JAL-3397 final update

[jalview.git] / src / jalview / datamodel / features / FeatureStoreImpl.java

diff --git a/src/jalview/datamodel/features/FeatureStoreImpl.java b/src/jalview/datamodel/features/FeatureStoreImpl.java
index 47c1dd4..63ee678 100644 (file)
--- a/src/jalview/datamodel/features/FeatureStoreImpl.java
+++ b/src/jalview/datamodel/features/FeatureStoreImpl.java
@@ -25,7 +25,6 @@ import jalview.datamodel.SequenceFeature;
 import java.util.ArrayList;
 import java.util.List;
 
-import intervalstore.api.IntervalStoreI;
 import intervalstore.impl.BinarySearcher;
 
 /**
@@ -39,18 +38,14 @@ import intervalstore.impl.BinarySearcher;
 public class FeatureStoreImpl extends FeatureStore
 {
 
-  /**
-   * Default constructor uses NCList
-   */
   public FeatureStoreImpl()
   {
-    this(true);
+    super();
   }
 
-  public FeatureStoreImpl(boolean useNCList)
+  public FeatureStoreImpl(int option)
   {
-    features = (useNCList ? new intervalstore.impl.IntervalStore<>()
-            : new intervalstore.nonc.IntervalStore<>(false));
+    super(option);
   }
 
   /**
@@ -75,7 +70,7 @@ public class FeatureStoreImpl extends FeatureStore
      * insert into list sorted by start (first contact position):
      * binary search the sorted list to find the insertion point
      */
-    int insertPosition = findFirstBeginStatic(contactFeatureStarts,
+    int insertPosition = findFirstBegin(contactFeatureStarts,
             feature.getBegin());
     contactFeatureStarts.add(insertPosition, feature);
 
@@ -83,7 +78,7 @@ public class FeatureStoreImpl extends FeatureStore
      * insert into list sorted by end (second contact position):
      * binary search the sorted list to find the insertion point
      */
-    insertPosition = findFirstEndStatic(contactFeatureEnds,
+    insertPosition = findFirstEnd(contactFeatureEnds,
             feature.getEnd());
     contactFeatureEnds.add(insertPosition, feature);
 
@@ -95,9 +90,10 @@ public class FeatureStoreImpl extends FeatureStore
    * (creating the IntervalStore if necessary)
    */
   @Override
-  protected synchronized void addPositionalFeature(SequenceFeature feature)
+  protected synchronized boolean addPositionalFeature(
+          SequenceFeature feature)
   {
-    features.add(feature);
+    return features.add(feature);
   }
 
   /**
@@ -142,7 +138,7 @@ public class FeatureStoreImpl extends FeatureStore
      * find the first contact feature (if any) 
      * whose end point is not before the target range
      */
-    int index = findFirstEndStatic(contactFeatureEnds, from);
+    int index = findFirstEnd(contactFeatureEnds, from);
 
     int n = contactFeatureEnds.size();
     while (index < n)
@@ -252,46 +248,21 @@ public class FeatureStoreImpl extends FeatureStore
   private void findOverlaps(long start, long end,
           List<SequenceFeature> result)
   {
-    result.addAll(((IntervalStoreI<SequenceFeature>) features)
+    result.addAll(features
             .findOverlaps(start, end));
   }
 
   @Override
   protected int findFirstBegin(List<SequenceFeature> list, long pos)
   {
-    return findFirstBeginStatic(list, pos);
-  }
-
-  /**
-   * Possibly a bit faster using a static method.
-   * 
-   * @param list
-   * @param pos
-   * @return
-   */
-  private static int findFirstBeginStatic(List<SequenceFeature> list,
-          long pos)
-  {
-    return BinarySearcher.findFirst(list, f -> f.getBegin() >= pos);
+    return BinarySearcher.findFirst(list, (int) pos,
+            BinarySearcher.fbegin);
   }
 
   @Override
   protected int findFirstEnd(List<SequenceFeature> list, long pos)
   {
-    return findFirstEndStatic(list, pos);
-  }
-
-  /**
-   * Possibly a bit faster using a static method.
-   * 
-   * @param list
-   * @param pos
-   * @return
-   */
-  private static int findFirstEndStatic(List<SequenceFeature> list,
-          long pos)
-  {
-    return BinarySearcher.findFirst(list, f -> f.getEnd() >= pos);
+    return BinarySearcher.findFirst(list, (int) pos, BinarySearcher.fend);
   }
 
   @Override