70 lines
2.6 KiB
Java
70 lines
2.6 KiB
Java
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package org.broadinstitute.sting.utils.analysis;
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import java.util.HashMap;
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* @author chartl
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* @since June 28, 2010
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*/
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public class AminoAcidTable {
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public HashMap<String,AminoAcid> tableByCodon = new HashMap<String,AminoAcid>(21);
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public HashMap<String,AminoAcid> tableByCode = new HashMap<String,AminoAcid>(21);
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public AminoAcidTable() {
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for ( AminoAcid acid : AminoAcid.values() ) {
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tableByCode.put(acid.getCode(),acid);
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for ( String codon : acid.codons ) {
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tableByCodon.put(codon,acid);
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}
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}
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}
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// todo -- these functions are for the genomic annotator and are named too generally -- they are
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// todo -- actually accessors by codon; thus should be more specific.
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public AminoAcid getEukaryoticAA(String codon) {
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return tableByCodon.get(codon.toUpperCase());
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}
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public AminoAcid getMitochondrialAA(String codon, boolean isFirst) {
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String upperCodon = codon.toUpperCase();
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if ( isFirst && upperCodon.equals("ATT") || upperCodon.equals("ATA") ) {
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return AminoAcid.Methionine;
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} else if ( upperCodon.equals("AGA") || upperCodon.equals("AGG") ) {
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return AminoAcid.Stop_codon;
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} else if ( upperCodon.equals("TGA") ) {
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return AminoAcid.Tryptophan;
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} else {
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return tableByCodon.get(upperCodon);
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}
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}
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public AminoAcid getAminoAcidByCode(String code) {
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return tableByCode.get(code);
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}
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}
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