From ee2af3b423ab51ca4efdc4b3df4ebce66a391e0a Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 25 Jun 2009 20:49:12 +0000
Subject: [PATCH] I committed this too soon... reverting...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1106 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/secondarybase/FourProb.java         | 63 +++++++++----------
 1 file changed, 31 insertions(+), 32 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/secondarybase/FourProb.java b/java/src/org/broadinstitute/sting/secondarybase/FourProb.java
index af945ba91..49e4a9d04 100755
--- a/java/src/org/broadinstitute/sting/secondarybase/FourProb.java
+++ b/java/src/org/broadinstitute/sting/secondarybase/FourProb.java
@@ -1,8 +1,7 @@
 package org.broadinstitute.sting.secondarybase;
 
-import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.QualityUtils;
 
 /**
  * FourProb represents four base hypotheses, their probabilities, and the ranking among one another.
@@ -10,8 +9,8 @@ import org.broadinstitute.sting.utils.BaseUtils;
  * @author Kiran Garimella
  */
 public class FourProb {
-    private int[] baseIndices;
     private double[] baseProbs;
+    private int[] baseIndices;
 
     /**
      * Constructor for FourProb.
@@ -26,33 +25,18 @@ public class FourProb {
             }
         }
 
+        int[] baseIndices = {0, 1, 2, 3};
+        
+        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];
 
-        // store this information in sorted form
         for (int i = 0; i < 4; i++) {
-            if (baseProbs[i] > this.baseProbs[0]) {
-                this.baseProbs[1] = this.baseProbs[0];
-                this.baseIndices[1] = this.baseIndices[0];
-
-                this.baseProbs[0] = baseProbs[i];
-                this.baseIndices[0] = i;
-            } else if (baseProbs[i] > this.baseProbs[1]) {
-                this.baseProbs[2] = this.baseProbs[1];
-                this.baseIndices[2] = this.baseIndices[1];
-
-                this.baseProbs[1] = baseProbs[i];
-                this.baseIndices[1] = i;
-            } else if (baseProbs[i] > this.baseProbs[2]) {
-                this.baseProbs[3] = this.baseProbs[2];
-                this.baseIndices[3] = this.baseIndices[2];
-
-                this.baseProbs[2] = baseProbs[i];
-                this.baseIndices[2] = i;
-            } else {
-                this.baseProbs[3] = baseProbs[i];
-                this.baseIndices[3] = i;
-            }
+            this.baseProbs[i] = ascendingBaseProbs[3 - i];
+            this.baseIndices[i] = ascendingBaseIndices[3 - i];
         }
     }
 
@@ -70,8 +54,7 @@ public class FourProb {
      * @param rank (0 = best, 3 = worst) the rank of the base whose index should be returned
      * @return the base label (A, C, G, T).
      */
-    //public char baseAtRank(int rank) { return baseIndexToBase(indexAtRank(rank)); }
-    public char baseAtRank(int rank) { return BaseUtils.baseIndexToSimpleBase(indexAtRank(rank)); }
+    public char baseAtRank(int rank) { return baseIndexToBase(indexAtRank(rank)); }
 
     /**
      * Returns the probability of the base at the specified rank.
@@ -89,6 +72,22 @@ public class FourProb {
      */
     public byte qualAtRank(int rank) { return QualityUtils.probToQual(probAtRank(rank)); }
 
+    /**
+     * A utility method to convert a base index into a base label.
+     *
+     * @param baseIndex the index of the base (0, 1, 2, 3).
+     * @return A, C, G, T, or '.' if the base index can't be understood.
+     */
+    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 '.';
+        }
+    }
+
     /**
      * Prettily formats the FourProb info.
      * 
@@ -96,10 +95,10 @@ public class FourProb {
      */
     public String toString() {
         return (
-                "[" + baseAtRank(0) + ":" + probAtRank(0) + " "
-                    + baseAtRank(1) + ":" + probAtRank(1) + " "
-                    + baseAtRank(2) + ":" + probAtRank(2) + " "
-                    + baseAtRank(3) + ":" + probAtRank(3) + "]"
+                "[" + baseAtRank(0) + ":" + qualAtRank(0) + " "
+                    + baseAtRank(1) + ":" + qualAtRank(1) + " "
+                    + baseAtRank(2) + ":" + qualAtRank(2) + " "
+                    + baseAtRank(3) + ":" + qualAtRank(3) + "]"
                );
     }
 }