Merge branch 'documentation/JAL-3111_release_211' into bug/JAL-2830_editManglesDatase...

[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 e506be2..8545e94 100644 (file)
--- a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
@@ -58,7 +58,7 @@ 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)
@@ -66,6 +66,9 @@ public class FeatureDistanceModel extends DistanceScoreModel
       System.err.println("Error in " + getClass().getName()
               + ".getInstance(): " + e.getMessage());
       return null;
+    } catch (ReflectiveOperationException roe)
+    {
+      return null;
     }
   }
 
@@ -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);
@@ -197,7 +200,7 @@ public class FeatureDistanceModel extends DistanceScoreModel
         /*
          * position is not a gap
          */
-        Set<String> types = new HashSet<String>();
+        Set<String> types = new HashSet<>();
         List<SequenceFeature> sfs = fr.findFeaturesAtResidue(
                 seq.getRefSeq(), spos);
         for (SequenceFeature sf : sfs)