X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=ab4bc595f9b9f4d9a65f3d456469abff638d40d1;hb=94f96a9c993be278b360ad15965715063db72520;hp=81325d5068b9a9356da357ab4163902d3ed13af7;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 81325d5..ab4bc59 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -46,8 +46,8 @@ public class GAlignFrame extends JInternalFrame {
     protected JMenuItem remove2RightMenuItem = new JMenuItem();
     protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
     protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
-    protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
-    protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
     protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
     protected JMenuItem sortIDMenuItem = new JMenuItem();
     protected JMenuItem sortGroupMenuItem = new JMenuItem();
@@ -74,21 +74,21 @@ public class GAlignFrame extends JInternalFrame {
     protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
     JMenuItem njTreeBlosumMenuItem = new JMenuItem();
     JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
-    protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
-    protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
     JMenuItem htmlMenuItem = new JMenuItem();
     JMenuItem overviewMenuItem = new JMenuItem();
     protected JMenuItem undoMenuItem = new JMenuItem();
     protected JMenuItem redoMenuItem = new JMenuItem();
-    protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
     JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-    protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
     JMenuItem printMenuItem = new JMenuItem();
-    protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
     JMenuItem findMenuItem = new JMenuItem();
     JMenu searchMenu = new JMenu();
-    protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
-    protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
     protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
     JMenuItem deleteGroups = new JMenuItem();
     JMenuItem delete = new JMenuItem();
@@ -97,16 +97,16 @@ public class GAlignFrame extends JInternalFrame {
     JMenu jMenu1 = new JMenu();
     JMenuItem pasteNew = new JMenuItem();
     JMenuItem pasteThis = new JMenuItem();
-    protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
     JMenuItem createPNG = new JMenuItem();
     protected JMenuItem font = new JMenuItem();
-    protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
     JMenuItem epsFile = new JMenuItem();
     JMenuItem LoadtreeMenuItem = new JMenuItem();
     JMenuItem jpred = new JMenuItem();
-    protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
-    protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
-    protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+    public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
     JMenuItem modifyPID = new JMenuItem();
     JMenuItem modifyConservation = new JMenuItem();
     protected JMenu sortByTreeMenu = new JMenu();
@@ -219,6 +219,7 @@ public class GAlignFrame extends JInternalFrame {
         } catch (Exception e) {
             e.printStackTrace();
         }
+
     }
 
     private void jbInit() throws Exception {