Changeset 873

Timestamp:

Dec 4, 2008, 11:53:05 AM (13 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #151: Use two queries instead of one in DetectionPValue.run() method

File:

• plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/DetectionPValue.java (modified) (5 diffs, 2 props)

plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/DetectionPValue.java

@@ -2 +2 @@
   $Id$
 
-  Copyright (C) 2008 Jari Häkkinen
+  Copyright (C) 2008 Jari Hakkinen
 
   This file is part of BASE - BioArray Software Environment.
@@ -394 +394 @@
       dc.saveItem(child);
 
+      // Create restriction: column = :bioAssayColumn
+      Restriction bioAssayRestriction = Restrictions.eq(
+        Dynamic.column(VirtualColumn.COLUMN), 
+        Expressions.parameter("bioAssayColumn")
+        );
+      // Channel one contains the data
+      Expression ch1=Dynamic.rawData("mean");
+
+      // Prepare query to retrieve spot data. We use a parameter to
+      // restrict the query to return data for one bioassay at a time
+      DynamicSpotQuery mainQuery = source.getSpotData();
+      mainQuery.joinRawData(JoinType.INNER);
+      mainQuery.selectPermanent(Dynamic.select(VirtualColumn.COLUMN));
+      mainQuery.selectPermanent(Dynamic.select(VirtualColumn.POSITION));
+      mainQuery.selectPermanent(Selects.expression(ch1,"ch1"));
+      mainQuery.restrictPermanent(bioAssayRestriction);
+
+      // Prepare a second query to retrieve control data
       // Create restriction: negative control beads only (background spots)
       Expression control = Dynamic.reporter("controlGroupName");
@@ -399 +417 @@
         Restrictions.eq(control, Expressions.string("negative")) 
         );
-
-      // Create restriction: column = :bioAssayColumn
-      Restriction bioAssayRestriction = Restrictions.eq(
-        Dynamic.column(VirtualColumn.COLUMN), 
-        Expressions.parameter("bioAssayColumn")
-        );
-
-      // Prepare query to retrieve spot data. We use a parameter to
-      // restrict the query to return data for one bioassay at a time
-      DynamicSpotQuery query = source.getSpotData();
-      query.joinRawData(JoinType.INNER);
-      query.selectPermanent(Dynamic.select(VirtualColumn.COLUMN));
-      query.selectPermanent(Dynamic.select(VirtualColumn.POSITION));
-      Expression ch1=Dynamic.rawData("mean");
-      query.selectPermanent(Selects.expression(ch1,"ch1"));
-      query.restrictPermanent(bioAssayRestriction);
-      query.setReturnTotalCount(true);
-
+      DynamicSpotQuery controlQuery = source.getSpotData();
+      controlQuery.joinRawData(JoinType.INNER);
+      controlQuery.selectPermanent(Selects.expression(ch1,"ch1"));
+      controlQuery.restrictPermanent(bioAssayRestriction);
+      controlQuery.restrict(controlRestriction);
+      controlQuery.order(Orders.asc(ch1));
+      controlQuery.setReturnTotalCount(true);
+      
       try
       {
@@ -440 +448 @@
           // extract negative control intensities for this bioassay
           short bioassayColumn = assay.getDataCubeColumnNo();
-          query.setParameter("bioAssayColumn", (int)bioassayColumn, Type.INT);
-          query.restrict(controlRestriction);
-          query.order(Orders.asc(ch1));
-          DynamicResultIterator dri = query.iterate(dc);
+          controlQuery.setParameter("bioAssayColumn", (int)bioassayColumn, Type.INT);
+          DynamicResultIterator dri = controlQuery.iterate(dc);
           int ch1Index = dri.getIndex(VirtualColumn.channel(1).getName());
           float[] sortedControlIntensity=new float[(int)dri.getTotalCount()];
@@ -459 +465 @@
 
           // calculate detection P-value for all beadsets
-          query.reset();  // remove controlRestriction and ordering
-          query.setParameter("bioAssayColumn", (int)bioassayColumn, Type.INT);
-          dri = query.iterate(dc);
+          mainQuery.setParameter("bioAssayColumn", (int)bioassayColumn, Type.INT);
+          dri = mainQuery.iterate(dc);
           int positionIndex = dri.getIndex(VirtualColumn.POSITION.getName());
           int columnIndex = dri.getIndex(VirtualColumn.COLUMN.getName());