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[jalview.git] / src / jalview / jbgui / GAlignFrame.java
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index f4502e5..1b89d71 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -24,10 +24,6 @@ import javax.swing.*;
 import javax.swing.event.*;\r
 \r
 import jalview.schemes.*;\r
-import java.awt.BorderLayout;\r
-\r
-\r
-\r
 \r
 public class GAlignFrame\r
     extends JInternalFrame\r
@@ -140,16 +136,15 @@ public class GAlignFrame
   JMenuItem invertColSel = new JMenuItem();\r
   protected JTabbedPane tabbedPane = new JTabbedPane();\r
   JMenuItem save = new JMenuItem();\r
-  JMenuItem jMenuItem1 = new JMenuItem();\r
   protected JMenuItem reload = new JMenuItem();\r
   JMenuItem newView = new JMenuItem();\r
   JMenuItem textColour = new JMenuItem();\r
   JMenu formatMenu = new JMenu();\r
-  JCheckBoxMenuItem jCheckBoxMenuItem1 = new JCheckBoxMenuItem();\r
   JMenu selectMenu = new JMenu();\r
   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();\r
   protected JMenuItem gatherViews = new JMenuItem();\r
   protected JMenuItem expandViews = new JMenuItem();\r
+  JMenuItem pageSetup = new JMenuItem();\r
   public GAlignFrame()\r
   {\r
     try\r
@@ -160,7 +155,8 @@ public class GAlignFrame
       // dynamically fill save as menu with available formats\r
       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
       {\r
-        JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
+        JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.\r
+                                       WRITEABLE_FORMATS[i]);\r
 \r
         item.addActionListener(new java.awt.event.ActionListener()\r
         {\r
@@ -189,45 +185,49 @@ public class GAlignFrame
       reload.setMnemonic('R');\r
     }\r
 \r
-\r
-    if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\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
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(\r
+            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
-              public void mousePressed(MouseEvent evt)\r
+              radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
+\r
+              int option = JOptionPane.showInternalConfirmDialog(jalview.gui.\r
+                  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
-                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
+                jalview.gui.UserDefinedColours.removeColourFromDefaults(\r
+                    radioItem.getText());\r
+                colourMenu.remove(radioItem);\r
+              }\r
+              else\r
+              {\r
+                radioItem.addActionListener(new ActionListener()\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
+                  public void actionPerformed(ActionEvent evt)\r
                   {\r
-                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
-                    colourMenu.remove(radioItem);\r
+                    userDefinedColour_actionPerformed(evt);\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
-            });\r
+            }\r
+          }\r
+        });\r
         radioItem.addActionListener(new ActionListener()\r
         {\r
           public void actionPerformed(ActionEvent evt)\r
@@ -255,7 +255,6 @@ public class GAlignFrame
 \r
     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 \r
-\r
   }\r
 \r
   public void setColourSelected(String defaultColour)\r
@@ -268,8 +267,8 @@ public class GAlignFrame
       switch (index)\r
       {\r
         case ColourSchemeProperty.NONE:\r
-              noColourmenuItem.setSelected(true);\r
-              break;\r
+          noColourmenuItem.setSelected(true);\r
+          break;\r
         case ColourSchemeProperty.CLUSTAL:\r
           clustalColour.setSelected(true);\r
 \r
@@ -340,7 +339,8 @@ public class GAlignFrame
     saveAs.setText("Save As...");\r
     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
         KeyEvent.VK_S,\r
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false));\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
+        java.awt.event.KeyEvent.SHIFT_MASK, false));\r
     saveAs.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -400,7 +400,8 @@ public class GAlignFrame
     });\r
     remove2LeftMenuItem.setText("Remove Left");\r
     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
-        awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+        awt.event.KeyEvent.VK_L,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -410,7 +411,8 @@ public class GAlignFrame
     });\r
     remove2RightMenuItem.setText("Remove Right");\r
     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
-        awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+        awt.event.KeyEvent.VK_R,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -433,7 +435,8 @@ public class GAlignFrame
     removeAllGapsMenuItem.setText("Remove All Gaps");\r
     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_E,\r
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
+        java.awt.event.KeyEvent.SHIFT_MASK, false));\r
     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -485,7 +488,8 @@ public class GAlignFrame
     });\r
     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
-        java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+        java.awt.event.KeyEvent.VK_D,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
                                                ActionListener()\r
     {\r
@@ -645,7 +649,8 @@ public class GAlignFrame
     });\r
     annotationPanelMenuItem.setActionCommand("");\r
     annotationPanelMenuItem.setText("Show Annotations");\r
-    annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
+    annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(\r
+        "SHOW_ANNOTATIONS", true));\r
     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -724,7 +729,7 @@ public class GAlignFrame
         wrapMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    printMenuItem.setText("Print");\r
+    printMenuItem.setText("Print ...");\r
     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
         event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
@@ -825,7 +830,8 @@ public class GAlignFrame
     pasteNew.setText("To New Alignment");\r
     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_V,\r
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false));\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
+        java.awt.event.KeyEvent.SHIFT_MASK, false));\r
     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -871,7 +877,7 @@ public class GAlignFrame
     });\r
 \r
     seqLimits.setText("Show Sequence Limits");\r
-    seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
+    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));\r
     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -943,11 +949,26 @@ public class GAlignFrame
     });\r
     sortByTreeMenu.setText("By Tree Order");\r
     sort.setText("Sort");\r
+    sort.addMenuListener(new MenuListener()\r
+    {\r
+      public void menuSelected(MenuEvent e)\r
+      {\r
+        buildTreeMenu();\r
+      }\r
+\r
+      public void menuDeselected(MenuEvent e)\r
+      {\r
+      }\r
+\r
+      public void menuCanceled(MenuEvent e)\r
+      {\r
+      }\r
+    });\r
     calculate.setText("Calculate Tree");\r
 \r
     jMenu2.setText("Export Image");\r
     padGapsMenuitem.setText("Pad Gaps");\r
-    padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
+    padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
     padGapsMenuitem.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -973,7 +994,6 @@ public class GAlignFrame
       }\r
     });\r
 \r
-\r
     featureSettings.setText("Feature Settings...");\r
     featureSettings.addActionListener(new ActionListener()\r
     {\r
@@ -1008,7 +1028,7 @@ public class GAlignFrame
       }\r
     });\r
     autoCalculate.setText("Autocalculate Consensus");\r
-    autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
+    autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
     autoCalculate.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -1104,7 +1124,7 @@ public class GAlignFrame
     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
         event.KeyEvent.VK_I,\r
         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()\r
-        |java.awt.event.KeyEvent.ALT_MASK,\r
+        | java.awt.event.KeyEvent.ALT_MASK,\r
         false));\r
     invertColSel.addActionListener(new ActionListener()\r
     {\r
@@ -1115,12 +1135,12 @@ public class GAlignFrame
     });\r
     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
     {\r
-        public void stateChanged(ChangeEvent evt)\r
-        {\r
-            JTabbedPane pane = (JTabbedPane)evt.getSource();\r
-            int sel = pane.getSelectedIndex();\r
-            tabSelectionChanged(sel);\r
-        }\r
+      public void stateChanged(ChangeEvent evt)\r
+      {\r
+        JTabbedPane pane = (JTabbedPane) evt.getSource();\r
+        int sel = pane.getSelectedIndex();\r
+        tabSelectionChanged(sel);\r
+      }\r
     });\r
     tabbedPane.addMouseListener(new MouseAdapter()\r
     {\r
@@ -1166,7 +1186,8 @@ public class GAlignFrame
       }\r
     });\r
     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"\r
-                              +"<br> Press X to eXpand tabs, G to reGroup.</i></html>");\r
+                              +\r
+        "<br> Press X to eXpand tabs, G to reGroup.</i></html>");\r
     textColour.setText("Text Colour");\r
     textColour.addActionListener(new ActionListener()\r
     {\r
@@ -1176,7 +1197,6 @@ public class GAlignFrame
       }\r
     });\r
     formatMenu.setText("Format");\r
-    jCheckBoxMenuItem1.setText("Right Align Ids");\r
     selectMenu.setText("Select");\r
     idRightAlign.setText("Right Align Sequence Id");\r
     idRightAlign.addActionListener(new ActionListener()\r
@@ -1208,6 +1228,14 @@ public class GAlignFrame
         expandViews_actionPerformed(e);\r
       }\r
     });\r
+    pageSetup.setText("Page Setup ...");\r
+    pageSetup.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        pageSetup_actionPerformed(e);\r
+      }\r
+    });\r
 \r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
@@ -1225,6 +1253,7 @@ public class GAlignFrame
     fileMenu.add(save);\r
     fileMenu.add(saveAs);\r
     fileMenu.add(outputTextboxMenu);\r
+    fileMenu.add(pageSetup);\r
     fileMenu.add(printMenuItem);\r
     fileMenu.addSeparator();\r
     fileMenu.add(jMenu2);\r
@@ -1291,12 +1320,14 @@ public class GAlignFrame
     calculateMenu.addSeparator();\r
     calculateMenu.add(showTranslation);\r
     calculateMenu.add(autoCalculate);\r
-    webServiceNoServices=new JMenuItem("<No Services>");\r
-    webService.add(webServiceNoServices);pasteMenu.add(pasteNew);\r
+    webServiceNoServices = new JMenuItem("<No Services>");\r
+    webService.add(webServiceNoServices);\r
+    pasteMenu.add(pasteNew);\r
     pasteMenu.add(pasteThis);\r
     sort.add(sortIDMenuItem);\r
     sort.add(sortGroupMenuItem);\r
     sort.add(sortPairwiseMenuItem);\r
+    sort.add(sortByTreeMenu);\r
     calculate.add(averageDistanceTreeMenuItem);\r
     calculate.add(neighbourTreeMenuItem);\r
     calculate.add(avDistanceTreeBlosumMenuItem);\r
@@ -1594,7 +1625,6 @@ public class GAlignFrame
 \r
   }\r
 \r
-\r
   public void createEPS(java.io.File f)\r
   {\r
   }\r
@@ -1627,8 +1657,6 @@ public class GAlignFrame
   {\r
   }\r
 \r
-\r
-\r
   protected void saveAs_actionPerformed(ActionEvent e)\r
   {\r
   }\r
@@ -1637,7 +1665,6 @@ public class GAlignFrame
   {\r
   }\r
 \r
-\r
   public void vamsasStore_actionPerformed(ActionEvent e)\r
   {\r
 \r
@@ -1673,7 +1700,6 @@ public class GAlignFrame
 \r
   }\r
 \r
-\r
   public void associatedData_actionPerformed(ActionEvent e)\r
   {\r
 \r
@@ -1778,4 +1804,14 @@ public class GAlignFrame
   {\r
 \r
   }\r
+\r
+  public void buildTreeMenu()\r
+  {\r
+\r
+  }\r
+\r
+  public void pageSetup_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
 }\r