Remove user colour menu item

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index e4842ee..7d09f1b 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,7 +23,6 @@ import java.awt.event.*;
 import javax.swing.*;\r
 import javax.swing.event.*;\r
 \r
-import jalview.gui.*;\r
 import jalview.schemes.*;\r
 \r
 public class GAlignFrame\r
@@ -115,10 +114,88 @@ public class GAlignFrame
   JMenu jMenu2 = new JMenu();\r
   JMenuItem padGapsMenuitem = new JMenuItem();\r
   JMenuItem ClustalRealign = new JMenuItem();\r
+  protected ButtonGroup colours = new ButtonGroup();\r
 \r
   public GAlignFrame()\r
   {\r
-    ButtonGroup colours = new ButtonGroup();\r
+\r
+\r
+    try\r
+    {\r
+      jbInit();\r
+      setJMenuBar(alignFrameMenuBar);\r
+\r
+      // dynamically fill save as menu with available formats\r
+      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
+      {\r
+        JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
+                             elementAt(\r
+                                 i));\r
+        item.addActionListener(new java.awt.event.ActionListener()\r
+        {\r
+          public void actionPerformed(ActionEvent e)\r
+          {\r
+            outputText_actionPerformed(e);\r
+          }\r
+        });\r
+\r
+        outputTextboxMenu.add(item);\r
+      }\r
+    }\r
+    catch (Exception e)\r
+    {\r
+    }\r
+\r
+\r
+    if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
+    {\r
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
+          getUserColourSchemes().keys();\r
+\r
+      while (userColours.hasMoreElements())\r
+      {\r
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
+            nextElement().toString());\r
+        radioItem.setName("USER_DEFINED");\r
+        radioItem.addMouseListener(new MouseAdapter()\r
+            {\r
+              public void mousePressed(MouseEvent evt)\r
+              {\r
+                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
+                {\r
+                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
+\r
+                  int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
+                      "Remove from default list?",\r
+                      "Remove user defined colour",\r
+                      JOptionPane.YES_NO_OPTION);\r
+                  if(option == JOptionPane.YES_OPTION)\r
+                  {\r
+                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
+                    colourMenu.remove(radioItem);\r
+                  }\r
+                  else\r
+                    radioItem.addActionListener(new ActionListener()\r
+                    {\r
+                      public void actionPerformed(ActionEvent evt)\r
+                      {\r
+                        userDefinedColour_actionPerformed(evt);\r
+                      }\r
+                    });\r
+                }\r
+              }\r
+            });\r
+        radioItem.addActionListener(new ActionListener()\r
+        {\r
+          public void actionPerformed(ActionEvent evt)\r
+          {\r
+            userDefinedColour_actionPerformed(evt);\r
+          }\r
+        });\r
+        colourMenu.insert(radioItem, 15);\r
+        colours.add(radioItem);\r
+      }\r
+    }\r
     colours.add(noColourmenuItem);\r
     colours.add(clustalColour);\r
     colours.add(zappoColour);\r
@@ -133,9 +210,13 @@ public class GAlignFrame
     colours.add(BLOSUM62Colour);\r
     colours.add(nucleotideColour);\r
 \r
-    noColourmenuItem.setSelected(true);\r
+    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
+\r
 \r
-    String defaultColour = Preferences.defaultColour;\r
+  }\r
+\r
+  public void setColourSelected(String defaultColour)\r
+  {\r
 \r
     if (defaultColour != null)\r
     {\r
@@ -143,6 +224,9 @@ public class GAlignFrame
 \r
       switch (index)\r
       {\r
+        case ColourSchemeProperty.NONE:\r
+              noColourmenuItem.setSelected(true);\r
+              break;\r
         case ColourSchemeProperty.CLUSTAL:\r
           clustalColour.setSelected(true);\r
 \r
@@ -163,6 +247,10 @@ public class GAlignFrame
 \r
           break;\r
 \r
+        case ColourSchemeProperty.TAYLOR:\r
+          taylorColour.setSelected(true);\r
+          break;\r
+\r
         case ColourSchemeProperty.HYDROPHOBIC:\r
           hydrophobicityColour.setSelected(true);\r
 \r
@@ -200,34 +288,6 @@ public class GAlignFrame
       }\r
     }\r
 \r
-    try\r
-    {\r
-      jbInit();\r
-      setJMenuBar(alignFrameMenuBar);\r
-\r
-      JMenuItem item;\r
-\r
-      // dynamically fill save as menu with available formats\r
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
-      {\r
-        item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
-                             elementAt(\r
-                                 i));\r
-        item.addActionListener(new java.awt.event.ActionListener()\r
-        {\r
-          public void actionPerformed(ActionEvent e)\r
-          {\r
-            outputText_actionPerformed(e);\r
-          }\r
-        });\r
-\r
-        outputTextboxMenu.add(item);\r
-      }\r
-    }\r
-    catch (Exception e)\r
-    {\r
-    }\r
-\r
   }\r
 \r
   private void jbInit()\r
@@ -237,6 +297,8 @@ public class GAlignFrame
     fileMenu.setText("File");\r
     saveAlignmentMenu.setMnemonic('L');\r
     saveAlignmentMenu.setText("Save As");\r
+    saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
+        awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     saveAlignmentMenu.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -549,7 +611,7 @@ public class GAlignFrame
     });\r
     annotationPanelMenuItem.setActionCommand("");\r
     annotationPanelMenuItem.setText("Show Annotations");\r
-    annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);\r
+    annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r