(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

[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 64d00ff..e264b68 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -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