Changeset 3575

Timestamp:

Jul 19, 2007, 3:42:17 PM (16 years ago)

Author:

Martin Svensson

Message:

Fixes #685 Add plugin parameter asking for bioassays to AbstractAnalysisPlugin?

File:

• trunk/src/core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java (modified) (4 diffs)

trunk/src/core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java

@@ -25 +25 @@
 
 import java.util.Collections; 
+import java.util.List;
 import java.util.Set; 
 
+import net.sf.basedb.core.BioAssay;
 import net.sf.basedb.core.BioAssaySet;
 import net.sf.basedb.core.DbControl;
@@ -107 +109 @@
   
   /**
+    The bioAssays subset parameter.
+    To use when working on subset of bioassays in a bioAssaySet
+    @see #getSourceBioAssaysSubSetParameter(String, String, List<BioAssay>)
+   */
+  private PluginParameter<BioAssay> sourceSubSetParameter = null;
+  
+  /**
     Create a new <code>AbstractAnalysisPlugin</code>.
   */
@@ -200 +209 @@
     }
     return sourceParameter;
+  }
+  
+  protected static final String SOURCE_BIOASSAYS = "source_subset";
+  
+  /**
+    Gets a plugin parameter that asks for a subset of bioassays to use as data source
+    for the plugin. 
+      @param label The parameter's label. Uses a default value if null.
+   * @param description Description of the parameter. Uses a default value if null.
+    @return A plugin parameter
+    @since 2.4
+  */
+  protected PluginParameter<BioAssay> getSourceBioAssaysParameter(String label, String description)
+  {
+    if (sourceSubSetParameter == null)
+    {
+      if (label == null) label = "Source bioassays";
+      if (description == null) description = "Select the bioassays that should be filtered. " +
+          "If no bioassay is selected all will be filtered.";
+      sourceSubSetParameter = new PluginParameter<BioAssay>
+        (
+          SOURCE_BIOASSAYS, label, description, 
+          new ItemParameterType<BioAssay>(BioAssay.class, null, false, 0, null)
+        );    
+    }
+    return sourceSubSetParameter;
   }
   
@@ -336 +371 @@
   
   /**
+    Gets a list of bioassays that were selected from the current bioassay set, to use for the analysis.
+      @param dc The DbControl to access the database with
+      @return A list with bioassays or null.
+      @since 2.4
+   */
+  @SuppressWarnings("unchecked")
+  protected List<BioAssay> getSourceBioAssays(DbControl dc)
+  {
+    List<BioAssay> bioAssaySubset = (List<BioAssay>)job.getValues(SOURCE_BIOASSAYS);
+    if (bioAssaySubset != null) 
+    {
+      for (BioAssay ba : bioAssaySubset)
+      {
+        dc.reattachItem(ba);
+      }
+    }
+    return bioAssaySubset;
+  }
+  
+  /**
     Generate a name for the transformation based on the plugin and it's
     configuration. The name is created by taking the name of the plugin from the