X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=e264b689c0d45787ddfe4e97b24675748ce51d48;hb=c5677e9860106a821a3e6e0429b20ede7b9a732a;hp=64d00ffef113a5396165b52f39ae19f7a55659f7;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 64d00ff..e264b68 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -271,7 +271,7 @@ public class Jalview2XML_V1
 
     for (int i = 0; i < JSEQ.length; i++)
     {
-      af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
+      af.viewport.setSequenceColour(af.viewport.getAlignment().getSequenceAt(i),
               new java.awt.Color(JSEQ[i].getColour()));
     }
 
@@ -371,7 +371,7 @@ public class Jalview2XML_V1
       if (cs != null)
       {
         cs.setThreshold(view.getPidThreshold(), true);
-        cs.setConsensus(af.viewport.hconsensus);
+        cs.setConsensus(af.viewport.getSequenceConsensusHash());
       }
     }