Å).
- getStepSize() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
how many pairs should be requested for alignment from server?
- getStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getStop() - Method in class org.biojava.nbio.structure.cath.CathFragment
-
- getStop() - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- getStopCodonSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
- getStrain() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getStrain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getStrain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- getStrand() - Method in class org.biojava.nbio.core.sequence.CDSSequence
-
- getStrand() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
A gene should have Strand
- getStrand() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getStrand() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
Strand which the location is located on
- getStrand() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
- getStrata() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getStrataInfoHashMap() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
-
- getStrategy() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
- getStretch(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the stretch in Å for the given base pair
- getString(String) - Method in class org.biojava.nbio.structure.align.util.ResourceManager
-
- getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- getStringForCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- getStringForCompound(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
-
- getStringRepresentation() - Method in enum org.biojava.nbio.core.sequence.Strand
-
- getStructAssemblies() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
- getStructAssemblyGens() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
- getStructOpers() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
- getStructuralTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
-
Calculate a phylogenetic tree of the MultipleAlignment using RMSD
distances and the Neighbor Joining algorithm from forester.
- getStructure() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
Return the current Structure in the AlignmentJmol instance.
- getStructure(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Request a Structure based on a name.
- getStructure(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructure() - Method in interface org.biojava.nbio.structure.Chain
-
Returns the parent Structure of this chain.
- getStructure() - Method in class org.biojava.nbio.structure.ChainImpl
-
Returns the parent Structure of this chain.
- getStructure() - Method in class org.biojava.nbio.structure.cluster.Subunit
-
The parent Structure from which the Subunit atoms were obtained.
- getStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- getStructure(URL) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- getStructure(File) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Handles the actual parsing of the file into a Structure object.
- getStructure() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
This method will return the parsed protein structure, once the parsing has been finished
- getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
-
- getStructure() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
-
Gets the structure.
- getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.MMTFFileReader
-
- getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.PDBFileReader
-
- getStructure(String) - Method in interface org.biojava.nbio.structure.io.StructureIOFile
-
Open filename and return a Structure object.
- getStructure(File) - Method in interface org.biojava.nbio.structure.io.StructureIOFile
-
Read file from File and returns
a Structure object.
- getStructure(String) - Static method in class org.biojava.nbio.structure.StructureIO
-
Loads a structure based on a name.
- getStructure(String) - Static method in class org.biojava.nbio.structure.StructureTools
-
- getStructure(String, PDBFileParser, AtomCache) - Static method in class org.biojava.nbio.structure.StructureTools
-
Flexibly get a structure from an input String.
- getStructure() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getStructure1() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
-
- getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBDirPanel
-
- getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBServerPanel
-
- getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
-
- getStructure1() - Method in class org.biojava.nbio.structure.gui.util.ScopSelectPanel
-
- getStructure1() - Method in interface org.biojava.nbio.structure.gui.util.StructurePairSelector
-
- getStructure2() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
-
- getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBDirPanel
-
- getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBServerPanel
-
- getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
-
- getStructure2() - Method in class org.biojava.nbio.structure.gui.util.ScopSelectPanel
-
- getStructure2() - Method in interface org.biojava.nbio.structure.gui.util.StructurePairSelector
-
- getStructureAlignment() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
-
- getStructureAlignment() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- getStructureAtom(Atom, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
- getStructureAtomLinkage(Atom, boolean, Atom, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
- getStructureById(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- getStructureById(String) - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
-
- getStructureById(String) - Method in interface org.biojava.nbio.structure.io.StructureProvider
-
Get the structure for a PDB ID
- getStructureCoverageThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
The minimum coverage of the structure alignment between two subunits to be
clustered together.
- getStructureForCathDomain(StructureName) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForCathDomain(StructureName, CathDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns a
Structure corresponding to the CATH identifier supplied in
structureName, using the specified
CathDatabase.
- getStructureForDomain(ScopDomain) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForDomain(ScopDomain, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForDomain(ScopDomain, ScopDatabase, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForDomain(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForDomain(String, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Loads a structure directly by PDB ID
- getStructureFromFasta() - Static method in class demo.DemoStructureFromFasta
-
- getStructureGroup(Group, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
- getStructureId() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
- getStructureIdentifier(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Returns the StructureIdentifier associated with the structure index from
its parent Ensemble.
- getStructureIdentifier(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- getStructureIdentifier() - Method in interface org.biojava.nbio.structure.Structure
-
Get an identifier corresponding to this structure
- getStructureIdentifier() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getStructureIdentifiers() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Returns a List containing the names of the structures aligned
(i.e.: PDB code, SCOP domain, etc.).
- getStructureIdentifiers() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
-
- getStructureInfo(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get summary information for the structure.
- getStructurePairAligner() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
- getStructures() - Method in class org.biojava.nbio.structure.gui.util.SelectMultiplePanel
-
- getStructures() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
-
Gets the protein structures mapped from the Fasta file.
- getSubject() - Method in interface org.biojava.nbio.ontology.Triple
-
Return the subject term of this triple
- getSubject() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getSubLocations() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getSubLocations() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
Gives access to the sub locations for this location.
- getSubproblems(List<AlignerHelper.Anchor>, int, int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
-
Convert a list of anchors into a subproblem list.
- getSubProfile(Location) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
-
- getSubProfile(Location) - Method in interface org.biojava.nbio.core.alignment.template.Profile
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getSubSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
If circular this will return the sequence represented by the sub
locations joined.
- getSubSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
Will return a SequenceReader object which represents the outer bounds
of this Location
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getSubSequence(int, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns a sub sequence view
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getSubSequence(Integer, Integer) - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Returns a portion of the sequence from the different positions.
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getSubstitutionMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Returns the substitution matrix.
- getSubstitutionMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
- getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getSubstitutionScoreVector(int) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Returns score for the alignment of the query column to all target columns
- getSubstitutionScoreVector(int, AlignerHelper.Subproblem) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Returns score for the alignment of the query column to all target columns
- getSubstructureMatchingProteinSequence(ProteinSequence, Structure) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher
-
Get a substructure of
wholeStructure containing only the
Groups that are included in
sequence.
- getSubunitClusters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
Returns the List of SubunitCluster used to calculate symmetry.
- getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
Return the number of Subunits involved in the symmetry.
- getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getSubunitMap() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
Map of Subunit equivalencies from the first to the second group.
- getSubunitRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getSubunits() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
Subunits contained in the SubunitCluster.
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
Returns the List of Subunits used to calculate symmetry.
- getSubunits1() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
Original Subunits of the first group.
- getSubunits2() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
Original Subunits of the second group.
- getSubunitTypeCount() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
-
- getSuggestion(String) - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
-
get a list of suggestions for a userInput
- getSuggestion(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
-
- getSuggestion(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
-
- getSummaryPos() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
- getSummaryPos() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
- getSunID() - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- getSunid() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode
-
- getSuperfamilyId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getSuperpositionAlgorithm() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Method to superpose subunits (i.e., structural aligner).
- getSurfaceResidues(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Returns the residues belonging to the surface
- getSurname() - Method in class org.biojava.nbio.structure.Author
-
- getSurv() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getSurvivalFitInfo() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getSurvivalInfoList() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getSurvivalInfoList() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
-
The data used to draw the graph
- getSurvivalTimePercentile(String, double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
To get the median percentile for a particular group pass the value of
.50.
- getSwissprotId() - Method in interface org.biojava.nbio.structure.Chain
-
Gets the Swissprot id of this chain.
- getSwissprotId() - Method in class org.biojava.nbio.structure.ChainImpl
-
get the Swissprot id of this chains .
- getSym1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getSym2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getSymbol() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- getSymbolSet() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
-
- getSymDeviation() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getSymmClash() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the symmClash property.
- getSymmetry() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
-
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getSymmetry_operation() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getSymmetryAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
-
Return all symmetry axes of of the structure: the set of axes that
describe all parts of the structure.
- getSymmetryClass(double) - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
-
- getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.C2RotationSolver
-
- getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.HelixSolver
-
- getSymmetryOperations() - Method in interface org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver
-
- getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.RotationSolver
-
- getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.SystematicSolver
-
- getSymmetryOrder(Map<Integer, Integer>, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
- getSymmetryOrder(Map<Integer, Integer>, Map<Integer, Integer>, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Tries to detect symmetry in an alignment.
- getSymmetryOrder(AFPChain, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
- getSymmGroup() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
- getSymmLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getSymmLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
- getSymmTitle(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
-
Create a symmetry title for a display frame (Jmol, alignment, etc).
- getSymmType() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getSymmType() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
-
- getSymop() - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Gets the value of the symop property.
- getSynonyms() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getSynonyms() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
-
- getSynonyms() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- getSynonyms() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
-
- getSynonyms() - Method in interface org.biojava.nbio.ontology.Term
-
Return the synonyms for this term.
- getSynonyms() - Method in class org.biojava.nbio.ontology.Term.Impl
-
- getSynonyms() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getSynonyms() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getSynonyms() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getSynthetic() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getSystematicName() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getSystematicName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getT() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getTable(String) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser
-
Returns a table by its name
- getTable(Integer) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser
-
Returns a table by its identifier i.e. 1 means universal codon tables
- getTable() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getTables() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser
-
Returns a list of all available IUPAC tables
- getTabPane() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- getTarget() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
-
- getTarget() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
-
- getTarget() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
-
- getTarget() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getTarget() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getTarget() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceScorer
-
Returns the second sequence of the pair.
- getTarget() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileScorer
-
Returns the second profile of the pair.
- getTarget() - Method in class org.biojava.nbio.core.alignment.SimpleProfilePair
-
- getTarget() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
-
- getTarget() - Method in interface org.biojava.nbio.core.alignment.template.ProfilePair
-
Returns the second
Profile of the pair.
- getTarget() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair
-
- getTargetEndIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
-
- getTargetIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
-
- getTargetIndex(int) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
-
- getTargetOntology() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- getTargetSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
Returns the Sequence which is our edit.
- getTargetStartIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
-
- getTaxonomicDivision() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
-
- getTaxonomy() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getTaxonomy() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getTempBuffer() - Method in class org.biojava.nbio.ontology.obo.OboFileParser
-
- getTempFactor() - Method in interface org.biojava.nbio.structure.Atom
-
Get temp factor.
- getTempFactor() - Method in class org.biojava.nbio.structure.AtomImpl
-
- getTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- getTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Fetch the term with the specified name.
- getTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- getTerms() - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- getTerms() - Method in interface org.biojava.nbio.ontology.Ontology
-
Return all the terms in this ontology
- getTerms() - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- getTest() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
-
- getText(Group) - Method in class org.biojava.nbio.structure.io.GroupToSDF
-
- getText() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
-
- getText() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
-
- getTGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getTGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getThePdbId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
Returns the PDB ID.
- getThreadPool() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
-
Returns current shared thread pool.
- getThreads() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getThree() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getThree() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
-
- getThree() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getThree_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
Should return the 3-prime end of the given Sequence according to
the edit.
- getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
-
- getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Insert
-
- getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute
-
- getTilt(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the tilt for the given base pair, relative to the one before it.
- getTime() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getTime() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getTime() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getTimeAxisIncrementPercentage() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
Get the percentage increment for the time axis
- getTimeout() - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getTissue() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getTissue() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getTissue_fraction() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getTitle() - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference
-
The title that retrieved from the Reference section.
- getTitle() - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
-
- getTitle() - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface
-
Get the title that retrieved from Reference section.
- getTitle() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
Return the title of the AlignmentJmol window.
- getTitle() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getTitle() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- getTitle() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the value of title
- getTitle() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getTmIntra() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getTMScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Returns the tmScore of the alignment.
- getTMScore(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPChainScorer
-
- getTMScore(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.util.AFPChainScorer
-
- getTMScore(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.Calc
-
Calculate the TM-Score for the superposition.
- getTMScore(Atom[], Atom[], int, int, boolean) - Static method in class org.biojava.nbio.structure.Calc
-
Calculate the TM-Score for the superposition.
- getTMThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters
-
Structure similarity threshold (measured with TMScore) to consider for the
structural subunit clustering.
- getTo() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
-
- getTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getToCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
-
- getTool() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
Get the tool identifier for QBlast.
- getTop() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getTopology() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
-
- getTopologyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getTorsionPenalty() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getTotal() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
-
- getTotalArea() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Returns the total area buried upon formation of this interface,
defined as: 1/2[ (ASA1u-ASA1c) + (ASA2u-ASA2u) ] , with:
ASAxu = ASA of first/second unbound chain
ASAxc = ASA of first/second complexed chain
In the area calculation HETATOM groups not part of the main protein/nucleotide chain
are not included.
- getTotalArea() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
Return the average buried surface area for this interface cluster
- getTotalLenIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getTotalLenOpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getTotalRmsdIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
this is the init-RMSD, not the final RMSD after refinement.
- getTotalRmsdOpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The RMSD of the final alignment.
- getTraceRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getTraces() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getTraceTmScoreMin() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getTrans() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getTranscoefpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getTranscript(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Get the transcript sequence by accession
- getTranscriptDNASequence(TwoBitFacade, GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Extracts the DNA sequence transcribed from the input genetic coordinates.
- getTranscriptDNASequence(TwoBitFacade, String, List<Integer>, List<Integer>, int, int, Character) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Extracts the DNA sequence transcribed from the input genetic coordinates.
- getTranscriptionEnd() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getTranscriptionStart() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getTranscripts() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Get the collection of transcription sequences assigned to this gene
- getTransfAlgebraic(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets a transformation algebraic string given its index.
- getTransfAlgebraic() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getTransform() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult
-
The transformation 4D matrix that needs to be applied to the second group
of Subunits to superimpose them onto the first group of Subunits, given
the equivalent residues in the SubunitCluster and the Subunit
equivalencies.
- getTransformation(Matrix, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Convert JAMA rotation and translation to a Vecmath transformation matrix.
- getTransformation(Matrix, Matrix) - Static method in class org.biojava.nbio.structure.geometry.Matrices
-
Convert JAMA rotation and translation to a Vecmath transformation matrix.
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns transformation matrix to orient structure
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getTransformation(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets a transformation by index expressed in crystal axes basis.
- getTransformationMap() - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser
-
Returns a map of bioassembly transformations
- getTransformationMatrix() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Return the transformation (both rotational and translational component) as a 4x4 transformation matrix.
- getTransformations() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
-
Returns a transformation matrix for each structure giving the
3D superimposition information of the multiple structure alignment.
- getTransformations() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
-
- getTransformations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets all transformations except for the identity in crystal axes basis.
- getTransformationsOrthonormal() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Gets all symmetry transformation operators corresponding to this structure's space group
(including the identity, at index 0) expressed in the orthonormal basis.
- getTransformId() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
- getTransformMap(BioAssemblyInfo, Map<String, Integer>) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Convert a bioassembly information into a map of transform, chainindices it relates to.
- getTransforms() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Return the 2 crystal transform operations performed on each of the
molecules of this interface.
- getTransforms() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
-
- getTransformType() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
Returns the TransformType of this transformation: AU, crystal translation, fractional translation
, 2 3 4 6-fold rotations, 2 3 4 6-fold screw rotations, -1 -3 -2 -4 -6 inversions/rotoinversions.
- getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
- getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getTransition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
An adaptor method which returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
- getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getTransition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getTransition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getTransition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getTransition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getTransition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getTranslatedBbs(Vector3d) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox
-
Returns a new BoundingBoxes object containing the same bounds as this
BoundingBoxes object translated by the given translation
- getTranslation(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- getTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
- getTranslationVector(Matrix4d) - Static method in class org.biojava.nbio.structure.Calc
-
Extract the translational vector as an Atom of a transformation matrix.
- getTranslationVector(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices
-
Extract the translational vector of a transformation matrix.
- getTranslScrewComponent() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
- getTranslScrewComponent(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
Given a transformation matrix containing a rotation and translation returns the
screw component of the rotation.
- getTransmembraneProteins() - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
-
get all Transmembrane proteins
- getTransNCS() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the transNCS property.
- getTree(CathDomain) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return the CATH sub-tree for a particular domain.
- getTree(CathDomain) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getTree(ScopDomain) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
get the SCOP sub-tree for a particular domain.
- getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getTreshold(int) - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
-
- getTriples(Term, Term, Term) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- getTriples(Term, Term, Term) - Method in interface org.biojava.nbio.ontology.Ontology
-
Return all triples from this ontology which match the supplied
pattern.
- getTriples(Term, Term, Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- getTriplet() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getTrustedCutoffs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
Not always 2.
- getTurn() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getTwi() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getTwinFraction() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the twinFraction property.
- getTwinL() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the twinL property.
- getTwinL2() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the twinL2 property.
- getTwist(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the twist for the given base pair, relative to the one before it.
- getTwistedGroups() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
-
- getTwo() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getTwo() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
-
- getTwo() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getTwoBitURL(String) - Static method in class org.biojava.nbio.genome.parsers.twobit.SimpleTwoBitFileProvider
-
- getTwoFoldsPerpendicular() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- getType() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
-
- getType() - Method in interface org.biojava.nbio.alignment.template.GapPenalty
-
- getType() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
The feature type
- getType() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getType() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
The type of the feature.
- getType() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- getType() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
- getType() - Method in class org.biojava.nbio.structure.EntityInfo
-
Get the type of entity this EntityInfo describes.
- getType() - Method in interface org.biojava.nbio.structure.Group
-
- getType() - Method in class org.biojava.nbio.structure.HetatomImpl
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPoly
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getType() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- getType() - Method in class org.biojava.nbio.structure.NucleotideImpl
-
- getType() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getType() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getType() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
-
- getType() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement
-
- getType() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
-
- getType_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPoly
-
- getType_symbol() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getType_symbol() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getTypeField() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getU() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
-
Return upper triangular factor
- getU() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Return the left singular vectors
- getUid() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getUnalignedGroups(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
List of groups from the structure not included in ca (e.g. ligands).
- getUnaryOperators() - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver
-
Returns a list of operators for this assembly.
- getUnderlyingCompound() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- getUnidentifiableAtomLinkages() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- getUnidentifiableModifiedResidues() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- getUniprot() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getUniprot() - Method in class org.biojava.nbio.phosphosite.Site
-
- getUniProtAccessionId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getUniprotbaseURL() - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
The current UniProt URL to deal with caching issues. www.uniprot.org is load balanced
but you can access pir.uniprot.org directly.
- getUniprotDirectoryCache() - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Local directory cache of XML that can be downloaded
- getUniprotEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getUniProtId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getUniProtId() - Method in interface org.biojava.nbio.structure.SeqMisMatch
-
- getUniProtId() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl
-
- getUniProtPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getUniProtResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getUniprotStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getUniqueID() - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
Need a unique id from String
- getUniqueInterfaces() - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder
-
Returns the list of unique interfaces that the given Structure has upon
generation of all crystal symmetry mates.
- getUniqueInterfaces(double) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder
-
Returns the list of unique interfaces that the given Structure has upon
generation of all crystal symmetry mates.
- getUnitCellAsArray(PDBCrystallographicInfo) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Get the length six array of the unit cell information.
- getUnitv() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getUnitVectors() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getUnknownDataTypeVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getUnrefinedScoreThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getUnweightedStrataInfoHashMap() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
-
- getUpdateFrequency() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
The expected ECOD update frequency determines whether the version
"latest" should be re-downloaded
- getUpdates() - Method in class org.biojava.nbio.structure.rcsb.RCSBUpdates
-
- getUpper() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getUpperBound() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits
-
- getUpperedBase() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- getUpperLimit() - Method in class org.biojava.nbio.structure.io.mmcif.chem.MetalBondDistance
-
- getUrl() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
Get the top-level ECOD server URL.
- getUrl() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
-
- getURL() - Method in class org.biojava.nbio.structure.URLIdentifier
-
- getUsed() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getUsedAtomNames() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getUserCollection() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Provided for convince if the developer needs to associate data with a sequence
- getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getUserConfigHelp() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
-
The help text for each of these parameters.
- getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
- getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getUserConfigHelp() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getUserConfigParameterNames() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
-
The labels to be displayed to the user for each parameter
- getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
- getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getUserConfigParameters() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
-
get the list of parameters that the user can change through the user interface.
- getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
- getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getUserConfigParameters() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getUserConfigTypes() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
-
Get the data types of the parameters
- getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
- getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
-
- getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getUserConfigTypes() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getUsername() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getUserObject() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
- getUserObject() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getUserObject() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
- getUserOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- getV() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition
-
Return the eigenvector matrix
- getV() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Return the right singular vectors
- getValenceElectronCount() - Method in enum org.biojava.nbio.structure.Element
-
Returns the number of valence electrons for this Element.
- getValidFolds(List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
Find valid symmetry orders for a given stoichiometry.
- getValue(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
-
- getValue(C, C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
-
- getValue(C, C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
-
Returns value in matrix for conversion from first
Compound to the second.
- getValue() - Method in class org.biojava.nbio.core.sequence.features.Qualifier
-
- getValue() - Method in class org.biojava.nbio.core.util.CRC64Checksum
-
- getValue() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
-
- getValue() - Method in class org.biojava.nbio.structure.align.helper.GapArray
-
- getValue_order() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getValues() - Method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
-
- getVarhaz() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getVariableResiduals() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getVariance() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getVariant() - Method in class org.biojava.nbio.genome.io.fastq.Fastq
-
Return the FASTQ sequence format variant for this FASTQ formatted sequence.
- getVariant() - Method in class org.biojava.nbio.genome.io.fastq.IlluminaFastqReader
-
- getVariant() - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqReader
-
- getVariant() - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqReader
-
- getVariant() - Method in class org.biojava.nbio.structure.EntityInfo
-
- getVDWRadius() - Method in enum org.biojava.nbio.structure.Element
-
Returns the van der Waals radius of this Element.
- getVector() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getVector1() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getVector1() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getVector2() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getVector2() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getVector3() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getVector3() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getVector3dScrewTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
- getVersion() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getVersion() - Method in class org.biojava.nbio.core.search.io.Result
-
- getVersion() - Method in class org.biojava.nbio.core.sequence.AccessionID
-
- getVersion() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
-
- getVersion() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
-
- getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeCPMain
-
- getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeMain
-
- getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
-
- getVersion() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
-
- getVersion() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
-
- getVersion() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
-
- getVersion() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getVersion() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
-
- getVersion() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Returns the version of the algorithm used to generate the
MultipleAlignment objects.
- getVersion() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
-
- getVersion() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner
-
Get the Version information for this Algorithm.
- getVersion() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
-
- getVersion() - Method in interface org.biojava.nbio.structure.align.StructureAlignment
-
Get the Version information for this Algorithm.
- getVersion() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getVersion() - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase
-
Return the release version.
- getVersion() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
-
- getVersion() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
Return the ECOD version, as parsed from the file.
- getVersion() - Method in class org.biojava.nbio.structure.validation.Program
-
Gets the value of the version property.
- getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
- getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
Returns the vertices of an n-fold polygon of given radius and center
- getVertices() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
-
- getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
Returns the vertices of an n-fold polygon of given radius and center
- getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
Returns the vertices of an n-fold polygon of given radius and center
- getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
Returns the vertices of an n-fold polygon of given radius and center
- getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
- getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getViewCount() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
-
- getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
- getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
- getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
- getViewedProfile() - Method in interface org.biojava.nbio.core.alignment.template.ProfileView
-
Returns the entire
Profile being viewed
- getViewedSequence() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getViewedSequence() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView
-
- getViewer() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
- getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
- getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getViewMatrix(int) - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
-
- getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
- getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
- getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
- getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
- getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getViewName(int) - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
-
- getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
- getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
- getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
- getVolume() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getVolume() - Method in class org.biojava.nbio.structure.JournalArticle
-
- getVolume() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
Returns the volume of this unit cell.
- getWaldTestInfo() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getWaterChain(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a water Chain based on the 'internal' chain id (asymId)
for the first model
- getWaterChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a water chain based on the 'internal' chain id (asymId)
for the given model index
- getWaterChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getWaterChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getWaterChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a water Chain based on the 'public' chain name (authId)
for the first model
- getWaterChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a water Chain based on the 'public' chain name (authId)
for the given model index
- getWaterChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getWaterChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getWaterChains() - Method in class org.biojava.nbio.structure.Model
-
- getWaterChains() - Method in interface org.biojava.nbio.structure.Structure
-
Return all water chains for the first model
- getWaterChains(int) - Method in interface org.biojava.nbio.structure.Structure
-
Return all water chains for the given model index
- getWaterChains() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getWaterChains(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getWebStartConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
-
- getWeight() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getWeight() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getWeight() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getWeight() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getWeighted() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getWeightedRmsd(Point3d[], Point3d[], double[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP
-
- getWidth() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
Returns the radius of an inscribed sphere, that is tangent to each
of the octahedron's faces
- getWikipediaLink() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getWilsonBaniso() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the wilsonBaniso property.
- getWilsonBestimate() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the wilsonBestimate property.
- getWindowSize() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
-
Access the current window size
- getWinSize() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
The window size to look at
- getWinSize() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- getX() - Method in interface org.biojava.nbio.structure.Atom
-
Get coordinate X.
- getX() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get coordinate X.
- getxAxisTimeCoordinates() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getxAxisTimeValues() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getXGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getXGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- getXMLcreationDate() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the xmLcreationDate property.
- getXtriageInputColumns() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the xtriageInputColumns property.
- getXYZEuler(Matrix) - Static method in class org.biojava.nbio.structure.Calc
-
Convert a rotation Matrix to Euler angles.
- getY() - Method in interface org.biojava.nbio.structure.Atom
-
Get coordinate Y.
- getY() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get coordinate Y.
- getZ() - Method in interface org.biojava.nbio.structure.Atom
-
Get coordinate Z.
- getZ() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get coordinate Z.
- getZ() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the z property.
- getZ() - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Gets the value of the z property.
- getZ() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getZ_PDB() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns the Jmol zoom to fit polyhedron and symmetry axes.
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorI
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorO
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorT
-
- getZscore() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the zscore property.
- getZscore() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the zscore property.
- getZYZEuler(Matrix) - Static method in class org.biojava.nbio.structure.Calc
-
Gets euler angles for a matrix given in ZYZ convention.
- GFF3FromUniprotBlastHits - Class in org.biojava.nbio.genome.homology
-
- GFF3FromUniprotBlastHits() - Constructor for class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
-
- GFF3Reader - Class in org.biojava.nbio.genome.parsers.gff
-
http://www.bioperl.org/wiki/GTF
Read and write FeatureLists as GFF/GTF formatted files.
- GFF3Reader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GFF3Reader
-
- GFF3Writer - Class in org.biojava.nbio.genome.parsers.gff
-
- GFF3Writer() - Constructor for class org.biojava.nbio.genome.parsers.gff.GFF3Writer
-
- GLOBAL_ALIGN1 - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- GLOBAL_ALIGN2 - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- gold - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
-
- GOParser - Class in org.biojava.nbio.ontology.io
-
Simple parser for the Gene Ontology (GO) flatfile format.
- GOParser() - Constructor for class org.biojava.nbio.ontology.io.GOParser
-
- Gotoh - Class in org.biojava.nbio.structure.align.pairwise
-
a class to perform Gotoh algorithm
- Gotoh(Alignable) - Constructor for class org.biojava.nbio.structure.align.pairwise.Gotoh
-
- GradientMapper - Class in org.biojava.nbio.structure.gui.util.color
-
Maps a set of real values onto a gradient.
- GradientMapper() - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- GradientMapper(Color, Color) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- GradientMapper(Color, Color, ColorSpace) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- GradientPanel - Class in org.biojava.nbio.structure.gui.util.color
-
- GradientPanel(ContinuousColorMapper, double, double) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientPanel
-
- GradientRenderer() - Constructor for class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer
-
- gradients - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- GraphComponentOrderDetector - Class in org.biojava.nbio.structure.symmetry.internal
-
The GraphOrderDetector transforms the self-alignment into a Graph and
extracts its maximally connected Components.
- GraphComponentOrderDetector() - Constructor for class org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector
-
- GraphComponentRefiner - Class in org.biojava.nbio.structure.symmetry.internal
-
The GraphRefiner transforms the self-alignment into a Graph and extracts its
maximally connected Components.
- GraphComponentRefiner() - Constructor for class org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner
-
- grayOutCEOrig(Atom[], int, int, CECalculator, Matrix, int, double[], double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
Grays out the main diagonal of a duplicated distance matrix.
- grayOutPreviousAlignment(AFPChain, Atom[], int, int, CECalculator, Matrix, int, double[], double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
- Grid - Class in org.biojava.nbio.structure.contact
-
A grid to be used for calculating atom contacts through a spatial hashing algorithm.
- Grid(double) - Constructor for class org.biojava.nbio.structure.contact.Grid
-
Creates a Grid, the cutoff is in the same units as the coordinates
(Angstroms if they are atom coordinates) and can
be specified to a precision of 0.01.
- GridCell - Class in org.biojava.nbio.structure.contact
-
A grid cell to be used in contact calculation via spatial hashing algorithm.
- GridCell(Grid) - Constructor for class org.biojava.nbio.structure.contact.GridCell
-
- group() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
Get the first item (everything before first semicolon, if it has one)
in the attribute field, which is assumed to
be a group identifer.
- group() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
-
Get the group id of the feature.
- Group - Interface in org.biojava.nbio.structure
-
This is the data structure for a single Group of atoms.
- group - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
-
- group1 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf
An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.
- group1 - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
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- group1WorseOutcome - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
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- group2 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
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- group2 - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
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- group3 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
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- GroupAsa - Class in org.biojava.nbio.structure.asa
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A class to store the results of ASA calculations, it can
hold ASA values per atom present in
Group
- GroupAsa(Group) - Constructor for class org.biojava.nbio.structure.asa.GroupAsa
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- groupByRange(double[], String, String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
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Need to allow a range of values similar to cut in R and a continuous c
- GroupContact - Class in org.biojava.nbio.structure.contact
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A pair of residues that are in contact
- GroupContact() - Constructor for class org.biojava.nbio.structure.contact.GroupContact
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- GroupContactSet - Class in org.biojava.nbio.structure.contact
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A set of residue-residue contacts.
- GroupContactSet() - Constructor for class org.biojava.nbio.structure.contact.GroupContactSet
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- GroupContactSet(AtomContactSet) - Constructor for class org.biojava.nbio.structure.contact.GroupContactSet
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Constructs a GroupContactSet by collapsing the given AtomContactSet into
residue-residue (group-group) contacts.
- GroupIterator - Class in org.biojava.nbio.structure
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An iterator over all groups of a structure.
- GroupIterator(Structure) - Constructor for class org.biojava.nbio.structure.GroupIterator
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Constructs a GroupIterator object over all models
- GroupIterator(Structure, int) - Constructor for class org.biojava.nbio.structure.GroupIterator
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Constructs a GroupIterator object over a specific model
- GroupLocation(List) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
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- GroupLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
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- GroupLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
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- GroupLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
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- GroupLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
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- GroupLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
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- GroupLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
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- GroupLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
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- GroupResults - Class in org.biojava.nbio.survival.kaplanmeier.figure
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- GroupResults() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
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- GroupToSDF - Class in org.biojava.nbio.structure.io
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- GroupToSDF() - Constructor for class org.biojava.nbio.structure.io.GroupToSDF
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- GroupType - Enum in org.biojava.nbio.structure
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This contains basic categories for Group types.
- groupValues() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
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Create a collection of all unique group ids in the list, as defined
by the group() method of the features.
- GTSlikeScore(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
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- GuanUberbacher<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.routines
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Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last
Compound of each
Sequence).
- GuanUberbacher() - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher
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- GuanUberbacher(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher
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Prepares for a pairwise global sequence alignment.
- GuanUberbacher(S, S, GapPenalty, SubstitutionMatrix<C>, int) - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher
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Prepares for a pairwise global sequence alignment.
- guessFiletype(String) - Static method in class org.biojava.nbio.structure.StructureIO
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Attempts to guess the type of a structure file based on the extension
- guessOrderFromAngle(double, int) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
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Returns the rotation order o that gives the lowest value of |2PI / o - theta,
given that the value is strictly lower than threshold, for orders {@code o=1,...
- guessPDBID(String) - Static method in class org.biojava.nbio.structure.URLIdentifier
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Recognizes PDB IDs that occur at the beginning of name followed by some
delimiter.
- guessScopDomain(String, ScopDatabase) - Static method in class org.biojava.nbio.structure.align.client.StructureName
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Guess a scop domain.
- guessSequentialAlignment(Map<Integer, Integer>, boolean) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
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Takes a potentially non-sequential alignment and guesses a sequential
version of it.
- GUIAlignmentProgressListener - Class in org.biojava.nbio.structure.align.gui
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a GUI that allows to watch progress as multiple alignments are being processed.
- GUIAlignmentProgressListener() - Constructor for class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
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- GuideTree<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
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Implements a data structure for a guide tree used during progressive multiple sequence alignment.
- GuideTree(List<S>, List<PairwiseSequenceScorer<S, C>>) - Constructor for class org.biojava.nbio.alignment.GuideTree
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Creates a guide tree for use during progressive multiple sequence alignment.
- GuideTree.Node - Class in org.biojava.nbio.alignment
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Implements a data structure for the node in a guide tree used during progressive multiple sequence alignment.
- GuideTreeNode<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template
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Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
- GUIFarmJobRunnable - Class in org.biojava.nbio.structure.align.gui
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- GUIFarmJobRunnable(FarmJobParameters) - Constructor for class org.biojava.nbio.structure.align.gui.GUIFarmJobRunnable
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- GuiWrapper - Class in org.biojava.nbio.structure.align.ce
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A class to wrap some of the strucutre.gui classes using Reflection
- GuiWrapper() - Constructor for class org.biojava.nbio.structure.align.ce.GuiWrapper
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- GZIP_MAGIC - Static variable in class org.biojava.nbio.core.util.InputStreamProvider
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The magic number found at the start of a GZIP stream.