org.biojava.nbio.core.sequence.transcription

Interface Table

All Known Implementing Classes:

IUPACParser.IUPACTable

public interface Table

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

Author:

ayates

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
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

Modifier and Type	Method and Description
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.