Changeset 4359

Timestamp:

Jul 1, 2008, 11:40:28 AM (15 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1076: Backwards incompatible change in MedianRatioNormalization? plugin

File:

• branches/2.7-stable/src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java (modified) (9 diffs)

branches/2.7-stable/src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java

@@ -237 +237 @@
     if (command.equals(Request.COMMAND_EXECUTE))
     {
-      if (progress != null) progress.display(0, "Preparing to normalize...");
-
       DbControl dc = null;
       try
@@ -250 +248 @@
         float highExclude = (Float) job.getValue(highExcludeParameter.getName());
         Job thisJob = getCurrentJob(dc);
-
-        // Create Transformation
-        Transformation t = source.newTransformation(getCurrentJob(dc));
-        t.setName(about.getName());
-        dc.saveItem(t);
-
-        // Create the normalized bioassay set
-        BioAssaySet child = t.newProduct(null, "new", true);
-        dc.saveItem(child);
-
-        // Batcher for inserting normalized data
-        SpotBatcher batcher = child.getSpotBatcher();
-
-        int nofChannels=source.getRawDataType().getChannels();
-        switch (nofChannels)
+        
+        BioAssaySet child = null;
+        int rawChannels = source.getRawDataType().getChannels();
+        switch (rawChannels)
         {
-            case 1:
-              String method = (String) job.getValue(methodParameter.getName());
-              normalize1ch(dc, source, batcher, minIntensity, lowExclude,
-                           highExclude, method.equals("Scale"), progress);
+          case 1:
+            String method = (String) job.getValue(methodParameter.getName());
+            child = normalize1ch(dc, source, thisJob, minIntensity, lowExclude,
+                    highExclude, method.equals("Scale"), progress);
+            break;
+          case 2:
+            int blockGroupSize =
+              (Integer) job.getValue(blockGroupParameter.getName());
+            child = normalize(dc, source, thisJob, minIntensity, lowExclude, 
+                highExclude, blockGroupSize, progress);
               break;
-            case 2:
-              int blockGroupSize =
-                (Integer) job.getValue(blockGroupParameter.getName());
-              normalize2ch(dc, source, batcher, minIntensity, lowExclude,
-                           highExclude, blockGroupSize, progress);
-              break;
-            default:
-              throw new InvalidDataException(nofChannels +
-                                             "-channel arrays not supported");
-        }
-
-        batcher.close();
+          default:
+              throw new InvalidDataException(rawChannels + 
+                "-channel arrays not supported");
+        }
+        
         child.setName(childName);
         child.setDescription(childDescription);
         dc.commit();
-
         int normalizedSpots = child.getNumSpots();
         response.setDone(normalizedSpots + " spots normalized, " + (source.getNumSpots() - normalizedSpots) + " spots removed");
@@ -416 +401 @@
     @since 2.7
   */
-  private void
-  normalize1ch(DbControl dc, BioAssaySet source, SpotBatcher batcher,
+  private BioAssaySet
+  normalize1ch(DbControl dc, BioAssaySet source, Job job,
                float minIntensity, float lowExclude, float highExclude,
                boolean scale, ProgressReporter progress)
   {
+    // Create Transformation
+    Transformation t = source.newTransformation(job);
+    t.setName(about.getName());
+    dc.saveItem(t);
+
+    // Create the normalized bioassay set
+    BioAssaySet child = t.newProduct(null, "new", true);
+    dc.saveItem(child);
+
+    // Batcher for inserting normalized data
+    SpotBatcher batcher = child.getSpotBatcher();
+    
     // Expressions used to get data
     Expression ch1 = Dynamic.column(VirtualColumn.channel(1));
@@ -504 +501 @@
       throw new BaseException(e);
     }
+    return child;
   }
 
   /**
-    Normalise the source bioassay set using MEDIAN-RATIO normalization.
+    Normalise the source bioassay set using MEDIAN-RATIO normalization. NOTE!
+    This normalization method only works with 2-channel data.
+    
     @param dc The DbControl to use for database access
     @param source The source bioassay set that is going to be normalized
+    @param job The job that is doing the normalization, or null
     @param minIntensity All spots which have a lower intensity value in either channel
       will be filtered out
@@ -519 +520 @@
     @param progress Progress reporter for the caller to keep track of the plugin's progress. Null is allowed. 
     @return The normalized bioassayset
-    @since 2.5
-  */
-  private void
-  normalize2ch(DbControl dc, BioAssaySet source, SpotBatcher batcher,
-               float minIntensity, float lowExclude, float highExclude,
-               int blockGroupSize, ProgressReporter progress)
-  {
+    @since 2.5; This method was removed in 2.7.0 by accident, added in 2.7.2 again
+  */
+  public BioAssaySet normalize(DbControl dc, BioAssaySet source, Job job, 
+      float minIntensity, float lowExclude, float highExclude, 
+      int blockGroupSize, ProgressReporter progress)
+  {
+    if (progress != null) progress.display(0, "Preparing to normalize...");
+  
+    // Create Transformation
+    Transformation t = source.newTransformation(job);
+    t.setName(about.getName());
+    dc.saveItem(t);
+    
+    // Create the normalized bioassay set
+    BioAssaySet child = t.newProduct(null, "new", true);
+    dc.saveItem(child);
+    
+    // Batcher for inserting normalized data
+    SpotBatcher batcher = child.getSpotBatcher();
+    
     // Expressions used to get data
     Expression block = Dynamic.rawData("block");
@@ -560 +574 @@
     query.restrict(bioAssayRestriction);
     query.order(Orders.asc(block));
-
+  
     // Normalize one bioassay at a time
     List<BioAssay> assays = source.getBioAssays().list(dc);
@@ -568 +582 @@
       {
         checkInterrupted();
-
+  
         // Prepare list for holding data
         int assaySpots = assay.getNumSpots();
@@ -650 +664 @@
           fromBlock = toBlock + 1;
         }
-        batcher.flush();
-      }
+      }
+      batcher.flush();
       batcher.close();
     }
@@ -658 +672 @@
       throw new BaseException(e);
     }
+    return child;
   }