X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FColumnCounterWorker.java;h=dd56aaf78c070fd68801536b57aa9d4453bad4dc;hb=refs%2Fheads%2Ffeatures%2FJAL-653_JAL-1766_htslib_refseqsupport;hp=69f4265d3b6b4685767645297b6f60d9cc5e061c;hpb=25551bf7f81cd62e7b427f5787f2879eab2afed7;p=jalview.git

diff --git a/src/jalview/workers/ColumnCounterWorker.java b/src/jalview/workers/ColumnCounterWorker.java
index 69f4265..dd56aaf 100644
--- a/src/jalview/workers/ColumnCounterWorker.java
+++ b/src/jalview/workers/ColumnCounterWorker.java
@@ -20,14 +20,14 @@
  */
 package jalview.workers;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
+import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 
@@ -53,9 +53,10 @@ class ColumnCounterWorker extends AlignCalcWorker
    * @param af
    * @param counter
    */
-  public ColumnCounterWorker(AlignFrame af, FeatureCounterI counter)
+  public ColumnCounterWorker(AlignViewportI viewport,
+          AlignmentViewPanel panel, FeatureCounterI counter)
   {
-    super(af.getViewport(), af.alignPanel);
+    super(viewport, panel);
     ourAnnots = new ArrayList<AlignmentAnnotation>();
     this.counter = counter;
     calcMan.registerWorker(this);
@@ -88,7 +89,6 @@ class ColumnCounterWorker extends AlignCalcWorker
         return;
       }
 
-      removeAnnotation();
       if (alignViewport.getAlignment() != null)
       {
         try
@@ -123,7 +123,7 @@ class ColumnCounterWorker extends AlignCalcWorker
    */
   void computeAnnotations()
   {
-    FeatureRenderer fr = new FeatureRenderer((AlignmentPanel) ap);
+    FeatureRenderer fr = new FeatureRenderer(alignViewport);
     // TODO use the commented out code once JAL-2075 is fixed
     // to get adequate performance on genomic length sequence
     AlignmentI alignment = alignViewport.getAlignment();
@@ -158,20 +158,28 @@ class ColumnCounterWorker extends AlignCalcWorker
       {
         Color color = ColorUtils.getGraduatedColour(count, 0, Color.cyan,
                 max, Color.blue);
-        anns[i] = new Annotation(String.valueOf(count),
-                String.valueOf(count), '0', count, color);
+        String str = String.valueOf(count);
+        anns[i] = new Annotation(str, str, '0', count, color);
       }
     }
 
     /*
-     * construct the annotation, save it and add it to the displayed alignment
+     * construct or update the annotation
      */
-    AlignmentAnnotation ann = new AlignmentAnnotation(counter.getName(),
-            counter.getDescription(), anns);
+    AlignmentAnnotation ann = alignViewport.getAlignment()
+            .findOrCreateAnnotation(counter.getName(),
+                    counter.getDescription(), false, null, null);
+    ann.description = counter.getDescription();
     ann.showAllColLabels = true;
+    ann.scaleColLabel = true;
     ann.graph = AlignmentAnnotation.BAR_GRAPH;
-    ourAnnots.add(ann);
-    alignViewport.getAlignment().addAnnotation(ann);
+    ann.annotations = anns;
+    setGraphMinMax(ann, anns);
+    ann.validateRangeAndDisplay();
+    if (!ourAnnots.contains(ann))
+    {
+      ourAnnots.add(ann);
+    }
   }
 
   /**