Merge branch 'develop' into features/JAL-2446NCList

[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 afa31e8..a6a23e7 100644 (file)
--- a/src/jalview/datamodel/features/NCList.java
+++ b/src/jalview/datamodel/features/NCList.java
@@ -1,8 +1,10 @@
 package jalview.datamodel.features;
 
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.Range;
+
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.Comparator;
 import java.util.List;
 
 /**
@@ -28,12 +30,6 @@ public class NCList<T extends ContiguousI>
    */
   private List<NCNode<T>> subranges;
 
-  /*
-   * a comparator to sort intervals by start position ascending, with
-   * longer (enclosing) intervals preceding those they enclose 
-   */
-  Comparator<ContiguousI> intervalSorter = new RangeComparator(true);
-
   /**
    * Constructor given a list of things that are each located on a contiguous
    * interval. Note that the constructor may reorder the list.
@@ -61,18 +57,18 @@ public class NCList<T extends ContiguousI>
      * sort by start ascending so that contained intervals 
      * follow their containing interval
      */
-    Collections.sort(ranges, intervalSorter);
+    Collections.sort(ranges, RangeComparator.BY_START_POSITION);
 
-    List<SubList> sublists = buildSubranges(ranges);
+    List<Range> sublists = buildSubranges(ranges);
 
     /*
      * convert each subrange to an NCNode consisting of a range and
      * (possibly) its contained NCList
      */
-    for (SubList sublist : sublists)
+    for (Range sublist : sublists)
     {
-      subranges.add(new NCNode<T>(ranges.subList(sublist.startIndex,
-              sublist.endIndex + 1)));
+      subranges.add(new NCNode<T>(ranges.subList(sublist.start,
+              sublist.end + 1)));
     }
 
     size = ranges.size();
@@ -97,9 +93,9 @@ public class NCList<T extends ContiguousI>
    * @param ranges
    * @return
    */
-  protected List<SubList> buildSubranges(List<T> ranges)
+  protected List<Range> buildSubranges(List<T> ranges)
   {
-    List<SubList> sublists = new ArrayList<SubList>();
+    List<Range> sublists = new ArrayList<Range>();
     
     if (ranges.isEmpty())
     {
@@ -120,13 +116,13 @@ public class NCList<T extends ContiguousI>
          * this interval is not contained in the preceding one 
          * close off the last sublist
          */
-        sublists.add(new SubList(listStartIndex, i - 1));
+        sublists.add(new Range(listStartIndex, i - 1));
         listStartIndex = i;
       }
       lastEndPos = nextEnd;
     }
 
-    sublists.add(new SubList(listStartIndex, ranges.size() - 1));
+    sublists.add(new Range(listStartIndex, ranges.size() - 1));
     return sublists;
   }
 
@@ -412,8 +408,12 @@ public class NCList<T extends ContiguousI>
    */
   protected int findFirstOverlap(long from)
   {
-    // TODO binary search
-    // for now quick cheat linear search
+    /*
+     * The NCList paper describes binary search for this step,
+     * but this not implemented here as (a) I haven't understood it yet
+     * and (b) it seems to imply complications for adding to an NCList
+     */
+
     int i = 0;
     if (subranges != null)
     {
@@ -606,7 +606,7 @@ public class NCList<T extends ContiguousI>
         if (subRegions != null)
         {
           subranges.addAll(subRegions.subranges);
-          Collections.sort(subranges, intervalSorter);
+          Collections.sort(subranges, RangeComparator.BY_START_POSITION);
         }
         size--;
         return true;