Changeset 1211

Timestamp:

Mar 26, 2010, 11:22:14 AM (13 years ago)

Author:

Jari Häkkinen

Message:

Addresses #248 and #252. Do not use 'externalId' field if save to file is not requested.

File:

• plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BackgroundCorrection.java (modified) (5 diffs)

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

@@ -197 +197 @@
     private int externalIdIndex;
     private int positionIndex;
+    // keep track if to save to file since externalId is only
+    // available when saving of background expression values is
+    // requested (avoid left joins in SQL).
+    private Boolean saveBG;
 
     /**
@@ -210 +214 @@
       this.intensity=sd.intensity;
     }
-    public SData(DynamicResultIterator dri) throws SQLException
-    {
+    public SData(DynamicResultIterator dri, Boolean sBG) throws SQLException
+    {
+      saveBG=sBG;
       ch1Index = dri.getIndex(VirtualColumn.channelIntensity(1).getName());
-      externalIdIndex = dri.getIndex("externalId");
+      externalIdIndex = (saveBG ? dri.getIndex("externalId") : -1);
       positionIndex = dri.getIndex(VirtualColumn.POSITION.getName());
     }
@@ -219 +224 @@
     {
       intensity  = sr.getFloat(ch1Index);
-      externalId = new String(sr.getString(externalIdIndex));
+      externalId = (saveBG ? new String(sr.getString(externalIdIndex)) : null);
       return sr.getInt(positionIndex);
     }
@@ -409 +414 @@
     int nofSpots=0;
     HashMap<Integer,SData> hmap=(saveBG ? new HashMap<Integer,SData>() : null);
-    SData sdata=new SData(dri);
+    SData sdata=new SData(dri,saveBG);
 
     while (dri.hasNext())
@@ -442 +447 @@
     float median=0;
     HashMap<Integer,SData> hmap=(saveBG ? new HashMap<Integer,SData>() : null);
-    SData sdata=new SData(dri);
+    SData sdata=new SData(dri,saveBG);
 
     while (dri.hasNext())