JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / util / MapList.java

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index ab811a9..58abdc3 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -88,8 +88,6 @@ public class MapList
   @Override
   public boolean equals(Object o)
   {
-    // TODO should also override hashCode to ensure equal objects have equal
-    // hashcodes
     if (o == null || !(o instanceof MapList))
     {
       return false;
@@ -112,6 +110,19 @@ public class MapList
   }
 
   /**
+   * Returns a hashcode made from the fromRatio, toRatio, and from/to ranges
+   */
+  @Override
+  public int hashCode()
+  {
+    int hashCode = 31 * fromRatio;
+    hashCode = 31 * hashCode + toRatio;
+    hashCode = 31 * hashCode + fromShifts.toArray().hashCode();
+    hashCode = 31 * hashCode + toShifts.toArray().hashCode();
+    return hashCode;
+  }
+
+  /**
    * Returns the 'from' ranges as {[start1, end1], [start2, end2], ...}
    * 
    * @return
@@ -331,7 +342,8 @@ public class MapList
    */
   public static List<int[]> coalesceRanges(final List<int[]> ranges)
   {
-    if (ranges == null || ranges.size() < 2) {
+    if (ranges == null || ranges.size() < 2)
+    {
       return ranges;
     }
 
@@ -342,7 +354,7 @@ public class MapList
     lastRange = new int[] { lastRange[0], lastRange[1] };
     merged.add(lastRange);
     boolean first = true;
-    
+
     for (final int[] range : ranges)
     {
       if (first)
@@ -376,7 +388,8 @@ public class MapList
        * if next range is in the same direction as last and contiguous,
        * just update the end position of the last range
        */
-      boolean sameDirection = range[1] == range[0] || direction == lastDirection;
+      boolean sameDirection = range[1] == range[0]
+              || direction == lastDirection;
       boolean extending = range[0] == lastRange[1] + lastDirection;
       boolean overlapping = (lastDirection == 1 && range[0] >= lastRange[0] && range[0] <= lastRange[1])
               || (lastDirection == -1 && range[0] <= lastRange[0] && range[0] >= lastRange[1]);
@@ -393,7 +406,7 @@ public class MapList
         lastDirection = (range[1] == range[0]) ? lastDirection : direction;
       }
     }
-    
+
     return changed ? merged : ranges;
   }
 
@@ -992,6 +1005,10 @@ public class MapList
    */
   public void addMapList(MapList map)
   {
+    if (this.equals(map))
+    {
+      return;
+    }
     this.fromLowest = Math.min(fromLowest, map.fromLowest);
     this.toLowest = Math.min(toLowest, map.toLowest);
     this.fromHighest = Math.max(fromHighest, map.fromHighest);
@@ -1087,4 +1104,15 @@ public class MapList
     }
     return forwardStrand;
   }
+
+  /**
+   * 
+   * @return true if from, or to is a three to 1 mapping
+   */
+  public boolean isTripletMap()
+  {
+    return (toRatio == 3 && fromRatio == 1)
+            || (fromRatio == 3 && toRatio == 1);
+  }
+
 }