Changeset 4540

Timestamp:

Jan 8, 2014, 10:48:49 AM (10 years ago)

Author:

Fredrik Levander

Message:

Refs #819, Refs #821. Clearing cluster IDs before matching. Fix when multiple hits with same FDR but different e-values.

Location:

trunk

Files:

• client/servlet/src/org/proteios/action/ActionFactory.java (modified) (2 diffs)
• client/servlet/src/org/proteios/action/hit/ViewHitFeature.java (added)
• plugin/src/org/proteios/plugins/ClearFeatures.java (modified) (8 diffs)
• plugin/src/org/proteios/plugins/FeatureHitMatcher.java (modified) (7 diffs)
• plugin/src/org/proteios/plugins/FeatureSequencePropagator.java (modified) (2 diffs)

trunk/client/servlet/src/org/proteios/action/ActionFactory.java

@@ -48 +48 @@
 import org.proteios.action.hit.ViewHit;
 import org.proteios.action.hit.ViewHitExternalId;
+import org.proteios.action.hit.ViewHitFeature;
 import org.proteios.action.hit.ViewHitPDBFile;
 import org.proteios.action.hit.ViewHitSearchResultFile;
@@ -683 +684 @@
                 link = getActionLink(ViewHitSubHits.class, label);
             }
+            else if (key.equals("PrecursorQuantity"))
+            {
+                link = getActionLink(ViewHitFeature.class, label);
+            }
             else if (key.equals("Protein"))
             {

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

@@ -76 +76 @@
   {
     return new AboutImpl("Clear Features", "Clear features in project",
-      "0.1", "2012, Fredrik Levander", null, null,
+      "0.2", "2012-2014, Fredrik Levander", null, null,
       "http://www.proteios.org");
   }
@@ -118 +118 @@
         int updatedFeatures = removeFeatureSequences(project, dc);
         dc.commit();
+        int deletedIds = clearClusterIds(project,sc);
         response
-          .setDone(updatedFeatures + " feature sequences removed. " + updatedHits + " hits updated. " + removedAligned + " aligned hits deleted.");
+          .setDone(updatedFeatures + " feature sequences removed. " + updatedHits + " hits updated. " + removedAligned + " aligned hits deleted. " + deletedIds + " cluster IDs removed.");
       }
       else
@@ -146 +147 @@
     QueryFactory qf = new QueryFactory();
     ItemQuery<Hit> hitQuery = qf.select(Hit.class);
-    hitQuery.restrictPermanent(Restrictions.eq(Hql.property("project"), Hql
-      .entity(project)));
+    hitQuery.restrictPermanent(Restrictions.eq(Hql.property("project"),
+      Hql.entity(project)));
     hitQuery.restrictPermanent(Restrictions.eq(Hql.property("scoreType"),
       Expressions.string("Proteios aligned")));
@@ -176 +177 @@
     QueryFactory qf = new QueryFactory();
     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));
+    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();)
     {
@@ -189 +190 @@
     }
     hitQuery = qf.select(Hit.class);
-    hitQuery.restrictPermanent(Restrictions.eq(Hql.property("project"), Hql
-      .entity(project)));
-    hitQuery.restrictPermanent(Restrictions.eq(Hql
-      .property("precursorQuantity"), null));
+    hitQuery.restrictPermanent(Restrictions.eq(Hql.property("project"),
+      Hql.entity(project)));
+    hitQuery.restrictPermanent(Restrictions.eq(
+      Hql.property("precursorQuantity"), null));
     hitQuery.restrictPermanent(Restrictions.neq(Hql.property("feature"),
       null));
@@ -216 +217 @@
     QueryFactory qf = new QueryFactory();
     ItemQuery<Feature> query = qf.select(Feature.class);
-    query.restrictPermanent(Restrictions.eq(Hql.property("project"), Hql
-      .entity(project)));
+    query.restrictPermanent(Restrictions.eq(Hql.property("project"),
+      Hql.entity(project)));
     query.restrict(Restrictions.neq(Hql.property("peptideSequence"), null));
     for (Iterator<Feature> iter = query.iterate(dc); iter.hasNext();)
@@ -247 +248 @@
     for (File msFile : files)
     {
-      log
-        .debug("Deleting features for file " + (++count) + " of " + nFiles);
+      log.debug("Deleting features for file " + (++count) + " of " + nFiles);
       nDeleted += Feature.deleteAllFeatures(project, msFile, sessc);
     }
@@ -254 +254 @@
     return nDeleted;
   }
+
+
+  /**
+   * Delete all cluster Ids for features in project. This is performed for one msFile at
+   * the time to avoid stalling. The deletions are committed to the database
+   * after each batch delete.
+   * 
+   * @return the number of deleted rows
+   */
+  public static int clearClusterIds(Project project, SessionControl sessc)
+  {
+    int nDeleted = 0;
+    DbControl dc = sessc.newDbControl();
+    List<File> files = Feature.getUniqueMsFiles(project, dc);
+    int nFiles = files.size();
+    int count = 0;
+    for (File msFile : files)
+    {
+      log.debug("Deleting features for file " + (++count) + " of " + nFiles);
+      nDeleted += clearClusterIds(project, msFile, sessc);
+    }
+    dc.close();
+    return nDeleted;
+  }
+
+
+  /**
+   * Delete all cluster Ids for features from a msFile in a project
+   * 
+   * @param project
+   * @param msFile File
+   * @param sessc Session Control
+   * @return number of updated rows
+   */
+  public static int clearClusterIds(Project project, File msFile,
+      SessionControl sessc)
+  {
+    int nUpdated = 0;
+    DbControl dc = sessc.newDbControl();
+    QueryFactory qf = new QueryFactory();
+    ItemQuery<Feature> featureQuery = qf.select(Feature.class);
+
+    // Only features in project should be retrieved
+    // OBS! has hql object as input
+    featureQuery.restrictPermanent(Restrictions.eq(Hql.property("project"),
+      Hql.entity(project)));
+    featureQuery.restrict(Restrictions.eq(Hql.property("msFile"),
+      Hql.entity(msFile)));
+    featureQuery
+      .restrict(Restrictions.neq(Hql.property("clusterId"), null));
+
+    for (Iterator<Feature> iter = featureQuery.iterate(dc); iter.hasNext();)
+    {
+      Feature feature = iter.next();
+      dc.reattachItem(feature);
+      feature.setClusterId(null);
+      nUpdated++;
+    }
+    dc.commit();
+    return nUpdated;
+  }
 }

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

@@ -99 +99 @@
     return new AboutImpl("Match features to hits",
         "Match features to hits for a project", "0.5",
-        "2009-2013, Marianne Sandin, Fredrik Levander", null, null,
+        "2009-2014, Marianne Sandin, Fredrik Levander", null, null,
         "http://www.proteios.org");
   }
@@ -123 +123 @@
       // Start by removing previous matches
       if (progress != null) {
-        progress.display(5, "Removing previous matches");
+        progress.display(2, "Removing previous matches");
       }
       Project project = (Project) job.getValue("project");
@@ -129 +129 @@
       dc.commit();
       if (progress != null) {
-        progress.display(5, "Removed aligned hits");
+        progress.display(4, "Removed aligned hits");
       }
       dc = sc.newDbControl();
@@ -136 +136 @@
       dc.commit();
       if (progress != null) {
-        progress.display(5, "Removed feature and hits connections");
+        progress.display(6, "Removed feature and hits connections");
       }
       dc = sc.newDbControl();
@@ -143 +143 @@
       dc.commit();
       if (progress != null) {
-        progress.display(5, "Removed feature sequences");
-      }
+        progress.display(8, "Removed feature sequences");
+      }
+      ClearFeatures.clearClusterIds(project, sc);
+      if (progress != null) {
+        progress.display(10, "Removed feature cluster Ids");
+      }     
       // Done with init
       dc = sc.newDbControl();
@@ -486 +490 @@
                         .getCombinedFDR())
                       best = false;
-                    if (hh.getCombinedFDR() == h.getCombinedFDR())
+                    if (hh.getCombinedFDR().equals(h.getCombinedFDR()))
                       if (hh.getExpectationValue()<=h.getExpectationValue())
                         best = false;
@@ -713 +717 @@
     hitQuery.order(Orders.asc(Hql.property("charge")));
     hitQuery.order(Orders.asc(Hql.property("experimentalMassInDaltons")));
+    hitQuery.order(Orders.asc(Hql.property("combinedFDR")));
+    hitQuery.order(Orders.asc(Hql.property("expectationValue")));
     ItemResultList<Hit> hitlist = hitQuery.list(dc);
     for (Hit h : hitlist) {

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

@@ -268 +268 @@
 
           dc.commit();
-          dc = sc.newDbControl();
-
-          featureQuery.restrict(Restrictions.eq(
-              Hql.property("msFile"), Hql.entity(currentMsFile)));
-          featureQuery.restrict(Restrictions.neq(
-              Hql.property("clusterId"), null));
-
-          List<Feature> allClusterIdFeatures = featureQuery.list(dc);
-
+          
           if (progress != null) {
             progress.display((fileNbr + 1) / nbrOfFiles,
@@ -282 +274 @@
                     + (fileNbr + 1));
           }
-
-          for (Feature clusterF : allClusterIdFeatures) {
-
-            clusterF.setClusterId(null);
-            dc.reattachItem(clusterF);
-
-          }
-
-          dc.commit();
+          
+          ClearFeatures.clearClusterIds(project, currentMsFile, sc);
+          
           dc = sc.newDbControl();