java.lang.Object

org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable

All Implemented Interfaces:: Table

Enclosing class:: IUPACParser

public static class IUPACParser.IUPACTable extends Object implements Table

Holds the concept of a codon table from the IUPAC format

Author:: Andy Yates

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.core.sequence.transcription.Table
Table.CaseInsensitiveTriplet, Table.Codon
Constructor Summary

Constructors

Constructor

Description

IUPACTable(String name, int id, String aminoAcidString, String startCodons, String baseOne, String baseTwo, String baseThree)

IUPACTable(String name, Integer id, String aminoAcidString, String startCodons)

Constructor which uses the basic IUPAC codon table format.
Method Summary

Modifier and Type

Method

Description

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()

String

getName()

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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- IUPACTable
  
  public IUPACTable(String name, int id, String aminoAcidString, String startCodons, String baseOne, String baseTwo, String baseThree)
- IUPACTable
  
  public IUPACTable(String name, Integer id, String aminoAcidString, String startCodons)
  
  Constructor which uses the basic IUPAC codon table format. Useful if you need to specify your own IUPAC table with minimal definitions from your side.
Method Details
- getId
  
  public Integer getId()
- getName
  
  public String getName()
- isStart
  
  public boolean isStart(AminoAcidCompound compound) throws IllegalStateException
  
  Returns true if the given compound was a start codon in this codon table. This will report true if the compound could ever have been a start codon.
  
  Specified by:
  
  isStart in interface Table
  
  Throws:
  
  IllegalStateException - Thrown if getCodons(CompoundSet, CompoundSet) was not called first.
- getCodons
  
  public 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.
  
  Specified by:
  
  getCodons in interface Table
  
  Parameters:
  
  nucleotides - The nucleotide set to use when building BioJava representations of codons
  
  aminoAcids - The target amino acid compounds objects
- getCodonCompoundSet
  
  public CompoundSet<Table.Codon> getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds)
  
  Returns the compound set of codons
  
  Specified by:
  
  getCodonCompoundSet in interface Table

Class IUPACParser.IUPACTable

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.core.sequence.transcription.Table

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

IUPACTable

IUPACTable

Method Details

getId

getName

isStart

getCodons

getCodonCompoundSet