Changeset 3912

Timestamp:

Oct 21, 2010, 3:10:49 PM (13 years ago)

Author:

Fredrik Levander

Message:

Refs #672. Handling spectrum lookup problems.

File:

• trunk/plugin/src/org/proteios/plugins/ProteiosProteinAssembly.java (modified) (4 diffs)

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

@@ -141 +141 @@
     };
   private int label_index = 0;
-
+  private List<String> problems = new ArrayList<String>();
 
   public ProteiosProteinAssembly()
@@ -614 +614 @@
               .write("" + f.getId() + " - " + f.getName() + "\n");
           }
+        }
+        if (!problems.isEmpty())
+        {
+          output.write("WARNING!!! Problems in report generation:\n");
+          for (String s:problems)
+          {
+            output.write(s+"\n");           
+          }
+          output.write("======================================\n");
         }
         output
@@ -1167 +1176 @@
         protein.scores.add(peptide.getExpectationValue());
       }
-      if (prot.getTotalIntensity()!=null && peptide.getTotalIntensity()!=null)
+      if (prot.getTotalIntensity() != null && peptide.getTotalIntensity() != null)
       {
         prot.setTotalIntensity(prot.getTotalIntensity() + peptide
-        .getTotalIntensity());
+          .getTotalIntensity());
       }
       log.debug("Added sequence to protein");
@@ -1323 +1332 @@
           .debug("Spectrum:" + requestSpectraNr + ", id:" + nextSpectrum);
         SpectrumInterface spec = specit.next();
-        double[] intensities = spec.listIntensities();
-        double[] mzs = spec.listMass();
-        /*
-         * If the mz values starts higher than the labels we might have
-         * to check in the next spectrum in the special case of mixed
-         * CID and HCD spectra...Only try this for mzData files.
-         */
-        if (checknext && (hcdOnly || (mzs[0] > reporterMasses[label_index][reporterMasses[label_index].length - 1])))
-        {
-          if (spec.getPrecursors() != null && spec.getPrecursors()
-            .size() > 0 && (pklFile.getFileType().getSystemId()
-            .equals(FileType.MZDATA) || pklFile.getFileType()
-            .getSystemId().equals(FileType.MZML)))
-          {
-            if (spec.getPrecursors().get(0).getFragmentationType() == FragmentationType.CID)
-            {
-              log
-                .debug("Checking next spectrum for spectrum id:" + nextSpectrum);
-              needNewCheck = true;
-              try
+        double[] reporterInt = new double[reporterMasses[label_index].length];
+        double[] reporterMz = new double[reporterMasses[label_index].length];
+        if (spec != null)
+        {
+          double[] intensities = spec.listIntensities();
+          double[] mzs = spec.listMass();
+          /*
+           * If the mz values starts higher than the labels we might
+           * have to check in the next spectrum in the special case of
+           * mixed CID and HCD spectra...Only try this for mzData
+           * files.
+           */
+          if (checknext && (hcdOnly || (mzs[0] > reporterMasses[label_index][reporterMasses[label_index].length - 1])))
+          {
+            if (spec.getPrecursors() != null && spec
+              .getPrecursors().size() > 0 && (pklFile
+              .getFileType().getSystemId()
+              .equals(FileType.MZDATA) || pklFile.getFileType()
+              .getSystemId().equals(FileType.MZML)))
+            {
+              if (spec.getPrecursors().get(0)
+                .getFragmentationType() == FragmentationType.CID)
               {
-                nextSpectrum = String.valueOf(Integer
-                  .parseInt(nextSpectrum) + 1);
-              }
-              catch (NumberFormatException e)
-              {
-                if (nextSpectrum.contains("scan="))
+                log
+                  .debug("Checking next spectrum for spectrum id:" + nextSpectrum);
+                needNewCheck = true;
+                try
                 {
-                  String oldScan = nextSpectrum
-                    .substring(nextSpectrum
-                      .indexOf("scan=") + "scan="
-                      .length());
-                  if (oldScan.contains(" "))
+                  nextSpectrum = String.valueOf(Integer
+                    .parseInt(nextSpectrum) + 1);
+                }
+                catch (NumberFormatException e)
+                {
+                  if (nextSpectrum.contains("scan="))
                   {
-                    oldScan = oldScan.substring(0, oldScan
-                      .indexOf(" "));
+                    String oldScan = nextSpectrum
+                      .substring(nextSpectrum
+                        .indexOf("scan=") + "scan="
+                        .length());
+                    if (oldScan.contains(" "))
+                    {
+                      oldScan = oldScan.substring(0,
+                        oldScan.indexOf(" "));
+                    }
+                    String newScan = Integer
+                      .toString(Integer.parseInt(oldScan) + 1);
+                    nextSpectrum = nextSpectrum.replace(
+                      oldScan, newScan);
+                    log
+                      .debug("Next spectrum id:" + nextSpectrum);
                   }
-                  String newScan = Integer.toString(Integer
-                    .parseInt(oldScan) + 1);
-                  nextSpectrum = nextSpectrum.replace(
-                    oldScan, newScan);
-                  log
-                    .debug("Next spectrum id:" + nextSpectrum);
                 }
               }
-            }
-            else if (spec.getPrecursors().get(0)
-              .getFragmentationType() == FragmentationType.HCD)
-            {
-              log.debug("HCD spectrum:" + nextSpectrum);
-            }
-          }
-        }
-        double[] reporterInt = new double[reporterMasses[label_index].length];
-        double[] reporterMz = new double[reporterMasses[label_index].length];
-        for (int i = 0; i < mzs.length; i++)
-        {
-          for (int j = 0; j < reporterMasses[label_index].length; j++)
-          {
-            if (Math.abs(reporterMasses[label_index][j] - mzs[i]) < matchTolerance)
-            {
-              // Use the closest match (Maybe better with most
-              // intense?)
+              else if (spec.getPrecursors().get(0)
+                .getFragmentationType() == FragmentationType.HCD)
+              {
+                log.debug("HCD spectrum:" + nextSpectrum);
+              }
+            }
+          }
+
+          for (int i = 0; i < mzs.length; i++)
+          {
+            for (int j = 0; j < reporterMasses[label_index].length; j++)
+            {
               if (Math
-                .abs(reporterMasses[label_index][j] - mzs[i]) < Math
-                .abs(reporterMz[j] - reporterMasses[label_index][j]))
+                .abs(reporterMasses[label_index][j] - mzs[i]) < matchTolerance)
               {
-                reporterMz[j] = mzs[i];
-                reporterInt[j] = intensities[i];
+                // Use the closest match (Maybe better with most
+                // intense?)
+                if (Math
+                  .abs(reporterMasses[label_index][j] - mzs[i]) < Math
+                  .abs(reporterMz[j] - reporterMasses[label_index][j]))
+                {
+                  reporterMz[j] = mzs[i];
+                  reporterInt[j] = intensities[i];
+                }
               }
             }
           }
+        }
+        else
+        {
+          String prob="Couldn't retrieve reporters from spectrum:" + nextSpectrum + "from file:"+pklFile.getName();
+          problems.add(prob);
+          log.warn(prob);
         }
         String reporterString = new String();