Changeset 2132

Timestamp:

Mar 30, 2006, 1:26:37 PM (17 years ago)

Author:

Johan Enell

Message:

Lowess is pinbased

Location:

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

Files:

• LowessNormalization.java (modified) (7 diffs)
• MedianRatioNormalization.java (modified) (1 diff)

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

@@ -52 +52 @@
 import net.sf.basedb.core.plugin.Request;
 import net.sf.basedb.core.plugin.Response;
+import net.sf.basedb.core.query.Aggregations;
 import net.sf.basedb.core.query.Dynamic;
 import net.sf.basedb.core.query.Expressions;
+import net.sf.basedb.core.query.JoinType;
 import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.core.query.Restriction;
@@ -130 +132 @@
     new ItemParameterType<BioAssaySet>(BioAssaySet.class, null, true, 1, null)
   );
+  
+  private static final PluginParameter<Integer> blockGroupParameter = new PluginParameter<Integer>
+  (
+    "blockGroup",
+    "Blockgroup size",
+    "The number of arraydesign blocks in each group",
+    new IntegerParameterType(1, null, 1, true)
+  );
 
   private static double ywRangeFactor = 6;
@@ -163 +173 @@
     parameters.add(iterParameter);
     parameters.add(bioAssaySetParameter);
+    parameters.add(blockGroupParameter);
     configureJob = new RequestInformation
     (
@@ -181 +192 @@
   public void run(Request request, Response response, ProgressReporter progress)
   {
+    DbControl dc = sc.newDbControl();
     String command = request.getCommand();
     if (command.equals(Request.COMMAND_EXECUTE))
     {
       SpotBatcher batcher = null;
-      DbControl dc = null;
       try
       {
-        dc = sc.newDbControl();
+        int blockGroupSize = (Integer) job.getValue(blockGroupParameter.getName());
         BioAssaySet bioAssaySet = (BioAssaySet) job.getValue(bioAssaySetParameter.getName());
         bioAssaySet = BioAssaySet.getById(dc, bioAssaySet.getId());
@@ -218 +229 @@
           "a"
         );
-        Restriction restriction = Restrictions.and
+        Restriction intensityRestriction = Restrictions.and
         (
           Restrictions.gt(Dynamic.column(VirtualColumn.channel(1)), Expressions.aFloat(0)), 
@@ -224 +235 @@
         );
 
+        DynamicSpotQuery query;
+        DynamicResultIterator resultIter;
         List<BioAssay> assays = bioAssaySet.getBioAssays().list(dc);
         for (BioAssay assay : assays)
         {
-          BioAssay childBioAssay = childBioAssaySet.newBioAssay(assay);
-          childBioAssay.setName(assay.getName());
-          dc.saveItem(childBioAssay);
-          
-          DynamicSpotQuery query = assay.getSpotData();
-          query.restrictPermanent(restriction);
-          query.select(M);
-          query.select(A);
-          query.orderPermanent(Orders.asc(Expressions.selected(A)));
-
-          int count = query.count(dc);
-          numSpots -= assay.getNumSpots() - count;
-          progress.display((normalizedSpots * 100) / numSpots, (assay.getNumSpots() - count)+ " spots removed from assay " + assay.getName());
-
-          ArrayList<Double> mValues = new ArrayList<Double>();
-          ArrayList<Double> aValues = new ArrayList<Double>();
-          DynamicResultIterator it = query.iterate(dc);
-          
-          while (it.hasNext())
+          dc.saveItem(childBioAssaySet.newBioAssay(assay));
+
+          query = assay.getSpotData();
+          query = assay.getSpotData();
+          query.restrict(intensityRestriction);
+          query.joinRawData(JoinType.LEFT);
+          query.select(Selects.expression(Aggregations.max(Expressions.selected(Dynamic.selectRawData("block"))), "max"));
+          resultIter = query.iterate(dc);
+          int maxBlock = resultIter.next().getInt(resultIter.getIndex("max"));
+
+          for (int i = 0; i < maxBlock; i += blockGroupSize)
           {
-            SqlResult r = it.next();
-            aValues.add((double) r.getFloat(it.getIndex(A.getAlias())));
-            mValues.add((double) r.getFloat(it.getIndex(M.getAlias())));
+            Restriction blockRestriction = Restrictions.between
+            ( 
+              Expressions.selected(Dynamic.selectRawData("block")),
+              Expressions.integer(i),
+              Expressions.integer(i+blockGroupSize)
+            );
+            
+            query = assay.getSpotData();
+            query.select(M);
+            query.select(A);
+            query.select(Dynamic.selectRawData("block"));
+            query.joinRawData(JoinType.LEFT);
+            query.restrictPermanent(intensityRestriction);
+            query.restrictPermanent(blockRestriction);
+            query.orderPermanent(Orders.asc(Expressions.selected(A)));
+  
+            if (query.count(dc) <= 0) continue;
+  
+            ArrayList<Double> mValues = new ArrayList<Double>();
+            ArrayList<Double> aValues = new ArrayList<Double>();
+            DynamicResultIterator it = query.iterate(dc);
+            
+            while (it.hasNext())
+            {
+              SqlResult r = it.next();
+              aValues.add((double) r.getFloat(it.getIndex(A.getAlias())));
+              mValues.add((double) r.getFloat(it.getIndex(M.getAlias())));
+            }
+            
+            List<Double> smoothCurve = lowess(aValues, mValues, fitFraction, iter, delta);
+  
+            query.reset();
+            query.select(Dynamic.select(VirtualColumn.COLUMN));
+            query.select(Dynamic.select(VirtualColumn.POSITION));
+            query.select(Dynamic.select(VirtualColumn.channel(1)));
+            query.select(Dynamic.select(VirtualColumn.channel(2)));
+            query.select(A);
+            query.joinRawData(JoinType.LEFT);
+            
+            it = query.iterate(dc);
+            int column = it.getIndex(VirtualColumn.COLUMN.getName());
+            int position = it.getIndex(VirtualColumn.POSITION.getName());
+            int ch1Col = it.getIndex(VirtualColumn.channel(1).getName());
+            int ch2Col = it.getIndex(VirtualColumn.channel(2).getName());
+            
+            for (int j = 0; j < smoothCurve.size() && it.hasNext(); j++)
+            {
+              SqlResult r = it.next();
+  
+              double factor = Math.exp(smoothCurve.get(j) * 0.5);
+              double ch1 = r.getFloat(ch1Col)/factor;
+              double ch2 = r.getFloat(ch2Col)*factor;
+              batcher.insert(r.getShort(column), r.getInt(position), (float) ch1, (float) ch2);
+            }
+            
+            normalizedSpots += smoothCurve.size();
+            progress.display((normalizedSpots * 100) / numSpots, normalizedSpots + " spots normalized");
           }
-          
-          List<Double> smoothCurve = lowess(aValues, mValues, fitFraction, iter, delta);
-
-          query.reset();
-          query.select(Dynamic.select(VirtualColumn.COLUMN));
-          query.select(Dynamic.select(VirtualColumn.POSITION));
-          query.select(Dynamic.select(VirtualColumn.channel(1)));
-          query.select(Dynamic.select(VirtualColumn.channel(2)));
-          query.select(A);
-          
-          it = query.iterate(dc);
-          int column = it.getIndex(VirtualColumn.COLUMN.getName());
-          int position = it.getIndex(VirtualColumn.POSITION.getName());
-          int ch1Col = it.getIndex(VirtualColumn.channel(1).getName());
-          int ch2Col = it.getIndex(VirtualColumn.channel(2).getName());
-          
-          for (int i = 0; i < smoothCurve.size() && it.hasNext(); i++)
-          {
-            SqlResult r = it.next();
-
-            double factor = Math.exp(smoothCurve.get(i) * 0.5);
-            double ch1 = r.getFloat(ch1Col)/factor;
-            double ch2 = r.getFloat(ch2Col)*factor;
-            batcher.insert(r.getShort(column), r.getInt(position), (float) ch1, (float) ch2);
-          }
-          
-          normalizedSpots += smoothCurve.size();
-          progress.display((normalizedSpots * 100) / numSpots, normalizedSpots + " spots normalized");
         }
         batcher.close();
@@ -354 +385 @@
         storeValue(job, request, iterParameter);
         storeValue(job, request, bioAssaySetParameter);
+        storeValue(job, request, blockGroupParameter);
         response.setDone("Job configuration complete", Job.ExecutionTime.SHORT);
       }

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

@@ -216 +216 @@
         for (BioAssay assay : assays)
         {
-          //TODO use block numbers to create subgroups
           dc.saveItem(child.newBioAssay(assay));