X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=8d1eacd3ca43096e9e0df4fd4d0c46d7196e11f7;hb=9debcac658224e1a84ddff4c4fd9f696e812913f;hp=dff20d3d76aa41d4411a7ce7852085a373ca7ecb;hpb=92bd4313e2f23a65df1eb965e836d178c1eacdd1;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index dff20d3..8d1eacd 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -25,7 +25,7 @@ import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
-import jalview.io.FileFormat;
+import jalview.io.FileFormats;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
@@ -65,8 +65,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem closeMenuItem = new JMenuItem();
 
-  protected JMenu colourMenu = new JMenu();
-
   protected JMenu webService = new JMenu();
 
   protected JMenuItem webServiceNoServices;
@@ -81,8 +79,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu outputTextboxMenu = new JMenu();
 
-  protected JRadioButtonMenuItem textColour;
-
   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
@@ -93,14 +89,10 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem redoMenuItem = new JMenuItem();
 
-  protected JCheckBoxMenuItem conservationMenuItem;
-
   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 
-  protected JCheckBoxMenuItem abovePIDThreshold;
-
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 
   JMenuItem copy = new JMenuItem();
@@ -109,8 +101,6 @@ public class GAlignFrame extends JInternalFrame
 
   JMenu pasteMenu = new JMenu();
 
-  protected JCheckBoxMenuItem applyToAllGroups;
-
   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
@@ -119,10 +109,20 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 
-  protected JMenuItem modifyPID;
+  protected JCheckBoxMenuItem applyToAllGroups;
+
+  protected JMenu colourMenu = new JMenu();
+
+  protected JMenuItem textColour;
+
+  protected JCheckBoxMenuItem conservationMenuItem;
 
   protected JMenuItem modifyConservation;
 
+  protected JCheckBoxMenuItem abovePIDThreshold;
+
+  protected JMenuItem modifyPID;
+
   protected JMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
@@ -211,7 +211,7 @@ public class GAlignFrame extends JInternalFrame
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (String ff : FileFormat.getWritableFormats(true))
+      for (String ff : FileFormats.getInstance().getWritableFormats(true))
       {
         JMenuItem item = new JMenuItem(ff);
 
@@ -1917,12 +1917,12 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        applyToAllGroups_actionPerformed();
+        applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
       }
     });
 
-    textColour = new JRadioButtonMenuItem(
-            MessageManager.getString("action.set_text_colour"));
+    textColour = new JMenuItem(
+            MessageManager.getString("label.text_colour"));
     textColour.addActionListener(new ActionListener()
     {
       @Override
@@ -1939,7 +1939,8 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed();
+        conservationMenuItem_actionPerformed(conservationMenuItem
+                .isSelected());
       }
     });
 
@@ -1950,7 +1951,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDThreshold_actionPerformed();
+        abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
       }
     });
     modifyPID = new JMenuItem(
@@ -2342,7 +2343,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void conservationMenuItem_actionPerformed()
+  protected void conservationMenuItem_actionPerformed(boolean selected)
   {
   }
 
@@ -2358,7 +2359,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void abovePIDThreshold_actionPerformed()
+  protected void abovePIDThreshold_actionPerformed(boolean selected)
   {
   }
 
@@ -2398,7 +2399,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void applyToAllGroups_actionPerformed()
+  protected void applyToAllGroups_actionPerformed(boolean selected)
   {
   }