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

Packages that use AminoAcidCompound

Package	Description
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

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 and 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 and 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>	DefaultAAIndexProvider.getMatrix(String matrixName)
SubstitutionMatrix<AminoAcidCompound>	AAIndexProvider.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 and 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 and 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 and Description
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.
ProteinSequence(String seqString, CompoundSet<AminoAcidCompound> compoundSet) Create a protein from a string with a 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 and 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 and 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 and 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 and 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 and Description
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(List<AminoAcidCompound> list)
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(List<AminoAcidCompound> list) Assumes all compounds were uppercase
AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(List<AminoAcidCompound> list) Not sure of use case and currently not supported
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
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>	CasePreservingProteinSequenceCreator.getSequence(String sequence, 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.

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

Modifier and Type	Method and 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 and Description
CompoundSet<Table.Codon>	IUPACParser.IUPACTable.getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds) Returns the compound set of codons
List<Table.Codon>	IUPACParser.IUPACTable.getCodons(CompoundSet<NucleotideCompound> nucelotides, CompoundSet<AminoAcidCompound> aminoAcids) Returns a list of codons where the source and target compounds are the same as those given by the parameters.
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(List<AminoAcidCompound> list)
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(List<AminoAcidCompound> list) Assumes all compounds were uppercase
AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(List<AminoAcidCompound> list) Not sure of use case and currently not supported
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
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.

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

Constructor and 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 and 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 and 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 and 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 and Description
TranscriptionEngine.Builder	TranscriptionEngine.Builder.aminoAcidsCompounds(CompoundSet<AminoAcidCompound> compounds)
CompoundSet<Table.Codon>	Table.getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds)
List<Table.Codon>	Table.getCodons(CompoundSet<NucleotideCompound> nucelotides, CompoundSet<AminoAcidCompound> aminoAcids)
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 and 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 and 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)
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)