Uses of Class
org.biojava.nbio.core.sequence.compound.AminoAcidCompound

Packages that use AminoAcidCompound

Package	Description
org.biojava.nbio.aaproperties	Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
org.biojava.nbio.aaproperties.xml	Set of classes that handles the reading and writing of xml files.
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.matrices
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.compound
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.transcription
org.biojava.nbio.structure.align.ce	Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.multiple.util
org.biojava.nbio.structure.cluster
org.biojava.nbio.structure.io	Input and Output of Structures

Uses of AminoAcidCompound in org.biojava.nbio.aaproperties

Fields in org.biojava.nbio.aaproperties declared as AminoAcidCompound

Modifier and Type	Field	Description
static AminoAcidCompound	Constraints.A
static AminoAcidCompound	Constraints.C
static AminoAcidCompound	Constraints.D
static AminoAcidCompound	Constraints.E
static AminoAcidCompound	Constraints.F
static AminoAcidCompound	Constraints.G
static AminoAcidCompound	Constraints.H
static AminoAcidCompound	Constraints.I
static AminoAcidCompound	Constraints.K
static AminoAcidCompound	Constraints.L
static AminoAcidCompound	Constraints.M
static AminoAcidCompound	Constraints.N
static AminoAcidCompound	Constraints.P
static AminoAcidCompound	Constraints.Q
static AminoAcidCompound	Constraints.R
static AminoAcidCompound	Constraints.S
static AminoAcidCompound	Constraints.T
static AminoAcidCompound	Constraints.V
static AminoAcidCompound	Constraints.W
static AminoAcidCompound	Constraints.Y

Fields in org.biojava.nbio.aaproperties with type parameters of type AminoAcidCompound

Modifier and Type	Field	Description
static Map<AminoAcidCompound,Double>	Constraints.aa2CTerminalPka
static Map<AminoAcidCompound,Double>	Constraints.aa2ExtinctionCoefficient
static Map<AminoAcidCompound,Double>	Constraints.aa2Hydrophathicity
static Map<AminoAcidCompound,Double>	Constraints.aa2MolecularWeight
static Map<AminoAcidCompound,Double>	Constraints.aa2NTerminalPka
static Map<AminoAcidCompound,Double>	Constraints.aa2PKa

Methods in org.biojava.nbio.aaproperties that return types with arguments of type AminoAcidCompound

Modifier and Type	Method	Description
Map<AminoAcidCompound,Double>	IPeptideProperties.getAAComposition(ProteinSequence sequence)	Returns the composition of the 20 standard amino acid in the sequence.
static Map<AminoAcidCompound,Double>	PeptideProperties.getAAComposition(String sequence)	An adaptor method to return the composition of the 20 standard amino acid in the sequence.
Map<AminoAcidCompound,Double>	PeptidePropertiesImpl.getAAComposition(ProteinSequence sequence)

Methods in org.biojava.nbio.aaproperties with parameters of type AminoAcidCompound

Modifier and Type	Method	Description
double	IPeptideProperties.getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode)	Returns the composition of specified amino acid in the sequence.
double	PeptidePropertiesImpl.getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode)

Uses of AminoAcidCompound in org.biojava.nbio.aaproperties.xml

Methods in org.biojava.nbio.aaproperties.xml that return AminoAcidCompound

Modifier and Type	Method	Description
AminoAcidCompound	CaseFreeAminoAcidCompoundSet.getCompoundForString(String string)
AminoAcidCompound	ModifiedAminoAcidCompoundSet.getCompoundForString(String string)

Methods in org.biojava.nbio.aaproperties.xml that return types with arguments of type AminoAcidCompound

Modifier and Type	Method	Description
List<AminoAcidCompound>	CaseFreeAminoAcidCompoundSet.getAllCompounds()
List<AminoAcidCompound>	ModifiedAminoAcidCompoundSet.getAllCompounds()
Set<AminoAcidCompound>	CaseFreeAminoAcidCompoundSet.getEquivalentCompounds(AminoAcidCompound compound)
Set<AminoAcidCompound>	ModifiedAminoAcidCompoundSet.getEquivalentCompounds(AminoAcidCompound compound)

Methods in org.biojava.nbio.aaproperties.xml with parameters of type AminoAcidCompound

Modifier and Type	Method	Description
boolean	CaseFreeAminoAcidCompoundSet.compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo)
boolean	ModifiedAminoAcidCompoundSet.compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo)
Set<AminoAcidCompound>	CaseFreeAminoAcidCompoundSet.getEquivalentCompounds(AminoAcidCompound compound)
Set<AminoAcidCompound>	ModifiedAminoAcidCompoundSet.getEquivalentCompounds(AminoAcidCompound compound)
String	CaseFreeAminoAcidCompoundSet.getStringForCompound(AminoAcidCompound compound)
String	ModifiedAminoAcidCompoundSet.getStringForCompound(AminoAcidCompound compound)
boolean	CaseFreeAminoAcidCompoundSet.hasCompound(AminoAcidCompound compound)
boolean	ModifiedAminoAcidCompoundSet.hasCompound(AminoAcidCompound compound)

Method parameters in org.biojava.nbio.aaproperties.xml with type arguments of type AminoAcidCompound

Modifier and Type	Method	Description
boolean	CaseFreeAminoAcidCompoundSet.isValidSequence(Sequence<AminoAcidCompound> sequence)
boolean	ModifiedAminoAcidCompoundSet.isValidSequence(Sequence<AminoAcidCompound> sequence)

Uses of AminoAcidCompound in org.biojava.nbio.core.alignment

Fields in org.biojava.nbio.core.alignment with type parameters of type AminoAcidCompound

Modifier and Type	Field	Description
protected static SubstitutionMatrix<AminoAcidCompound>	SimpleProfile.matrix

Uses of AminoAcidCompound in org.biojava.nbio.core.alignment.matrices

Methods in org.biojava.nbio.core.alignment.matrices that return types with arguments of type AminoAcidCompound

Modifier and Type	Method	Description
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getAminoAcidSubstitutionMatrix(String name)	Returns a substitution matrix for amino acids given by the name name.
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum100()	Returns Blosum 100 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum30()	Returns Blosum 30 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum35()	Returns Blosum 35 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum40()	Returns Blosum 40 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum45()	Returns Blosum 45 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum50()	Returns Blosum 50 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum55()	Returns Blosum 55 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum60()	Returns Blosum 60 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SimpleSubstitutionMatrix.getBlosum62()
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum62()	Returns Blosum 62 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum65()	Returns Blosum 65 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum70()	Returns Blosum 70 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum75()	Returns Blosum 75 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum80()	Returns Blosum 80 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum85()	Returns Blosum 85 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum90()	Returns Blosum 90 matrix by Henikoff & Henikoff
List<AminoAcidCompound>	ScaledSubstitutionMatrix.getCols()
Map<AminoAcidCompound,Short>	ScaledSubstitutionMatrix.getColumn(AminoAcidCompound column)
CompoundSet<AminoAcidCompound>	ScaledSubstitutionMatrix.getCompoundSet()
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getGonnet250()	Returns PAM 250 matrix by Gonnet, Cohen & Benner
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getIdentity()
Map<String,SubstitutionMatrix<AminoAcidCompound>>	AAIndexFileParser.getMatrices()
SubstitutionMatrix<AminoAcidCompound>	AAIndexProvider.getMatrix(String matrixName)
SubstitutionMatrix<AminoAcidCompound>	DefaultAAIndexProvider.getMatrix(String matrixName)
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getMatrixFromAAINDEX(String matrixName)	Returns any matrix from the AAINDEX database file
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getPAM250()	Returns PAM 250 matrix by Dayhoff
Map<AminoAcidCompound,Short>	ScaledSubstitutionMatrix.getRow(AminoAcidCompound row)
List<AminoAcidCompound>	ScaledSubstitutionMatrix.getRows()
SubstitutionMatrix<AminoAcidCompound>	ScaledSubstitutionMatrix.normalizeMatrix(short scale)

Methods in org.biojava.nbio.core.alignment.matrices with parameters of type AminoAcidCompound

Modifier and Type	Method	Description
Map<AminoAcidCompound,Short>	ScaledSubstitutionMatrix.getColumn(AminoAcidCompound column)
Map<AminoAcidCompound,Short>	ScaledSubstitutionMatrix.getRow(AminoAcidCompound row)
short	ScaledSubstitutionMatrix.getValue(AminoAcidCompound from, AminoAcidCompound to)

Method parameters in org.biojava.nbio.core.alignment.matrices with type arguments of type AminoAcidCompound

Modifier and Type	Method	Description
void	ScaledSubstitutionMatrix.setCols(List<AminoAcidCompound> cols)
void	ScaledSubstitutionMatrix.setRows(List<AminoAcidCompound> rows)

Uses of AminoAcidCompound in org.biojava.nbio.core.sequence

Constructor parameters in org.biojava.nbio.core.sequence with type arguments of type AminoAcidCompound

Constructor	Description
ProteinSequence(String seqString, CompoundSet<AminoAcidCompound> compoundSet)	Create a protein from a string with a user defined set of amino acids
ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader)	A protein sequence where the storage of the sequence is somewhere else.
ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, CompoundSet<AminoAcidCompound> compoundSet)	A protein sequence where the storage of the sequence is somewhere else with user defined set of amino acids.
ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, CompoundSet<AminoAcidCompound> compoundSet)	A protein sequence where the storage of the sequence is somewhere else with user defined set of amino acids.

Uses of AminoAcidCompound in org.biojava.nbio.core.sequence.compound

Methods in org.biojava.nbio.core.sequence.compound that return AminoAcidCompound

Modifier and Type	Method	Description
AminoAcidCompound	AminoAcidCompoundSet.getCompoundForString(String string)

Methods in org.biojava.nbio.core.sequence.compound that return types with arguments of type AminoAcidCompound

Modifier and Type	Method	Description
List<AminoAcidCompound>	AminoAcidCompoundSet.getAllCompounds()
CompoundSet<AminoAcidCompound>	AminoAcidCompound.getCompoundSet()
Set<AminoAcidCompound>	AminoAcidCompoundSet.getEquivalentCompounds(AminoAcidCompound compound)

Methods in org.biojava.nbio.core.sequence.compound with parameters of type AminoAcidCompound

Modifier and Type	Method	Description
boolean	AminoAcidCompoundSet.compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo)
Set<AminoAcidCompound>	AminoAcidCompoundSet.getEquivalentCompounds(AminoAcidCompound compound)
String	AminoAcidCompoundSet.getStringForCompound(AminoAcidCompound compound)
boolean	AminoAcidCompoundSet.hasCompound(AminoAcidCompound compound)

Method parameters in org.biojava.nbio.core.sequence.compound with type arguments of type AminoAcidCompound

Modifier and Type	Method	Description
boolean	AminoAcidCompoundSet.isValidSequence(Sequence<AminoAcidCompound> sequence)

Uses of AminoAcidCompound in org.biojava.nbio.core.sequence.io

Methods in org.biojava.nbio.core.sequence.io that return types with arguments of type AminoAcidCompound

Modifier and Type	Method	Description
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(String sequence, long index)
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(List<AminoAcidCompound> list)	Assumes all compounds were uppercase
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(String sequence, long index)	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.
AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(List<AminoAcidCompound> list)	Not sure of use case and currently not supported
AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)	Should be able to extend the same concept to a remote URL call or database connection.
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(String sequence, long index)
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(List<AminoAcidCompound> list)
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)

Methods in org.biojava.nbio.core.sequence.io with parameters of type AminoAcidCompound

Modifier and Type	Method	Description
boolean	IUPACParser.IUPACTable.isStart(AminoAcidCompound compound)	Returns true if the given compound was a start codon in this codon table.

Method parameters in org.biojava.nbio.core.sequence.io with type arguments of type AminoAcidCompound

Modifier and Type	Method	Description
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(List<AminoAcidCompound> list)	Assumes all compounds were uppercase
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(List<AminoAcidCompound> list)	Not sure of use case and currently not supported
AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)	Should be able to extend the same concept to a remote URL call or database connection.
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(List<AminoAcidCompound> list)
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)

Constructor parameters in org.biojava.nbio.core.sequence.io with type arguments of type AminoAcidCompound

Constructor	Description
CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)
FileProxyProteinSequenceCreator(File file, CompoundSet<AminoAcidCompound> compoundSet, SequenceParserInterface sequenceParser)	Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
ProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)

Uses of AminoAcidCompound in org.biojava.nbio.core.sequence.transcription

Methods in org.biojava.nbio.core.sequence.transcription that return AminoAcidCompound

Modifier and Type	Method	Description
AminoAcidCompound	Table.Codon.getAminoAcid()

Methods in org.biojava.nbio.core.sequence.transcription that return types with arguments of type AminoAcidCompound

Modifier and Type	Method	Description
List<Sequence<AminoAcidCompound>>	RNAToAminoAcidTranslator.createSequences(Sequence<NucleotideCompound> originalSequence)	Performs the core conversion of RNA to Peptide.
CompoundSet<AminoAcidCompound>	TranscriptionEngine.getAminoAcidCompounds()
SequenceCreatorInterface<AminoAcidCompound>	TranscriptionEngine.getProteinSequenceCreator()
Map<Frame,Sequence<AminoAcidCompound>>	TranscriptionEngine.multipleFrameTranslation(Sequence<NucleotideCompound> dna, Frame... frames)	A way of translating DNA in a number of frames
Sequence<AminoAcidCompound>	TranscriptionEngine.translate(Sequence<NucleotideCompound> dna)	Quick method to let you go from a CDS to a Peptide quickly.

Methods in org.biojava.nbio.core.sequence.transcription with parameters of type AminoAcidCompound

Modifier and Type	Method	Description
boolean	Table.isStart(AminoAcidCompound compound)	Returns true if the given compound could have been a start amino acid; this does not assert if the codon that actually coded for the amino acid was a start codon.

Method parameters in org.biojava.nbio.core.sequence.transcription with type arguments of type AminoAcidCompound

Modifier and Type	Method	Description
TranscriptionEngine.Builder	TranscriptionEngine.Builder.aminoAcidsCompounds(CompoundSet<AminoAcidCompound> compounds)
protected void	RNAToAminoAcidTranslator.postProcessCompoundLists(List<List<AminoAcidCompound>> compoundLists)	Performs the trimming of stop codons and the conversion of a valid start amino acid to M
TranscriptionEngine.Builder	TranscriptionEngine.Builder.proteinCreator(SequenceCreatorInterface<AminoAcidCompound> creator)
protected void	RNAToAminoAcidTranslator.trimStop(List<AminoAcidCompound> sequence)	Imperfect code.

Constructors in org.biojava.nbio.core.sequence.transcription with parameters of type AminoAcidCompound

Constructor	Description
Codon(Table.CaseInsensitiveTriplet triplet, AminoAcidCompound aminoAcid, boolean start, boolean stop)

Constructor parameters in org.biojava.nbio.core.sequence.transcription with type arguments of type AminoAcidCompound

Constructor	Description
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons, boolean stopAtStopCodons, boolean waitForStartCodon)

Uses of AminoAcidCompound in org.biojava.nbio.structure.align.ce

Fields in org.biojava.nbio.structure.align.ce with type parameters of type AminoAcidCompound

Modifier and Type	Field	Description
protected SubstitutionMatrix<AminoAcidCompound>	CeParameters.substitutionMatrix

Methods in org.biojava.nbio.structure.align.ce that return types with arguments of type AminoAcidCompound

Modifier and Type	Method	Description
SubstitutionMatrix<AminoAcidCompound>	CeParameters.getSubstitutionMatrix()	Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.

Method parameters in org.biojava.nbio.structure.align.ce with type arguments of type AminoAcidCompound

Modifier and Type	Method	Description
void	CeParameters.setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound> substitutionMatrix)	Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.

Uses of AminoAcidCompound in org.biojava.nbio.structure.align.multiple.util

Methods in org.biojava.nbio.structure.align.multiple.util that return types with arguments of type AminoAcidCompound

Modifier and Type	Method	Description
static MultipleSequenceAlignment<ProteinSequence,AminoAcidCompound>	MultipleAlignmentTools.toProteinMSA(MultipleAlignment msta)	Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid residues.

Uses of AminoAcidCompound in org.biojava.nbio.structure.cluster

Method parameters in org.biojava.nbio.structure.cluster with type arguments of type AminoAcidCompound

Modifier and Type	Method	Description
boolean	SubunitCluster.mergeSequence(SubunitCluster other, SubunitClustererParameters params, Alignments.PairwiseSequenceAlignerType alignerType, GapPenalty gapPenalty, SubstitutionMatrix<AminoAcidCompound> subsMatrix)	Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).

Uses of AminoAcidCompound in org.biojava.nbio.structure.io

Method parameters in org.biojava.nbio.structure.io with type arguments of type AminoAcidCompound

Modifier and Type	Method	Description
static AFPChain	FastaAFPChainConverter.fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>,AminoAcidCompound> alignment, Structure structure1, Structure structure2)	Provided only for convenience.
static AFPChain	FastaAFPChainConverter.fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>,AminoAcidCompound> alignment, Structure structure1, Structure structure2)	Provided only for convenience.

Constructor parameters in org.biojava.nbio.structure.io with type arguments of type AminoAcidCompound

Constructor	Description
FastaStructureParser(File file, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(File file, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(InputStream is, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(InputStream is, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(FastaReader<ProteinSequence,AminoAcidCompound> reader, AtomCache cache)