Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / analysis / scoremodels / FeatureDistanceModel.java

diff --git a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
index c20d4f1..e506be2 100644 (file)
--- a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
@@ -177,10 +177,12 @@ public class FeatureDistanceModel extends DistanceScoreModel
   /**
    * Builds and returns a map containing a (possibly empty) list (one per
    * SeqCigar) of visible feature types at the given column position. The map
-   * has no entry for sequences which are gapped at the column position.
+   * does not include entries for features which straddle a gapped column
+   * positions.
    * 
    * @param seqs
    * @param columnPosition
+   *          (0..)
    * @return
    */
   protected Map<SeqCigar, Set<String>> findFeatureTypesAtColumn(
@@ -192,9 +194,12 @@ public class FeatureDistanceModel extends DistanceScoreModel
       int spos = seq.findPosition(columnPosition);
       if (spos != -1)
       {
+        /*
+         * position is not a gap
+         */
         Set<String> types = new HashSet<String>();
-        List<SequenceFeature> sfs = fr.findFeaturesAtRes(seq.getRefSeq(),
-                spos);
+        List<SequenceFeature> sfs = fr.findFeaturesAtResidue(
+                seq.getRefSeq(), spos);
         for (SequenceFeature sf : sfs)
         {
           types.add(sf.getType());