X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=056555aace3be923fb80832e769cf562c236f44d;hb=b3b59df08fc4183bb35e4ed5a54841a990b71346;hp=a38c5301c946ae980a2baf926e31ab3f01b0265b;hpb=d69ea8f1997771890b44e4b332a7ca84fe6f0893;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index a38c530..056555a 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -645,10 +645,7 @@ public class Jalview2XML
         view.setShowAnnotation(av.getShowAnnotation());
         view.setShowBoxes(av.getShowBoxes());
         view.setShowColourText(av.getColourText());
-        view.setShowConservation(av.showConservation);
         view.setShowFullId(av.getShowJVSuffix());
-        view.setShowIdentity(av.showIdentity);
-        view.setShowQuality(av.showQuality);
         view.setShowSequenceFeatures(av.showSequenceFeatures);
         view.setShowText(av.getShowText());
         view.setWrapAlignment(av.getWrapAlignment());
@@ -1341,9 +1338,10 @@ public class Jalview2XML
         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.showConservation = !hideConservation;
+        af.viewport.showQuality = !hideQuality;
+        af.viewport.showIdentity = !hideConsensus;
+
         af.viewport.setAbovePIDThreshold(view.getPidSelected());
         af.abovePIDThreshold.setSelected(view.getPidSelected());
         af.viewport.setColourText(view.getShowColourText());