X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=55d29d514fd6e0997df57a344edb5e965070e601;hb=d559b47886de6427219011e6e355320a0babd757;hp=d5ec6ac5cbb9ae95dbddf713c02ea4edf8a9414a;hpb=b2b7e99113e1f0962140fc72d989cc826799a2d4;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d5ec6ac..55d29d5 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1270,8 +1270,8 @@ public class Jalview2XML
       view.setWidth(size.width);
       view.setHeight(size.height);
 
-      view.setStartRes(av.startRes);
-      view.setStartSeq(av.startSeq);
+      view.setStartRes(av.getStartRes());
+      view.setStartSeq(av.getStartSeq());
 
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
@@ -1294,7 +1294,7 @@ public class Jalview2XML
                 .getGlobalColourScheme()));
       }
 
-      ResidueShaderI vcs = av.getViewportColourScheme();
+      ResidueShaderI vcs = av.getResidueShading();
       ColourSchemeI cs = av.getGlobalColourScheme();
 
       if (cs != null)
@@ -4474,15 +4474,15 @@ public class Jalview2XML
     }
 
     af.viewport.setGlobalColourScheme(cs);
-    af.viewport.getViewportColourScheme().setThreshold(
+    af.viewport.getResidueShading().setThreshold(
             view.getPidThreshold(), true);
-    af.viewport.getViewportColourScheme().setConsensus(
+    af.viewport.getResidueShading().setConsensus(
             af.viewport.getSequenceConsensusHash());
     af.viewport.setColourAppliesToAllGroups(false);
 
     if (view.getConservationSelected() && cs != null)
     {
-      af.viewport.getViewportColourScheme().setConservationInc(
+      af.viewport.getResidueShading().setConservationInc(
               view.getConsThreshold());
     }