protected now public

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