Changeset 4352

Timestamp:

Sep 27, 2012, 10:23:17 AM (11 years ago)

Author:

Fredrik Levander

Message:

Refs #755. Corrected bug in k-score import introduced in 4198

File:

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

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

@@ -238 +238 @@
     {
       ItemQuery<SpectrumSearch> ssQuery = SpectrumSearch.getQuery();
-      ssQuery.restrict(Restrictions.eq(Hql.property("resultFile"), Hql
-        .entity(resultsFile)));
+      ssQuery.restrict(Restrictions.eq(Hql.property("resultFile"),
+        Hql.entity(resultsFile)));
       DbControl dc = sc.newDbControl();
       ItemResultIterator<SpectrumSearch> iri = ssQuery.iterate(dc);
@@ -577 +577 @@
           if ((line = inreader.readLine()) != null)
           {
-            log
-              .info("TandemImport isImportable() File line3=" + line);
+            log.info("TandemImport isImportable() File line3=" + line);
             ok = line.startsWith("<bioml");
           }
@@ -814 +813 @@
         {
           // Add other annotations to the SpectrumSearch.
-          log
-            .info("Add annotation:" + param_name + " value:" + buffer
-              .toString());
+          log.info("Add annotation:" + param_name + " value:" + buffer
+            .toString());
           anna.addAnnotation(spectrumSearch, param_name, Type.STRING,
             buffer.toString());
@@ -848 +846 @@
     private List<String> protein_uids = new ArrayList<String>();
     private String param_name;
-    private boolean inside_parameters = false;
     String inputSpectrumFileName = null;
 
@@ -964 +961 @@
           .getIndex("modified")) + "@" + attrs.getValue(
           attrs.getIndex("type")).charAt(0) + "" + pos;
-        log
-          .debug("Sequence:" + current_peptide.getDescription() + " current_start:" + current_start + " pos:" + pos + " mod:" + modifiedAminoAcid);
+        log.debug("Sequence:" + current_peptide.getDescription() + " current_start:" + current_start + " pos:" + pos + " mod:" + modifiedAminoAcid);
         current_peptide
           .setDescription(current_peptide.getDescription() + " " + modifiedAminoAcid);
@@ -1015 +1011 @@
         }
       }
-      else if (qName.equals("note") && !inside_parameters)
+      else if (qName.equals("note"))
       {
         if (param_name.equals("description") && !protein_exists)
@@ -1023 +1019 @@
           current_protein.setDescription(tempname);
         }
-        if (param_name.equals("Description"))
+        else if (param_name.equals("Description"))
         {
           // Will equal MGF title if file is MGF
@@ -1038 +1034 @@
           }
         }
-      }
-
-      else if (param_name.equals("scoring, algorithm") && !buffer
-        .toString().equals("native"))
-      {
-        // Change name of score algorithm for all search results.
-        for (AHit sr : protein_results)
-        {
-          sr.setScoreType(buffer.toString() + " protein score");
-        }
-        for (AHit sr : peptide_results)
-        {
-          sr.setScoreType(buffer.toString() + " peptide score");
-        }
-      }
-
+        else if (param_name.equals("scoring, algorithm") && !buffer
+          .toString().equals("native"))
+        {
+          // Change name of score algorithm for all search results.
+          for (AHit sr : protein_results)
+          {
+            sr.setScoreType(buffer.toString() + " protein score");
+          }
+          for (AHit sr : peptide_results)
+          {
+            sr.setScoreType(buffer.toString() + " peptide score");
+          }
+        }
+      }
       // End of file.
       else if (qName.equals("bioml"))