X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=f1879c1fb95084bd8d52554135d2316badc770ab;hb=497958b4e5217efaa3ddeece38f38c3a6e98cb96;hp=9263cd982d475cec57f86abedea3433394902a60;hpb=70fd4c40d0b2046c6d402e365e4d04f9cfbb68ef;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 9263cd9..f1879c1 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -49,7 +49,10 @@ import java.util.jar.JarInputStream;
 
 import javax.swing.JOptionPane;
 
+import jalview.util.MessageManager;
+import jalview.util.jarInputStreamProvider;
 import org.exolab.castor.xml.IDResolver;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 
 /**
  * DOCUMENT ME!
@@ -411,29 +414,31 @@ public class Jalview2XML_V1
     }
 
     af.viewport.setColourAppliesToAllGroups(true);
-    af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
+    af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
 
     if (jms.getFeatureSettings() != null)
     {
-      af.viewport.featuresDisplayed = new Hashtable();
+      Hashtable featuresDisplayed = new Hashtable();
+      Hashtable featureColours = new Hashtable();
       String[] renderOrder = new String[jms.getFeatureSettings()
               .getSettingCount()];
       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
       {
         Setting setting = jms.getFeatureSettings().getSetting(fs);
 
-        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+        featureColours.put(
                 setting.getType(), new java.awt.Color(setting.getColour()));
 
         renderOrder[fs] = setting.getType();
 
         if (setting.getDisplay())
         {
-          af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+          featuresDisplayed.put(setting.getType(), new Integer(
                   setting.getColour()));
         }
       }
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+      FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null);
+      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(frs);
     }
 
     af.setMenusFromViewport(af.viewport);