pal.datatype
Interface CodonTable

All Superinterfaces:
java.io.Serializable

public interface CodonTable
extends java.io.Serializable

Describes a device for translating Nucleotide triplets or codon indices into amino acid codes


Method Summary
 char getAminoAcidChar(char[] codon)
          Returns the char associated with AminoAcid represented by 'codon'
 char getAminoAcidCharFromCodonIndex(int codonIndex)
          Returns the amino acid char at the corresponding codonIndex
 int getAminoAcidState(char[] codon)
          Returns the state associated with AminoAcid represented by 'codon'
 int getAminoAcidStateFromCodonIndex(int codonIndex)
          Returns the amino acid state at the corresponding codonIndex
 char[][] getCodonsFromAminoAcidChar(char aminoAcidChar)
           
 char[][] getCodonsFromAminoAcidState(int aminoAcidState)
           
 int getNumberOfTerminatorIndexes()
          Returns the number of terminator amino acids.
 int[] getTerminatorIndexes()
          Returns the codon indexes of terminator amino acids.
 

Method Detail

getAminoAcidChar

public char getAminoAcidChar(char[] codon)
Returns the char associated with AminoAcid represented by 'codon'
Returns:
state for '?' if codon unknown or wrong length
See Also:
AminoAcids

getAminoAcidState

public int getAminoAcidState(char[] codon)
Returns the state associated with AminoAcid represented by 'codon'
Returns:
'?' if codon unknown or wrong length
See Also:
AminoAcids

getCodonsFromAminoAcidState

public char[][] getCodonsFromAminoAcidState(int aminoAcidState)
Returns:
all the possible codons for a given amino acid

getCodonsFromAminoAcidChar

public char[][] getCodonsFromAminoAcidChar(char aminoAcidChar)

getAminoAcidCharFromCodonIndex

public char getAminoAcidCharFromCodonIndex(int codonIndex)
Returns the amino acid char at the corresponding codonIndex

getAminoAcidStateFromCodonIndex

public int getAminoAcidStateFromCodonIndex(int codonIndex)
Returns the amino acid state at the corresponding codonIndex

getTerminatorIndexes

public int[] getTerminatorIndexes()
Returns the codon indexes of terminator amino acids.

getNumberOfTerminatorIndexes

public int getNumberOfTerminatorIndexes()
Returns the number of terminator amino acids.