94 lines
2.8 KiB
Java
Executable File
94 lines
2.8 KiB
Java
Executable File
/*
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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
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils;
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/**
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* Represents a single amino acid.
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*/
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public class AminoAcid {
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private String name;
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private String threeLetterCode;
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private String letter;
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/**
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* Constructor.
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*
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* @param letter The 1 letter code. (eg. I). This is '*' for the stop codon.
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* @param name The full name of the AA (eg. Isoleucine).
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* @param code The 3 letter code. (eg. Ile).
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*/
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public AminoAcid( String letter, String name, String code) {
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this.name = name;
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this.threeLetterCode = code;
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this.letter = letter;
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}
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/** Equality based on the amino acid code. */
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public boolean equals(Object o) {
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if (this == o) { return true; }
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if (o == null || !(o instanceof AminoAcid)) { return false; }
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final AminoAcid aminoAcid = (AminoAcid) o;
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return !(getCode() != null ? !getCode().equals(aminoAcid.getCode()) : aminoAcid.getCode() != null);
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}
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/** Hashes the three letter code. */
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public int hashCode() {
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return (getCode() != null ? getCode().hashCode() : 0);
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}
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/**
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* Returns the full name of this AA.
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*/
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public String getName() { return name; }
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/**
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* Returns the 1 letter code for this AA.
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*/
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public String getLetter() { return letter; }
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/**
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* Returns the 3 letter code.
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*/
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public String getCode() { return threeLetterCode; }
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/** Returns true if the amino acid is really just a stop codon. */
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public boolean isStop() {
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return "*".equals(getLetter());
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}
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/** Returns true if the amino acid is really just a stop codon. */
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public boolean isUnknown() {
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return "X".equals(getLetter());
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}
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public String toString() {
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return name;
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}
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}
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