Changeset 833

Timestamp:

Nov 28, 2008, 2:15:23 PM (14 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #150: Fix layout of DetectionPValue.java

File:

• plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/DetectionPValue.java (modified) (15 diffs)

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

@@ -63 +63 @@
 import net.sf.basedb.core.query.SqlResult;
 import net.sf.basedb.core.signal.SignalHandler;
-import net.sf.basedb.core.signal.SignalReceivedException;
 import net.sf.basedb.core.signal.SignalTarget;
 import net.sf.basedb.core.signal.ThreadSignalHandler;
@@ -123 +122 @@
       "Illumina Focused Arrays (not yet implemented)",
       new StringParameterType(255, "Whole Genome BeadChip", true, 1, 0, 0,
-                              Arrays.asList(
-                                new String[] { "Whole Genome BeadChip" ,
-                                               "Focused Array (not yet implemented)" }
-                                )
+        Arrays.asList(
+          new String[] { "Whole Genome BeadChip", "Focused Array (not yet implemented)" }
         )
-      );
+      )
+    );
 
   private static final String defaultChildName="Detection P-value";
@@ -167 +165 @@
         {
           response.setError(errors.size() +
-                            " invalid parameter(s) were found in the request",
-                            errors);
+            " invalid parameter(s) were found in the request", errors);
           return;
         }
@@ -186 +183 @@
         Job.ExecutionTime execTime = Job.ExecutionTime.SHORT;
         DbControl dc = sc.newDbControl();
-        try {
+        try 
+        {
           BioAssaySet source = getSourceBioAssaySet(dc);
           int nofAssays = source.getBioAssays().list(dc).size();
           if (nofAssays>10 && nofAssays<30)
+          {
             execTime = Job.ExecutionTime.MEDIUM;
+          }
           else if (nofAssays>=30)
+          {
             execTime = Job.ExecutionTime.LONG;
+          }
         }
-        finally {
-          if (dc != null)
-            dc.close();
+        finally 
+        {
+          if (dc != null) dc.close();
         }
         response.setDone("Job configuration complete", execTime);
       }
-    }
-    catch (SignalReceivedException ex)
-    {
-      response.setError("Aborted by user", Arrays.asList(ex));
     }
     catch (Throwable ex)
@@ -259 +257 @@
     if (permissions.size() == 0)
     {
-      permissions.add(new Permissions(Item.EXPERIMENT, null,
-                                      EnumSet.of(Permission.USE)));
-      permissions.add(new Permissions(Item.EXTRAVALUETYPE, null,
-                                      EnumSet.of(Permission.USE)));
-      permissions.add(new Permissions(Item.JOB, null,
-                                      EnumSet.of(Permission.READ)));
+      permissions.add(new Permissions(Item.EXPERIMENT, null, EnumSet.of(Permission.USE)));
+      permissions.add(new Permissions(Item.EXTRAVALUETYPE, null, EnumSet.of(Permission.USE)));
+      permissions.add(new Permissions(Item.JOB, null, EnumSet.of(Permission.READ)));
     }
     return permissions;
@@ -276 +271 @@
   {
     if (cmd.equals(Request.COMMAND_CONFIGURE_JOB))
+    {
       return getConfigureJobParameters();
+    }
     return null;
   }
@@ -303 +300 @@
       DbControl dc = null;
       Experiment experiment = null;
-      try {
+      try 
+      {
         dc = sc.newDbControl();
         experiment=getCurrentExperiment(dc);
@@ -309 +307 @@
       finally
       {
-        if (dc != null)
-          dc.close();
+        if (dc != null) dc.close();
       }
       if (Illumina.getBeadSummaryType() != experiment.getRawDataType())
       {
-        message = ("The experiment (" + experiment +
-                   ") is not Illumina expression data");
+        message = "The experiment (" + experiment + ") is not Illumina expression data";
       }
     }
@@ -328 +324 @@
     float[] absMedianDistance=new float[sortedIntensity.length];
     for (int i=0; i<absMedianDistance.length; ++i)
+    {
       absMedianDistance[i]=Math.abs(sortedIntensity[i]-controlMedian);
+    }
     Arrays.sort(absMedianDistance);
     float MAD=median(absMedianDistance);
@@ -335 +333 @@
     int controlstart=0;
     while ((controlMedian-sortedIntensity[controlstart]) > MADcut)
+    {
       controlstart++;
+    }
     int controlend=sortedIntensity.length;
     while ((sortedIntensity[--controlend]-controlMedian) > MADcut);
@@ -380 +380 @@
       dc = sc.newDbControl();
       BioAssaySet source = getSourceBioAssaySet(dc);
-      String childName = Values.getString((String)job.getValue(CHILD_NAME),
-                                          source.getName());
+      String childName = Values.getString((String)job.getValue(CHILD_NAME), source.getName());
       String childDescription = (String)job.getValue(CHILD_DESCRIPTION);
 
@@ -421 +420 @@
       {
         // Batcher for inserting child data
-        SpotExtraValueBatcher<Float> batcher=
-          child.getSpotExtraValueBatcher(Float.class,
-                                         ExtraValueType.getByExternalId(dc,Illumina.DETECTION_PVALUE_ID),
-                                         thisJob);
+        SpotExtraValueBatcher<Float> batcher = child.getSpotExtraValueBatcher(
+          Float.class,
+          ExtraValueType.getByExternalId(dc, Illumina.DETECTION_PVALUE_ID),
+          thisJob);
 
         // Caluclate one bioassay at a time
@@ -435 +434 @@
           if (progress != null)
           {
-            progress.display(100*assayNo/nofAssays, "Treating assay " +
-                             (assayNo+1) + " of " + nofAssays + ".");
+            progress.display(100*assayNo/nofAssays, 
+                "Treating assay " + (assayNo+1) + " of " + nofAssays + ".");
           }
 
@@ -454 +453 @@
           }
           dri.close();
-          int[] controlStartStop=
-            locateOutlierBoundary(sortedControlIntensity,
-                                  (Float)job.getValue(outlierParameter.getName()));
+          int[] controlStartStop =  locateOutlierBoundary(sortedControlIntensity, 
+            (Float)job.getValue(outlierParameter.getName()));
 
           checkInterrupted();
@@ -471 +469 @@
             SqlResult result = dri.next();
             batcher.insert(result.getShort(columnIndex), result.getInt(positionIndex),
-                           pvalue(sortedControlIntensity, controlStartStop[0],
-                                  controlStartStop[1], result.getFloat(ch1Index)));
+              pvalue(sortedControlIntensity, controlStartStop[0],
+              controlStartStop[1], result.getFloat(ch1Index)));
           }
           dri.close();