X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=1d52819e428269a9bbeb0ac9af5601dcd05ba1e3;hb=a452823dc1f0f02a366ea432cb161a7e1b1570ca;hp=bb5a1aca46605a5893e3fcda6d1dab3adde72222;hpb=3596077c79b7aa2051b9aaa978481004b513101c;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index bb5a1ac..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
@@ -113,10 +113,8 @@ public class Jalview2XML_V1
                 for (int i = 0; i < entryCount; i++)
                 {
                     jarentry = jin.getNextJarEntry();
-
                   }
 
-
                   class NoDescIDResolver implements IDResolver
                   {
                     public Object resolve(String idref)
@@ -269,7 +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() );
@@ -295,7 +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();
@@ -336,9 +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());
@@ -388,7 +385,7 @@ public class Jalview2XML_V1
             if(cs!=null)
             {
               cs.setThreshold(view.getPidThreshold(), true);
-              cs.setConsensus(af.viewport.vconsensus);
+              cs.setConsensus(af.viewport.hconsensus);
             }
         }