X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMapList.java;h=8ff640b582b417f46353d282c47b22f61c942a89;hb=5bc9afbf74ecf25e146938049d01ea36c18fd578;hp=e456dabdc281946dae004e527487d07569a7d11b;hpb=ab9351a591e5295be9e41bfa86238ccc2a8024f8;p=jalview.git

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index e456dab..8ff640b 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -41,12 +41,12 @@ public class MapList
   /*
    * Subregions (base 1) described as { [start1, end1], [start2, end2], ...}
    */
-  private List<int[]> fromShifts = new ArrayList<int[]>();
+  private List<int[]> fromShifts;
 
   /*
    * Same format as fromShifts, for the 'mapped to' sequence
    */
-  private List<int[]> toShifts = new ArrayList<int[]>();
+  private List<int[]> toShifts;
 
   /*
    * number of steps in fromShifts to one toRatio unit
@@ -73,6 +73,15 @@ public class MapList
   private int toHighest;
 
   /**
+   * Constructor
+   */
+  public MapList()
+  {
+    fromShifts = new ArrayList<int[]>();
+    toShifts = new ArrayList<int[]>();
+  }
+
+  /**
    * Two MapList objects are equal if they are the same object, or they both
    * have populated shift ranges and all values are the same.
    */
@@ -180,7 +189,8 @@ public class MapList
   }
 
   /**
-   * Constructor.
+   * Constructor given from and to ranges as [start1, end1, start2, end2,...].
+   * If any end is equal to the next start, the ranges will be merged.
    * 
    * @param from
    *          contiguous regions as [start1, end1, start2, end2, ...]
@@ -193,25 +203,47 @@ public class MapList
    */
   public MapList(int from[], int to[], int fromRatio, int toRatio)
   {
+    this();
     this.fromRatio = fromRatio;
     this.toRatio = toRatio;
     fromLowest = from[0];
     fromHighest = from[1];
+    int added = 0;
+
     for (int i = 0; i < from.length; i += 2)
     {
       fromLowest = Math.min(fromLowest, from[i]);
       fromHighest = Math.max(fromHighest, from[i + 1]);
-
-      fromShifts.add(new int[] { from[i], from[i + 1] });
+      if (added > 0 && from[i] == fromShifts.get(added - 1)[1])
+      {
+        /*
+         * this range starts where the last ended - just extend it
+         */
+        fromShifts.get(added - 1)[1] = from[i + 1];
+      }
+      else
+      {
+        fromShifts.add(new int[] { from[i], from[i + 1] });
+        added++;
+      }
     }
 
     toLowest = to[0];
     toHighest = to[1];
+    added = 0;
     for (int i = 0; i < to.length; i += 2)
     {
       toLowest = Math.min(toLowest, to[i]);
       toHighest = Math.max(toHighest, to[i + 1]);
-      toShifts.add(new int[] { to[i], to[i + 1] });
+      if (added > 0 && to[i] == toShifts.get(added - 1)[1])
+      {
+        toShifts.get(added - 1)[1] = to[i + 1];
+      }
+      else
+      {
+        toShifts.add(new int[] { to[i], to[i + 1] });
+        added++;
+      }
     }
   }
 
@@ -222,6 +254,7 @@ public class MapList
    */
   public MapList(MapList map)
   {
+    this();
     // TODO not used - remove?
     this.fromLowest = map.fromLowest;
     this.fromHighest = map.fromHighest;
@@ -257,6 +290,7 @@ public class MapList
   public MapList(List<int[]> fromRange, List<int[]> toRange, int fromRatio,
           int toRatio)
   {
+    this();
     this.fromShifts = fromRange;
     this.toShifts = toRange;
     this.fromRatio = fromRatio;