JAL-3140 NCList now via IntervalStore library

[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 727d3ef..bd102f6 100644 (file)
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -20,7 +20,6 @@
  */
 package jalview.datamodel.features;
 
-import jalview.datamodel.ContiguousI;
 import jalview.datamodel.SequenceFeature;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
@@ -36,6 +35,8 @@ import java.util.Map.Entry;
 import java.util.Set;
 import java.util.TreeMap;
 
+import intervalstore.api.IntervalI;
+
 /**
  * A class that stores sequence features in a way that supports efficient
  * querying by type and location (overlap). Intended for (but not limited to)
@@ -49,10 +50,10 @@ public class SequenceFeatures implements SequenceFeaturesI
   /**
    * a comparator for sorting features by start position ascending
    */
-  private static Comparator<ContiguousI> FORWARD_STRAND = new Comparator<ContiguousI>()
+  private static Comparator<IntervalI> FORWARD_STRAND = new Comparator<IntervalI>()
   {
     @Override
-    public int compare(ContiguousI o1, ContiguousI o2)
+    public int compare(IntervalI o1, IntervalI o2)
     {
       return Integer.compare(o1.getBegin(), o2.getBegin());
     }
@@ -61,10 +62,10 @@ public class SequenceFeatures implements SequenceFeaturesI
   /**
    * a comparator for sorting features by end position descending
    */
-  private static Comparator<ContiguousI> REVERSE_STRAND = new Comparator<ContiguousI>()
+  private static Comparator<IntervalI> REVERSE_STRAND = new Comparator<IntervalI>()
   {
     @Override
-    public int compare(ContiguousI o1, ContiguousI o2)
+    public int compare(IntervalI o1, IntervalI o2)
     {
       return Integer.compare(o2.getEnd(), o1.getEnd());
     }