JAL-1687 ignore case when determining if sequence matches consensus

[jalview.git] / src / jalview / io / VamsasAppDatastore.java

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 1d36865..7df7cb2 100644 (file)
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -2570,15 +2570,15 @@ public class VamsasAppDatastore
    * initialise a range type object from a set of start/end inclusive intervals
    * 
    * @param mrt
-   * @param range
+   * @param ranges
    */
-  private void initRangeType(RangeType mrt, int[] range)
+  private void initRangeType(RangeType mrt, List<int[]> ranges)
   {
-    for (int i = 0; i < range.length; i += 2)
+    for (int[] range : ranges)
     {
       Seg vSeg = new Seg();
-      vSeg.setStart(range[i]);
-      vSeg.setEnd(range[i + 1]);
+      vSeg.setStart(range[0]);
+      vSeg.setEnd(range[1]);
       mrt.addSeg(vSeg);
     }
   }