Changeset 791

Timestamp:

Sep 24, 2008, 9:16:08 PM (14 years ago)

Author:

Jari Häkkinen

Message:

References #129. Removed unused code, moved common code to super class, added a few comments.

Location:

plugins/base1/se.lu.onk.ReplicateError/trunk/src/replicateerror

Files:

• AcrossAssays/ReplicateErrorAA.java (modified) (5 diffs)
• ReplicateError.java (modified) (1 diff)
• WithinAssays/ReplicateErrorWA.java (modified) (4 diffs)

plugins/base1/se.lu.onk.ReplicateError/trunk/src/replicateerror/AcrossAssays/ReplicateErrorAA.java

@@ -209 +209 @@
       
       Iterator<String> it = groups.keySet().iterator();
-      PrintStream groupsFile = new PrintStream(new File("data", "groups.data"));
       while (it.hasNext())
       {
@@ -222 +221 @@
         else
         {
-          groupsFile.println(key);
           HTML.addGroup(key, assayIdToName(group));
         }
@@ -325 +323 @@
         }
 
-        Iterator<Integer> i = replicates.keySet().iterator();
-        while (i.hasNext())
-        {
-          Integer reporter = i.next();
-          Replicate r = replicates.get(reporter);
-          if (r.valid())
-          {
-            Iterator<Spot[]> dupI = r.duplicateIterator();
-            while (dupI.hasNext())
-            {
-              Spot[] d = dupI.next();
-              R.replica1Range(d[0].getM());
-              R.replica2Range(d[1].getM());
-              R.replicaMRange(Replicate.getReplicateM(d[0], d[1]));
-            }
-          }
-          else
-          {
-            i.remove();
-            if (leaveSingletons && r.size() == 1)
-            {
-              singletons.put(reporter, r);
-            }
-          }
-        }
+        // remove unusable replicates
+        purgeUnusableReplicates(replicates, singletons);
         
         // calculate mean or median befor filter
@@ -368 +343 @@
         R.setABRBefore(groupName, caluculateABR(replicates.values()));
 
-        // print result
+        // print result to file for later use in R
         printDuplicates(replicates.values(), groupName + ".data");
         
@@ -376 +351 @@
           r.filter(averageBefore, sdLimit * sdBefore);
         }
+        // print result to file for later use in R
         printDuplicates(replicates.values(), groupName + "good.data");
         

plugins/base1/se.lu.onk.ReplicateError/trunk/src/replicateerror/ReplicateError.java

@@ -241 +241 @@
   }
 
+  protected void purgeUnusableReplicates(HashMap<Integer, Replicate> replicates,
+                                         HashMap<Integer, Replicate> singletons)
+  { 
+    Iterator<Integer> i = replicates.keySet().iterator();
+    while (i.hasNext())
+    {
+      Integer reporter = i.next();
+      Replicate r = replicates.get(reporter);
+      if (r.valid())
+      {
+        Iterator<Spot[]> dupI = r.duplicateIterator();
+        while (dupI.hasNext())
+        {
+          Spot[] d = dupI.next();
+          R.replica1Range(d[0].getM());
+          R.replica2Range(d[1].getM());
+          R.replicaMRange(Replicate.getReplicateM(d[0], d[1]));
+        }
+      }
+      else
+      {
+        i.remove();
+        if (leaveSingletons && r.size() == 1) singletons.put(reporter, r);
+      }
+    }
+  }
+
   protected List<Float> getMList(Collection<Replicate> replicates)
   {

plugins/base1/se.lu.onk.ReplicateError/trunk/src/replicateerror/WithinAssays/ReplicateErrorWA.java

@@ -61 +61 @@
     {
       HTML.openGroup();
-      PrintStream groupsFile = new PrintStream(new File("data", "groups.data"));
       String[] vals;
       while ((vals = bfr.readDataRow()) != null)
       {
         assayName.put(new Integer(vals[idCol]), vals[nameCol]);
-        groupsFile.println(vals[nameCol]);
       }
-      groupsFile.close();
       HTML.closeGroup();
     }
@@ -139 +136 @@
         
         // remove unusable replicates
-        Iterator<Integer> it = replicates.keySet().iterator();
-        while (it.hasNext())
-        {
-          Integer reporter = it.next();
-          Replicate r = replicates.get(reporter);
-          if (leaveSingletons && r.size() == 1)
-          {
-            singletons.put(reporter, r);
-            it.remove();
-          }
-          else
-          {
-            Iterator<Spot[]> dupI = r.duplicateIterator();
-            while (dupI.hasNext())
-            {
-              Spot[] d = dupI.next();
-              R.replica1Range(d[0].getM());
-              R.replica2Range(d[1].getM());
-              R.replicaMRange(Replicate.getReplicateM(d[0], d[1])); 
-            }
-          }
-        }
+        purgeUnusableReplicates(replicates, singletons);
         
         int nbrBefore = replicates.size();
@@ -180 +156 @@
         R.setABRBefore(assayName.get(assay), caluculateABR(replicates.values()));
         
-        // print result
+        // print result to file for later use in R
         printDuplicates(replicates.values(), assayName.get(assay) + ".data");
         
@@ -188 +164 @@
           r.filter(averageBefore, sdLimit * sdBefore);
         }
+        // print result to file for later use in R
         printDuplicates(replicates.values(), assayName.get(assay) + "good.data");