X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=58da0748dcf176ace9c2f484eb36084f6dd3cf55;hb=6312ff96a7669b59327d583d1dc64b0b96647d67;hp=89ff20fc2254536d5e1e4b2a22d6c0fe5cf0af12;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 89ff20f..58da074 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,13 +1,35 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
 package jalview.appletgui;
 
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.jbappletgui.GTreePanel;
-import java.awt.event.*;
 import java.util.*;
 
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbappletgui.*;
 
-public class TreePanel extends GTreePanel
+public class TreePanel
+    extends GTreePanel
 {
   SequenceI[] seq;
   String type;
@@ -23,7 +45,8 @@ public class TreePanel extends GTreePanel
     return tree;
   }
 
-  public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
+  public TreePanel(AlignViewport av, Vector seqVector, String type,
+                   String pwtype, int s, int e)
   {
     super();
 
@@ -34,12 +57,14 @@ public class TreePanel extends GTreePanel
     end = e;
 
     String longestName = "";
-    seq = new Sequence [seqVector.size()];
-    for (int i=0;i < seqVector.size();i++)
+    seq = new Sequence[seqVector.size()];
+    for (int i = 0; i < seqVector.size(); i++)
     {
       seq[i] = (Sequence) seqVector.elementAt(i);
-      if(seq[i].getName().length()>longestName.length())
+      if (seq[i].getName().length() > longestName.length())
+      {
         longestName = seq[i].getName();
+      }
     }
 
     tree = new NJTree(seq, type, pwtype, start, end);
@@ -52,10 +77,60 @@ public class TreePanel extends GTreePanel
 
   }
 
+  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
+                   String type, String pwtype)
+  {
+    super();
+    // These are probably only  arbitrary strings reflecting source of tree
+    this.type = type;
+    this.pwtype = pwtype;
+
+    start = 0;
+    end = seqVector.size();
 
-public String getText(String format) {
-  return null;
-}
+    String longestName = "";
+    seq = new Sequence[seqVector.size()];
+    for (int i = 0; i < seqVector.size(); i++)
+    {
+      seq[i] = (Sequence) seqVector.elementAt(i);
+    }
+    // This constructor matches sequence names to treenodes and sets up the tree layouts.
+    tree = new NJTree(seq, newtree);
+    // Now have to calculate longest name based on the leaves
+    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+
+    for (int i = 0; i < leaves.size(); i++)
+    {
+      if (longestName.length() <
+          ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).getName().
+          length())
+      {
+        longestName = TreeCanvas.PLACEHOLDER +
+            ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).
+            getName();
+      }
+    }
+
+    tree.reCount(tree.getTopNode());
+    tree.findHeight(tree.getTopNode());
+
+    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+    treeCanvas.setShowBootstrap(newtree.HasBootstrap());
+    treeCanvas.setShowDistances(newtree.HasDistances());
+    distanceMenu.setState(newtree.HasDistances());
+    bootstrapMenu.setState(newtree.HasBootstrap());
+    if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
+    {
+      placeholdersMenu.setState(treeCanvas.markPlaceholders);
+    }
+    scrollPane.add(treeCanvas);
+
+  }
+
+  public String getText(String format)
+  {
+    return null;
+  }
 
   protected void fitToWindow_actionPerformed(ActionEvent e)
   {
@@ -63,29 +138,39 @@ public String getText(String format) {
     repaint();
   }
 
+  public void newickOutput_actionPerformed(ActionEvent actionEvent)
+  {
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+    String output = fout.print(false, true);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    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)
   {
- /*   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);
-*/
+    /*   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);
+     */
   }
 
   protected void distanceMenu_actionPerformed(ActionEvent e)
@@ -98,4 +183,9 @@ public String getText(String format) {
     treeCanvas.setShowBootstrap(bootstrapMenu.getState());
   }
 
+  protected void placeholdersMenu_actionPerformed(ActionEvent e)
+  {
+    treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+  }
+
 }