A class that represents the model parameters for all of the Gaussian models for all cycles.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@273 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/fourbasecaller/BasecallingReadModel.java

@@ -0,0 +1,44 @@
+package org.broadinstitute.sting.playground.fourbasecaller;
+
+import org.broadinstitute.sting.utils.Utils;
+
+public class BasecallingReadModel {
+    private BasecallingBaseModel[] basemodels = null;
+
+    public BasecallingReadModel(int readLength) {
+        basemodels = new BasecallingBaseModel[readLength];
+
+        for (int i = 0; i < readLength; i++) {
+            basemodels[i] = new BasecallingBaseModel();
+        }
+    }
+
+    public void addTrainingPoint(int cycle, char basePrev, char baseCur, byte qualCur, double[] fourintensity) {
+        basemodels[cycle].addTrainingPoint(basePrev, baseCur, qualCur, fourintensity);
+    }
+
+    public double[][] computeLikelihoods(int cycle, char basePrev, byte qualPrev, double[] fourintensity) {
+        return basemodels[cycle].computeLikelihoods(cycle, basePrev, qualPrev, fourintensity);
+    }
+
+    public FourProb computeProbabilities(int cycle, char basePrev, byte qualPrev, double[] fourintensity) {
+        double[][] likes = computeLikelihoods(cycle, basePrev, qualPrev, fourintensity);
+
+        double[] probs = new double[4];
+        int[] baseindices = { 0, 1, 2, 3 };
+        double total = 0;
+
+        for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) {
+            for (int basePrevIndex = 0; basePrevIndex < 4; basePrevIndex++) {
+                probs[baseCurIndex] += likes[basePrevIndex][baseCurIndex];
+            }
+            total += probs[baseCurIndex];
+        }
+
+        for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) {
+            probs[baseCurIndex] /= total;
+        }
+
+        return new FourProb(baseindices, probs);
+    }
+}