@@ -0,0 +1,1569 @@
+package org.broadinstitute.sting.playground.gatk.walkers.annotator;%0A%0A/**%0A * Represents a single amino acid.%0A */%0Apublic class AminoAcid %7B%0A    private String name;%0A    private String code;%0A    private String letter;%0A%0A%0A    /**%0A     * Constructor.%0A     *%0A     * @param letter The 1 letter code. (eg. I). This is '*' for the stop codon.%0A     * @param name The full name of the AA (eg. Isoleucine).%0A     * @param code The 3 letter code. (eg. Ile).%0A     */%0A    public AminoAcid( String letter, String name, String code) %7B%0A        this.name = name;%0A        this.code = code;%0A        this.letter = letter;%0A    %7D%0A%0A    /** Equality based on the amino acid code. */%0A    public boolean equals(Object o) %7B%0A        if (this == o) %7B return true; %7D%0A        if (o == null %7C%7C !(o instanceof AminoAcid)) %7B return false; %7D%0A%0A        final AminoAcid aminoAcid = (AminoAcid) o;%0A        return !(getCode() != null ? !getCode().equals(aminoAcid.getCode()) : aminoAcid.getCode() != null);%0A    %7D%0A%0A    /** Hashes the three letter code. */%0A    public int hashCode() %7B%0A        return (getCode() != null ? getCode().hashCode() : 0);%0A    %7D%0A%0A    /**%0A     * Returns the full name of this AA.%0A     */%0A    public String getName() %7B return name; %7D%0A%0A    /**%0A     * Returns the 1 letter code for this AA.%0A     */%0A    public String getLetter() %7B return letter; %7D%0A%0A    /**%0A     * Returns the 3 letter code.%0A     */%0A    public String getCode() %7B return code; %7D%0A%0A%0A    /** Returns true if the amino acid is really just a stop codon. */%0A    public boolean isStop() %7B%0A        return %22*%22.equals(getLetter());%0A    %7D%0A%7D%0A

Data object for representing a single amino acid