Can edit in wrapped view

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 345bcf5..4c5cdfe 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -36,6 +36,7 @@ public class GAlignFrame
   protected JMenu colourMenu = new JMenu();\r
   protected JMenu calculateMenu = new JMenu();\r
   protected JMenu webService = new JMenu();\r
+  protected JMenuItem webServiceNoServices;\r
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
@@ -101,7 +102,6 @@ public class GAlignFrame
   public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
   JMenuItem epsFile = new JMenuItem();\r
   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
-  JMenuItem jnet = new JMenuItem();\r
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
@@ -110,10 +110,8 @@ public class GAlignFrame
   protected JMenu sortByTreeMenu = new JMenu();\r
   protected JMenu sort = new JMenu();\r
   JMenu calculate = new JMenu();\r
-  JMenuItem msaAlignMenuItem = new JMenuItem();\r
   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
@@ -154,9 +152,37 @@ public class GAlignFrame
 \r
       while (userColours.hasMoreElements())\r
       {\r
-        JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\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
@@ -443,14 +469,6 @@ public class GAlignFrame
         neighbourTreeMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    clustalAlignMenuItem.setText("Clustal Alignment");\r
-    clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        clustalAlignMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
     this.getContentPane().setLayout(borderLayout1);\r
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
     alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
@@ -830,14 +848,6 @@ public class GAlignFrame
         LoadtreeMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    jnet.setText("JNet");\r
-    jnet.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        jpred_actionPerformed(e);\r
-      }\r
-    });\r
     scaleAbove.setVisible(false);\r
     scaleAbove.setText("Scale Above");\r
     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
@@ -886,14 +896,7 @@ public class GAlignFrame
     sortByTreeMenu.setText("By Tree Order");\r
     sort.setText("Sort");\r
     calculate.setText("Calculate Tree");\r
-    msaAlignMenuItem.setText("Muscle Alignment");\r
-    msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        msaAlignMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
+\r
     jMenu2.setText("Export");\r
     padGapsMenuitem.setText("Pad Gaps");\r
     padGapsMenuitem.addActionListener(new ActionListener()\r
@@ -903,20 +906,13 @@ public class GAlignFrame
         padGapsMenuitem_actionPerformed(e);\r
       }\r
     });\r
-    ClustalRealign.setText("Clustal Realign");\r
-    ClustalRealign.addActionListener(new ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        ClustalRealign_actionPerformed(e);\r
-      }\r
-    });\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
     alignFrameMenuBar.add(viewMenu);\r
     alignFrameMenuBar.add(colourMenu);\r
     alignFrameMenuBar.add(calculateMenu);\r
+    alignFrameMenuBar.add(webService);\r
     fileMenu.add(saveAlignmentMenu);\r
     fileMenu.add(jMenu2);\r
     fileMenu.add(outputTextboxMenu);\r
@@ -985,12 +981,8 @@ public class GAlignFrame
     calculateMenu.addSeparator();\r
     calculateMenu.add(pairwiseAlignmentMenuItem);\r
     calculateMenu.add(PCAMenuItem);\r
-    calculateMenu.addSeparator();\r
-    calculateMenu.add(webService);\r
-    webService.add(clustalAlignMenuItem);\r
-    webService.add(msaAlignMenuItem);\r
-    webService.add(jnet);\r
-    webService.add(ClustalRealign);\r
+    webServiceNoServices=new JMenuItem("<No Services>");\r
+    webService.add(webServiceNoServices);\r
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
     jMenu1.add(pasteNew);\r
     jMenu1.add(pasteThis);\r