Add support RNAML format

[jalview.git] / src / jalview / gui / Jalview2XML_V1.java

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 5d1a89b..e264b68 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,6 +1,6 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
  * \r
  * This file is part of Jalview.\r
  * \r
@@ -271,7 +271,7 @@ public class Jalview2XML_V1
 \r
     for (int i = 0; i < JSEQ.length; i++)\r
     {\r
-      af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),\r
+      af.viewport.setSequenceColour(af.viewport.getAlignment().getSequenceAt(i),\r
               new java.awt.Color(JSEQ[i].getColour()));\r
     }\r
 \r
@@ -371,7 +371,7 @@ public class Jalview2XML_V1
       if (cs != null)\r
       {\r
         cs.setThreshold(view.getPidThreshold(), true);\r
-        cs.setConsensus(af.viewport.hconsensus);\r
+        cs.setConsensus(af.viewport.getSequenceConsensusHash());\r
       }\r
     }\r
 \r