JAL-3140 reduced coupling to intervalstore.jar

[jalview.git] / src / jalview / datamodel / features / SequenceFeatures.java

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index bd102f6..5390975 100644 (file)
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -26,8 +26,6 @@ import jalview.io.gff.SequenceOntologyI;
 
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -47,29 +45,6 @@ import intervalstore.api.IntervalI;
  */
 public class SequenceFeatures implements SequenceFeaturesI
 {
-  /**
-   * a comparator for sorting features by start position ascending
-   */
-  private static Comparator<IntervalI> FORWARD_STRAND = new Comparator<IntervalI>()
-  {
-    @Override
-    public int compare(IntervalI o1, IntervalI o2)
-    {
-      return Integer.compare(o1.getBegin(), o2.getBegin());
-    }
-  };
-
-  /**
-   * a comparator for sorting features by end position descending
-   */
-  private static Comparator<IntervalI> REVERSE_STRAND = new Comparator<IntervalI>()
-  {
-    @Override
-    public int compare(IntervalI o1, IntervalI o2)
-    {
-      return Integer.compare(o2.getEnd(), o1.getEnd());
-    }
-  };
 
   /*
    * map from feature type to structured store of features for that type
@@ -436,11 +411,10 @@ 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);
+    IntervalI.sortIntervals(features, forwardStrand);
   }
 
   /**