JAL-4409 Allow more URI schemes (e.g. file) to be opened in Jalview

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index ccf6379..712c63b 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1403,7 +1403,9 @@ public abstract class AlignmentViewport
 
   protected boolean showQuality = true;
 
-  protected boolean showConsensus = true;
+  protected boolean showConsensus = true;  
+
+  protected boolean showSSConsensus = false;
 
   protected boolean showOccupancy = true;
 
@@ -1461,6 +1463,12 @@ public abstract class AlignmentViewport
     changeSupport.firePropertyChange(prop, oldvalue, newvalue);
   }
 
+  @Override
+  public void notifyAlignmentChanged()
+  {
+    firePropertyChange("alignment", null, alignment);
+  }
+
   // common hide/show column stuff
 
   public void hideSelectedColumns()
@@ -2041,7 +2049,7 @@ public abstract class AlignmentViewport
               MessageManager.getString("label.consensus_descr"),
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       
-      secondaryStructureConsensus = new AlignmentAnnotation("SecondaryStructureConsensus",
+      secondaryStructureConsensus = new AlignmentAnnotation(MessageManager.getString("label.ssconsensus_label"),
               MessageManager.getString("label.ssconsensus_descr"),
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       
@@ -2109,7 +2117,7 @@ public abstract class AlignmentViewport
     aa.hasText = true;
     aa.autoCalculated = true;
 
-    if (showConsensus)
+    if (showSSConsensus)
     {
       alignment.addAnnotation(aa);
     }