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 63da089..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.
  * 
@@ -1330,7 +1330,7 @@ public class VamsasAppDatastore
             };
             if (dojvsync)
             {
-              fromxml.LoadJalviewAlign(jprovider);
+              fromxml.loadJalviewAlign(jprovider);
             }
           } catch (Exception e)
           {
@@ -1378,7 +1378,7 @@ public class VamsasAppDatastore
           };
           if (dojvsync)
           {
-            fromxml.LoadJalviewAlign(jarstream);
+            fromxml.loadJalviewAlign(jarstream);
           }
         } catch (Exception e)
         {
@@ -1525,7 +1525,7 @@ public class VamsasAppDatastore
         jxml.setSkipList(skipList);
         if (dojvsync)
         {
-          jxml.SaveState(new JarOutputStream(cappdata
+          jxml.saveState(new JarOutputStream(cappdata
                   .getClientOutputStream()));
         }
 
@@ -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);
     }
   }