X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FColumnCounterSetWorker.java;h=6c5707de49350783762586db4085bbf6973f863a;hb=refs%2Fheads%2Fbug%2FJAL-2491;hp=cf6a229ba91c677fb60277ef0cc62f06f05ec29e;hpb=d0b6486ecb5c6572b823f9fd8676a603a4d493e9;p=jalview.git

diff --git a/src/jalview/workers/ColumnCounterSetWorker.java b/src/jalview/workers/ColumnCounterSetWorker.java
index cf6a229..6c5707d 100644
--- a/src/jalview/workers/ColumnCounterSetWorker.java
+++ b/src/jalview/workers/ColumnCounterSetWorker.java
@@ -69,6 +69,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
   @Override
   public void run()
   {
+    boolean annotationAdded = false;
     try
     {
       calcMan.notifyStart(this);
@@ -93,7 +94,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
       {
         try
         {
-          computeAnnotations();
+          annotationAdded = computeAnnotations();
         } catch (IndexOutOfBoundsException x)
         {
           // probable race condition. just finish and return without any fuss.
@@ -111,7 +112,10 @@ class ColumnCounterSetWorker extends AlignCalcWorker
 
     if (ap != null)
     {
-      ap.adjustAnnotationHeight();
+      if (annotationAdded)
+      {
+        ap.adjustAnnotationHeight();
+      }
       ap.paintAlignment(true);
     }
 
@@ -120,8 +124,10 @@ class ColumnCounterSetWorker extends AlignCalcWorker
   /**
    * Scan each column of the alignment to calculate a count by feature type. Set
    * the count as the value of the alignment annotation for that feature type.
+   * 
+   * @return
    */
-  void computeAnnotations()
+  boolean computeAnnotations()
   {
     FeatureRenderer fr = new FeatureRenderer(alignViewport);
     // TODO use the commented out code once JAL-2075 is fixed
@@ -140,6 +146,12 @@ class ColumnCounterSetWorker extends AlignCalcWorker
     {
       max[crow] = 0;
     }
+
+    int[] minC = counter.getMinColour();
+    int[] maxC = counter.getMaxColour();
+    Color minColour = new Color(minC[0], minC[1], minC[2]);
+    Color maxColour = new Color(maxC[0], maxC[1], maxC[2]);
+
     for (int col = 0; col < width; col++)
     {
       int[] count = counts[col];
@@ -164,6 +176,9 @@ class ColumnCounterSetWorker extends AlignCalcWorker
         max[crow] = Math.max(count[crow], max[crow]);
       }
     }
+
+    boolean annotationAdded = false;
+
     for (int anrow = 0; anrow < rows; anrow++)
     {
       Annotation[] anns = new Annotation[width];
@@ -175,8 +190,8 @@ class ColumnCounterSetWorker extends AlignCalcWorker
         int count = counts[i][anrow];
         if (count > 0)
         {
-          Color color = ColorUtils.getGraduatedColour(count, 0, Color.cyan,
-                  max[anrow], Color.blue);
+          Color color = ColorUtils.getGraduatedColour(count, 0, minColour,
+                  max[anrow], maxColour);
           String str = String.valueOf(count);
           anns[i] = new Annotation(str, str, '0', count, color);
         }
@@ -185,11 +200,14 @@ class ColumnCounterSetWorker extends AlignCalcWorker
       /*
        * construct or update the annotation
        */
-      AlignmentAnnotation ann = alignViewport.getAlignment()
-              .findOrCreateAnnotation(counter.getNames()[anrow],
-                      counter.getDescriptions()[anrow], false, null,
-                      null);
-      ann.description = counter.getDescriptions()[anrow];
+      String description = counter.getDescriptions()[anrow];
+      if (!alignment.findAnnotation(description).iterator().hasNext())
+      {
+        annotationAdded = true;
+      }
+      AlignmentAnnotation ann = alignment.findOrCreateAnnotation(
+              counter.getNames()[anrow], description, false, null, null);
+      ann.description = description;
       ann.showAllColLabels = true;
       ann.scaleColLabel = true;
       ann.graph = AlignmentAnnotation.BAR_GRAPH;
@@ -201,6 +219,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
         ourAnnots.add(ann);
       }
     }
+    return annotationAdded;
   }
 
   /**