X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FColumnCounterSetWorker.java;h=a711f2bd91c869437b1131cc8f0ecb731dd8f246;hb=bbc8fc127287ad3a11f0b470d37d741ddca162ff;hp=b6b64fcd11fbdb9e7b86f32927d0177c6daab2e9;hpb=9603ccdf9190d748728b4fb2fdd14533ca4e1a38;p=jalview.git

diff --git a/src/jalview/workers/ColumnCounterSetWorker.java b/src/jalview/workers/ColumnCounterSetWorker.java
index b6b64fc..a711f2b 100644
--- a/src/jalview/workers/ColumnCounterSetWorker.java
+++ b/src/jalview/workers/ColumnCounterSetWorker.java
@@ -57,7 +57,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
           AlignmentViewPanel panel, FeatureSetCounterI counter)
   {
     super(viewport, panel);
-    ourAnnots = new ArrayList<AlignmentAnnotation>();
+    ourAnnots = new ArrayList<>();
     this.counter = counter;
     calcMan.registerWorker(this);
   }
@@ -70,44 +70,22 @@ class ColumnCounterSetWorker extends AlignCalcWorker
   public void run()
   {
     boolean annotationAdded = false;
-    try
+    if (alignViewport.isClosed())
     {
-      calcMan.notifyStart(this);
+      abortAndDestroy();
+      return;
+    }
 
-      while (!calcMan.notifyWorking(this))
+    if (alignViewport.getAlignment() != null)
+    {
+      try
       {
-        try
-        {
-          Thread.sleep(200);
-        } catch (InterruptedException ex)
-        {
-          ex.printStackTrace();
-        }
-      }
-      if (alignViewport.isClosed())
+        annotationAdded = computeAnnotations();
+      } catch (IndexOutOfBoundsException x)
       {
-        abortAndDestroy();
+        // probable race condition. just finish and return without any fuss.
         return;
       }
-
-      if (alignViewport.getAlignment() != null)
-      {
-        try
-        {
-          annotationAdded = computeAnnotations();
-        } catch (IndexOutOfBoundsException x)
-        {
-          // probable race condition. just finish and return without any fuss.
-          return;
-        }
-      }
-    } catch (OutOfMemoryError error)
-    {
-      ap.raiseOOMWarning("calculating feature counts", error);
-      calcMan.disableWorker(this);
-    } finally
-    {
-      calcMan.workerComplete(this);
     }
 
     if (ap != null)
@@ -116,7 +94,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
       {
         ap.adjustAnnotationHeight();
       }
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
     }
 
   }
@@ -191,10 +169,10 @@ class ColumnCounterSetWorker extends AlignCalcWorker
         int count = counts[i][anrow];
 
         Color color = ColorUtils.getGraduatedColour(count, 0, minColour,
-                  max[anrow], maxColour);
-          String str = String.valueOf(count);
-          anns[i] = new Annotation(str, str, '0', count, color);
-          rmax = Long.max(count, rmax);
+                max[anrow], maxColour);
+        String str = String.valueOf(count);
+        anns[i] = new Annotation(str, str, '0', count, color);
+        rmax = Math.max(count, rmax);
       }
 
       /*
@@ -229,6 +207,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
    * 
    * @param alignment
    * @param col
+   *          (0..)
    * @param row
    * @param fr
    */
@@ -249,14 +228,12 @@ class ColumnCounterSetWorker extends AlignCalcWorker
     {
       return null;
     }
-    int pos = seq.findPosition(col);
 
     /*
      * compute a count for any displayed features at residue
      */
-    // NB have to adjust pos if using AlignmentView.getVisibleAlignment
     // see JAL-2075
-    List<SequenceFeature> features = fr.findFeaturesAtRes(seq, pos);
+    List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, col + 1);
     int[] count = this.counter.count(String.valueOf(res), features);
     return count;
   }