JAL-1933 showOccupancy applet parameter and SHOW_OCCUPANCY .jalview_properties setting

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 065c503..e50cc09 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -149,6 +149,9 @@ public class AlignViewport extends AlignmentViewport implements
       showConsensus = applet.getDefaultParameter("showConsensus",
               showConsensus);
 
+      showOccupancy = applet.getDefaultParameter("showOccupancy",
+              showOccupancy);
+
       setShowUnconserved(applet.getDefaultParameter("showUnconserved",
               getShowUnconserved()));
 

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 602e3a1..992ec54 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -279,6 +279,8 @@ public class AlignViewport extends AlignmentViewport implements
               false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+      showOccupancy = Cache.getDefault("SHOW_OCCUPANCY", true);
     }
     initAutoAnnotation();
     String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC