From 4ea44eaccf82b15dafb8dd53f5c71de5e9d0d551 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 16 Dec 2016 15:31:53 +0000
Subject: [PATCH] JAL-2346 ensure view updates when annotation options are
 rebuilt

---
 src/jalview/gui/AnnotationRowFilter.java |   17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 128b99c..7bf8721 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -88,8 +88,6 @@ public abstract class AnnotationRowFilter extends JPanel
    */
   private Map<AlignmentAnnotation, String> annotationLabels;
 
-  private boolean enableSeqAss = false;
-
   private AlignmentAnnotation currentAnnotation;
 
   /**
@@ -176,6 +174,7 @@ public abstract class AnnotationRowFilter extends JPanel
     Vector<String> list = new Vector<String>();
     int index = 1;
     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
+    seqAssociated.setEnabled(false);
     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
     {
       AlignmentAnnotation annotation = av.getAlignment()
@@ -189,7 +188,7 @@ public abstract class AnnotationRowFilter extends JPanel
       }
       else
       {
-        enableSeqAss = true;
+        seqAssociated.setEnabled(true);
       }
       String label = annotation.label;
       // add associated sequence ID if available
@@ -234,11 +233,6 @@ public abstract class AnnotationRowFilter extends JPanel
     return selectedThresholdItem;
   }
 
-  public void modelChanged()
-  {
-    seqAssociated.setEnabled(enableSeqAss);
-  }
-
   public void ok_actionPerformed()
   {
     try
@@ -313,7 +307,8 @@ public abstract class AnnotationRowFilter extends JPanel
   {
     adjusting = true;
     String cursel = (String) anns.getSelectedItem();
-    boolean isvalid = false, isseqs = seqAssociated.isSelected();
+    boolean isvalid = false;
+    boolean isseqs = seqAssociated.isSelected();
     anns.removeAllItems();
     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
     {
@@ -324,7 +319,6 @@ public abstract class AnnotationRowFilter extends JPanel
       }
       anns.addItem(anitem);
     }
-    adjusting = false;
     if (isvalid)
     {
       anns.setSelectedItem(cursel);
@@ -336,6 +330,9 @@ public abstract class AnnotationRowFilter extends JPanel
         anns.setSelectedIndex(0);
       }
     }
+    adjusting = false;
+
+    updateView();
   }
 
   protected void propagateSeqAssociatedThreshold(boolean allAnnotation,
-- 
1.7.10.2