JAL-2446 fix size maintenance during add

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

diff --git a/src/jalview/datamodel/features/NCList.java b/src/jalview/datamodel/features/NCList.java
index 9906884..afa31e8 100644 (file)
--- a/src/jalview/datamodel/features/NCList.java
+++ b/src/jalview/datamodel/features/NCList.java
@@ -50,6 +50,9 @@ public class NCList<T extends ContiguousI>
   }
 
   /**
+   * Sort and group ranges into sublists where each sublist represents a region
+   * and its contained subregions
+   * 
    * @param ranges
    */
   protected void build(List<T> ranges)
@@ -78,9 +81,8 @@ public class NCList<T extends ContiguousI>
   public NCList(T entry)
   {
     this();
-    List<T> ranges = new ArrayList<T>();
-    ranges.add(entry);
-    build(ranges);
+    subranges.add(new NCNode<T>(entry));
+    size = 1;
   }
 
   public NCList()
@@ -326,7 +328,7 @@ public class NCList<T extends ContiguousI>
           final int j)
   {
     NCList<T> newNCList = new NCList<T>();
-    newNCList.subranges.addAll(subranges.subList(i, j + 1));
+    newNCList.addNodes(subranges.subList(i, j + 1));
     NCNode<T> newNode = new NCNode<T>(entry, newNCList);
     for (int k = j; k >= i; k--)
     {
@@ -335,6 +337,15 @@ public class NCList<T extends ContiguousI>
     subranges.add(i, newNode);
   }
 
+  protected void addNodes(List<NCNode<T>> nodes)
+  {
+    for (NCNode<T> node : nodes)
+    {
+      subranges.add(node);
+      size += node.size();
+    }
+  }
+
   /**
    * Returns a (possibly empty) list of items whose extent overlaps the given
    * range
@@ -531,7 +542,7 @@ public class NCList<T extends ContiguousI>
    * 
    * @return
    */
-  public int getSize()
+  public int size()
   {
     return size;
   }
@@ -594,7 +605,7 @@ public class NCList<T extends ContiguousI>
         subranges.remove(i);
         if (subRegions != null)
         {
-          subranges.addAll(i, subRegions.subranges);
+          subranges.addAll(subRegions.subranges);
           Collections.sort(subranges, intervalSorter);
         }
         size--;
@@ -605,6 +616,7 @@ public class NCList<T extends ContiguousI>
         if (subRegions != null && subRegions.delete(entry))
         {
           size--;
+          subrange.deleteSubRegionsIfEmpty();
           return true;
         }
       }