Merge branch 'features/JAL-2446NCList' into

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index cd71bbd..103025c 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -220,8 +220,7 @@ public class CrossRef
 
     rseqs = new ArrayList<SequenceI>();
     AlignedCodonFrame cf = new AlignedCodonFrame();
-    matcher = new SequenceIdMatcher(
-            dataset.getSequences());
+    matcher = new SequenceIdMatcher(dataset.getSequences());
 
     for (SequenceI seq : fromSeqs)
     {
@@ -620,29 +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)
@@ -667,6 +662,7 @@ public class CrossRef
     }
     return imported;
   }
+
   /**
    * Sets the inverse sequence mapping in the corresponding dbref of the mapped
    * to sequence (if any). This is used after fetching a cross-referenced
@@ -866,8 +862,8 @@ public class CrossRef
     MapList mapping = null;
     SequenceI dsmapFrom = mapFrom.getDatasetSequence() == null ? mapFrom
             : mapFrom.getDatasetSequence();
-    SequenceI dsmapTo = mapTo.getDatasetSequence() == null ? mapTo
-            : mapTo.getDatasetSequence();
+    SequenceI dsmapTo = mapTo.getDatasetSequence() == null ? mapTo : mapTo
+            .getDatasetSequence();
     /*
      * look for a reverse mapping, if found make its inverse. 
      * Note - we do this on dataset sequences only.