JAL-2754 Sequence.findFeatures(fromCol, toCol)

[jalview.git] / src / jalview / workers / ColumnCounterSetWorker.java

diff --git a/src/jalview/workers/ColumnCounterSetWorker.java b/src/jalview/workers/ColumnCounterSetWorker.java
index 6c5707d..ba627a8 100644 (file)
--- a/src/jalview/workers/ColumnCounterSetWorker.java
+++ b/src/jalview/workers/ColumnCounterSetWorker.java
@@ -228,6 +228,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
    * 
    * @param alignment
    * @param col
+   *          (0..)
    * @param row
    * @param fr
    */
@@ -248,14 +249,12 @@ 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;
   }