Changeset 4270

Timestamp:

Jan 2, 2012, 3:07:11 PM (11 years ago)

Author:

Fredrik Levander

Message:

Refs #773. Updated querying for peptide-based non-gel reports.

File:

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

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

@@ -56 +56 @@
 import org.proteios.core.query.Restrictions;
 import java.io.BufferedWriter;
+import java.io.IOException;
 import java.io.OutputStream;
 import java.io.OutputStreamWriter;
@@ -111 +112 @@
       "Combined hits report",
       "Combine scores for different hits and extract hits which pass the given false discovery rate threshold. The Hits report is updated with the calculated combined FDRs",
-      "1.3", "2007-2011, Protein Technology, Lund University", null,
+      "1.4", "2007-2012, Protein Technology, Lund University", null,
       null, "http://www.proteios.org  ");
   }
@@ -364 +365 @@
           hitQuery.setPermanentParameter("localSampleId",
             localSampleId, null);
+          hitQuery.orderPermanent(Orders.asc(Hql
+            .property("peakListFile")));
+          hitQuery.orderPermanent(Orders.asc(Hql
+            .property("spectrumStringId")));
         }
       }
@@ -383 +388 @@
       {
         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);
@@ -417 +425 @@
         }
         boolean first = true;
+        int last_index = 0, last_rev_index = 0, forwardSize = combinedHits
+          .size(), reverseSize = revCombinedHits.size();
         while (hitit.hasNext())
         {
@@ -544 +554 @@
               else
               {
+                // There is a local sample id
+                Integer currentFileId = currenthit
+                  .getPeakListFile().getId();
                 // If there is a sample id we sort on input
                 // filename
                 if (!reverse)
                 {
-                  for (int j = 0; (j < combinedHits.size() && (!existed)); j++)
+                  if (!proteins)
                   {
-                    if (proteins && currenthit
-                      .getPeakListFile().equals(
-                        combinedHits.get(j).hit
-                          .getPeakListFile()) && currenthit
-                      .getExternalId().equals(
-                        combinedHits.get(j).hit
-                          .getExternalId()))
+                    for (int j = last_index; j < forwardSize; j++)
                     {
-                      existed = true;
-                      currentcombined = combinedHits
-                        .get(j);
+                      if (currenthit
+                        .getSpectrumStringId().equals(
+                          combinedHits.get(j).hit
+                            .getSpectrumStringId()) && currentFileId
+                        .equals(combinedHits.get(j).hitPeakListFileId) && combinedHits
+                        .get(j).hit.getDescription()
+                        .startsWith(seqstart))
+                      {
+                        existed = true;
+                        currentcombined = combinedHits
+                          .get(j);
+                        last_index = j;
+                        break;
+                      }
                     }
-                    else if (!proteins && currenthit
-                      .getPeakListFile().equals(
-                        combinedHits.get(j).hit
-                          .getPeakListFile()) && currenthit
-                      .getSpectrumStringId().equals(
-                        combinedHits.get(j).hit
-                          .getSpectrumStringId()) && combinedHits
-                      .get(j).hit.getDescription()
-                      .startsWith(seqstart))
+                  }
+                  else
+                  {
+                    for (int j = 0; (j < combinedHits
+                      .size() && (!existed)); j++)
                     {
-                      existed = true;
-                      currentcombined = combinedHits
-                        .get(j);
+                      if (currenthit.getExternalId()
+                        .equals(
+                          combinedHits.get(j).hit
+                            .getExternalId()) && currentFileId
+                        .equals(combinedHits.get(j).hitPeakListFileId))
+                      {
+                        existed = true;
+                        currentcombined = combinedHits
+                          .get(j);
+                      }
                     }
                   }
@@ -580 +601 @@
                 else
                 {
-                  for (int j = 0; (j < revCombinedHits.size() && (!existed)); j++)
+                  if (proteins)
                   {
-                    if (proteins && currenthit
-                      .getPeakListFile().equals(
-                        revCombinedHits.get(j).hit
-                          .getPeakListFile()) && currenthit
-                      .getExternalId().equals(
-                        revCombinedHits.get(j).hit
-                          .getExternalId()))
+                    for (int j = 0; (j < revCombinedHits
+                      .size() && (!existed)); j++)
                     {
-                      existed = true;
-                      currentcombined = revCombinedHits
-                        .get(j);
+                      if (currentFileId
+                        .equals(revCombinedHits.get(j).hitPeakListFileId) && currenthit
+                        .getExternalId().equals(
+                          revCombinedHits.get(j).hit
+                            .getExternalId()))
+                      {
+                        existed = true;
+                        currentcombined = revCombinedHits
+                          .get(j);
+                      }
                     }
-                    else if (!proteins && currenthit
-                      .getPeakListFile().equals(
-                        revCombinedHits.get(j).hit
-                          .getPeakListFile()) && currenthit
-                      .getSpectrumStringId().equals(
-                        revCombinedHits.get(j).hit
-                          .getSpectrumStringId()) && revCombinedHits
-                      .get(j).hit.getDescription()
-                      .startsWith(seqstart))
+                  }
+                  else
+                  {
+                    for (int j = last_rev_index; j < reverseSize; j++)
+
                     {
-                      existed = true;
-                      currentcombined = revCombinedHits
-                        .get(j);
+                      if (currenthit
+                        .getSpectrumStringId().equals(
+                          revCombinedHits.get(j).hit
+                            .getSpectrumStringId()) && currentFileId
+                        .equals(revCombinedHits.get(j).hitPeakListFileId) && revCombinedHits
+                        .get(j).hit.getDescription()
+                        .startsWith(seqstart))
+                      {
+                        existed = true;
+                        currentcombined = revCombinedHits
+                          .get(j);
+                        last_rev_index = j;
+                        break;
+                      }
                     }
                   }
@@ -624 +654 @@
             {
               currentcombined.hit = currenthit;
+              currentcombined.hitPeakListFileId = currenthit
+                .getPeakListFile().getId();
               if (reverse)
               {
@@ -634 +666 @@
             }
             // Point to first in combination
-            else if (!reverse)
+            else if (!reverse || keepDecoys)
             {
               currenthit
@@ -641 +673 @@
             }
             if (first)
-            // Try to find number of db_entries
-            {
-              File searchFile = currenthit
-                .getIdentificationResultFile();
-              ItemQuery<SpectrumSearch> ssQuery = SpectrumSearch
-                .getQuery();
-              ssQuery.restrict(Restrictions
-                .eq(Hql.property("resultFile"), Hql
-                  .entity(searchFile)));
-              ItemResultIterator<SpectrumSearch> ssit = ssQuery
-                .iterate(dc);
-              if (ssit.hasNext())
-              {
-                SpectrumSearch ss = (SpectrumSearch) ssit
-                  .next();
-                Iterator<SearchDatabase> sdit = ss
-                  .getSearchDatabases().iterator();
-                if (sdit.hasNext())
-                {
-                  SearchDatabase sdb = sdit.next();
-                  if (db_entries != 0)
-                  {
-                    if (db_entries != sdb
-                      .getNumberOfEntriesAfterTaxonomy())
-                    {
-                      output
-                        .write("WARNING!!! Number of database entries seems to differ between search engines!\n");
-                    }
-                  }
-                  db_entries = sdb
-                    .getNumberOfEntriesAfterTaxonomy();
-                  output
-                    .write("Score type " + score_types[i] + ", database ");
-                  if (sdb.getVersionIdentifier() != null && sdb
-                    .getVersionIdentifier().length() > 0)
-                  {
-                    output
-                      .write(sdb.getVersionIdentifier());
-                  }
-                  else
-                  {
-                    output.write(sdb.getName());
-                  }
-                  output
-                    .write(", number of database entries: " + db_entries + "\n");
-                  log
-                    .info("CombinedHitsReport: database entries:" + db_entries);
-                }
-              }
-            }
+              db_entries = retrieveNumberOfDbEntries(dc,
+                currenthit, db_entries, i, output);
             first = false;
             querycount++;
@@ -702 +686 @@
           }
         }
+        // Now sort
+        if (!proteins && localSampleId != null)
+        {
+          Comparator<CombinedHit> hitSort = new HitFileAndSpectrumStringIdAndDescriptionSort();
+          Collections.sort(combinedHits, hitSort);
+          Collections.sort(revCombinedHits, hitSort);
+        }
         hitQuery.reset();
       }
       if (progress != null)
       {
-        progress.display(60, "Querying done. Calculating FDRs.");
+        progress.display(60,
+          "Querying done. Setting default score values.");
       }
       // The actual filtering:
@@ -781 +773 @@
       }
       // double total_number = db_entries * decoyPart * spots;
+      if (progress != null)
+      {
+        progress.display(65, "Querying done. Calculating scores.");
+      }
       countBetterRandomHits(combinedHits, revCombinedHits);
       countBetterRandomHits(revCombinedHits, revCombinedHits);
+      if (progress != null)
+      {
+        progress.display(70, "Querying done. Calculating FDRs.");
+      }
       // Now sort according to pValues
       Comparator<CombinedHit> hitPValueSort = new HitPValueSort();
@@ -973 +973 @@
   }
 
+
+  int retrieveNumberOfDbEntries(DbControl dc, Hit currenthit, int db_entries,
+      int score_type_idx, BufferedWriter output)
+      throws IOException
+  // Try to find number of db_entries
+  {
+    File searchFile = currenthit.getIdentificationResultFile();
+    ItemQuery<SpectrumSearch> ssQuery = SpectrumSearch.getQuery();
+    ssQuery.restrict(Restrictions.eq(Hql.property("resultFile"), Hql
+      .entity(searchFile)));
+    ItemResultIterator<SpectrumSearch> ssit = ssQuery.iterate(dc);
+    if (ssit.hasNext())
+    {
+      SpectrumSearch ss = (SpectrumSearch) ssit.next();
+      Iterator<SearchDatabase> sdit = ss.getSearchDatabases().iterator();
+      if (sdit.hasNext())
+      {
+        SearchDatabase sdb = sdit.next();
+        if (db_entries != 0)
+        {
+          if (db_entries != sdb.getNumberOfEntriesAfterTaxonomy())
+          {
+            output
+              .write("WARNING!!! Number of database entries seems to differ between search engines!\n");
+          }
+        }
+        db_entries = sdb.getNumberOfEntriesAfterTaxonomy();
+        output
+          .write("Score type " + score_types[score_type_idx] + ", database ");
+        if (sdb.getVersionIdentifier() != null && sdb
+          .getVersionIdentifier().length() > 0)
+        {
+          output.write(sdb.getVersionIdentifier());
+        }
+        else
+        {
+          output.write(sdb.getName());
+        }
+        output
+          .write(", number of database entries: " + db_entries + "\n");
+        log.info("CombinedHitsReport: database entries:" + db_entries);
+      }
+    }
+    return db_entries;
+  }
+
   public class CombinedHit
       implements Comparable<CombinedHit>
@@ -979 +1025 @@
     double fdr = 0D;
     Hit hit;
+    Integer hitPeakListFileId = 0;
     Float scores[];
 
@@ -1001 +1048 @@
       else
       {
-        retval = hit.getPeakListFile().getName().compareTo(
-          o.hit.getPeakListFile().getName());
+        retval = hitPeakListFileId.compareTo(o.hitPeakListFileId);
       }
       return retval;
@@ -1126 +1172 @@
     }
   }
+
+  public class HitFileAndSpectrumStringIdAndDescriptionSort
+      implements Comparator<CombinedHit>
+  {
+    public int compare(CombinedHit o1, CombinedHit o2)
+    {
+      if (o1.hitPeakListFileId.equals(o2.hitPeakListFileId))
+      {
+        if (o1.hit.getSpectrumStringId().equals(
+          o2.hit.getSpectrumStringId()))
+        {
+          return o1.hit.getDescription().compareTo(
+            o2.hit.getDescription());
+        }
+        else
+        {
+          return o1.hit.getSpectrumStringId().compareTo(
+            o2.hit.getSpectrumStringId());
+        }
+      }
+      else
+        return (o1.hitPeakListFileId.compareTo(o2.hitPeakListFileId));
+    }
+  }
+
 }