From a72a5a7b1a488ce10d9d148ad046b0154dd455d1 Mon Sep 17 00:00:00 2001
From: weisburd <weisburd@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 23 Apr 2010 15:49:06 +0000
Subject: [PATCH] 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
---
 .../gatk/walkers/annotator/AminoAcid.java     | 59 +++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcid.java

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcid.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcid.java
new file mode 100755
index 000000000..98c9415d4
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcid.java
@@ -0,0 +1,59 @@
+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());
+    }
+}