Changeset 4284

Timestamp:

Feb 10, 2012, 4:25:09 PM (12 years ago)

Author:

Fredrik Levander

Message:

Refs #777. Now summing if multiple values. Corrected so that also writing last cluster. Indicating sequence conflicts.

File:

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

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

@@ -192 +192 @@
     String currentSequence = "";
     String currentAcc = "";
-    Float[] values = null;
+    boolean conflict = false;
+    float[] values = null;
     writer
       .println("Cluster ID\tPeptide Sequence\tExternal IDs\tCharge\tAverage RT");
@@ -201 +202 @@
       if (!feature.getClusterId().equals(currentCluster))
       {
-        if (values != null)
-        {
-          writer
-            .print(currentCluster + "\t" + currentSequence + "\t" + currentAcc + "\t" + currentCharge + "\t" + (rtSum / nValues));
-          for (Float value : values)
-          {
-            writer.print("\t" + value);
-          }
-          writer.println();
-        }
-        values = new Float[entries];
+        printRow(writer, values, currentCluster, currentSequence,
+          currentAcc, currentCharge, rtSum, nValues, conflict);
+        values = new float[entries];
+        conflict = false;
         currentAcc = "";
         currentCharge = 0;
@@ -219 +213 @@
         nValues = 0;
       }
-      if (currentSequence.equals("") && feature.getPeptideSequence() != null)
-      {
-        currentSequence = feature.getPeptideSequence();
-        for (Hit hit : feature.getHits())
+      if (currentSequence.equals(""))
+      {
+        if (feature.getPeptideSequence() != null)
         {
-          if (currentSequence.startsWith(hit.getDescription()))
+          currentSequence = feature.getPeptideSequence();
+          for (Hit hit : feature.getHits())
           {
-            currentAcc = hit.getExternalId();
+            if (currentSequence.startsWith(hit.getDescription()))
+            {
+              currentAcc = hit.getExternalId();
+            }
           }
         }
       }
-      values[msFiles.indexOf(feature.getMsFile())] = feature
-        .getIntegratedIntensity();
+      else if (!feature.getPeptideSequence().equals(currentSequence))
+      {
+        conflict = true;
+      }
+      values[msFiles.indexOf(feature.getMsFile())] += feature
+        .getIntegratedIntensity().floatValue();
       nValues++;
       if (currentCharge == 0)
@@ -237 +238 @@
       rtSum += feature.getApexRetentionTimeInMinutes();
 
+    }
+    printRow(writer, values, currentCluster, currentSequence, currentAcc,
+      currentCharge, rtSum, nValues, conflict);
+  }
+
+
+  private void printRow(PrintWriter writer, float[] values,
+      Long currentCluster, String currentSequence, String currentAcc,
+      int currentCharge, float rtSum, float nValues, boolean conflict)
+  {
+    if (values != null)
+    {
+      writer.print(currentCluster + "\t" + currentSequence);
+      if (conflict)
+        writer.print(",+");
+      writer
+        .print("\t" + currentAcc + "\t" + currentCharge + "\t" + (rtSum / nValues));
+      for (float value : values)
+      {
+        writer.print("\t" + value);
+      }
+      writer.println();
     }