JAL-3621 update to intervalstore v1.1

[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 db2f0e1..70485b6 100644 (file)
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -20,11 +20,8 @@
  */
 package jalview.datamodel.features;
 
-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.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -33,6 +30,9 @@ 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
@@ -44,7 +44,6 @@ import intervalstore.api.IntervalI;
  */
 public class SequenceFeatures implements SequenceFeaturesI
 {
-
   /*
    * map from feature type to structured store of features for that type
    * null types are permitted (but not a good idea!)
@@ -414,7 +413,9 @@ public class SequenceFeatures implements SequenceFeaturesI
   public static void sortFeatures(List<? extends IntervalI> features,
           final boolean forwardStrand)
   {
-    IntervalI.sortIntervals(features, forwardStrand);
+    Collections.sort(features,
+            forwardStrand ? IntervalI.COMPARE_BEGIN_ASC_END_ASC
+                    : IntervalI.COMPARE_END_DESC);
   }
 
   /**