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

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

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 Details
- 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.