Changeset 3766

Timestamp:

Aug 16, 2010, 2:14:37 PM (13 years ago)

Author:

Fredrik Levander

Message:

Refs #614. Added log file for matching features to hits.

File:

• trunk/plugin/src/org/proteios/plugins/FeatureHitMatcher.java (modified) (9 diffs)

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

@@ -34 +34 @@
 import org.proteios.core.Hit;
 import org.proteios.core.Include;
+import org.proteios.core.ItemFactory;
 import org.proteios.core.ItemQuery;
 import org.proteios.core.ItemResultList;
@@ -51 +52 @@
 import org.proteios.core.query.Restrictions;
 
+import java.io.OutputStream;
+import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -121 +124 @@
       boolean matchRelated = ((Boolean) job.getValue("secondary"))
         .booleanValue();
-      /* Check that the feature file hasn't been imported already */
       QueryFactory qf = new QueryFactory();
       try
       {
+        ItemFactory factory = new ItemFactory(dc);
+        File outCoreFile = factory.create(File.class);
+        dc.reattachItem(project);
+        outCoreFile.setDirectory(project.getProjectDirectory());
+        outCoreFile.setName("MatchLog-" + job.getId() + ".txt");
+        dc.saveItem(outCoreFile);
+        OutputStream outstream = outCoreFile.getUploadStream(false);
+        PrintWriter writer = new PrintWriter(outstream);
+        writer.println("Matching report for project:" + project
+          .getName());
+        writer.println("m/z tolerance:" + tolerance);
+        writer
+          .println("RT (minutes) tolerance - start:" + startTimeTol + " end:" + endTimeTol);
+        writer.println("Matching with related files" + matchRelated);
         List<File> uniqueMsFiles = Feature
           .getUniqueMsFiles(project, dc);
+        writer
+          .println("Number of files with MS features:" + uniqueMsFiles
+            .size() + "\n");
         ItemQuery<Feature> featureQuery = qf.select(Feature.class);
         featureQuery.restrictPermanent(Restrictions.eq(Hql
@@ -135 +154 @@
             .property("msFile"), Hql.entity(currentMsFile)));
           log.debug("Matching for file:" + currentMsFile);
+          writer.println("File:" + currentMsFile);
           List<Hit> hits = retrieveHits(currentMsFile, project, dc,
             matchRelated);
           List<Feature> features = featureQuery.list(dc);
           count += matchFeatures(features, hits, dc, tolerance,
-            startTimeTol, endTimeTol);
+            startTimeTol, endTimeTol, writer);
           featureQuery.reset();
         }
+        writer.close();
         dc.commit();
         response
@@ -164 +185 @@
   private int matchFeatures(List<Feature> features, List<Hit> hits,
       DbControl dc, double tolerance, double startTimeTol,
-      double endTimeTol)
+      double endTimeTol, PrintWriter writer)
   {
     log.debug("Features to match:" + features.size());
     log.debug("Hits to match:" + hits.size());
+    writer.println("Features to match:" + features.size());
+    writer.println("MS/MS identifications to match:" + hits.size());
     int count = 0;
+    int newmatches = 0;
+    int replaced = 0;
+    int ambiguities = 0;
     for (Feature f : features)
     {
@@ -199 +225 @@
               {
                 h.setPrecursorQuantity(f.getApexIntensity());
+                replaced++;
               }
               f.setPeptideSequence(h.getDescription());
               f.addHit(h);
+              newmatches++;
             }
             else
@@ -209 +237 @@
                * Use the feature with the highest intensity
                */
-              if (h.getPrecursorQuantity() == null || (h
+              if (h.getPrecursorQuantity() == null && (h
                 .getPrecursorQuantity() < f.getApexIntensity()))
               {
                 h.setPrecursorQuantity(f.getApexIntensity());
+                if (!h.getDescription().equals(
+                  f.getPeptideSequence()))
+                {
+                  f.setPeptideSequence(h.getDescription());
+                  ambiguities++;
+                }
+                replaced++;
               }
               f.addHit(h);
@@ -257 +292 @@
               f.setPeptideSequence(h.getDescription());
               count++;
+              newmatches++;
             }
           }
@@ -262 +298 @@
       }
     }
+    writer.println("New features matched:" + newmatches);
+    writer.println("Multiply matched features:" + replaced);
+    writer.println("Matched hits:" + count);
+    writer
+      .println("Ambiguous matches (different sequences from MS/MS identifications):" + ambiguities);
+    writer.println("===============================");
     return count;
   }