Changeset 1210

Timestamp:

Mar 23, 2010, 3:47:51 PM (13 years ago)

Author:

Jari Häkkinen

Message:

Addresses #248 and #252. Median fixed.

File:

• plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BackgroundCorrection.java (modified) (1 diff)

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

@@ -440 +440 @@
 
     int nofSpots=0;
-    SqlResult r = null;
-    while (nofSpots++<count) r=dri.next();
-
-    // odd number, next number is the median
-    if (!even) return dri.next().getFloat(index);
-    // even number, median is average of this and next number
-    return (r.getFloat(index) + dri.next().getFloat(index))/2;
+    float median=0;
+    HashMap<Integer,SData> hmap=(saveBG ? new HashMap<Integer,SData>() : null);
+    SData sdata=new SData(dri);
+
+    while (dri.hasNext())
+    {
+      SqlResult sr=dri.next();
+      ++nofSpots;
+      // odd number, median is the centre
+      // even number, median is the average of two values in the centre
+      if ((nofSpots==count) || (even && nofSpots==(count+1))) median+=sr.getFloat(index);
+
+      if (saveBG)
+      {
+        Integer position=sdata.extractData(sr);
+        allNegPos.add(position);
+        hmap.put(position,new SData(sdata));
+      }
+    }
+
+    if (saveBG) negSData.add(hmap);
+
+    // even number of spot,  median is an average of two values
+    return (even ? median/2 : median);
   }