Uses of Class
org.biojava3.core.sequence.compound.AminoAcidCompound

Packages that use AminoAcidCompound

Package	Description
org.biojava3.core.sequence
org.biojava3.core.sequence.compound
org.biojava3.core.sequence.io
org.biojava3.core.sequence.transcription

Uses of AminoAcidCompound in org.biojava3.core.sequence

Constructor parameters in org.biojava3.core.sequence with type arguments of type AminoAcidCompound

Modifier	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.biojava3.core.sequence.compound

Methods in org.biojava3.core.sequence.compound that return AminoAcidCompound

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

Methods in org.biojava3.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.biojava3.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.biojava3.core.sequence.compound with type arguments of type AminoAcidCompound

Modifier and Type	Method	Description
void	AminoAcidCompoundSet.verifySequence(Sequence<AminoAcidCompound> sequence)

Uses of AminoAcidCompound in org.biojava3.core.sequence.io

Methods in org.biojava3.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.biojava3.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.biojava3.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.biojava3.core.sequence.io with type arguments of type AminoAcidCompound

Modifier	Constructor	Description
	CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)
	FileProxyProteinSequenceCreator(File fastaFile, CompoundSet<AminoAcidCompound> compoundSet)	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.biojava3.core.sequence.transcription

Methods in org.biojava3.core.sequence.transcription that return AminoAcidCompound

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

Methods in org.biojava3.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.biojava3.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.biojava3.core.sequence.transcription with type arguments of type AminoAcidCompound

Modifier and Type	Method	Description
TranscriptionEngine.Builder	TranscriptionEngine.Builder.aminoAcidsCompounds(CompoundSet<AminoAcidCompound> compounds)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.proteinCreator(SequenceCreatorInterface<AminoAcidCompound> creator)

Constructors in org.biojava3.core.sequence.transcription with parameters of type AminoAcidCompound

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

Constructor parameters in org.biojava3.core.sequence.transcription with type arguments of type AminoAcidCompound

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