org.biojava3.core.sequence.transcription
Interface Table

All Known Implementing Classes:
IUPACParser.IUPACTable

public interface Table

Provides a way of separating us from the specific IUPACTable even though this is the only implementing class for the interface.

Author:
ayates

Nested Class Summary
static class Table.CaseInsensitiveTriplet
          Class used to hold three nucleotides together and allow for equality to be assessed in a case insensitive manner.
static class Table.Codon
          Instance of a Codon which is 3 NucleotideCompounds, its corresponding AminoAcidCompound and if it is a start or stop codon.
 
Method Summary
 CompoundSet<Table.Codon> getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds)
           
 List<Table.Codon> getCodons(CompoundSet<NucleotideCompound> nucelotides, CompoundSet<AminoAcidCompound> aminoAcids)
           
 boolean 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 Detail

getCodons

List<Table.Codon> getCodons(CompoundSet<NucleotideCompound> nucelotides,
                            CompoundSet<AminoAcidCompound> aminoAcids)

getCodonCompoundSet

CompoundSet<Table.Codon> getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds,
                                             CompoundSet<AminoAcidCompound> aminoAcidCompounds)

isStart

boolean 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. This is as accurate a call as we can make with an AminoAcidCompound.