showConservation, quality, identity not used

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index e118309..fef8a83 100755 (executable)
--- 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 +1338,6 @@ 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.setAbovePIDThreshold(view.getPidSelected());
         af.abovePIDThreshold.setSelected(view.getPidSelected());
         af.viewport.setColourText(view.getShowColourText());
@@ -1481,7 +1475,7 @@ public class Jalview2XML
             if(cs!=null)
             {
               cs.setThreshold(view.getPidThreshold(), true);
-              cs.setConsensus(af.viewport.vconsensus);
+              cs.setConsensus(af.viewport.hconsensus);
             }
         }