JAL-3187 save and restore flags for show complement features

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 9a303e2..5b1c0a3 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -1501,6 +1501,9 @@ public class Jalview2XML
       view.setFollowHighlight(av.isFollowHighlight());
       view.setFollowSelection(av.followSelection);
       view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
+      view.setShowComplementFeatures(av.isShowComplementFeatures());
+      view.setShowComplementFeaturesOnTop(
+              av.isShowComplementFeaturesOnTop());
       if (av.getFeaturesDisplayed() != null)
       {
         FeatureSettings fs = new FeatureSettings();
@@ -5019,6 +5022,9 @@ public class Jalview2XML
     viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
     viewport.setShowGroupConsensus(view.isShowGroupConsensus());
     viewport.setShowGroupConservation(view.isShowGroupConservation());
+    viewport.setShowComplementFeatures(view.isShowComplementFeatures());
+    viewport.setShowComplementFeaturesOnTop(
+            view.isShowComplementFeaturesOnTop());
 
     // recover feature settings
     if (jm.getFeatureSettings() != null)