X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=1d52819e428269a9bbeb0ac9af5601dcd05ba1e3;hb=b3b59df08fc4183bb35e4ed5a54841a990b71346;hp=d84b8dbf73f317152eb5b8334b31d07fdaf340a7;hpb=2be3bda24ceee2da9d3c41723b5bc1e660948a20;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index d84b8db..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();
@@ -318,7 +318,7 @@ public class Jalview2XML_V1
                 if (groups[i].getConsThreshold() != 0)
                 {
                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
-                            ResidueProperties.propHash, 3, sg.sequences, 0,
+                            ResidueProperties.propHash, 3, sg.getSequences(false), 0,
                             sg.getWidth() - 1);
                     c.calculate();
                     c.verdict(false, 25);
@@ -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());
@@ -359,16 +356,13 @@ public class Jalview2XML_V1
         af.viewport.setWrapAlignment(view.getWrapAlignment());
         af.wrapMenuItem.setSelected(view.getWrapAlignment());
 
-        if (view.getWrapAlignment())
-        {
-            af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-        }
-        else
-        {
-            af.annotationPanelMenuItem.setState(view.getShowAnnotation());
-            af.viewport.setShowAnnotation(view.getShowAnnotation());
-            af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
-        }
+
+        af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+
+        af.annotationPanelMenuItem.setState(view.getShowAnnotation());
+        af.viewport.setShowAnnotation(view.getShowAnnotation());
+        af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+
 
         af.viewport.setShowBoxes(view.getShowBoxes());
         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
@@ -391,7 +385,7 @@ public class Jalview2XML_V1
             if(cs!=null)
             {
               cs.setThreshold(view.getPidThreshold(), true);
-              cs.setConsensus(af.viewport.vconsensus);
+              cs.setConsensus(af.viewport.hconsensus);
             }
         }