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. Codon Indexes (or states) are defined as in GeneralizedCodons

Version:
$Id: CodonTable.java,v 1.10 2003/09/04 03:22:34 matt Exp $
Author:
Matthew Goode, Alexei Drummond

Field Summary
static int ALTERNATIVE_YEAST
          TypeID for Alternative Yeast
static int ASCIDIAN_MITOCHONDRIAL
          TypeID for Ascidian Mitochondrial
static int BACTERIAL
          TypeID for Bacterial
static int BLEPHARISMA_NUCLEAR
          TypeID for Blepharisma Nuclear
static int CILATE
          TypeID for Cilate
static int ECHINODERM_MITOCHONDRIAL
          TypeID for Echinoderm Mitochondrial
static int EUPLOTID_NUCLEAR
          TypeID for Euplotid Nuclear
static int FLATWORM_MITOCHONDRIAL
          TypeID for Flatworm Mitochondrial
static int INVERTEBRATE_MITOCHONDRIAL
          TypeID for Invertebrate Mitochondrial
static int MOLD_PROTOZOAN_MITOCHONDRIAL
          TypeID for Mold Protozoan Mitochondrial
static int MYCOPLASMA
          TypeID for Mycoplasma
static java.lang.String[] ORGANISM_TYPE_NAMES
          A textual version of an organism type - type is index into array
static int UNIVERSAL
          TypeID for Universal
static int VERTEBRATE_MITOCHONDRIAL
          TypeID for Vertebrate Mitochondrial
static int YEAST
          TypeID for Yeast
 
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
 int getAminoAcidStateFromStates(int[] states)
           
 char[][] getCodonsFromAminoAcidChar(char aminoAcidChar)
           
 char[][] getCodonsFromAminoAcidState(int aminoAcidState)
           
 int[] getIUPACStatesFromAminoAcidState(int aminoAcid)
           
 int getNumberOfTerminatorIndexes()
          Returns the number of terminator amino acids.
 int getOrganismTypeID()
           
 int[] getStatesFromAminoAcidState(int aminoAcid)
           
 int[] getTerminatorIndexes()
           
 boolean isSynonymous(int codonIndexOne, int codonIndexTwo)
           
 

Field Detail

UNIVERSAL

static final int UNIVERSAL
TypeID for Universal

See Also:
Constant Field Values

VERTEBRATE_MITOCHONDRIAL

static final int VERTEBRATE_MITOCHONDRIAL
TypeID for Vertebrate Mitochondrial

See Also:
Constant Field Values

YEAST

static final int YEAST
TypeID for Yeast

See Also:
Constant Field Values

MOLD_PROTOZOAN_MITOCHONDRIAL

static final int MOLD_PROTOZOAN_MITOCHONDRIAL
TypeID for Mold Protozoan Mitochondrial

See Also:
Constant Field Values

MYCOPLASMA

static final int MYCOPLASMA
TypeID for Mycoplasma

See Also:
Constant Field Values

INVERTEBRATE_MITOCHONDRIAL

static final int INVERTEBRATE_MITOCHONDRIAL
TypeID for Invertebrate Mitochondrial

See Also:
Constant Field Values

CILATE

static final int CILATE
TypeID for Cilate

See Also:
Constant Field Values

ECHINODERM_MITOCHONDRIAL

static final int ECHINODERM_MITOCHONDRIAL
TypeID for Echinoderm Mitochondrial

See Also:
Constant Field Values

EUPLOTID_NUCLEAR

static final int EUPLOTID_NUCLEAR
TypeID for Euplotid Nuclear

See Also:
Constant Field Values

ASCIDIAN_MITOCHONDRIAL

static final int ASCIDIAN_MITOCHONDRIAL
TypeID for Ascidian Mitochondrial

See Also:
Constant Field Values

FLATWORM_MITOCHONDRIAL

static final int FLATWORM_MITOCHONDRIAL
TypeID for Flatworm Mitochondrial

See Also:
Constant Field Values

BLEPHARISMA_NUCLEAR

static final int BLEPHARISMA_NUCLEAR
TypeID for Blepharisma Nuclear

See Also:
Constant Field Values

BACTERIAL

static final int BACTERIAL
TypeID for Bacterial

See Also:
Constant Field Values

ALTERNATIVE_YEAST

static final int ALTERNATIVE_YEAST
TypeID for Alternative Yeast

See Also:
Constant Field Values

ORGANISM_TYPE_NAMES

static final java.lang.String[] ORGANISM_TYPE_NAMES
A textual version of an organism type - type is index into array

Method Detail

getAminoAcidChar

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

int getAminoAcidState(char[] codon)
Returns the state associated with AminoAcid represented by 'codon'

Returns:
'?' if codon unknown or wrong length
See Also:
AminoAcids

getCodonsFromAminoAcidState

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

getCodonsFromAminoAcidChar

char[][] getCodonsFromAminoAcidChar(char aminoAcidChar)

getAminoAcidCharFromCodonIndex

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


getAminoAcidStateFromCodonIndex

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


getIUPACStatesFromAminoAcidState

int[] getIUPACStatesFromAminoAcidState(int aminoAcid)

getStatesFromAminoAcidState

int[] getStatesFromAminoAcidState(int aminoAcid)

getAminoAcidStateFromStates

int getAminoAcidStateFromStates(int[] states)
Returns:
The AminoAcid states given the nucleotides states (array should be of size 3)

getTerminatorIndexes

int[] getTerminatorIndexes()
Returns:
the codon states of terminator amino acids.

getNumberOfTerminatorIndexes

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


getOrganismTypeID

int getOrganismTypeID()
Returns:
the type of this organism (see defined type constants)

isSynonymous

boolean isSynonymous(int codonIndexOne,
                     int codonIndexTwo)
Returns:
true if the amino acids that map to two codons are the same (synonymous). False otherwise