Changeset 4362

Timestamp:

Oct 24, 2012, 8:24:43 AM (10 years ago)

Author:

Fredrik Levander

Message:

Refs #773. Further optimisation of counting.

File:

• trunk/plugin/src/org/proteios/plugins/CombinedHitsReport.java (modified) (7 diffs)

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

@@ -699 +699 @@
       log.debug("First sorting done. Setting score values");
       // Set dummy scores
+      float[][] combScores = new float[combinedHits.size()][score_types.length];
+      int index=0;
       for (CombinedHit ch : combinedHits)
       {
@@ -714 +716 @@
             }
           }
-        }
+          combScores[index][i]=ch.scores[i];
+        }
+        index++;
       }
       float[][] revScores = new float[revCombinedHits.size()][score_types.length];
-      int index=0;
+      index=0;
       for (CombinedHit ch : revCombinedHits)
       {
@@ -737 +741 @@
         index++;
       }
-      log.debug("Adding of extreme scores done.");
+      log.debug("Addition of extreme scores done.");
       // count spots
       int spots = 0;
@@ -778 +782 @@
       }
       log.debug("Counting better hits for targets.");
-      countBetterRandomHits(combinedHits, revScores);
+      countBetterRandomHits(combinedHits, combScores, revScores);
       log.debug("Counting better hits for decoys.");
-      countBetterRandomHits(revCombinedHits, revScores);
+      countBetterRandomHits(revCombinedHits, revScores, revScores);
       log.debug("Counting done. Sorting after score counts");
       if (progress != null)
@@ -957 +961 @@
 
 
-  private void countBetterRandomHits(List<CombinedHit> combinedHits,
+  private void countBetterRandomHits(List<CombinedHit> combinedHits, float[][] combScores,
       float[][] revScores)
   {
@@ -969 +973 @@
        * Count how many reverse hits that have better score of any type.
        * If the reverse hit has all the score types that the forward hit
-       * has, and any of them is above those of the forward hit, it should
+       * has, and all of them are above those of the forward hit, it should
        * be counted.
        */
@@ -977 +981 @@
         for (int k = 0; k < scoreSize; k++)
         {
-            if ((!compareE[k] && (revScores[j][k] < combinedHits
-              .get(i).scores[k])) || (compareE[k] && (revScores
-              [j][k] > combinedHits.get(i).scores[k])))
-            {
-              above = false;
-            }
+          if (compareE[k])
+          {
+            if (revScores[j][k]>combScores[i][k]) above=false;
+          }
+          else
+          {
+            if (revScores[j][k]<combScores[i][k]) above=false;
+          }
         }
         if (above)