X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FColumnCounterSetWorker.java;h=74695fe2bd494f63ce4d866f3f16b02ee2a8691d;hb=refs%2Fheads%2Fbug%2FJAL-2851;hp=2422748086a2ad248e453f5e07333137e3eaf012;hpb=9cee9c3255a397e190ec7f12f86bab7a2f6bc45a;p=jalview.git

diff --git a/src/jalview/workers/ColumnCounterSetWorker.java b/src/jalview/workers/ColumnCounterSetWorker.java
index 2422748..74695fe 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);
   }
@@ -116,7 +116,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
       {
         ap.adjustAnnotationHeight();
       }
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
     }
 
   }
@@ -229,6 +229,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
    * 
    * @param alignment
    * @param col
+   *          (0..)
    * @param row
    * @param fr
    */
@@ -249,14 +250,12 @@ 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;
   }