X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;fp=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=82772bccd3077659ab13fb3c1afd802a16b53c1a;hb=586ade46bdcd05ff028a1cff82c3c527326d28ec;hp=db2f0e1bb9950587e78519087fc8232151d57425;hpb=adcef27f5747b4e70e89a56c3735bc3afb8ce9bf;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index db2f0e1..82772bc 100644
--- 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!)
@@ -373,7 +372,7 @@ public class SequenceFeatures implements SequenceFeaturesI
     {
       return true;
     }
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     for (String term : soTerm)
     {
       if (type.equals(term) || so.isA(type, term))
@@ -414,7 +413,10 @@ 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_DESC
+                    : IntervalI.COMPARE_END_DESC);
   }
 
   /**