fixing kiran's busted build

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@686 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 21:29:04 +00:00 · 2009-05-12 21:29:04 +00:00 · 5b47c5ab6c
parent 4f2c8bf0a3
commit 5b47c5ab6c
1 changed files with 100 additions and 0 deletions
--- a/java/src/org/broadinstitute/sting/secondarybase/FourProb.java
+++ b/java/src/org/broadinstitute/sting/secondarybase/FourProb.java
@ -0,0 +1,100 @@
+package org.broadinstitute.sting.secondarybase;
+
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.QualityUtils;
+
+/**
+ * FourProb represents four base hypotheses, their probabilities, and the ranking among one another.
+ *
+ * @author Kiran Garimella
+ */
+public class FourProb {
+    private double[] baseProbs;
+    private int[] baseIndices;
+
+    /**
+     * Constructor for FourProb.
+     *
+     * @param baseLikes  the unsorted base hypothesis probabilities (in ACGT order).
+     */
+    public FourProb(double[][] baseLikes) {
+        double[] baseProbs = new double[4];
+        for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) {
+            for (int basePrevIndex = 0; basePrevIndex < baseLikes.length; basePrevIndex++) {
+                baseProbs[baseCurIndex] += baseLikes[basePrevIndex][baseCurIndex];
+            }
+        }
+
+        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];
+
+        for (int i = 0; i < 4; i++) {
+            this.baseProbs[i] = ascendingBaseProbs[3 - i];
+            this.baseIndices[i] = ascendingBaseIndices[3 - i];
+        }
+    }
+
+    /**
+     * Returns the index of the base at the specified rank.
+     *
+     * @param rank (0 = best, 3 = worst) the rank of the base whose index should be returned
+     * @return the index (0, 1, 2, 3).
+     */
+    public int indexAtRank(int rank) { return baseIndices[rank]; }
+
+    /**
+     * Returns the base label of the base at the specified rank.
+     * @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)); }
+
+    /**
+     * Returns the probability of the base at the specified rank.
+     * @param rank (0 = best, 3 = worst) the rank of the base whose index should be returned
+     * @return the probability of the base (0.0-1.0)
+     */
+    public double probAtRank(int rank) { return baseProbs[rank]; }
+
+    /**
+     * Returns the quality score of the base at the specified rank.
+     * @param rank (0 = best, 3 = worst) the rank of the base whose index should be returned
+     * @return the quality score of the base (0-40)
+     */
+    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.
+     * 
+     * @return a prettily formatted Sting containing the base and quality score in rank order.
+     */
+    public String toString() {
+        return (
+                "[" + baseAtRank(0) + ":" + qualAtRank(0) + " "
+                    + baseAtRank(1) + ":" + qualAtRank(1) + " "
+                    + baseAtRank(2) + ":" + qualAtRank(2) + " "
+                    + baseAtRank(3) + ":" + qualAtRank(3) + "]"
+               );
+    }
+}