JAL-1933 gap value as description; minor formatting

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 560ff59..da05a09 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,6 +20,17 @@
  */
 package jalview.viewmodel;
 
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
@@ -57,17 +68,6 @@ import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -1913,7 +1913,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       initConsensus(consensus);
       gapcounts = new AlignmentAnnotation("Gaps", "Number of Gaps",
               new Annotation[1], 0f, alignment.getHeight(),
-              AlignmentAnnotation.LINE_GRAPH);
+              AlignmentAnnotation.BAR_GRAPH);
       initGapCounts(gapcounts);
 
       initComplementConsensus();
@@ -1969,15 +1969,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   // these should be extracted from the view model - style and settings for
   // derived annotation
-  private void initGapCounts(AlignmentAnnotation gapcounts)
+  private void initGapCounts(AlignmentAnnotation counts)
   {
-    gapcounts.hasText = false;
-    gapcounts.autoCalculated = true;
-    gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+    counts.hasText = false;
+    counts.autoCalculated = true;
+    counts.graph = AlignmentAnnotation.BAR_GRAPH;
 
     if (showConsensus)
     {
-      alignment.addAnnotation(gapcounts);
+      alignment.addAnnotation(counts);
     }
   }
 
@@ -2851,7 +2851,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   private boolean selectionIsDefinedGroup = false;
 
-
   @Override
   public boolean isSelectionDefinedGroup()
   {