Proceed with upperCase residue
[jalview.git] / src / jalview / jbappletgui / GTreePanel.java
index f5f7ab1..1810719 100755 (executable)
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+*/\r
 package jalview.jbappletgui;\r
 \r
 import java.awt.*;\r
 import java.awt.event.*;\r
 \r
-public class GTreePanel extends Frame\r
-{\r
-  BorderLayout borderLayout1 = new BorderLayout();\r
-  protected ScrollPane scrollPane = new ScrollPane();\r
-  MenuBar jMenuBar1 = new MenuBar();\r
-  Menu jMenu2 = new Menu();\r
-  protected MenuItem fontSize = new MenuItem();\r
-  protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();\r
-  protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();\r
-  protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();\r
-  Menu fileMenu = new Menu();\r
-  MenuItem newickOutput = new MenuItem();\r
 \r
-  public GTreePanel()\r
-  {\r
-    try\r
-    {\r
-      jbInit();\r
-      this.setMenuBar(jMenuBar1);\r
+public class GTreePanel extends Frame {\r
+    BorderLayout borderLayout1 = new BorderLayout();\r
+    protected ScrollPane scrollPane = new ScrollPane();\r
+    MenuBar jMenuBar1 = new MenuBar();\r
+    Menu jMenu2 = new Menu();\r
+    protected MenuItem fontSize = new MenuItem();\r
+    protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();\r
+    protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();\r
+    protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();\r
+    protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();\r
+    Menu fileMenu = new Menu();\r
+    MenuItem newickOutput = new MenuItem();\r
+\r
+    public GTreePanel() {\r
+        try {\r
+            jbInit();\r
+            this.setMenuBar(jMenuBar1);\r
+        } catch (Exception e) {\r
+            e.printStackTrace();\r
+        }\r
     }\r
-    catch(Exception e)\r
-    {\r
-      e.printStackTrace();\r
-    }\r
-\r
-  }\r
-  private void jbInit() throws Exception\r
-  {\r
-    setLayout(borderLayout1);\r
-    this.setBackground(Color.white);\r
-    this.setFont(new java.awt.Font("Verdana", 0, 12));\r
-    jMenu2.setLabel("View");\r
-    fontSize.setLabel("Font Size - 12");\r
-    fontSize.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        fontSize_actionPerformed(e);\r
-      }\r
-    });\r
-    bootstrapMenu.setLabel("Show Bootstrap values");\r
-    bootstrapMenu.addItemListener(new java.awt.event.ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent e)\r
-      {\r
-        bootstrapMenu_actionPerformed(null);\r
-      }\r
-    });\r
-    distanceMenu.setLabel("Show Distances");\r
-    distanceMenu.addItemListener(new java.awt.event.ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent e)\r
-      {\r
-        distanceMenu_actionPerformed(null);\r
-      }\r
-    });\r
-    fitToWindow.setState(true);\r
-    fitToWindow.setLabel("Fit to window");\r
-    fitToWindow.addItemListener(new java.awt.event.ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent e)\r
-      {\r
-        fitToWindow_actionPerformed(null);\r
-      }\r
-    });\r
-    fileMenu.setLabel("File");\r
-    newickOutput.setLabel("Newick format");\r
-    newickOutput.addActionListener(new ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent actionEvent)\r
-      {\r
-        newickOutput_actionPerformed(actionEvent);\r
-      }\r
-    });\r
-    add(scrollPane, BorderLayout.CENTER);\r
-    jMenuBar1.add(fileMenu);\r
-    jMenuBar1.add(jMenu2);\r
-    jMenu2.add(fitToWindow);\r
-    jMenu2.add(fontSize);\r
-    jMenu2.add(distanceMenu);\r
-    jMenu2.add(bootstrapMenu);\r
-    fileMenu.add(newickOutput);\r
-  }\r
-\r
-\r
-  protected void printMenu_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void fontSize_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void distanceMenu_actionPerformed(ActionEvent e)\r
-  {\r
 \r
-  }\r
+    private void jbInit() throws Exception {\r
+        setLayout(borderLayout1);\r
+        this.setBackground(Color.white);\r
+        this.setFont(new java.awt.Font("Verdana", 0, 12));\r
+        jMenu2.setLabel("View");\r
+        fontSize.setLabel("Font Size - 12");\r
+        fontSize.addActionListener(new java.awt.event.ActionListener() {\r
+                public void actionPerformed(ActionEvent e) {\r
+                    fontSize_actionPerformed(e);\r
+                }\r
+            });\r
+        bootstrapMenu.setLabel("Show Bootstrap Values");\r
+        bootstrapMenu.addItemListener(new java.awt.event.ItemListener() {\r
+                public void itemStateChanged(ItemEvent e) {\r
+                    bootstrapMenu_actionPerformed(null);\r
+                }\r
+            });\r
+        distanceMenu.setLabel("Show Distances");\r
+        distanceMenu.addItemListener(new java.awt.event.ItemListener() {\r
+                public void itemStateChanged(ItemEvent e) {\r
+                    distanceMenu_actionPerformed(null);\r
+                }\r
+            });\r
+        placeholdersMenu.setLabel("Mark Unassociated Leaves");\r
+        placeholdersMenu.addItemListener(new java.awt.event.ItemListener() {\r
+                public void itemStateChanged(ItemEvent e) {\r
+                    placeholdersMenu_actionPerformed(null);\r
+                }\r
+            });\r
+        fitToWindow.setState(true);\r
+        fitToWindow.setLabel("Fit To Window");\r
+        fitToWindow.addItemListener(new java.awt.event.ItemListener() {\r
+                public void itemStateChanged(ItemEvent e) {\r
+                    fitToWindow_actionPerformed(null);\r
+                }\r
+            });\r
+        fileMenu.setLabel("File");\r
+        newickOutput.setLabel("Newick Format");\r
+        newickOutput.addActionListener(new ActionListener() {\r
+                public void actionPerformed(ActionEvent actionEvent) {\r
+                    newickOutput_actionPerformed(actionEvent);\r
+                }\r
+            });\r
+        add(scrollPane, BorderLayout.CENTER);\r
+        jMenuBar1.add(fileMenu);\r
+        jMenuBar1.add(jMenu2);\r
+        jMenu2.add(fitToWindow);\r
+        jMenu2.add(fontSize);\r
+        jMenu2.add(distanceMenu);\r
+        jMenu2.add(bootstrapMenu);\r
+        jMenu2.add(placeholdersMenu);\r
+        fileMenu.add(newickOutput);\r
+    }\r
 \r
-  protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
-  {\r
+    protected void printMenu_actionPerformed(ActionEvent e) {\r
+    }\r
 \r
-  }\r
+    protected void fontSize_actionPerformed(ActionEvent e) {\r
+    }\r
 \r
-  protected void fitToWindow_actionPerformed(ActionEvent e)\r
-  {\r
+    protected void distanceMenu_actionPerformed(ActionEvent e) {\r
+    }\r
 \r
-  }\r
+    protected void bootstrapMenu_actionPerformed(ActionEvent e) {\r
+    }\r
 \r
-  public void newickOutput_actionPerformed(ActionEvent actionEvent)\r
-  {\r
+    protected void placeholdersMenu_actionPerformed(ActionEvent e) {\r
+    }\r
 \r
-  }\r
+    protected void fitToWindow_actionPerformed(ActionEvent e) {\r
+    }\r
 \r
+    public void newickOutput_actionPerformed(ActionEvent actionEvent) {\r
+    }\r
 }\r