Changeset 4272

Timestamp:

Jan 2, 2012, 6:29:50 PM (11 years ago)

Author:

Fredrik Levander

Message:

Refs #773. Updated FDR calculation for performance.

File:

• trunk/plugin/src/org/proteios/plugins/CombinedHitsReport.java (modified) (4 diffs)

trunk/plugin/src/org/proteios/plugins/CombinedHitsReport.java

@@ -400 +400 @@
         // Restrict so that the score type starts with:
         hitQuery.setParameter("scoretype", score_types[i] + "%", null);
+        if (progress != null)
+        {
+          progress.display((50 * i / score_types.length),
+            "Query " + (i + 1) + " of " + score_types.length);
+        }
         Iterator<Hit> hitIt = hitQuery.iterate(dc);
         List<Hit> hitlist = new ArrayList<Hit>();
@@ -422 +427 @@
 
         Iterator<Hit> hitit = hitlist.iterator();
-        if (progress != null)
-        {
-          progress.display((50 * i / score_types.length),
-            "Query " + (i + 1) + " of " + score_types.length);
-        }
         boolean first = true;
         int last_index = 0, last_rev_index = 0, forwardSize = combinedHits
@@ -799 +799 @@
       int combinedHitsSize = combinedHits.size();
       int revCombinedHitsSize = revCombinedHits.size();
+      int forward_idx=0;
+      int reverse_idx=0;
       for (int i = 0; i < combinedHitsSize; i++)
       {
-        int forwardCount = 0;
+        //int forwardCount = 0;
         int count = combinedHits.get(i).count;
-        for (int j = 0; j < combinedHitsSize; j++)
+        for (int j = forward_idx; j < combinedHitsSize; j++)
         {
           if (count >= combinedHits.get(j).count)
           {
-            forwardCount++;
+            forward_idx=j;
           }
           else
             break;
         }
-        int reverseCount = 0;
-        for (int j = 0; j < revCombinedHitsSize; j++)
+        //int reverseCount = 0;
+        for (int j = reverse_idx; j < revCombinedHitsSize; j++)
         {
           if (count >= revCombinedHits.get(j).count)
           {
-            reverseCount++;
+            reverse_idx=j++;
           }
           else
             break;
         }
-        double combinedFDR = ((double) reverseCount / (decoySize * (double) forwardCount));
+        double combinedFDR = ((double) reverse_idx / (decoySize * (double) forward_idx));
         // Conservative estimate
         if (combinedFDR == 0)
@@ -840 +842 @@
       if (keepDecoys)
       {
+        forward_idx=0;
+        reverse_idx=0;
         for (int i = 0; i < revCombinedHitsSize; i++)
         {
-          double forwardCount = 0d;
-          double count = revCombinedHits.get(i).count;
-          for (int j = 0; j < combinedHitsSize; j++)
+          int count = revCombinedHits.get(i).count;
+          for (int j = forward_idx; j < combinedHitsSize; j++)
           {
             if (count >= combinedHits.get(j).count)
             {
-              forwardCount++;
+              forward_idx=j;
             }
             else
               break;
           }
-          double reverseCount = 0d;
-          for (int j = 0; j < revCombinedHitsSize; j++)
+          for (int j = reverse_idx; j < revCombinedHitsSize; j++)
           {
             if (count >= revCombinedHits.get(j).count)
             {
-              reverseCount++;
+              reverse_idx=j;
             }
             else
               break;
           }
-          double combinedFDR = (reverseCount / (decoySize * forwardCount));
+          double combinedFDR = ((double) reverse_idx / (decoySize * (double) forward_idx));
           revCombinedHits.get(i).fdr = combinedFDR;
           // Now set the fdr value in the hit