Merge branch 'feature/JAL-3187linkedFeatures' into feature/JAL-3251biotypedMappings

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index a5585ce..e9b6f8c 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -161,10 +161,6 @@ public class FeatureSettings extends JPanel
 
   JSlider transparency = new JSlider();
 
-  JCheckBox showComplement;
-
-  JCheckBox showComplementOnTop;
-
   /*
    * when true, constructor is still executing - so ignore UI events
    */
@@ -1275,7 +1271,7 @@ public class FeatureSettings extends JPanel
             MessageManager.getString("label.transparency_tip"));
 
     boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
-    showComplement = new JCheckBox(
+    JCheckBox showComplement = new JCheckBox(
             "Show " + (nucleotide ? "protein" : "CDS") + " features");
     showComplement.setSelected(af.getViewport().isShowComplementFeatures());
     showComplement.addActionListener(new ActionListener()
@@ -1289,7 +1285,7 @@ public class FeatureSettings extends JPanel
       }
     });
 
-    showComplementOnTop = new JCheckBox("on top");
+    JCheckBox showComplementOnTop = new JCheckBox("on top");
     showComplementOnTop
             .setSelected(af.getViewport().isShowComplementFeaturesOnTop());
     showComplementOnTop.addActionListener(new ActionListener()

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)