Changeset 5147

Timestamp:

Oct 20, 2009, 12:33:46 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1389: Cache annotation summary groups in experiment explorer

The in-memory cache is now cleared every time the selected annotation types are modified.

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/ExperimentExplorer.java (modified) (9 diffs)
• www/views/experiments/explorer/view/index.jsp (modified) (1 diff)

trunk/src/clients/web/net/sf/basedb/clients/web/ExperimentExplorer.java

@@ -27 +27 @@
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -194 +195 @@
     The snapshot manager that loads annotation values.
   */
-  private final SnapshotManager snapshotManager;
+  private SnapshotManager snapshotManager;
   
   /**
@@ -234 +235 @@
     Caches annotation summaries.
   */
-  private Map<AnnotationType, AnnotationSummary> summaryCache;
+  private Map<Integer, AnnotationSummary> summaryCache;
   
   /**
@@ -244 +245 @@
     this.bioAssays = new HashMap<Short, Integer>();
     this.snapshotManager = new SnapshotManager();
-    this.summaryCache = new HashMap<AnnotationType, AnnotationSummary>();
+    this.summaryCache = new HashMap<Integer, AnnotationSummary>();
     for (BioAssay ba : bioAssaySet.getBioAssays().list(bioAssaySet.getDbControl()))
     {
@@ -412 +413 @@
     @return The id of the selected annotation type or 0 if no annotation type
       is selected
-    @deprecated Use {@link #getAnnotationTypeIds()} instead
+    @deprecated In 2.14, use {@link #getAnnotationTypeIds()} instead
   */
   public int getAnnotationTypeId()
@@ -425 +426 @@
     @param annotationTypeId The annotation type id or 0 if none is
       selected
-    @deprecated Use {@link #getAnnotationTypeIds()} instead
+    @deprecated In 2.14, use {@link #setAnnotationTypeIds(Collection)} instead
   */
   public void setAnnotationTypeId(int annotationTypeId)
@@ -435 +436 @@
   
   /**
-    Get a set for keeping track of the selected annotation types.
-    @return A set for storing integers (=the id of the selected annotation types)
+    Get the selected annotation types.
+    @return A set with the the id's of the selected annotation types
+    @since 2.14
   */
   public Set<Integer> getAnnotationTypeIds()
@@ -442 +444 @@
     if (annotationTypeIds == null) annotationTypeIds = new HashSet<Integer>();
     return annotationTypeIds;
+  }
+  
+  /**
+    Update the selected annotation types.
+    @param ids A collection containing the id's of all annotation types
+      that should currently be selected, all other annotation types are
+      automatically deselected
+    @since 2.14
+  */
+  public void setAnnotationTypeIds(Collection<Integer> ids)
+  {
+    Set<Integer> current = getAnnotationTypeIds();
+    current.clear();
+    for (Integer id : ids)
+    {
+      current.add(id);
+      summaryCache.remove(id);
+    }
+    // The snapshot manager also has an in-memory cache
+    snapshotManager = new SnapshotManager();
   }
   
@@ -500 +522 @@
   public AnnotationSummary getAnnotationSummary(DbControl dc, AnnotationType annotationType)
   {
-    AnnotationSummary summary = summaryCache.get(annotationType);
+    AnnotationSummary summary = summaryCache.get(annotationType.getId());
     if (summary == null)
     {
       summary = new AnnotationSummary(this, dc, annotationType);
-      summaryCache.put(annotationType, summary);
+      summaryCache.put(annotationType.getId(), summary);
     }
     else

trunk/www/views/experiments/explorer/view/index.jsp

@@ -86 +86 @@
   {
     Integer[] annotationTypes = Values.getInt(request.getParameter("annotationtype_id").split("\\|"));
-    Set<Integer> tmp = explorer.getAnnotationTypeIds();
-    tmp.clear();
-    tmp.addAll(Arrays.asList(annotationTypes));
+    explorer.setAnnotationTypeIds(Arrays.asList(annotationTypes));
     
     // If an annotation type is selected the annotation column must be visible as the first column