JAL-2383 restore PID colour threshold from project; enable/disable

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index cbeb93c..6530d3d 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,9 +23,10 @@ package jalview.jbgui;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
-import jalview.io.FileFormat;
+import jalview.io.FileFormats;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
 
@@ -51,7 +52,6 @@ import javax.swing.JLabel;
 import javax.swing.JMenu;
 import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JRadioButtonMenuItem;
 import javax.swing.JTabbedPane;
@@ -155,6 +155,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem modifyConservation = new JMenuItem();
 
+  protected JMenuItem modifyPID = new JMenuItem();
+
   protected JMenu sortByTreeMenu = new JMenu();
 
   protected JMenu sort = new JMenu();
@@ -245,7 +247,7 @@ 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);
 
@@ -314,13 +316,13 @@ public class GAlignFrame extends JInternalFrame
           {
             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
-            int option = JOptionPane.showInternalConfirmDialog(
+            int option = JvOptionPane.showInternalConfirmDialog(
                     jalview.gui.Desktop.desktop, MessageManager
                             .getString("label.remove_from_default_list"),
                     MessageManager
                             .getString("label.remove_user_defined_colour"),
-                    JOptionPane.YES_NO_OPTION);
-            if (option == JOptionPane.YES_OPTION)
+                    JvOptionPane.YES_NO_OPTION);
+            if (option == JvOptionPane.YES_OPTION)
             {
               jalview.gui.UserDefinedColours
                       .removeColourFromDefaults(radioItem.getText());
@@ -1118,7 +1120,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed(e);
+        conservationMenuItem_actionPerformed();
       }
     });
     noColourmenuItem.setText(MessageManager.getString("label.none"));
@@ -1189,7 +1191,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDThreshold_actionPerformed(e);
+        abovePIDThreshold_actionPerformed();
       }
     });
     showSeqFeatures.setText(MessageManager
@@ -1604,14 +1606,14 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    JMenuItem modifyPID = new JMenuItem(
+    modifyPID = new JMenuItem(
             MessageManager.getString("label.modify_identity_threshold"));
     modifyPID.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        modifyPID_actionPerformed(e);
+        modifyPID_actionPerformed();
       }
     });
     modifyConservation.setText(MessageManager
@@ -1621,7 +1623,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        modifyConservation_actionPerformed(e);
+        modifyConservation_actionPerformed();
       }
     });
     sortByTreeMenu
@@ -2319,7 +2321,7 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
     colourMenu.add(purinePyrimidineColour);
-    colourMenu.add(RNAInteractionColour);
+    // colourMenu.add(RNAInteractionColour);
     // colourMenu.add(covariationColour);
     colourMenu.add(tcoffeeColour);
     colourMenu.add(userDefinedColour);
@@ -2817,7 +2819,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void conservationMenuItem_actionPerformed()
   {
   }
 
@@ -2833,7 +2835,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+  protected void abovePIDThreshold_actionPerformed()
   {
   }
 
@@ -2954,11 +2956,11 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void modifyPID_actionPerformed(ActionEvent e)
+  protected void modifyPID_actionPerformed()
   {
   }
 
-  protected void modifyConservation_actionPerformed(ActionEvent e)
+  protected void modifyConservation_actionPerformed()
   {
   }