X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=ae4e55d3a31eea6ea64d8f4b742457627f03db1f;hb=65d6d09cd08743d481d39521bb0298ea683888f8;hp=c2cad1f8ef3e27d226f83e940c3607ef3f9db23b;hpb=4ad19b786f19aeadaf7a841e43ff8e490a39589d;p=jalview.git

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index c2cad1f..ae4e55d 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -770,7 +770,8 @@ public final class MappingUtils
   }
 
   /**
-   * Returns the total length of the supplied ranges
+   * Returns the total length of the supplied ranges, which may be as single
+   * [start, end] or multiple [start, end, start, end ...]
    * 
    * @param ranges
    * @return
@@ -784,7 +785,16 @@ public final class MappingUtils
     int length = 0;
     for (int[] range : ranges)
     {
-      length += Math.abs(range[1] - range[0]) + 1;
+      if (range.length % 2 != 0)
+      {
+        System.err.println("Error unbalance start/end ranges: "
+                + ranges.toString());
+        return 0;
+      }
+      for (int i = 0; i < range.length - 1; i += 2)
+      {
+        length += Math.abs(range[i + 1] - range[i]) + 1;
+      }
     }
     return length;
   }
@@ -848,7 +858,6 @@ public final class MappingUtils
     int cdspos = 0;
     for (int x = 0; x < copy.length && sxpos == -1; x += 2)
     {
-      // fixme handle reverse strand
       cdspos += Math.abs(copy[x + 1] - copy[x]) + 1;
       if (removeCount < cdspos)
       {