Changeset 698

Timestamp:

May 21, 2008, 11:57:29 PM (14 years ago)

Author:

Jari Häkkinen

Message:

Fixes #110.

File:

• plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/DetectionPValue.java (modified) (4 diffs)

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

@@ -114 +114 @@
      is added, or a corresponding list for 2-channel types must be
      added.
-
-     Note, changing the string in the list will affect the behaviour
-     of the plug-in and most certaintly unexpected results will be
-     generated. As an example, changing 'Whole Genome BeadChip'
-     will break the median method.
   */
   private static final
-  PluginParameter<String> arrayType1Parameter = new PluginParameter<String>
-    ( "method",
-      "Correction method",
-      "These methods are implemented:\n\n" +
-      "Detection P-value calculation for Illumine Whole Genome BeadChips\n" +
-      "Detection P-value calculation for Illumine Focused Arrays",
+  PluginParameter<String> arrayTypeParameter = new PluginParameter<String>
+    ( "arraytype",
+      "Array type",
+      "Detection P-value calculation for array types:\n\n" +
+      "Illumina Whole Genome BeadChips\n" +
+      "Illumina Focused Arrays (not yet implemented)",
       new StringParameterType(255, "Whole Genome BeadChip", true, 1, 0, 0,
                               Arrays.asList(
@@ -185 +180 @@
 
         // Plug-in options
-        storeValue(job, request, arrayType1Parameter);
+        storeValue(job, request, arrayTypeParameter);
         storeValue(job, request, outlierParameter);
 
@@ -241 +236 @@
 
         // background correction method
-        parameters.add(arrayType1Parameter);
+        parameters.add(arrayTypeParameter);
         parameters.add(outlierParameter);
   
@@ -382 +377 @@
     try
     {
-      String arrayType = (String)job.getValue(arrayType1Parameter.getName());
+      String arrayType = (String)job.getValue(arrayTypeParameter.getName());
       dc = sc.newDbControl();
       BioAssaySet source = getSourceBioAssaySet(dc);