X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=8ac4991d08fe5d6a8e0609e111e73e80d0c16245;hb=10b40b4ec840e5076c95109b0ea518928385821c;hp=1120291dcd3d6e78094b038f88f85555c8f512c8;hpb=3a9c9cd41358438efc1c4f365fecc7491592ca46;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 1120291..8ac4991 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -20,14 +20,8 @@
  */
 package jalview.datamodel.features;
 
-import jalview.datamodel.ContiguousI;
-import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.io.gff.SequenceOntologyI;
-
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.Comparator;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -35,6 +29,11 @@ import java.util.Map.Entry;
 import java.util.Set;
 import java.util.TreeMap;
 
+import intervalstore.api.IntervalI;
+import jalview.datamodel.SequenceFeature;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+
 /**
  * A class that stores sequence features in a way that supports efficient
  * querying by type and location (overlap). Intended for (but not limited to)
@@ -45,30 +44,6 @@ import java.util.TreeMap;
  */
 public class SequenceFeatures implements SequenceFeaturesI
 {
-  /**
-   * a comparator for sorting features by start position ascending
-   */
-  private static Comparator<ContiguousI> FORWARD_STRAND = new Comparator<ContiguousI>()
-  {
-    @Override
-    public int compare(ContiguousI o1, ContiguousI o2)
-    {
-      return Integer.compare(o1.getBegin(), o2.getBegin());
-    }
-  };
-
-  /**
-   * a comparator for sorting features by end position descending
-   */
-  private static Comparator<ContiguousI> REVERSE_STRAND = new Comparator<ContiguousI>()
-  {
-    @Override
-    public int compare(ContiguousI o1, ContiguousI o2)
-    {
-      return Integer.compare(o2.getEnd(), o1.getEnd());
-    }
-  };
-
   /*
    * map from feature type to structured store of features for that type
    * null types are permitted (but not a good idea!)
@@ -435,11 +410,13 @@ public class SequenceFeatures implements SequenceFeaturesI
    * @param features
    * @param forwardStrand
    */
-  public static void sortFeatures(List<SequenceFeature> features,
+  public static void sortFeatures(List<? extends IntervalI> features,
           final boolean forwardStrand)
   {
-    Collections.sort(features, forwardStrand ? FORWARD_STRAND
-            : REVERSE_STRAND);
+    Collections.sort(features,
+            forwardStrand
+                    ? IntervalI.COMPARE_BEGIN_ASC_END_DESC
+                    : IntervalI.COMPARE_END_DESC);
   }
 
   /**