Changeset 4277

Timestamp:

Jan 24, 2012, 9:51:45 AM (11 years ago)

Author:

Fredrik Levander

Message:

Fixes #775.

File:

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

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

@@ -133 +133 @@
   {
     return new AboutImpl("X!Tandem results importer",
-      "SpectrumSearch import from X!Tandem xml", "1.01",
-      "2006-2009, Protein Technology, Lund University", null, null,
+      "SpectrumSearch import from X!Tandem xml", "1.1",
+      "2006-2011, Protein Technology, Lund University", null, null,
       "http://www.proteios.org  ");
   }
@@ -318 +318 @@
           hit.setMatchedPeaks(new Integer(0));
           hit.setRMSError(new Float(0.0));
+        }
+        else if (hit.getDescription().contains("@"))
+        {
+          removeFixedMod(hit, ss);
         }
       }
@@ -381 +385 @@
 
 
+  private void removeFixedMod(AHit hit, SpectrumSearch ss)
+  // This function will remove fixed modifications from the hit description.
+  {
+    String desc = hit.getDescription();
+    for (SearchModification sm : ss.getSearchModifications())
+    {
+      if (sm.isFixed())
+      {
+        log.debug("Checking for " + sm.getName());
+        if (desc.contains("@" + sm.getAminoAcidSpecificity()))
+        {
+          String[] parts = hit.getDescription().split(" ");
+          String newdesc = parts[0];
+          boolean writeDelta = false;
+          for (int i = 1; i < parts.length; i++)
+          {
+            if (parts[i].contains("@"))
+            {
+              int index = parts[i].indexOf('@');
+              float mass = Float.parseFloat(parts[i].substring(0,
+                index));
+              String aa = parts[i]
+                .substring(index + 1, index + 2);
+              if (sm.getAminoAcidSpecificity().contains(aa) && Math
+                .abs(mass - sm.getMonoisotopicDeltaMass()) < 0.0002)
+              {}
+              else
+              {
+                newdesc += " " + parts[i];
+                writeDelta = true;
+              }
+            }
+            else if (writeDelta && parts[i].startsWith("delta:"))
+            {
+              newdesc += " " + parts[i];
+            }
+          }
+          log.debug("Old desc:" + desc + " new desc:" + newdesc);
+          desc = newdesc;
+          hit.setDescription(desc);
+        }
+      }
+    }
+  }
+
+
   public String getInputFileName()
   {
@@ -787 +837 @@
     public ProgressReporter progress;
     private AHit current_protein;
-    private int current_spectrum_id, current_charge;
+    private int current_spectrum_id, current_charge, current_start;
+    private float delta = 0;
     private AHit current_peptide;
     private StringBuffer buffer = null;
@@ -867 +918 @@
         current_peptide.setDescription(sequence);
         current_peptide.setExternalId(current_accession);
+        current_start = Integer.valueOf(attrs.getValue(attrs
+          .getIndex("start")));
         // Does this peptide result exist?
         boolean existed = false;
@@ -899 +952 @@
             .valueOf(exp_mass));
           current_peptide.setCharge(Integer.valueOf(current_charge));
+          delta = current_peptide.getScore() - Float.parseFloat(attrs
+            .getValue(attrs.getIndex("nextscore")));
           peptide_results.add(current_peptide);
         }
@@ -905 +960 @@
       {
         // om.setPosition(Integer.valueOf(attrs.getValue(attrs.getIndex("at"))).intValue());
+        int pos = Integer.valueOf(attrs.getValue(attrs.getIndex("at"))) - current_start + 1;
         String modifiedAminoAcid = attrs.getValue(attrs
           .getIndex("modified")) + "@" + attrs.getValue(
-          attrs.getIndex("type")).charAt(0);
+          attrs.getIndex("type")).charAt(0) + "" + pos;
+        log
+          .debug("Sequence:" + current_peptide.getDescription() + " current_start:" + current_start + " pos:" + pos + " mod:" + modifiedAminoAcid);
         current_peptide
           .setDescription(current_peptide.getDescription() + " " + modifiedAminoAcid);
@@ -948 +1006 @@
         throws SAXException
     {
-      if (qName.equals("score_record"))
-      {
-        // spectrumSearch.addSearchResult(current_result);
-        // current_result.addPolyPeptide(current_protein);
+      if (qName.equals("domain"))
+      {
+        if (current_peptide.getDescription().contains("@") && !current_peptide
+          .getDescription().contains("delta:"))
+        {
+          current_peptide.setDescription(current_peptide
+            .getDescription() + " delta:" + delta);
+        }
       }
       else if (qName.equals("note") && !inside_parameters)