org.biojava3.core.sequence.io
public static class IUPACParser.IUPACTable extends java.lang.Object implements Table
Table.CaseInsensitiveTriplet, Table.Codon
Constructor and Description |
---|
IUPACParser.IUPACTable(java.lang.String name,
java.lang.Integer id,
java.lang.String aminoAcidString,
java.lang.String startCodons)
Constructor which uses the basic IUPAC codon table format.
|
IUPACParser.IUPACTable(java.lang.String name,
int id,
java.lang.String aminoAcidString,
java.lang.String startCodons,
java.lang.String baseOne,
java.lang.String baseTwo,
java.lang.String baseThree) |
Modifier and Type | Method and Description |
---|---|
CompoundSet<Table.Codon> |
getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds,
CompoundSet<AminoAcidCompound> aminoAcidCompounds)
Returns the compound set of codons
|
java.util.List<Table.Codon> |
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.
|
java.lang.Integer |
getId() |
java.lang.String |
getName() |
boolean |
isStart(AminoAcidCompound compound)
Returns true if the given compound was a start codon in this
codon table.
|
public IUPACParser.IUPACTable(java.lang.String name, int id, java.lang.String aminoAcidString, java.lang.String startCodons, java.lang.String baseOne, java.lang.String baseTwo, java.lang.String baseThree)
public IUPACParser.IUPACTable(java.lang.String name, java.lang.Integer id, java.lang.String aminoAcidString, java.lang.String startCodons)
public java.lang.Integer getId()
public java.lang.String getName()
public boolean isStart(AminoAcidCompound compound) throws java.lang.IllegalStateException
isStart
in interface Table
java.lang.IllegalStateException
- Thrown if
getCodons(CompoundSet, CompoundSet)
was not called first.public java.util.List<Table.Codon> getCodons(CompoundSet<NucleotideCompound> nucelotides, CompoundSet<AminoAcidCompound> aminoAcids)
public CompoundSet<Table.Codon> getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds)
getCodonCompoundSet
in interface Table