Changeset 863

Timestamp:

Dec 2, 2008, 11:24:18 PM (13 years ago)

Author:

Jari Häkkinen

Message:

Addresses #50. Working on the Java wrapper.

File:

• plugins/base1/se.lu.thep.wenni/trunk/base/base2/WeNNI.java (modified) (4 diffs)

plugins/base1/se.lu.thep.wenni/trunk/base/base2/WeNNI.java

@@ -26 +26 @@
 import net.sf.basedb.plugins.AbstractRunBinaryPlugin;
 
-import net.sf.basedb.core.DbControl;
-import net.sf.basedb.core.Experiment;
+import net.sf.basedb.core.DbControl; // Jari, remove this?
+import net.sf.basedb.core.Experiment; // Jari, remove this?
+import net.sf.basedb.core.Item;
+import net.sf.basedb.core.Permission;
 import net.sf.basedb.core.ProgressReporter;
-import net.sf.basedb.core.RawBioAssay;
+import net.sf.basedb.core.RawBioAssay; // Jari, remove this?
 
 import net.sf.basedb.core.plugin.AboutImpl;
+import net.sf.basedb.core.plugin.Permissions;
 import net.sf.basedb.core.plugin.Plugin;
 
 import java.io.IOException;
 
+import java.util.EnumSet;
 import java.util.List;
 
@@ -57 +61 @@
 
   public WeNNI() {
-    // set about information
+
     about = new AboutImpl
-      ( "WeNNI plug-in", "An Unreliable expression value of a gene is " +
+      ( "WeNNI", "An Unreliable expression value of a gene is " +
         "imputed as the average expression in the most similar genes.\n" +
         "\nThe method is published in \"Improving missing value imputation " +
@@ -69 +73 @@
         null, null,
         "http://baseplugins.thep.lu.se/wiki/se.lu.thep.WeNNI" );
+
+    defaultChildName = "WeNNI imputed bioassayset";
+
+    // Permisssions to request
+    permissions.add(new Permissions(Item.EXPERIMENT, null,
+                                    EnumSet.of(Permission.USE)));
+    permissions.add(new Permissions(Item.JOB, null,
+                                    EnumSet.of(Permission.READ)));
+
     // set the type of the plug-in
     plugin_maintype=Plugin.MainType.ANALYZE;
   }
 
+  /**
+     List of background correction methods.
+
+     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 'Illumina BeadStudio median'
+     will break the median method.
+
+  private static final
+  PluginParameter<String> methodParameter = new PluginParameter<String>
+    ( "method",
+      "Correction method",
+      "These methods are implemented:\n\n" +
+      "Illumina BeadStudio inspired mean 'negative control'\n" +
+      "Illumina BeadStudio inspired median 'negative control'",
+      new StringParameterType(255, "Illumina BeadStudio median", true, 1, 0, 0,
+                              Arrays.asList(
+                                new String[] { "Illumina BeadStudio mean" ,
+                                               "Illumina BeadStudio median" }
+                                )
+        )
+      );
+  */
 
   protected void runBinary(List<RawBioAssay> sources,
@@ -78 +114 @@
     throws InterruptedException, IOException
   {
+    String[] cmd = { getBinaryPath(this.getClass(),"nni") , "--help" };
+    execute(cmd,progress);
   }