Changeset 2154

Timestamp:

Dec 4, 2013, 12:37:11 PM (10 years ago)

Author:

olle

Message:

Refs #228. Classes/files AverageNormalization.java and QuantileNormalization.java updated to determine the default averaging method based on the intensity transform information for the BioAssaySet to work on, instead of what is returned from the Formula.AverageMethod getAverage() method for the IntensityTransform of the latter:

1. Private method RequestInformation getConfiguredJobParameters() is updated to check the intensity transform set for the BioAssaySet, and select the default averaging method based on that. This makes the choice of default averaging method independent on the value of the getAverage() method.

Location:

plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins

Files:

• AverageNormalization.java (modified) (2 diffs)
• QuantileNormalization.java (modified) (3 diffs)

plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/AverageNormalization.java

@@ -31 +31 @@
 import net.sf.basedb.core.DynamicResultIterator;
 import net.sf.basedb.core.DynamicSpotQuery;
+import net.sf.basedb.core.Formula;
+import net.sf.basedb.core.IntensityTransform;
 import net.sf.basedb.core.FloatParameterType;
 import net.sf.basedb.core.InvalidUseOfNullException;
@@ -345 +347 @@
         parameters.add(getChildDescriptionParameter(null, null, null)); 
         // Average normalization options        
+        Formula.AverageMethod defaultAverageMethod = Formula.AverageMethod.ARITHMETIC_MEAN;
+        IntensityTransform transform = bas.getIntensityTransform();
+        if (transform == IntensityTransform.NONE)
+        {
+          defaultAverageMethod = Formula.AverageMethod.GEOMETRIC_MEAN;
+        }
         StringParameterType spt = new StringParameterType
         (
             null, 
-            bas.getIntensityTransform().getAverageMethod().toString(), 
+            defaultAverageMethod.toString(), 
             true, 1, 0, 0, 
             Arrays.asList(arithmeticOption, geometricOption)

plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/QuantileNormalization.java

@@ -29 +29 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.DynamicSpotQuery;
+import net.sf.basedb.core.Formula;
+import net.sf.basedb.core.IntensityTransform;
 import net.sf.basedb.core.Job;
 import net.sf.basedb.core.PluginParameter;
@@ -250 +252 @@
         
         // Average normalization options
+        Formula.AverageMethod defaultAverageMethod = Formula.AverageMethod.ARITHMETIC_MEAN;
+        IntensityTransform transform = bas.getIntensityTransform();
+        if (transform == IntensityTransform.NONE)
+        {
+          defaultAverageMethod = Formula.AverageMethod.GEOMETRIC_MEAN;
+        }
         StringParameterType spt = new StringParameterType
         (
             null, 
-            bas.getIntensityTransform().getAverageMethod().toString(), 
+            defaultAverageMethod.toString(), 
             true, 1, 0, 0, 
             Arrays.asList(arithmeticOption, geometricOption)
@@ -323 +331 @@
       
       // Control that the number of spots per assay is the same in all assays
-      if (spotsPerAssay > -1 && spotsPerAssay != assay.getNumSpots()) 
+      if (spotsPerAssay > -1 && spotsPerAssay != assay.getNumSpots())
         throw new BaseException("The number of spots are not equal between the dispal\n " +
             "The normalization can not be done.");
       else if (spotsPerAssay == -1)
-        spotsPerAssay = assay.getNumSpots();  
+        spotsPerAssay = assay.getNumSpots();
       
       // Get spot data and sort it ascending