Changeset 3770

Timestamp:

Aug 17, 2010, 12:31:01 PM (13 years ago)

Author:

Fredrik Levander

Message:

Refs #614. Logging more parameters, and updating of hits when deleting features.

Location:

trunk

Files:

• api/core/src/org/proteios/core/Hit.java (modified) (1 diff)
• api/core/src/org/proteios/core/data/FeatureData.java (modified) (1 diff)
• client/servlet/src/org/proteios/action/feature/ClearFeatures.java (modified) (3 diffs)
• plugin/src/org/proteios/plugins/FeatureHitMatcher.java (modified) (2 diffs)

trunk/api/core/src/org/proteios/core/Hit.java

@@ -721 +721 @@
   public void setFeature(Feature feature)
   {
-    getData().setFeature(feature.getData());
-  }
+    if (feature!=null)
+    {
+      getData().setFeature(feature.getData());
+    }
+    else
+    {
+      getData().setFeature(null);
+    }
+  }
+  
 }

trunk/api/core/src/org/proteios/core/data/FeatureData.java

@@ -260 +260 @@
 
   /**
-   * Get the Hits matched to this feature.
+   * Get the Hits matched to this feature. Note that the there is no cascading for delete 
    * 
-   * @hibernate.set table="`Hits`" cascade="delete" lazy="true" inverse="true"
+   * @hibernate.set table="`Hits`" cascade="none" lazy="true" inverse="true"
    * @hibernate.collection-one-to-many class="org.proteios.core.data.HitData"
    *                                   not-null="false"

trunk/client/servlet/src/org/proteios/action/feature/ClearFeatures.java

@@ -37 +37 @@
 import org.proteios.core.DbControl;
 import org.proteios.core.Feature;
+import org.proteios.core.Hit;
 import org.proteios.core.ItemQuery;
 import org.proteios.core.Project;
@@ -71 +72 @@
     Project project = isProjectActive(dc);
     /***********************************************************************
-     * Drop all hits in the active project
+     * update relevant hits in the active project
      */
+    int counter = 0, counter2=0;
     QueryFactory qf = getQueryFactory();
+    ItemQuery<Hit> hitQuery = qf.select(Hit.class);
+    hitQuery.restrictPermanent(Restrictions.eq(Hql.property("project"), Hql
+      .entity(project)));
+    hitQuery.restrictPermanent(Restrictions.neq(Hql.property("precursorQuantity"), null));
+    for (Iterator<Hit> iter = hitQuery.iterate(dc); iter.hasNext();)
+    {
+      Hit element = iter.next();
+      dc.reattachItem(element);
+      element.setPrecursorQuantity(null);
+      element.setFeature(null);
+      counter2++;
+    }   
+    log.debug("Done with hits");
+    dc.commit();
+    log.debug("Commit done");
+    /****
+     * And delete all features
+     */
+    dc = newDbControl();    
     ItemQuery<Feature> query = qf.select(Feature.class);
     query.restrictPermanent(Restrictions.eq(Hql.property("project"), Hql
       .entity(project)));
-    int counter = 0;
     for (Iterator<Feature> iter = query.iterate(dc); iter.hasNext();)
     {
@@ -84 +104 @@
       counter++;
     }
+    log.debug("Done with features");
     dc.commit();
-    setMessage(counter + " features removed");
+    log.debug("... and commit");
+    setMessage(counter + " features removed. "+counter2+" hits updated.");
     setForwardTo(ConfigureTableFactory2.class);
   }

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

@@ -237 +237 @@
                * Use the feature with the highest intensity
                */
-              if (h.getPrecursorQuantity() == null && (h
+              if (h.getPrecursorQuantity() == null || (h
                 .getPrecursorQuantity() < f.getApexIntensity()))
               {
@@ -244 +244 @@
                   f.getPeptideSequence()))
                 {
-                  f.setPeptideSequence(h.getDescription());
+
+                  log.debug("Not matching: " + h
+                    .getDescription() + " and " + f
+                    .getPeptideSequence());
+                  writer
+                    .println("Ambiguity: " + h
+                      .getDescription() + " not matching feature sequence " + f
+                      .getPeptideSequence() + ", feature m/z:" + f
+                      .getMassToChargeRatio());
+                  boolean best = true;
+                  for (Hit hh : f.getHits())
+                  {
+                    if (hh.getCombinedFDR() < h
+                      .getCombinedFDR())
+                      best = false;
+                  }
+                  if (best)
+                  {
+                    f
+                      .setPeptideSequence(h
+                        .getDescription());
+                    writer
+                      .println("Better scoring hit sequence replacing old");
+                  }
                   ambiguities++;
                 }