X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureDistanceModel.java;fp=src%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureDistanceModel.java;h=e506be2d295daccdd01670c0715e7a96d60c2b54;hb=2dd39c36211f947fda099c550e711ef5905efefd;hp=056ecdb750082e91fca85bfe28ee9154c7a44fb8;hpb=4dd40d33a5becefd51c31a426f2501b21029f82c;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
index 056ecdb..e506be2 100644
--- a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
@@ -124,8 +124,8 @@ public class FeatureDistanceModel extends DistanceScoreModel
         /*
          * first record feature types in this column for each sequence
          */
-        Map<SeqCigar, Set<String>> sfap = findFeatureTypesAtColumn(
-                seqs, cpos);
+        Map<SeqCigar, Set<String>> sfap = findFeatureTypesAtColumn(seqs,
+                cpos);
 
         /*
          * count feature types on either i'th or j'th sequence but not both
@@ -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());