X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=ddfcbe33e032665f2ba68402d92d4dfa9fd5713b;hb=54b44faea7413a39963c535fa728b6e415dfe989;hp=51ec4a0a0e27fa9e256225acf0c79e659009f88b;hpb=8a5c39442bced20fc95272efe6d3176719ca3f15;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 51ec4a0..ddfcbe3 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -22,23 +22,22 @@ package jalview.appletgui;
 import java.util.*;
 
 import java.awt.event.*;
+import java.awt.*;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.io.*;
-import jalview.jbappletgui.*;
 
-public class TreePanel
-    extends GTreePanel
+public class TreePanel extends Frame implements ActionListener, ItemListener
 {
   SequenceI[] seq;
   String type;
   String pwtype;
-  AlignmentPanel ap;
   int start;
   int end;
   TreeCanvas treeCanvas;
   NJTree tree;
+  AlignViewport av;
 
   public NJTree getTree()
   {
@@ -55,14 +54,19 @@ public class TreePanel
    * @param s DOCUMENT ME!
    * @param e DOCUMENT ME!
    */
-  public TreePanel(AlignViewport av, Vector seqVector, String type,
-                   String pwtype, int s, int e)
+  public TreePanel(AlignViewport av, String type, String pwtype)
   {
-    super();
-    initTreePanel(av, seqVector, type, pwtype, s, e, null);
+    try
+    {
+      jbInit();
+      this.setMenuBar(jMenuBar1);
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
 
-    // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
-    treeCanvas.setShowDistances(true);
+    initTreePanel(av, type, pwtype, null);
   }
 
   /**
@@ -74,32 +78,39 @@ public class TreePanel
    * @param type DOCUMENT ME!
    * @param pwtype DOCUMENT ME!
    */
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-                   String type, String pwtype)
+  public TreePanel(AlignViewport av,
+                   String type,
+                   String pwtype,
+                   NewickFile newtree)
   {
-    super();
-    initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
+    try
+    {
+      jbInit();
+      this.setMenuBar(jMenuBar1);
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    initTreePanel(av, type, pwtype, newtree);
   }
 
 
-  void initTreePanel(AlignViewport av, Vector seqVector, String type,
-                     String pwtype, int s, int e, NewickFile newTree)
+  void initTreePanel(AlignViewport av,
+                     String type,
+                     String pwtype,
+                     NewickFile newTree)
   {
 
+    this.av = av;
     this.type = type;
     this.pwtype = pwtype;
 
-    start = s;
-    end = e;
-
-    seq = new Sequence[seqVector.size()];
-    for(int i=0; i<seqVector.size(); i++)
-      seq[i] = (SequenceI)seqVector.elementAt(i);
-
-
     treeCanvas = new TreeCanvas(av, scrollPane);
     scrollPane.add(treeCanvas);
 
+
     TreeLoader tl = new TreeLoader(newTree);
     tl.start();
 
@@ -116,17 +127,42 @@ public class TreePanel
 
     public void run()
     {
-      NJTree tree;
-      if(newtree!=null)
-        tree = new NJTree(seq, newtree);
+      if (newtree != null)
+        tree = new NJTree(av.alignment.getSequencesArray(),
+                          newtree);
       else
-        tree = new NJTree(seq, type, pwtype, start, end);
+        {
+          int start, end;
+          SequenceI [] seqs;
+          CigarArray seqStrings = null;
+        //  if (av.hasHiddenColumns)
+          {
+        //    seqStrings = av.getSelectionAsString();
+          }
+
+          if(av.getSelectionGroup()==null)
+          {
+            start = 0;
+            end = av.alignment.getWidth();
+            seqs = av.alignment.getSequencesArray();
+          }
+          else
+          {
+            start = av.getSelectionGroup().getStartRes();
+            end = av.getSelectionGroup().getEndRes()+1;
+            seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+          }
+
+          tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+        }
 
       tree.reCount(tree.getTopNode());
       tree.findHeight(tree.getTopNode());
       treeCanvas.setTree(tree);
       if(newtree!=null)
       {
+        distanceMenu.setState(newtree.HasDistances());
+        bootstrapMenu.setState(newtree.HasBootstrap());
         treeCanvas.setShowBootstrap(newtree.HasBootstrap());
         treeCanvas.setShowDistances(newtree.HasDistances());
       }
@@ -134,68 +170,111 @@ public class TreePanel
 
       treeCanvas.repaint();
 
+      av.setCurrentTree(tree);
+
     }
   }
 
-  public String getText(String format)
+  public void actionPerformed(ActionEvent evt)
   {
-    return null;
+    if(evt.getSource()==newickOutput)
+      newickOutput_actionPerformed();
+    else if(evt.getSource()==fontSize)
+      fontSize_actionPerformed();
   }
 
-  protected void fitToWindow_actionPerformed(ActionEvent e)
+  public void itemStateChanged(ItemEvent evt)
   {
-    treeCanvas.fitToWindow = fitToWindow.getState();
-    repaint();
+    if(evt.getSource()==fitToWindow)
+      treeCanvas.fitToWindow = fitToWindow.getState();
+
+    else if(evt.getSource()==distanceMenu)
+      treeCanvas.setShowDistances(distanceMenu.getState());
+
+    else if(evt.getSource()==bootstrapMenu)
+      treeCanvas.setShowBootstrap(bootstrapMenu.getState());
+
+    else if(evt.getSource()==placeholdersMenu)
+      treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+
+    treeCanvas.repaint();
   }
 
-  public void newickOutput_actionPerformed(ActionEvent actionEvent)
+
+  public void newickOutput_actionPerformed()
   {
     jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
     String output = fout.print(false, true);
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
     cap.setText(output);
     java.awt.Frame frame = new java.awt.Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
   }
 
-  protected void fontSize_actionPerformed(ActionEvent e)
+  public java.awt.Font getTreeFont()
   {
-    /*   if( treeCanvas==null )
-        return;
-
-      String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
-
-      Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
-                                  "Select font size",
-                                  "Font size",
-                                  JOptionPane.QUESTION_MESSAGE,
-     null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
-                                  ,"Font Size - "+size);
-      if(selection!=null)
-      {
-        fontSize.setText("Font Size - " + selection);
-
-        int i = Integer.parseInt(selection.toString());
-        treeCanvas.setFontSize(i);
-      }
-       scrollPane.setViewportView(treeCanvas);
-     */
+    return treeCanvas.font;
   }
 
-  protected void distanceMenu_actionPerformed(ActionEvent e)
+  public void setTreeFont(java.awt.Font font)
   {
-    treeCanvas.setShowDistances(distanceMenu.getState());
+    treeCanvas.font = font;
+    treeCanvas.repaint();
   }
 
-  protected void bootstrapMenu_actionPerformed(ActionEvent e)
+  protected void fontSize_actionPerformed()
   {
-    treeCanvas.setShowBootstrap(bootstrapMenu.getState());
+     if( treeCanvas==null )
+        return;
+
+    new FontChooser(this);
   }
 
-  protected void placeholdersMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+
+
+
+  BorderLayout borderLayout1 = new BorderLayout();
+  protected ScrollPane scrollPane = new ScrollPane();
+  MenuBar jMenuBar1 = new MenuBar();
+  Menu jMenu2 = new Menu();
+  protected MenuItem fontSize = new MenuItem();
+  protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
+  protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
+  protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
+  protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
+  Menu fileMenu = new Menu();
+  MenuItem newickOutput = new MenuItem();
+
+  private void jbInit() throws Exception {
+      setLayout(borderLayout1);
+      this.setBackground(Color.white);
+      this.setFont(new java.awt.Font("Verdana", 0, 12));
+      jMenu2.setLabel("View");
+      fontSize.setLabel("Font...");
+      fontSize.addActionListener(this);
+      bootstrapMenu.setLabel("Show Bootstrap Values");
+      bootstrapMenu.addItemListener(this);
+      distanceMenu.setLabel("Show Distances");
+      distanceMenu.addItemListener(this);
+      placeholdersMenu.setLabel("Mark Unassociated Leaves");
+      placeholdersMenu.addItemListener(this);
+      fitToWindow.setState(true);
+      fitToWindow.setLabel("Fit To Window");
+      fitToWindow.addItemListener(this);
+      fileMenu.setLabel("File");
+      newickOutput.setLabel("Newick Format");
+      newickOutput.addActionListener(this);
+
+    add(scrollPane, BorderLayout.CENTER);
+      jMenuBar1.add(fileMenu);
+      jMenuBar1.add(jMenu2);
+      jMenu2.add(fitToWindow);
+      jMenu2.add(fontSize);
+      jMenu2.add(distanceMenu);
+      jMenu2.add(bootstrapMenu);
+      jMenu2.add(placeholdersMenu);
+    fileMenu.add(newickOutput);
   }
 
 }