Changeset 4271

Timestamp:

Jan 2, 2012, 5:41:40 PM (11 years ago)

Author:

Fredrik Levander

Message:

Refs #773. Updated sorting and some loops for better performance.

File:

• trunk/plugin/src/org/proteios/plugins/CombinedHitsReport.java (modified) (16 diffs)

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

@@ -36 +36 @@
 import org.proteios.core.ItemQuery;
 import org.proteios.core.ItemResultIterator;
-import org.proteios.core.ItemResultList;
 import org.proteios.core.Permission;
 import org.proteios.core.PermissionDeniedException;
@@ -365 +364 @@
           hitQuery.setPermanentParameter("localSampleId",
             localSampleId, null);
-          hitQuery.orderPermanent(Orders.asc(Hql
-            .property("peakListFile")));
-          hitQuery.orderPermanent(Orders.asc(Hql
-            .property("spectrumStringId")));
         }
       }
@@ -385 +380 @@
       output.write("False discovery rate cutoff: " + Float
         .valueOf((float) fdrCutOff) + "\n");
-      if (proteins)
-      {
-        output.write("Protein level report\n");
-        hitQuery.orderPermanent(Orders.asc(Hql.property("externalId")));
-      }
-      else
-      {
-        output.write("Peptide level report\n");
-        hitQuery
-          .orderPermanent(Orders.asc(Hql.property("description")));
-      }
       log.info("CombinedHitsReport: Random text prefix " + reverseText);
       log.info("CombinedHitsReport: FDR cutoff " + fdrCutOff);
@@ -402 +386 @@
         Expressions.parameter("protein")));
       hitQuery.setPermanentParameter("protein", proteins, null);
+      if (proteins)
+      {
+        output.write("Protein level report\n");
+      }
+      else
+      {
+        output.write("Peptide level report\n");
+      }
       for (int i = 0; i < score_types.length; i++)
       {
@@ -408 +400 @@
         // Restrict so that the score type starts with:
         hitQuery.setParameter("scoretype", score_types[i] + "%", null);
-        ItemResultList<Hit> hitlist = hitQuery.list(dc);
+        Iterator<Hit> hitIt = hitQuery.iterate(dc);
+        List<Hit> hitlist = new ArrayList<Hit>();
+        while (hitIt.hasNext())
+        {
+          hitlist.add(hitIt.next());
+        }
         output.write("Score type:" + score_types[i]);
         int queryhits = hitlist.size();
@@ -418 +415 @@
           actual_score_types++;
         }
+        if (!proteins && localSampleId != null)
+        {
+          Comparator<Hit> hitSorter = new HitFileAndSpectrumStringIdAndDescriptionSortForHit();
+          Collections.sort(hitlist, hitSorter);
+        }
+
         Iterator<Hit> hitit = hitlist.iterator();
         if (progress != null)
@@ -557 +560 @@
                 Integer currentFileId = currenthit
                   .getPeakListFile().getId();
+                log
+                  .debug("File ID:" + currentFileId + " spectrum: " + currenthit
+                    .getSpectrumStringId() + " description: " + currenthit
+                    .getDescription());
                 // If there is a sample id we sort on input
                 // filename
@@ -790 +797 @@
       double lowestFDR = 1d / (double) combinedHits.size();
       // Calculate FDR
-      for (int i = 0; i < combinedHits.size(); ++i)
-      {
-        double forwardCount = 0d;
-        for (int j = 0; j < combinedHits.size(); ++j)
-        {
-          if (combinedHits.get(i).count >= combinedHits.get(j).count)
+      int combinedHitsSize = combinedHits.size();
+      int revCombinedHitsSize = revCombinedHits.size();
+      for (int i = 0; i < combinedHitsSize; i++)
+      {
+        int forwardCount = 0;
+        int count = combinedHits.get(i).count;
+        for (int j = 0; j < combinedHitsSize; j++)
+        {
+          if (count >= combinedHits.get(j).count)
           {
             forwardCount++;
           }
-        }
-        double reverseCount = 0d;
-        for (int j = 0; j < revCombinedHits.size(); ++j)
-        {
-          if (combinedHits.get(i).count >= revCombinedHits.get(j).count)
+          else
+            break;
+        }
+        int reverseCount = 0;
+        for (int j = 0; j < revCombinedHitsSize; j++)
+        {
+          if (count >= revCombinedHits.get(j).count)
           {
             reverseCount++;
           }
-        }
-        double combinedFDR = (reverseCount / (decoySize * forwardCount));
+          else
+            break;
+        }
+        double combinedFDR = ((double) reverseCount / (decoySize * (double) forwardCount));
         // Conservative estimate
         if (combinedFDR == 0)
@@ -826 +840 @@
       if (keepDecoys)
       {
-        for (int i = 0; i < revCombinedHits.size(); ++i)
+        for (int i = 0; i < revCombinedHitsSize; i++)
         {
           double forwardCount = 0d;
-          for (int j = 0; j < combinedHits.size(); ++j)
+          double count = revCombinedHits.get(i).count;
+          for (int j = 0; j < combinedHitsSize; j++)
           {
-            if (revCombinedHits.get(i).count >= combinedHits.get(j).count)
+            if (count >= combinedHits.get(j).count)
             {
               forwardCount++;
             }
+            else
+              break;
           }
           double reverseCount = 0d;
-          for (int j = 0; j < revCombinedHits.size(); ++j)
+          for (int j = 0; j < revCombinedHitsSize; j++)
           {
-            if (revCombinedHits.get(i).count >= revCombinedHits
-              .get(j).count)
+            if (count >= revCombinedHits.get(j).count)
             {
               reverseCount++;
             }
+            else
+              break;
           }
           double combinedFDR = (reverseCount / (decoySize * forwardCount));
@@ -877 +895 @@
         if (progress != null)
         {
-          progress.display(90, "Wrote standard hits to file");
+          progress.display(90, "Wrote target hits to file");
         }
       }
@@ -917 +935 @@
       }
       output.close();
+      if (progress != null)
+      {
+        progress.display(95, "Wrote hits to file. Saving to database.");
+      }
       dc.commit();
       if (progress != null)
@@ -933 +955 @@
       List<CombinedHit> revCombinedHits)
   {
-    for (int i = 0; i < combinedHits.size(); i++)
+    int combinedHitsSize = combinedHits.size();
+    int revCombinedHitsSize = revCombinedHits.size();
+    int scoreSize = score_types.length;
+    for (int i = 0; i < combinedHitsSize; i++)
     {
       int scores_above = 0;
@@ -942 +967 @@
        * counted.
        */
-      for (int j = 0; j < revCombinedHits.size(); j++)
+      for (int j = 0; j < revCombinedHitsSize; j++)
       {
         boolean count = true;
         boolean above = true;
-        for (int k = 0; k < score_types.length; k++)
+        for (int k = 0; k < scoreSize; k++)
         {
           /*
@@ -969 +994 @@
         }
       }
-      combinedHits.get(i).count = (double) scores_above;
+      combinedHits.get(i).count = scores_above;
     }
   }
@@ -1022 +1047 @@
       implements Comparable<CombinedHit>
   {
-    double count = 0D;
+    int count = 0;
     double fdr = 0D;
     Hit hit;
@@ -1197 +1222 @@
   }
 
+  public class HitFileAndSpectrumStringIdAndDescriptionSortForHit
+      implements Comparator<Hit>
+  {
+    public int compare(Hit o1, Hit o2)
+    {
+      if (Integer.valueOf(o1.getPeakListFile().getId()).equals(
+        o2.getPeakListFile().getId()))
+      {
+        if (o1.getSpectrumStringId().equals(o2.getSpectrumStringId()))
+        {
+          return o1.getDescription().compareTo(o2.getDescription());
+        }
+        else
+        {
+          return o1.getSpectrumStringId().compareTo(
+            o2.getSpectrumStringId());
+        }
+      }
+      else
+        return (Integer.valueOf(o1.getPeakListFile().getId())
+          .compareTo(o2.getPeakListFile().getId()));
+    }
+  }
+
 }