Changeset 4274

Timestamp:

Jan 4, 2012, 1:38:40 PM (11 years ago)

Author:

Fredrik Levander

Message:

Refs #772. Updated protein assembly for optional per replicate assembly.

Location:

trunk

Files:

• client/servlet/src/org/proteios/action/hit/CreateProteinAssemblyJob.java (modified) (3 diffs)
• client/servlet/src/org/proteios/action/hit/ProteinAssembly1.java (modified) (2 diffs)
• plugin/src/org/proteios/plugins/ProteiosProteinAssembly.java (modified) (15 diffs)

trunk/client/servlet/src/org/proteios/action/hit/CreateProteinAssemblyJob.java

@@ -56 +56 @@
 {
   public static final VBoolean VFILEWISE = new VBoolean("isFileWise", false);
+  public static final VBoolean VREPLICATEWISE = new VBoolean("isReplicateWise", false);
   public static final VBoolean VOCCAMS = new VBoolean("isOccamsRazor", false);
   public static final VBoolean VUNIQUE = new VBoolean("isUnique", false);
@@ -106 +107 @@
     if (isFileWise == null)
       isFileWise = new Boolean(false);
+    Boolean isReplicateWise = getValidBoolean(VREPLICATEWISE);
+    if (isReplicateWise == null)
+      isReplicateWise = new Boolean(false);
     Boolean isOccamsRazor = getValidBoolean(VOCCAMS);
     if (isOccamsRazor == null)
@@ -164 +168 @@
     job.setParameterValue("fileWise", new BooleanParameterType(),
       isFileWise);
+    job.setParameterValue("replicateWise", new BooleanParameterType(),
+      isReplicateWise);
     job.setParameterValue("occamsRazor", new BooleanParameterType(),
       isOccamsRazor);

trunk/client/servlet/src/org/proteios/action/hit/ProteinAssembly1.java

@@ -80 +80 @@
     isProteinCB.setLabel("FileWise");
     isProteinCB.setValue("true");
-    isProteinCB.setHelp("Per peaklist file report");
+    isProteinCB.setHelp("Per peaklist file protein grouping");
     properties.add(isProteinCB);
+    Checkbox<VBoolean> isReplicateCB = new Checkbox<VBoolean>(
+      CreateProteinAssemblyJob.VREPLICATEWISE);
+    isReplicateCB.setLabel("ReplicateWise");
+    isReplicateCB.setValue("true");
+    isReplicateCB.setHelp("Per replicate protein grouping");
+    properties.add(isReplicateCB);
     Checkbox<VBoolean> isOccamCB = new Checkbox<VBoolean>(
       CreateProteinAssemblyJob.VOCCAMS);
@@ -186 +192 @@
     instruction += " If the search results combination has been performed, the peptide combined FDR can be used as cutoff, otherwise max E-value can be used.";
     instruction += " The report can be filtered based on protein FDR if decoy peptides are present (search in target-decoy database and decoys kept in combined hits report are the requirements).";
-    instruction += " Select whether to find proteins globally or per file or per sample. Also select whether peptide sequences should be counted once per unique";
+    instruction += " Select whether to assemble proteins globally per sample, or per replicate or per file. Also select whether peptide sequences should be counted once per unique";
     instruction += " Set the minimum nuber of peptides to the required number of significant peptides per protein.";
     instruction += " sequence. If the generate proteins checkbox is checked, new hits will be generated with score type Proteios Protein.";

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

@@ -113 +113 @@
   private boolean quantifyUsingUnique = false;
   private boolean peptideReport = false;
+  private boolean separateReplicates = false;
   private Integer minPep = 1;
   private int refIdx = 0;
@@ -181 +182 @@
       "Protein Assembly from Peptides",
       "Generate protein entries for Hits which pass a certain score limit. The Proteins are added to the hits report",
-      "1.9", "2008-2011, Fredrik Levander", null, null,
+      "1.10", "2008-2012, Fredrik Levander", null, null,
       "http://www.proteios.org  ");
   }
@@ -225 +226 @@
           .booleanValue();
         fileWise = ((Boolean) job.getValue("fileWise")).booleanValue();
+        separateReplicates = ((Boolean) job.getValue("replicateWise"))
+          .booleanValue();
         fdr = ((Boolean) job.getValue("fdr")).booleanValue();
         uniqueSequences = ((Boolean) job.getValue("unique"))
@@ -525 +528 @@
       Integer currentSpotId = null;
       String currentLocalSampleId = null;
+      String currentReplicateId = null;
       // First group peptides, if protein combination is not supposed to
       // be
@@ -541 +545 @@
           addFraction(peptideFraction, peptideFractions,
             currentSpotId, currentLocalSampleId,
-            currentPeakListFile, currentHit);
+            currentReplicateId, currentPeakListFile, currentHit);
           peptideFraction = new ArrayList<Hit>();
         }
@@ -547 +551 @@
         currentPeakListFile = currentHit.getPeakListFile();
         currentLocalSampleId = currentHit.getLocalSampleId();
+        currentReplicateId = currentHit.getReplicateId();
         peptideFraction.add(currentHit);
         if (!hitit.hasNext())
@@ -552 +557 @@
           addFraction(peptideFraction, peptideFractions,
             currentSpotId, currentLocalSampleId,
-            currentPeakListFile, currentHit);
+            currentReplicateId, currentPeakListFile, currentHit);
         }
       }
@@ -672 +677 @@
                 .getLocalSampleId() + "\n");
           }
+          if (separateReplicates && proteinHits.size() > 0)
+          {
+            output.write("Replicate id:" + proteinHits.get(0).hit
+              .getReplicateId() + "\n");
+          }
           if (fileWise && proteinHits.size() > 0)
           {
@@ -747 +757 @@
             output.write("Spot ID\t");
           }
-          else if (localSampleId == null)
+          else if (localSampleId != null)
           {
             output.write("Sample\t");
+            if (separateReplicates)
+            {
+              output.write("Replicate\t");
+            }
           }
           output
@@ -762 +776 @@
             }
           }
-          if (localSampleId != null && localSampleId.equals("all"))
-          {
-            output.write("\tSample");
+          if (localSampleId != null)
+          {
+            if (localSampleId.equals("all"))
+              output.write("\tSample");
+            if (separateReplicates)
+            {
+              output.write("\tReplicate");
+            }
           }
           output.write("\tLocal FDR\tTotal Intensity\n");
@@ -781 +800 @@
                 output.write("" + p.getSpotId() + "\t");
               }
-              else if (localSampleId == null)
+              else if (localSampleId != null)
               {
                 output.write("" + p.getLocalSampleId() + "\t");
+                if (separateReplicates)
+                {
+                  output
+                    .write("" + p.getReplicateId() + "\t");
+                }
               }
               output.write("" + p.getMatchedPeaks());
@@ -865 +889 @@
                   }
                 }
-                if (localSampleId != null && localSampleId
-                  .equals("all"))
+                if (localSampleId != null)
                 {
-                  output.write("\t" + p.getLocalSampleId());
+                  if (localSampleId.equals("all"))
+                  {
+                    output.write("\t" + p
+                      .getLocalSampleId());
+                  }
+                  if (separateReplicates)
+                    output.write("\t" + p.getReplicateId());
                 }
                 output
@@ -957 +986 @@
   private void addFraction(List<Hit> peptideFraction,
       List<List<Hit>> peptideFractions, Integer currentSpotId,
-      String currentLocalSampleId, File currentPeakListFile,
-      Hit currentHit)
+      String currentLocalSampleId, String currentReplicateId,
+      File currentPeakListFile, Hit currentHit)
   {
     if (label_index > 0)
@@ -993 +1022 @@
     }
     /*
-     * Start to collect new fraction if at new sample
+     * Start to collect new fraction if at new sample or new replicate
      */
-    if (localSampleId != null && localSampleId.equals("all") && (!currentLocalSampleId
-      .equals(currentHit.getLocalSampleId())))
-    {
-      peptideFractions.add(new ArrayList<Hit>());
+    if (localSampleId != null)
+    {
+      if (localSampleId.equals("all") && (!currentLocalSampleId
+        .equals(currentHit.getLocalSampleId())))
+      {
+        peptideFractions.add(new ArrayList<Hit>());
+      }
+      else if (separateReplicates && currentReplicateId != null && (!currentReplicateId
+        .equals(currentHit.getReplicateId())))
+      {
+        peptideFractions.add(new ArrayList<Hit>());
+      }
     }
 
@@ -1371 +1408 @@
     newHit.setMatchedPeaks(1);
     newHit.setLocalSampleId(currentHit.getLocalSampleId());
+    newHit.setReplicateId(currentHit.getReplicateId());
     // Set this to keep link to search settings
     newHit.setIdentificationResultFile(currentHit