after merge

[jalview.git] / src / jalview / appletgui / TreePanel.java

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 3e26a4b..99ad412 100755 (executable)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -22,19 +22,17 @@ package jalview.appletgui;
 import java.util.*;\r
 \r
 import java.awt.event.*;\r
+import java.awt.*;\r
 \r
 import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
 import jalview.io.*;\r
-import jalview.jbappletgui.*;\r
 \r
-public class TreePanel\r
-    extends GTreePanel\r
+public class TreePanel extends Frame\r
 {\r
   SequenceI[] seq;\r
   String type;\r
   String pwtype;\r
-  AlignmentPanel ap;\r
   int start;\r
   int end;\r
   TreeCanvas treeCanvas;\r
@@ -58,7 +56,16 @@ public class TreePanel
   public TreePanel(AlignViewport av, Vector seqVector, String type,\r
                    String pwtype, int s, int e)\r
   {\r
-    super();\r
+    try\r
+    {\r
+      jbInit();\r
+      this.setMenuBar(jMenuBar1);\r
+    }\r
+    catch (Exception ex)\r
+    {\r
+      ex.printStackTrace();\r
+    }\r
+\r
     initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
   }\r
 \r
@@ -74,7 +81,16 @@ public class TreePanel
   public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
                    String type, String pwtype)\r
   {\r
-    super();\r
+    try\r
+    {\r
+      jbInit();\r
+      this.setMenuBar(jMenuBar1);\r
+    }\r
+    catch (Exception e)\r
+    {\r
+      e.printStackTrace();\r
+    }\r
+\r
     initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
   }\r
 \r
@@ -151,7 +167,7 @@ public class TreePanel
   {\r
     jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
     String output = fout.print(false, true);\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);\r
     cap.setText(output);\r
     java.awt.Frame frame = new java.awt.Frame();\r
     frame.add(cap);\r
@@ -192,4 +208,71 @@ public class TreePanel
     treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
   }\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 placeholdersMenu = new CheckboxMenuItem();\r
+  protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();\r
+  Menu fileMenu = new Menu();\r
+  MenuItem newickOutput = new MenuItem();\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...");\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
+\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
 }\r