Changeset 2498

Timestamp:

Aug 8, 2006, 4:01:22 PM (17 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #314: Update documentation that shows code examples with Transformation.newProduct

Location:

trunk

Files:

• doc/development/overview/dynamic/filter.html (modified) (1 diff)
• doc/development/overview/dynamic/rootbioassayset.html (modified) (1 diff)
• doc/development/plugins/analysis/index.html (modified) (1 diff)
• src/core/net/sf/basedb/core/FilterBatcher.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/PositionExtraValueBatcher.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/SpotBatcher.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/SpotExtraValueBatcher.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/Transformation.java (modified) (2 diffs)
• src/examples/plugins/src/net/sf/basedb/exampleplugins/ExampleAnalyzer.java (modified) (1 diff)

trunk/doc/development/overview/dynamic/filter.html

@@ -116 +116 @@
   // Create Transformation
   Transformation t = source.newTransformation(null);
+  dc.saveItem(t);
 
   // Create a new BioAssaySet using the same data cube and layer
-  BioAssaySet filtered = t.newProduct(null, null);
+  BioAssaySet filtered = t.newProduct(null, null, true);
   filtered.setName("Filtered bioassayset");
-  dc.saveItem(t);
   dc.saveItem(filtered);
-
-  // Create BioAssay:s for each source BioAssay
-  for (BioAssay sourceBa : source.getBioAssays().list(dc))
-  {
-    BioAssay ba = filtered.newBioAssay(sourceBa);
-    dc.saveItem(ba);
-  }
 
   // Get all column and position coordinate for all spots that pass the filter

trunk/doc/development/overview/dynamic/rootbioassayset.html

@@ -140 +140 @@
   // Create Transformation
   Transformation t = e.newTransformation(null, rba);
+  dc.saveItem(t);
   
   // Create root BioAssaySet in new data cube and layer
-  BioAssaySet root = t.newProduct("new", "new");
+  BioAssaySet root = t.newProduct("new", "new", false);
   root.setName("New root bioassayset");
-  dc.saveItem(t);
   dc.saveItem(root);
   

trunk/doc/development/plugins/analysis/index.html

@@ -246 +246 @@
       Transformation t = source.newTransformation(j);
       t.setName("Copy spot intensities >= 0");
-      BioAssaySet result = t.newProduct(null, "new");
+      dc.saveItem(t);
+
+      BioAssaySet result = t.newProduct(null, "new", true);
       result.setName("After: Copying spot intensities");
-      dc.saveItem(t);
       dc.saveItem(result);
-      
-      // Create child bioassays for each source bioassay
-      for (BioAssay ba : source.getBioAssays.list(dc))
-      {
-         dc.saveItem(result.newBioAssay(ba));
-      }
 
       // Get query for source data

trunk/src/core/net/sf/basedb/core/FilterBatcher.java

@@ -49 +49 @@
 // filtered result
 Transformation t = source.newTransformation();
-BioAssaySet filtered = t.newProduct(null, null);
 dc.saveItem(t);
+BioAssaySet filtered = t.newProduct(null, null, true);
 dc.saveItem(filtered);
-
-// Create new bioassays for each bioassay in the source
-// bioassayset
-for (BioAssay sourceBa : source.getBioAssays().list(dc))
-{
-   dc.saveItem(bas.newBioAssay(sourceBa));
-}
 
 // Create a query that selects the column
@@ -258 +251 @@
 // filtered result
 Transformation t = source.newTransformation();
-BioAssaySet filtered = t.newProduct(null, null);
 dc.saveItem(t);
+BioAssaySet filtered = t.newProduct(null, null, true);
 dc.saveItem(filtered);
-
-// Create new bioassays for each bioassay in the source
-// bioassayset
-for (BioAssay sourceBa : source.getBioAssays().list(dc))
-{
-   dc.saveItem(bas.newBioAssay(sourceBa));
-}
 
 // Create a query that selects the column

trunk/src/core/net/sf/basedb/core/PositionExtraValueBatcher.java

@@ -46 +46 @@
 // new intensities, we use the same data cube and layer as the source
 Transformation t = source.newTransformation();
-BioAssaySet bas = t.newProduct(null, null);
 dc.saveItem(t);
+BioAssaySet bas = t.newProduct(null, null, true);
 dc.saveItem(bas);
-
-// Create new bioassays for each bioassay in the source
-// bioassayset
-for (BioAssay sourceBa : source.getBioAssays().list(dc))
-{
-   dc.saveItem(bas.newBioAssay(sourceBa));
-}
 
 // Create a query that selects the data of
@@ -282 +275 @@
 // new intensities, we use the same data cube and layer as the source
 Transformation t = source.newTransformation();
-BioAssaySet bas = t.newProduct(null, null);
 dc.saveItem(t);
+BioAssaySet bas = t.newProduct(null, null, true);
 dc.saveItem(bas);
 
-// Create new bioassays for each bioassay in the source
-// bioassayset
-for (BioAssay sourceBa : source.getBioAssays().list(dc))
-{
-   dc.saveItem(bas.newBioAssay(sourceBa));
-}
 
 // Create a query that selects the data of

trunk/src/core/net/sf/basedb/core/SpotBatcher.java

@@ -47 +47 @@
 // but a different layer
 Transformation t = source.newTransformation();
-BioAssaySet bas = t.newProduct(null, "new");
 dc.saveItem(t);
+BioAssaySet bas = t.newProduct(null, "new", true);
 dc.saveItem(bas);
-
-// Create new bioassays for each bioassay in the source
-// bioassayset
-for (BioAssay sourceBa : source.getBioAssays().list(dc))
-{
-   dc.saveItem(bas.newBioAssay(sourceBa));
-}
 
 // Create a query that selects the data of
@@ -274 +267 @@
 // but a different layer
 Transformation t = source.newTransformation();
-BioAssaySet bas = t.newProduct(null, "new");
 dc.saveItem(t);
+BioAssaySet bas = t.newProduct(null, "new", true);
 dc.saveItem(bas);
-
-// Create new bioassays for each bioassay in the source
-// bioassayset
-for (BioAssay sourceBa : source.getBioAssays().list(dc))
-{
-   dc.saveItem(bas.newBioAssay(sourceBa));
-}
 
 // Create a query that selects the data of

trunk/src/core/net/sf/basedb/core/SpotExtraValueBatcher.java

@@ -46 +46 @@
 // new intensities, we use the same data cube and layer as the source
 Transformation t = source.newTransformation();
-BioAssaySet bas = t.newProduct(null, null);
 dc.saveItem(t);
+BioAssaySet bas = t.newProduct(null, null, true);
 dc.saveItem(bas);
-
-// Create new bioassays for each bioassay in the source
-// bioassayset
-for (BioAssay sourceBa : source.getBioAssays().list(dc))
-{
-   dc.saveItem(bas.newBioAssay(sourceBa));
-}
 
 // Create a query that selects the data from
@@ -274 +267 @@
 // new intensities, we use the same data cube and layer as the source
 Transformation t = source.newTransformation();
-BioAssaySet bas = t.newProduct(null, null);
 dc.saveItem(t);
+BioAssaySet bas = t.newProduct(null, null, true);
 dc.saveItem(bas);
-
-// Create new bioassays for each bioassay in the source
-// bioassayset
-for (BioAssay sourceBa : source.getBioAssays().list(dc))
-{
-   dc.saveItem(bas.newBioAssay(sourceBa));
-}
 
 // Create a query that selects the data from

trunk/src/core/net/sf/basedb/core/Transformation.java

@@ -382 +382 @@
 Transformation t = ...
 
-// Use same data cube, but a new layer
-BioAssaySet bas = t.newProduct(null, "new");
-
-// Use same data cube and layer
-BioAssaySet filtered = t.newProduct(null, null);
-
-// Use new data cube and layer
-BioAsssySet merged = t.newProduct("new", "new");
+// Use same data cube, but a new layer; automatically create child bioassays
+BioAssaySet bas = t.newProduct(null, "new", true);
+
+// Use same data cube and layer; automatically create child bioassays
+BioAssaySet filtered = t.newProduct(null, null, true);
+
+// Use new data cube and layer; automatic creation of 
+// child bioassays is not supported
+BioAsssySet merged = t.newProduct("new", "new", false);
 
 // Create four new bioassaysets using two datacubes, one
 // with two layers and one with one layer
-BioAssaySet bas1 = t.newProduct("cube1", "layer1");
-BioAssaySet bas2 = t.newProduct("cube1", "layer2");
-BioAssaySet bas3 = t.newProduct("cube2", "layer3");
-BioAssaySet bas4 = t.newProduct("cube2", "layer3");
+BioAssaySet bas1 = t.newProduct("cube1", "layer1", false);
+BioAssaySet bas2 = t.newProduct("cube1", "layer2", false);
+BioAssaySet bas3 = t.newProduct("cube2", "layer3", false);
+BioAssaySet bas4 = t.newProduct("cube2", "layer3", false);
 </pre>
 
@@ -404 +405 @@
     <pre class="code">
 // Don't! We bas3 is now using the same cube and layer as bas1
-BioAssaySet bas3 = t.newProduct("cube2", "layer1");
+BioAssaySet bas3 = t.newProduct("cube2", "layer1", false);
 </pre>
 

trunk/src/examples/plugins/src/net/sf/basedb/exampleplugins/ExampleAnalyzer.java

@@ -151 +151 @@
         Transformation t = source.newTransformation(j);
         t.setName("Multiply " + factor + "; filter < " + cutoff);
-      BioAssaySet result = t.newProduct(null, "new");
+      BioAssaySet result = t.newProduct(null, "new", true);
       result.setName("After: multiply and filter");
       dc.saveItem(t);
       dc.saveItem(result);
-        
-        // Create child bioassays for each source bioassay
-        for (BioAssay ba : source.getBioAssays().list(dc))
-        {
-           dc.saveItem(result.newBioAssay(ba));
-        }
         
         //  Get query for source data