Changeset 2485

Timestamp:

Aug 3, 2006, 1:03:02 PM (17 years ago)

Author:

Johan Enell

Message:

Position batcher added

File:

• trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (9 diffs)

trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -52 +52 @@
 import net.sf.basedb.core.ProgressReporter;
 import net.sf.basedb.core.RawBioAssay;
+import net.sf.basedb.core.Reporter;
 import net.sf.basedb.core.RequestInformation;
 import net.sf.basedb.core.SpotBatcher;
@@ -702 +703 @@
     throws IOException
   {
+    int posCnt = 0;
+    
     BioAssaySet bas = null;
     SpotBatcher spotBatcher = null;
-    PositionBatcher posBatcher = null; 
+    PositionBatcher posBatcher = null;
 
     HashMap<String, BioAssay> idMap = new HashMap<String, BioAssay>();
+    HashMap<PosRep, Integer> posMap = new HashMap<PosRep, Integer>();
 
     FlatFileParser ffp = getInitializedFlatFileParser(new FileInputStream(new java.io.File(getExecDirectory(), "stdout.txt")));
@@ -756 +760 @@
       else if (section.name().equals("spots"))
       {
+        posBatcher = bas.getPositionBatcher(); // TODO: BioAssaySet can be null
         spotBatcher = bas.getSpotBatcher(); // TODO: BioAssaySet can be null
         List<String> columns = Arrays.asList(ffp.getHeader("columns").split("\\t"));
@@ -762 +767 @@
 
         ffp.setMinDataColumns(columns.size() - 1 + assays.size() * assayFields.size());
-        ffp.setUseNullIfEmpty(false);
 
         int posCol = columns.indexOf("position");
@@ -778 +782 @@
           {
             intCols = true;
-            int1Col += dataCol;
-            int2Col += dataCol;
           }
           else if (mCol > -1 && aCol > -1)
           {
             intCols = false;
-            mCol += dataCol;
-            aCol += dataCol;
           }
           else
@@ -798 +798 @@
         }
         
+        int1Col += dataCol;
+        int2Col += dataCol;
+        aCol += dataCol;
+        mCol += dataCol;
+        
         while (ffp.hasMoreData())
         {
@@ -804 +809 @@
           {
             BioAssay ba = idMap.get(assayId);
-
-            float int1;
-            float int2;
-
             try
             {
-              int position = Integer.parseInt(dataline.get(posCol));
+              Float int1;
+              Float int2;             
+              Integer reporter = dataline.get(repCol) == null ? null : new Integer(dataline.get(repCol));
+              Integer position = dataline.get(posCol) == null ? null : new Integer(dataline.get(posCol));
+              
               if (intCols)
               {
-                int1 = Float.parseFloat(dataline.get(int1Col));
-                int2 = Float.parseFloat(dataline.get(int2Col));
+                int1 = dataline.get(int1Col) == null ? Float.NaN : new Float(dataline.get(int1Col));
+                int2 = dataline.get(int2Col) == null ? Float.NaN : new Float(dataline.get(int2Col));
               }
               else
               {
-                double a = Double.parseDouble(dataline.get(aCol));
-                double m = Double.parseDouble(dataline.get(mCol));
+                float a = dataline.get(aCol) == null ? Float.NaN : new Float(dataline.get(aCol));
+                float m = dataline.get(mCol) == null ? Float.NaN : new Float(dataline.get(mCol));
 
                 // int2 = 10^a / 2^(0.5*m)
                 // int1 = int2 * 2^m
-                int2 = (float) (Math.pow(10, a) / Math.pow(2, 0.5 * m));
-                int1 = (float) (int2 * Math.pow(2, m));
+                int2 = new Float(Math.pow(10, a) / Math.pow(2, 0.5 * m));
+                int1 = new Float(int2 * Math.pow(2, m));
+              }
+              
+              PosRep pr = new PosRep(position, reporter);
+              position = posMap.get(pr);
+              if (position == null)
+              {
+                if (posMap.values().contains(position))
+                {
+                  position = pr.getPosition();
+                  if (position > posCnt)
+                  {
+                    posCnt = position;
+                  }
+                }
+                else
+                {
+                  posCnt++;
+                  position = posCnt;
+                }
+                posMap.put(pr, position);
               }
               
@@ -830 +855 @@
               {
                 spotBatcher.insert(ba.getDataCubeColumnNo(), position, int1, int2);
+                if (reporter != null)
+                {
+                  posBatcher.insert(position, Reporter.getById(dc, reporter));
+                }
+                else 
+                {
+                  posBatcher.insert(position, null);
+                }
               }
             }
@@ -1182 +1215 @@
     }
   }
+
+  
+  private class PosRep
+  {
+    Integer position;
+    
+    Integer reporter;
+
+    PosRep(Integer position, Integer reporter)
+    {
+      this.position = position;
+      this.reporter = reporter;
+    }
+
+    public final Integer getPosition()
+    {
+      return position;
+    }
+
+    public final Integer getReporter()
+    {
+      return reporter;
+    }
+
+    @Override
+    public boolean equals(Object o)
+    {
+      if (this == o)
+      {
+        return true;
+      }
+      else if (o instanceof PosRep)
+      {
+        PosRep pr = (PosRep) o;
+        return position.equals(pr.getPosition()) && (reporter == pr.getReporter() || reporter.equals(pr.getReporter()));
+      }
+      return false;
+    }
+    
+  }
 }