JAL-1933 only create and add occupancy row to alignment view if showOccupancy viewpor...

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 8d2580b..f4d8f59 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1284,6 +1284,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean showConsensus = true;
 
+  protected boolean showOccupancy = true;
+
   private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
 
   protected SequenceAnnotationOrder sortAnnotationsBy = null;
@@ -1893,11 +1895,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       consensus = new AlignmentAnnotation("Consensus", "PID",
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       initConsensus(consensus);
-      gapcounts = new AlignmentAnnotation("Occupancy",
-              "Number of aligned positions",
-              new Annotation[1], 0f, alignment.getHeight(),
-              AlignmentAnnotation.BAR_GRAPH);
-      initGapCounts(gapcounts);
+      initGapCounts();
 
       initComplementConsensus();
     }
@@ -1954,16 +1952,19 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   // these should be extracted from the view model - style and settings for
   // derived annotation
-  private void initGapCounts(AlignmentAnnotation counts)
+  private void initGapCounts()
   {
-    counts.hasText = true;
-    counts.autoCalculated = true;
-    counts.scaleColLabel = true;
-    counts.graph = AlignmentAnnotation.BAR_GRAPH;
-
-    if (showConsensus)
+    if (showOccupancy)
     {
-      alignment.addAnnotation(counts);
+      gapcounts = new AlignmentAnnotation("Occupancy",
+              "Number of aligned positions", new Annotation[1], 0f,
+              alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+      gapcounts.hasText = true;
+      gapcounts.autoCalculated = true;
+      gapcounts.scaleColLabel = true;
+      gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+      alignment.addAnnotation(gapcounts);
     }
   }