Changeset 3913

Timestamp:

Oct 21, 2010, 3:49:58 PM (13 years ago)

Author:

Fredrik Levander

Message:

Refs #672. Handling peptide total intensity of null

File:

• trunk/plugin/src/org/proteios/plugins/ProteiosProteinAssembly.java (modified) (5 diffs)

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

@@ -1111 +1111 @@
       .debug("Trying to add sequence:" + peptide.getDescription() + " to protein " + prot
         .getExternalId());
+    double pep_tot_int = peptide.getTotalIntensity() == null ? 0 : peptide.getTotalIntensity();
     List<String> sequences = protein.sequences;
     if (sequences.contains(peptide.getDescription()) && uniqueSequences)
@@ -1121 +1122 @@
       if (fdr)
         currentScore = peptide.getCombinedFDR();
-      if ((score >= currentScore) && tot_int <= peptide
-        .getTotalIntensity())
+      if ((score >= currentScore) && tot_int <= pep_tot_int)
       {
         // replace
@@ -1138 +1138 @@
         }
         protein.peptides.add(peptide);
-        protein.totalIntensities.add(peptide.getTotalIntensity());
+        protein.totalIntensities.add(pep_tot_int);
         protein.spectrumStringIds.add(peptide.getSpectrumStringId());
         protein.spectrumFileIds.add(peptide.getPeakListFile().getId());
@@ -1159 +1159 @@
       protein.peptides.add(peptide);
       protein.sequences.add(peptide.getDescription());
-      protein.totalIntensities.add(peptide.getTotalIntensity());
+      protein.totalIntensities.add(pep_tot_int);
       protein.spectrumStringIds.add(peptide.getSpectrumStringId());
       protein.spectrumFileIds.add(peptide.getPeakListFile().getId());
@@ -1176 +1176 @@
         protein.scores.add(peptide.getExpectationValue());
       }
-      if (prot.getTotalIntensity() != null && peptide.getTotalIntensity() != null)
-      {
-        prot.setTotalIntensity(prot.getTotalIntensity() + peptide
-          .getTotalIntensity());
+      if (prot.getTotalIntensity() != null)
+      {
+        prot.setTotalIntensity(prot.getTotalIntensity() + pep_tot_int);
       }
       log.debug("Added sequence to protein");