X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureDistanceModel.java;h=bcc085558a4beb19f18b3fe68ec95de58ad83177;hb=cd669a0e8c7b91b379bca8fe6e702cf0fcbd1ce0;hp=ddbaf73600e05204dc854519c81b72a93f967289;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
index ddbaf73..bcc0855 100644
--- a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
@@ -58,14 +58,17 @@ public class FeatureDistanceModel extends DistanceScoreModel
     FeatureDistanceModel instance;
     try
     {
-      instance = this.getClass().newInstance();
+      instance = this.getClass().getDeclaredConstructor().newInstance();
       instance.configureFromAlignmentView(view);
       return instance;
     } catch (InstantiationException | IllegalAccessException e)
     {
-      System.err.println("Error in " + getClass().getName()
+      jalview.bin.Console.errPrintln("Error in " + getClass().getName()
               + ".getInstance(): " + e.getMessage());
       return null;
+    } catch (ReflectiveOperationException roe)
+    {
+      return null;
     }
   }
 
@@ -124,8 +127,8 @@ 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
@@ -188,7 +191,7 @@ public class FeatureDistanceModel extends DistanceScoreModel
   protected Map<SeqCigar, Set<String>> findFeatureTypesAtColumn(
           SeqCigar[] seqs, int columnPosition)
   {
-    Map<SeqCigar, Set<String>> sfap = new HashMap<SeqCigar, Set<String>>();
+    Map<SeqCigar, Set<String>> sfap = new HashMap<>();
     for (SeqCigar seq : seqs)
     {
       int spos = seq.findPosition(columnPosition);
@@ -197,9 +200,9 @@ public class FeatureDistanceModel extends DistanceScoreModel
         /*
          * position is not a gap
          */
-        Set<String> types = new HashSet<String>();
-        List<SequenceFeature> sfs = fr.findFeaturesAtResidue(
-                seq.getRefSeq(), spos);
+        Set<String> types = new HashSet<>();
+        List<SequenceFeature> sfs = fr
+                .findFeaturesAtResidue(seq.getRefSeq(), spos, spos);
         for (SequenceFeature sf : sfs)
         {
           types.add(sf.getType());