JAL-2446 merged to spike branch

[jalview.git] / src / jalview / analysis / CrossRef.java

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 23308d6..103025c 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -619,28 +619,25 @@ public class CrossRef
                  * duplication (e.g. same variation from two 
                  * transcripts)
                  */
-                SequenceFeature[] sfs = ms.getSequenceFeatures();
-                if (sfs != null)
+                List<SequenceFeature> sfs = ms.getFeatures()
+                        .getAllFeatures();
+                for (SequenceFeature feat : sfs)
                 {
-                  for (SequenceFeature feat : sfs)
+                  /*
+                   * make a flyweight feature object which ignores Parent
+                   * attribute in equality test; this avoids creating many
+                   * otherwise duplicate exon features on genomic sequence
+                   */
+                  SequenceFeature newFeature = new SequenceFeature(feat)
                   {
-                    /*
-                     * make a flyweight feature object which ignores Parent
-                     * attribute in equality test; this avoids creating many
-                     * otherwise duplicate exon features on genomic sequence
-                     */
-                    SequenceFeature newFeature = new SequenceFeature(feat)
+                    @Override
+                    public boolean equals(Object o)
                     {
-                      @Override
-                      public boolean equals(Object o)
-                      {
-                        return super.equals(o, true);
-                      }
-                    };
-                    matched.addSequenceFeature(newFeature);
-                  }
+                      return super.equals(o, true);
+                    }
+                  };
+                  matched.addSequenceFeature(newFeature);
                 }
-
               }
               cf.addMap(retrievedSequence, map.getTo(), map.getMap());
             } catch (Exception e)