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Data object for representing a single amino acid 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3248 348d0f76-0448-11de-a6fe-93d51630548a
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weisburd 2010-04-23 15:49:06 +00:00
parent e7c0ded40e
commit a72a5a7b1a
1 changed files with 59 additions and 0 deletions
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59
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcid.java 100755
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package org.broadinstitute.sting.playground.gatk.walkers.annotator;
/**
* Represents a single amino acid.
*/
public class AminoAcid {
private String name;
private String code;
private String letter;
/**
* Constructor.
*
* @param letter The 1 letter code. (eg. I). This is '*' for the stop codon.
* @param name The full name of the AA (eg. Isoleucine).
* @param code The 3 letter code. (eg. Ile).
*/
public AminoAcid( String letter, String name, String code) {
this.name = name;
this.code = code;
this.letter = letter;
}
/** Equality based on the amino acid code. */
public boolean equals(Object o) {
if (this == o) { return true; }
if (o == null || !(o instanceof AminoAcid)) { return false; }
final AminoAcid aminoAcid = (AminoAcid) o;
return !(getCode() != null ? !getCode().equals(aminoAcid.getCode()) : aminoAcid.getCode() != null);
}
/** Hashes the three letter code. */
public int hashCode() {
return (getCode() != null ? getCode().hashCode() : 0);
}
/**
* Returns the full name of this AA.
*/
public String getName() { return name; }
/**
* Returns the 1 letter code for this AA.
*/
public String getLetter() { return letter; }
/**
* Returns the 3 letter code.
*/
public String getCode() { return code; }
/** Returns true if the amino acid is really just a stop codon. */
public boolean isStop() {
return "*".equals(getLetter());
}
}