X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=ba8396a97b6ed2be21faf7e066b47c26cad478d9;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=727d3ef8b243d5c45048845f7e81283f2649bb33;hpb=a4f2a7f356b8edab17a9a5bb6f2e71a1419792a9;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 727d3ef..ba8396a 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -20,15 +20,12 @@
  */
 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.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -36,6 +33,8 @@ 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)
@@ -46,29 +45,6 @@ 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
@@ -435,11 +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);
   }
 
   /**
@@ -472,13 +447,22 @@ public class SequenceFeatures implements SequenceFeaturesI
    * {@inheritDoc}
    */
   @Override
-  public boolean shiftFeatures(int shift)
+  public boolean shiftFeatures(int fromPosition, int shiftBy)
   {
     boolean modified = false;
     for (FeatureStore fs : featureStore.values())
     {
-      modified |= fs.shiftFeatures(shift);
+      modified |= fs.shiftFeatures(fromPosition, shiftBy);
     }
     return modified;
   }
-}
\ No newline at end of file
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public void deleteAll()
+  {
+    featureStore.clear();
+  }
+}