javadoc for jalview_properties tags

[jalview.git] / src / jalview / appletgui / AlignViewport.java

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index e5551e2..3418270 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -210,12 +210,12 @@ public class AlignViewport
                 AlignmentAnnotation.BAR_GRAPH);
         conservation.hasText = true;
         conservation.autoCalculated = true;
-        
+
         if (showConservation)
         {
           alignment.addAnnotation(conservation);
         }
-        
+
         if (showQuality)
         {
           quality = new AlignmentAnnotation("Quality",
@@ -226,11 +226,11 @@ public class AlignViewport
                   AlignmentAnnotation.BAR_GRAPH);
           quality.hasText = true;
           quality.autoCalculated = true;
-          
+
           alignment.addAnnotation(quality);
         }
       }
-      
+
       consensus = new AlignmentAnnotation("Consensus", "PID",
               new Annotation[1], 0f, 100f,
               AlignmentAnnotation.BAR_GRAPH);
@@ -242,7 +242,7 @@ public class AlignViewport
         alignment.addAnnotation(consensus);
       }
     }
-    
+
   }
 
   public void showSequenceFeatures(boolean b)
@@ -276,7 +276,7 @@ public class AlignViewport
           {
             if (ap != null)
             {
-              ap.paintAlignment(true);
+              ap.paintAlignment(false);
             }
             Thread.sleep(200);
           }
@@ -454,7 +454,7 @@ public class AlignViewport
         {
           if (ap != null)
           {
-            ap.paintAlignment(true);
+            ap.paintAlignment(false);
           }
 
           Thread.sleep(200);