X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureDistanceModel.java;h=38217e922aa0633089bffccaa105f03f85096ca5;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=c20d4f1a76353ee54adcb41221ce5175c607057a;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
index c20d4f1..38217e9 100644
--- a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
@@ -55,12 +55,12 @@ public class FeatureDistanceModel extends DistanceScoreModel
   @Override
   public ScoreModelI getInstance(AlignmentViewPanel view)
   {
-    FeatureDistanceModel instance;
+    FeatureDistanceModel model;
     try
     {
-      instance = this.getClass().newInstance();
-      instance.configureFromAlignmentView(view);
-      return instance;
+      model = this.getClass().newInstance();
+      model.configureFromAlignmentView(view);
+      return model;
     } catch (InstantiationException | IllegalAccessException e)
     {
       System.err.println("Error in " + getClass().getName()
@@ -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());