X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=8e12ff5c3a81e7eb49629ed6c40952ce85c4b5c3;hb=ed96e73a6db654d52a6a1b1d27c2ee707876a4c7;hp=34146dd579cf9fb33edb9b41408d1320de2c993a;hpb=eccc204bba7aab9101c16df03cc5f740241d9184;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 34146dd..8e12ff5 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -78,9 +78,9 @@ public class AlignViewport extends AlignmentViewport
 
   boolean antiAlias = false;
 
-  private Rectangle explodedGeometry;
+  private Rectangle explodedGeometry = null;
 
-  private String viewName;
+  private String viewName = null;
 
   /*
    * Flag set true on the view that should 'gather' multiple views of the same
@@ -207,7 +207,7 @@ public class AlignViewport extends AlignmentViewport
    */
   private void applyViewProperties()
   {
-    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+    antiAlias = Cache.getDefault("ANTI_ALIAS", true);
 
     viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
     setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
@@ -865,10 +865,9 @@ public class AlignViewport extends AlignmentViewport
     if (ap != null)
     {
       // modify GUI elements to reflect geometry change
-      Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
-              .getPreferredSize();
+      Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
       idw.width = i;
-      getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+      ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
     }
   }
 
@@ -993,8 +992,8 @@ 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());
@@ -1005,7 +1004,7 @@ 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?
     //
@@ -1037,6 +1036,10 @@ public class AlignViewport extends AlignmentViewport
         {
           displayed.setVisible(type);
         }
+        else if (featureSettings.isFeatureHidden(type))
+        {
+          displayed.setHidden(type);
+        }
       }
     }
 
@@ -1065,6 +1068,8 @@ public class AlignViewport extends AlignmentViewport
       fr.orderFeatures(featureSettings);
     }
     fr.setTransparency(featureSettings.getTransparency());
+
+    fr.notifyFeaturesChanged();
   }
 
   public String getViewName()