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java.lang.Objectorg.biojava3.core.sequence.io.IUPACParser.IUPACTable
public static class IUPACParser.IUPACTable
Holds the concept of a codon table from the IUPAC format
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava3.core.sequence.transcription.Table |
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Table.CaseInsensitiveTriplet, Table.Codon |
Constructor Summary | |
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IUPACParser.IUPACTable(String name,
Integer id,
String aminoAcidString,
String startCodons)
Constructor which uses the basic IUPAC codon table format. |
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IUPACParser.IUPACTable(String name,
int id,
String aminoAcidString,
String startCodons,
String baseOne,
String baseTwo,
String baseThree)
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Method Summary | |
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CompoundSet<Table.Codon> |
getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds,
CompoundSet<AminoAcidCompound> aminoAcidCompounds)
Returns the compound set of codons |
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. |
Integer |
getId()
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String |
getName()
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boolean |
isStart(AminoAcidCompound compound)
Returns true if the given compound was a start codon in this codon table. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public IUPACParser.IUPACTable(String name, int id, String aminoAcidString, String startCodons, String baseOne, String baseTwo, String baseThree)
public IUPACParser.IUPACTable(String name, Integer id, String aminoAcidString, String startCodons)
Method Detail |
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public Integer getId()
public String getName()
public boolean isStart(AminoAcidCompound compound) throws IllegalStateException
isStart
in interface Table
IllegalStateException
- Thrown if
getCodons(CompoundSet, CompoundSet)
was not called first.public List<Table.Codon> getCodons(CompoundSet<NucleotideCompound> nucelotides, CompoundSet<AminoAcidCompound> aminoAcids)
getCodons
in interface Table
nucleotides
- The nucleotide set to use when building BioJava
representations of codonsaminoAcids
- The target amino acid compounds objectspublic CompoundSet<Table.Codon> getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds)
getCodonCompoundSet
in interface Table
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