JAL-2557 removal of Sequence.sequenceFeatures

[jalview.git] / src / MCview / PDBChain.java

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index ef86cfd..8285d88 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -167,15 +167,14 @@ public class PDBChain
   }
 
   /**
-   * copy over the RESNUM seqfeatures from the internal chain sequence to the
+   * Copies over the RESNUM seqfeatures from the internal chain sequence to the
    * mapped sequence
    * 
    * @param seq
    * @param status
    *          The Status of the transferred annotation
-   * @return the features added to sq (or its dataset)
    */
-  public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
+  public void transferRESNUMFeatures(SequenceI seq,
           String status)
   {
     SequenceI sq = seq;
@@ -184,10 +183,11 @@ public class PDBChain
       sq = sq.getDatasetSequence();
       if (sq == sequence)
       {
-        return null;
+        return;
       }
     }
-    /**
+
+    /*
      * Remove any existing features for this chain if they exist ?
      * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
      * totfeat=seqsfeatures.length; // Remove any features for this exact chain
@@ -197,14 +197,10 @@ public class PDBChain
     {
       status = PDBChain.IEASTATUS;
     }
-    SequenceFeature[] features = sequence.getSequenceFeatures();
-    if (features == null)
-    {
-      return null;
-    }
-    for (int i = 0; i < features.length; i++)
+
+    List<SequenceFeature> features = sequence.getSequenceFeatures();
+    for (SequenceFeature feature : features)
     {
-      SequenceFeature feature = features[i];
       if (feature.getFeatureGroup() != null
               && feature.getFeatureGroup().equals(pdbid))
       {
@@ -223,7 +219,6 @@ public class PDBChain
         }
       }
     }
-    return features;
   }
 
   /**