JAL-653 handle reverse strand mappings also

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 47f7017..11597eb 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -621,8 +621,8 @@ public final class MappingUtils
   }
 
   /**
-   * Converts a series of [start, end] ranges into an array of individual
-   * positions.
+   * Converts a series of [start, end] range pairs into an array of individual
+   * positions. This also caters for 'reverse strand' (start > end) cases.
    * 
    * @param ranges
    * @return
@@ -635,17 +635,21 @@ public final class MappingUtils
     int count = 0;
     for (int i = 0; i < ranges.length - 1; i += 2)
     {
-      count += ranges[i + 1] - ranges[i] + 1;
+      count += Math.abs(ranges[i + 1] - ranges[i]) + 1;
     }
 
     int[] result = new int[count];
     int k = 0;
     for (int i = 0; i < ranges.length - 1; i += 2)
     {
-      for (int j = ranges[i]; j <= ranges[i + 1]; j++)
+      int from = ranges[i];
+      final int to = ranges[i + 1];
+      int step = from <= to ? 1 : -1;
+      do
       {
-        result[k++] = j;
-      }
+        result[k++] = from;
+        from += step;
+      } while (from != to + step);
     }
     return result;
   }