Changeset 4282

Timestamp:

Feb 10, 2012, 12:15:50 PM (12 years ago)

Author:

marianne

Message:

Refs #774. Alignment of charge states >1 and hits update.

File:

• trunk/plugin/src/org/proteios/plugins/FeatureSequencePropagator.java (modified) (8 diffs)

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

@@ -225 +225 @@
           featureQuery.restrict(Restrictions.eq(Hql
             .property("msFile"), Hql.entity(currentMsFile)));
-          featureQuery.restrict(Restrictions.eq(Hql
+          featureQuery.restrict(Restrictions.gt(Hql
             .property("chargeState"),Expressions.integer(2)));
           featureQuery.order(Orders.asc(Hql.property("apexRetentionTimeInMinutes")));
@@ -263 +263 @@
           featureQuery.restrict(Restrictions.neq(Hql
             .property("peptideSequence"), null));
-          featureQuery.restrict(Restrictions.eq(Hql
+          featureQuery.restrict(Restrictions.gt(Hql
             .property("chargeState"),Expressions.integer(2)));
           featureQuery.order(Orders.asc(Hql.property("apexRetentionTimeInMinutes")));
@@ -697 +697 @@
     featureQuery.restrict(Restrictions.eq(Hql
       .property("msFile"), Hql.entity(uniqueMsFiles.get(fp.getFirstFile()))));
-    featureQuery.restrict(Restrictions.eq(Hql
+    featureQuery.restrict(Restrictions.gt(Hql
       .property("chargeState"),Expressions.integer(2)));
     featureQuery.order(Orders.asc(Hql.property("apexRetentionTimeInMinutes")));
@@ -705 +705 @@
     
     featureQuery.restrict(Restrictions.eq(Hql
+        .property("msFile"), Hql.entity(uniqueMsFiles.get(fp.getFirstFile()))));
+      featureQuery.restrict(Restrictions.gt(Hql
+        .property("chargeState"),Expressions.integer(2)));
+      featureQuery.order(Orders.asc(Hql.property("apexRetentionTimeInMinutes")));
+    featureQuery.restrict(Restrictions.neq(Hql.property("peptideSequence"), null));
+    List<Feature> tempAllFeaturesSeq = featureQuery.list(dc);
+    ArrayList<Feature> allFeaturesSeq = new ArrayList<Feature>(tempAllFeaturesSeq);
+    featureQuery.reset();
+    
+    featureQuery.restrict(Restrictions.eq(Hql
       .property("msFile"), Hql.entity(uniqueMsFiles.get(fp.getSecondFile()))));
-    featureQuery.restrict(Restrictions.eq(Hql
+    featureQuery.restrict(Restrictions.gt(Hql
       .property("chargeState"),Expressions.integer(2)));
     featureQuery.order(Orders.asc(Hql.property("apexRetentionTimeInMinutes")));
@@ -1028 +1038 @@
 
         bestMatch.setClusterId(f.getClusterId());
+        
+        //updating hits
+        if (f.getPeptideSequence()!= null && bestMatch.getPeptideSequence()==null){
+          updateHitsList(f,bestMatch,localSampleId2,fractionId2,allFeaturesSeq,writer,dc,factory,project);
+        }
 
         log.debug("First feature after set: " +f.getClusterId() + " bestMatch feature: " +bestMatch.getClusterId());
@@ -1058 +1073 @@
 
   
-  private void updateHitsList(Feature f, Feature f2, String localSampleId2, String fractionId2, List<Feature> allFeatures, PrintWriter writer, DbControl dc, ItemFactory factory, Project project){
+  private void updateHitsList(Feature f, Feature f2, String localSampleId2, String fractionId2, ArrayList<Feature> allFeaturesSeq, PrintWriter writer, DbControl dc, ItemFactory factory, Project project){
         //create a hit in database for f2 (the feature whose sequence has been updated) 
         
@@ -1087 +1102 @@
                 fseq = fseq.substring(0, fseq
                   .lastIndexOf(' '));
-              for (Feature f3 : allFeatures)
+              for (Feature f3 : allFeaturesSeq)
               {
-                if(f3.getPeptideSequence()!=null){
-                  // Currently ignoring charge state of hit.
                   if ((fseq.equals(f3.getPeptideSequence()) || (fseq
                       .contains(" ") && f3
                       .getPeptideSequence().startsWith(fseq))) && !f3
-                      .getHits().isEmpty())
+                      .getHits().isEmpty() && f.getChargeState().equals(f3.getChargeState()))
                   {
                     for (Hit h1 : f3.getHits())
@@ -1112 +1125 @@
                     }
                   }
-                }
+                
               }
             }