X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=1d52819e428269a9bbeb0ac9af5601dcd05ba1e3;hb=b3b59df08fc4183bb35e4ed5a54841a990b71346;hp=d8dfe62bbd5e06e9fbc9952b41e83770d46916e0;hpb=61505ac1511435b067e647f5c7c9050e5c1eef41;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index d8dfe62..1d52819 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -267,7 +267,7 @@ public class Jalview2XML_V1
         Viewport[] views = jms.getViewport();
         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 
-        AlignFrame af = new AlignFrame(al);
+        AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 
 
         //  af.changeColour() );
@@ -293,7 +293,9 @@ public class Jalview2XML_V1
                                 groups[i].getColour());
                     }
 
-                    cs.setThreshold(groups[i].getPidThreshold(), true);
+                    if(cs!=null)
+                      cs.setThreshold(groups[i].getPidThreshold(), true);
+
                 }
 
                 Vector seqs = new Vector();
@@ -334,9 +336,6 @@ public class Jalview2XML_V1
         af.viewport.setStartRes(view.getStartRes());
         af.viewport.setStartSeq(view.getStartSeq());
         af.viewport.setShowAnnotation(view.getShowAnnotation());
-        af.viewport.showConservation = view.getShowConservation();
-        af.viewport.showQuality = view.getShowQuality();
-        af.viewport.showIdentity = view.getShowIdentity();
         af.viewport.setAbovePIDThreshold(view.getPidSelected());
         af.abovePIDThreshold.setSelected(view.getPidSelected());
         af.viewport.setColourText(view.getShowColourText());
@@ -386,7 +385,7 @@ public class Jalview2XML_V1
             if(cs!=null)
             {
               cs.setThreshold(view.getPidThreshold(), true);
-              cs.setConsensus(af.viewport.vconsensus);
+              cs.setConsensus(af.viewport.hconsensus);
             }
         }