X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStoreImpl.java;h=a90755dabd21efff3bc26a1338891d41a997ea6f;hb=28e9024f09a78a9625ed4defa2012bf342bec51e;hp=02394bb8275734de221eab070ee69148e041e719;hpb=8406f2ced29d2c04dbabaf1cde80b1a7fa8ce8ce;p=jalview.git

diff --git a/src/jalview/datamodel/features/FeatureStoreImpl.java b/src/jalview/datamodel/features/FeatureStoreImpl.java
index 02394bb..a90755d 100644
--- a/src/jalview/datamodel/features/FeatureStoreImpl.java
+++ b/src/jalview/datamodel/features/FeatureStoreImpl.java
@@ -27,7 +27,6 @@ import java.util.List;
 
 import intervalstore.api.IntervalStoreI;
 import intervalstore.impl.BinarySearcher;
-import intervalstore.impl.IntervalStore;
 
 /**
  * A data store for a set of sequence features that supports efficient lookup of
@@ -40,9 +39,18 @@ import intervalstore.impl.IntervalStore;
 public class FeatureStoreImpl extends FeatureStore
 {
 
+  /**
+   * Default constructor uses NCList
+   */
   public FeatureStoreImpl()
   {
-    features = new IntervalStore<>();
+    this(true);
+  }
+
+  public FeatureStoreImpl(boolean useNCList)
+  {
+    features = (useNCList ? new intervalstore.impl.IntervalStore<>()
+            : new intervalstore.nonc.IntervalStore<>(false));
   }
 
   /**
@@ -87,9 +95,10 @@ public class FeatureStoreImpl extends FeatureStore
    * (creating the IntervalStore if necessary)
    */
   @Override
-  protected synchronized void addNestedFeature(SequenceFeature feature)
+  protected synchronized boolean addPositionalFeature(
+          SequenceFeature feature)
   {
-    features.add(feature);
+    return features.add(feature);
   }
 
   /**
@@ -286,4 +295,10 @@ public class FeatureStoreImpl extends FeatureStore
     return BinarySearcher.findFirst(list, f -> f.getEnd() >= pos);
   }
 
+  @Override
+  protected boolean findAndRemoveNonContactFeature(SequenceFeature sf)
+  {
+    return features.remove(sf);
+  }
+
 }