X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=3c520e39690f88bb3c2b02edd69197f2fc2344fa;hb=1f029391e9e263b132a62eaefcc2fe68badacfd6;hp=0125f0db68d544c7d0b25cc22a0e74c9487b34a2;hpb=27eec0137f40a134a181b4738859a160749babe2;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 0125f0d..3c520e3 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1022,8 +1022,8 @@ public class AlignViewport extends AlignmentViewport
     
     FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
             .getFeatureRenderer();
-    List<String> origRenderOrder = new ArrayList(),
-            origGroups = new ArrayList();
+    List<String> origRenderOrder = new ArrayList<>();
+    List<String> origGroups = new ArrayList<>();
     // preserve original render order - allows differentiation between user configured colours and autogenerated ones
     origRenderOrder.addAll(fr.getRenderOrder());
     origGroups.addAll(fr.getFeatureGroups());
@@ -1034,7 +1034,7 @@ public class AlignViewport extends AlignmentViewport
     if (!mergeOnly)
     {
       // only clear displayed features if we are mergeing
-      displayed.clear();
+      // displayed.clear();
     }
     // TODO this clears displayed.featuresRegistered - do we care?
     //
@@ -1066,6 +1066,10 @@ public class AlignViewport extends AlignmentViewport
         {
           displayed.setVisible(type);
         }
+        else if (featureSettings.isFeatureHidden(type))
+        {
+          displayed.setHidden(type);
+        }
       }
     }