X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=233707b5de906247c5c8305bedcaab492c87e5f2;hb=abb4c1cc7383a54df59066186eb282588bb884e8;hp=9109fb22f7eef8756c465a02fc1ac56bd229eaaf;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 9109fb2..233707b 100644
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.analysis.AlignmentUtils;
@@ -18,6 +38,7 @@ import jalview.io.gff.SequenceOntologyI;
 import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
+import jalview.util.RangeComparator;
 
 import java.io.IOException;
 import java.net.MalformedURLException;
@@ -90,26 +111,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   }
 
   /**
-   * A comparator to sort ranges into ascending start position order
-   */
-  private class RangeSorter implements Comparator<int[]>
-  {
-    boolean forwards;
-
-    RangeSorter(boolean forward)
-    {
-      forwards = forward;
-    }
-
-    @Override
-    public int compare(int[] o1, int[] o2)
-    {
-      return (forwards ? 1 : -1) * Integer.compare(o1[0], o2[0]);
-    }
-
-  }
-
-  /**
    * Default constructor (to use rest.ensembl.org)
    */
   public EnsemblSeqProxy()
@@ -213,7 +214,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       EnsemblFeatureType[] features = getFeaturesToFetch();
       AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
               features);
-      if (geneFeatures.getHeight() > 0)
+      if (geneFeatures != null && geneFeatures.getHeight() > 0)
       {
         genomicSequence = geneFeatures.getSequenceAt(0);
       }
@@ -606,7 +607,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
      * a final sort is needed since Ensembl returns CDS sorted within source
      * (havana / ensembl_havana)
      */
-    Collections.sort(regions, new RangeSorter(direction == 1));
+    Collections.sort(regions, new RangeComparator(direction == 1));
 
     List<int[]> to = Arrays.asList(new int[] { start,
         start + mappedLength - 1 });