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// (c) 1999-2001 PAL Development Core Team
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// This package may be distributed under the
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// terms of the Lesser GNU General Public License (LGPL)
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* Describes a device for translating Nucleotide triplets
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* or codon indices into amino acid codes.
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* Codon Indexes (or states) are defined as in GeneralizedCodons
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* @author Matthew Goode
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* @author Alexei Drummond
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* <li> 19 August 2003 - Added getAminoAcidStateFromIUPACStates()
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* @version $Id: CodonTable.java,v 1.10 2003/09/04 03:22:34 matt Exp $
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public interface CodonTable extends java.io.Serializable {
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/** TypeID for Universal */
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static final int UNIVERSAL = 0;
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/** TypeID for Vertebrate Mitochondrial*/
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static final int VERTEBRATE_MITOCHONDRIAL = 1;
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/** TypeID for Yeast */
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static final int YEAST = 2;
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/** TypeID for Mold Protozoan Mitochondrial */
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static final int MOLD_PROTOZOAN_MITOCHONDRIAL = 3;
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/** TypeID for Mycoplasma */
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static final int MYCOPLASMA = 4;
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/** TypeID for Invertebrate Mitochondrial */
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static final int INVERTEBRATE_MITOCHONDRIAL = 5;
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/** TypeID for Cilate */
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static final int CILATE = 6;
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/** TypeID for Echinoderm Mitochondrial */
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static final int ECHINODERM_MITOCHONDRIAL = 7;
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/** TypeID for Euplotid Nuclear */
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static final int EUPLOTID_NUCLEAR = 8;
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/** TypeID for Ascidian Mitochondrial */
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static final int ASCIDIAN_MITOCHONDRIAL = 9;
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/** TypeID for Flatworm Mitochondrial */
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static final int FLATWORM_MITOCHONDRIAL = 10;
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/** TypeID for Blepharisma Nuclear */
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static final int BLEPHARISMA_NUCLEAR = 11;
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/** TypeID for Bacterial */
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static final int BACTERIAL = 12;
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/** TypeID for Alternative Yeast */
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static final int ALTERNATIVE_YEAST = 13;
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* A textual version of an organism type - type is index into array
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static final String[] ORGANISM_TYPE_NAMES = {
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"Vertebrate Mitochondrial",
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"Mold Protozoan Mitochondrial",
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"Invertebrate Mitochondrial",
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"Echinoderm Mitochondrial",
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"Ascidian Mitochondrial",
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"Flatworm Mitochondrial",
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"Blepharisma Nuclear",
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* Returns the char associated with AminoAcid represented by 'codon'
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* @note char is as defined by AminoAcids.java
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* @return state for '?' if codon unknown or wrong length
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char getAminoAcidChar(char[] codon);
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* Returns the state associated with AminoAcid represented by 'codon'
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* @note state is as defined by AminoAcids.java
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* @return '?' if codon unknown or wrong length
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int getAminoAcidState(char[] codon);
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* @return all the possible codons for a given amino acid
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char[][] getCodonsFromAminoAcidState(int aminoAcidState);
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* @return all the possible codons for a given amino acid
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char[][] getCodonsFromAminoAcidChar(char aminoAcidChar);
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/** Returns the amino acid char at the corresponding codonIndex */
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char getAminoAcidCharFromCodonIndex(int codonIndex);
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/** Returns the amino acid state at the corresponding codonIndex */
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int getAminoAcidStateFromCodonIndex(int codonIndex);
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* @returns three IUPAC states representing the given amino acid
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* @note The returned array should not be altered, and implementations
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* should attempt to implement this as efficiently as possible
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* @note the returned array may not be enough to accurately reconstruct the amino acid (as it may be too ambiguous)
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int[] getIUPACStatesFromAminoAcidState(int aminoAcid);
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int[] getStatesFromAminoAcidState(int aminoAcid);
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* @return The AminoAcid states given the nucleotides states (array should be of size 3)
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int getAminoAcidStateFromStates(int[] states);
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* @return the codon states of terminator amino acids.
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int[] getTerminatorIndexes();
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* Returns the number of terminator amino acids.
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int getNumberOfTerminatorIndexes();
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* @return the type of this organism (see defined type constants)
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int getOrganismTypeID();
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* @return true if the amino acids that map to two codons are the same (synonymous). False otherwise
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boolean isSynonymous(int codonIndexOne, int codonIndexTwo);
added
removed
src/pal/datatype/CodonTable.java
