Changeset 2133

Timestamp:

Mar 30, 2006, 3:49:24 PM (18 years ago)

Author:

Johan Enell

Message:

corrected the counter

Location:

trunk/src/core/net/sf/basedb/plugins

Files:

• LowessNormalization.java (modified) (2 diffs)
• MedianRatioNormalization.java (modified) (4 diffs)

trunk/src/core/net/sf/basedb/plugins/LowessNormalization.java

@@ -210 +210 @@
         
         batcher = childBioAssaySet.getSpotBatcher();
-        
-        int numSpots = bioAssaySet.getNumSpots();
-        int normalizedSpots = 0;
-        progress.display(normalizedSpots / numSpots * 100, normalizedSpots + " spots normalized");
-        
+
         float delta = (Float) job.getValue(deltaParameter.getName());
         float fitFraction = (Float) job.getValue(fitFractionParameter.getName());
@@ -237 +233 @@
         DynamicSpotQuery query;
         DynamicResultIterator resultIter;
+        query = bioAssaySet.getSpotData();
+        query.restrict(intensityRestriction);
+        int numSpots = query.count(dc);
+        int normalizedSpots = 0;
+        progress.display(normalizedSpots / numSpots * 100, normalizedSpots + " spots normalized");
+        
         List<BioAssay> assays = bioAssaySet.getBioAssays().list(dc);
         for (BioAssay assay : assays)

trunk/src/core/net/sf/basedb/plugins/MedianRatioNormalization.java

@@ -80 +80 @@
   private static final About about = new AboutImpl
   (
-    "Normalization: pin-based median ratio",
+    "Normalization: Median ratio",
     "This normalizer scales the intensities in such a way that their geometric mean (sqrt(i1 * i2))" +
     " is kept constant but the median of their ratios (i1/i2) is shifted to 1.\n" +
@@ -197 +197 @@
         dc.saveItem(child);
         batcher = child.getSpotBatcher();
-
-        int numSpots = bioAssaySet.getNumSpots();
-        int normalizedSpots = 0;
-        progress.display(normalizedSpots / numSpots * 100, normalizedSpots + " spots normalized");
-
+        
         Select ratio = Selects.expression(Expressions.divide(Dynamic.column(VirtualColumn.channel(1)), Dynamic.column(VirtualColumn.channel(2))), "ratio");
         Restriction intensityRestriction = Restrictions.and
@@ -213 +209 @@
         DynamicSpotQuery query;
         DynamicResultIterator resultIter;
+        query = bioAssaySet.getSpotData();
+        query.restrict(intensityRestriction);
+        int numSpots = query.count(dc);
+        int normalizedSpots = 0;
+        progress.display(normalizedSpots / numSpots * 100, normalizedSpots + " spots normalized");
+
         List<BioAssay> assays = bioAssaySet.getBioAssays().list(dc);
         for (BioAssay assay : assays)
@@ -248 +250 @@
             int lowCount = (int) Math.floor(count * lowExclude / 100);
             int highCount = (int) Math.floor(count * highExclude / 100);
-            numSpots -= assay.getNumSpots() - count;
-            progress.display((normalizedSpots * 100) / numSpots, (assay.getNumSpots() - count) + " spots removed from assay " + assay.getName());
 
             // check count > 0