From 59334b027086be540c8768888742312f3cb55f14 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 2 Apr 2009 22:08:31 +0000
Subject: [PATCH] A convenience class for manipulation base probability
 distributions.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@274 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/fourbasecaller/FourProb.java   | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/playground/fourbasecaller/FourProb.java

diff --git a/java/src/org/broadinstitute/sting/playground/fourbasecaller/FourProb.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/FourProb.java
new file mode 100755
index 000000000..6397ad911
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/fourbasecaller/FourProb.java
@@ -0,0 +1,47 @@
+package org.broadinstitute.sting.playground.fourbasecaller;
+
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.QualityUtils;
+
+public class FourProb {
+    private double[] baseProbs;
+    private int[] baseIndices;
+
+    public FourProb(int[] baseIndices, double[] baseProbs) {
+        Integer[] perm = Utils.SortPermutation(baseProbs);
+        double[] ascendingBaseProbs = Utils.PermuteArray(baseProbs, perm);
+        int[] ascendingBaseIndices = Utils.PermuteArray(baseIndices, perm);
+
+        this.baseProbs = new double[4];
+        this.baseIndices = new int[4];
+
+        for (int i = 0; i < 4; i++) {
+            this.baseProbs[i] = ascendingBaseProbs[3 - i];
+            this.baseIndices[i] = ascendingBaseIndices[3 - i];
+        }
+    }
+
+    public int indexAtRank(int rank) { return baseIndices[rank]; }
+    public char baseAtRank(int rank) { return baseIndexToBase(indexAtRank(rank)); }
+    public double probAtRank(int rank) { return baseProbs[rank]; }
+    public byte qualAtRank(int rank) { return QualityUtils.probToQual(probAtRank(rank)); }
+
+    private char baseIndexToBase(int baseIndex) {
+        switch (baseIndex) {
+            case 0: return 'A';
+            case 1: return 'C';
+            case 2: return 'G';
+            case 3: return 'T';
+            default: return '.';
+        }
+    }
+
+    public String toString() {
+        return (
+                "[" + baseAtRank(0) + ":" + qualAtRank(0) + " "
+                    + baseAtRank(1) + ":" + qualAtRank(1) + " "
+                    + baseAtRank(2) + ":" + qualAtRank(2) + " "
+                    + baseAtRank(3) + ":" + qualAtRank(3) + "]"
+               );
+    }
+}