Changeset 1143 for plugins/base2

Timestamp:

Jul 28, 2009, 3:48:40 PM (14 years ago)

Author:

Martin Svensson

Message:

References #228 Added parameter to define which average method to use when running the plugin. The functionality is not tested yet.

Location:

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

Files:

• AbstractNormalizationPlugin.java (modified) (3 diffs)
• AverageNormalization.java (modified) (10 diffs)
• QuantileNormalization.java (modified) (9 diffs)

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

@@ -32 +32 @@
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.Permission;
+import net.sf.basedb.core.PluginParameter;
 import net.sf.basedb.core.Type;
 import net.sf.basedb.core.VirtualColumn;
@@ -61 +62 @@
   extends AbstractAnalysisPlugin
 {
+  protected static final String arithmeticOption = "Arithmetic mean";
+  protected static final String geometricOption = "Geometric mean";
   
   private static final Set<Permissions> permissions = new HashSet<Permissions>();
   
+  protected  PluginParameter<String> averageMethodParameter = new PluginParameter<String>
+  (
+    "averageMethod",
+    "Average calculation method",
+    "Select which method to use when calculating the averages.\n" +
+    "Geometric mean is default for none-logged values and arithmetic " +
+    "is default for logged values.",
+    null
+  );  
   
   /**
@@ -210 +222 @@
     return data;
   }
+  
+  public class AverageCalculator
+  {
+    private double sum;
+    private int dataSize;
+    private final String avgMethod;
+    
+    public AverageCalculator(String avgMethod)
+    {
+      this.avgMethod = avgMethod;
+      sum = 0;
+      dataSize = 0;
+    }
+    
+    public void addNumber(float number)
+    {
+      if (arithmeticOption.equals(avgMethod))
+      {
+        sum = sum + number;
+      }
+      else if (geometricOption.equals(avgMethod))
+      {
+        sum = sum + Math.log(number);       
+      }
+      dataSize++;
+    }
+    
+    public Float getAverage()
+    {
+      Float average = null;
+      if (dataSize > 0)
+      {
+        if (arithmeticOption.equals(avgMethod))
+        {
+          average = (float)sum/dataSize;
+        }
+        else if (geometricOption.equals(avgMethod))
+        {
+          average = (float)Math.exp(sum/dataSize);
+        }
+      }
+      return average;
+    }
+  }
 }

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

@@ -32 +32 @@
 import net.sf.basedb.core.DynamicSpotQuery;
 import net.sf.basedb.core.FloatParameterType;
-import net.sf.basedb.core.IntensityTransform;
 import net.sf.basedb.core.InvalidUseOfNullException;
 import net.sf.basedb.core.Job;
@@ -89 +88 @@
 {
   private static final String yesOption = "yes";
-  private static final String noOption = "no";
-  private static final String geometricOption = "geometric";
-  private static final String arithmeticOption = "arithmetic";
+  private static final String noOption = "no";  
   
   /*
@@ -127 +124 @@
     new FloatParameterType(null, null, 100f, false)
   );
-  
-  /*
-    Define which average method to use when calculating.
-   */
-  private PluginParameter<String> averageMethodParameter = new PluginParameter<String>
-  (
-    "averageMethod",
-    "Average calculation method",
-    "Select which method to use when calculating the averages.\n" +
-    "Geometric mean is default for none-logged values and arithmetic " +
-    "is default for logged values.",
-    null
-  );
-    
+      
   /*
     Information about this plug-in
@@ -320 +304 @@
         if (useGlobalAvgInt)
         { 
-          refValue = getGlobalGeometricMeanIntensity(dc, source, minIntensity);
+          refValue = getGlobalGeometricMeanIntensity(dc, source, minIntensity, (String)job.getValue("averageMethod"));
         }
         else
@@ -389 +373 @@
         parameters.add(getChildNameParameter(null, null, bas.getName()));
         parameters.add(getChildDescriptionParameter(null, null, null)); 
-
-        // Average normalization options
+        // Average normalization options        
         StringParameterType spt = new StringParameterType
         (
             null, 
-            bas.getIntensityTransform().equals(IntensityTransform.NONE) ? geometricOption : arithmeticOption , 
+            bas.getIntensityTransform().getAverageMethod().toString(), 
             true, 1, 0, 0, 
-            Arrays.asList(new String[] {geometricOption, arithmeticOption} )
+            Arrays.asList(arithmeticOption, geometricOption)
         );
         averageMethodParameter = new PluginParameter<String>
@@ -437 +420 @@
     long numSpots;
     long normalizedSpots = 0;
-    
-    boolean useGeometricMean = geometricOption.equals(job.getParameterValue("averageMethod"));
     
     // Create Transformation
@@ -515 +496 @@
         if (dataSize == 0) continue;
         
-        // Calculate the average intensity for the current assay.
-        double sum = 0;
-        float assayAverage;
-        if (useGeometricMean)
+        // Get the average intensity for the current assay.
+        String configuredAverageMethod = (String)job.getParameterValue("averageMethod");
+        AverageCalculator avgCalc = new AverageCalculator(configuredAverageMethod);
+        for (Normalizable d : data)
         {
-          for (Normalizable d : data)
-          {
-            sum = sum + Math.log(d.getNormalizableData());
-          }
-          assayAverage = (float)Math.exp(sum/dataSize);       
-        }
-        else
-        {
-          for (Normalizable d : data)
-          {
-            sum = sum + d.getNormalizableData();            
-          }
-          assayAverage = (float)sum/dataSize;         
-        }
-        scaleFactor = refValue / assayAverage;
+          avgCalc.addNumber(d.getNormalizableData());
+        }
+        Float assayAverage = avgCalc.getAverage();        
+        scaleFactor = assayAverage != null ? refValue / assayAverage : scaleFactor;
         
         // Normalize data and put it into the child-bioassay set
@@ -560 +530 @@
     either 1-channel or 2-channel data.
    */
-  private float getGlobalGeometricMeanIntensity(DbControl dc, BioAssaySet source,
-                                                float minIntensity)
+  private float getGlobalGeometricMeanIntensity(DbControl dc, BioAssaySet source, float minIntensity, String averageMethod)
     throws SQLException, BaseException
   {
@@ -574 +543 @@
     {
     case 1: 
-      ratio = Expressions.ln(ch1);
+      ratio = ch1;
       break;
     case 2:
@@ -582 +551 @@
       throw new BaseException(noOfChannels + " channel-data is not supported by this plugin");
     }   
-    mean = Aggregations.mean(ratio);
+    
+        
+    if (arithmeticOption.equals(averageMethod)) mean = Aggregations.mean(ratio);
+    else if (geometricOption.equals(averageMethod)) mean = Aggregations.geometricMean(ratio);
+    
     query.select(Selects.expression(mean, "mean"));
     query.restrict(intensityRestriction);

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

@@ -34 +34 @@
 import net.sf.basedb.core.RequestInformation;
 import net.sf.basedb.core.SpotBatcher;
+import net.sf.basedb.core.StringParameterType;
 import net.sf.basedb.core.Transformation;
 import net.sf.basedb.core.VirtualColumn;
@@ -223 +224 @@
         storeValue(job, request, ri.getParameter(CHILD_DESCRIPTION)); 
         
+        storeValue(job, request, averageMethodParameter);
+        
         response.setDone("Job configuration completed", Job.ExecutionTime.MEDIUM);
       }
@@ -273 +276 @@
         parameters.add(getSourceBioAssaySetParameter(null, null));
         parameters.add(getChildNameParameter(null, null, bas.getName()));
-        parameters.add(getChildDescriptionParameter(null, null, null)); 
+        parameters.add(getChildDescriptionParameter(null, null, null));
+        
+        // Average normalization options
+        StringParameterType spt = new StringParameterType
+        (
+            null, 
+            bas.getIntensityTransform().getAverageMethod().toString(), 
+            true, 1, 0, 0, 
+            Arrays.asList(arithmeticOption, geometricOption)
+        );
+        averageMethodParameter = new PluginParameter<String>
+        (
+          averageMethodParameter.getName(),
+          averageMethodParameter.getLabel(),
+          averageMethodParameter.getDescription(),
+          spt
+        );        
+        parameters.add(averageMethodParameter);
 
         String description = "Set minimum intensity for each channel and properties for the child";
@@ -300 +320 @@
       Job job, ProgressReporter progress)
   {
+    String averageMethod = (String)(job.getParameterValue("averageMethod"));
+    
     int noOfChannels = source.getRawDataType().getChannels();
     long normalizedSpots = 0;
@@ -320 +342 @@
           normalizedSpots + " spots normalized");
     
-    double[] rowSummaries = null;
+    AverageCalculator[] rowCalculators = null;
     
     List<BioAssay> assays = source.getBioAssays().list(dc);
     Map<Integer, File> fileMap = new HashMap<Integer, File>();
+    String configuredAverageMethod = (String)job.getParameterValue(averageMethodParameter.getName());
     int spotsPerAssay = -1;
     
@@ -342 +365 @@
       
       // Write spot data to file and calculate row summaries
-      if (rowSummaries == null) rowSummaries = new double[data.size()];
+      if (rowCalculators == null) rowCalculators = new AverageCalculator[data.size()];
       FileWriter fw = null;
       try
@@ -351 +374 @@
         for (int i=0; i<data.size(); i++)
         {
-          AbstractSpotData spot = data.get(i);          
-          rowSummaries[i] += spot.getNormalizableData();
+          AbstractSpotData spot = data.get(i);
+          if (rowCalculators[i] == null) rowCalculators[i] = new AverageCalculator(configuredAverageMethod);
+          rowCalculators[i].addNumber(spot.getNormalizableData());
           
           if (i > 0)fw.write("\n");
@@ -378 +402 @@
       }
     } 
-    
-    // Calculate the row averages.
-    float[] rowAverages = new float[rowSummaries.length];
-    for (int i=0; i<rowSummaries.length; i++)
-    {
-      rowAverages[i] = (float)(rowSummaries[i]/assays.size());
-    }
-    
+        
     try
     {
@@ -418 +435 @@
           String[] lineInfo = line.split("\t");
           AbstractSpotData spot = getSpotDataFromString(lineInfo);
-          spot.setNormalizableData(rowAverages[rowIndex]);
+          spot.setNormalizableData(rowCalculators[rowIndex].getAverage());
           batcher.insert(columnNo, spot.getPosition(), spot.getChannelData());
           normalizedSpots++;