Changeset 4426

Timestamp:

Feb 27, 2013, 1:51:04 PM (10 years ago)

Author:

Fredrik Levander

Message:

Refs #777. Added fix for rare cases when external id previously could not be found.

File:

• trunk/plugin/src/org/proteios/plugins/FeatureComparison.java (modified) (3 diffs)

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

@@ -90 +90 @@
   {
     return new AboutImpl("Feature Comparison Report",
-      "Generate table with feature comparison", "0.1",
-      "2012, Immunotechnology, Lund University", null, null,
+      "Generate table with feature comparison", "0.2",
+      "2012-2103, Immunotechnology, Lund University", null, null,
       "http://www.proteios.org  ");
   }
@@ -186 +186 @@
     featureQuery
       .restrict(Restrictions.neq(Hql.property("clusterId"), null));
-    featureQuery.restrict(Restrictions.eq(Hql.property("project"), Hql
-      .entity(project)));
+    featureQuery.restrict(Restrictions.eq(Hql.property("project"),
+      Hql.entity(project)));
     featureQuery.order(Orders.asc(Hql.property("clusterId")));
     int entries = msFiles.size();
@@ -236 +236 @@
         }
       }
-      else if (feature.getPeptideSequence() != null && (!feature
-        .getPeptideSequence().equals(currentSequence)))
-      {
-        conflict = true;
+      else if (feature.getPeptideSequence() != null)
+      {
+        if (!feature.getPeptideSequence().equals(currentSequence))
+        {
+          conflict = true;
+        }
+        /*
+         * To rescue accession numbers in cases where no accession
+         * number could be obtained previously
+         */
+        else if (currentAcc.equals(""))
+        {
+          for (Hit hit : feature.getHits())
+          {
+            if (hit.getDescription().startsWith(currentSequence))
+            {
+              currentAcc = hit.getExternalId();
+            }
+          }
+        }
       }
       if (values[msFiles.indexOf(feature.getMsFile())] == null)