X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=103c96ba54cce439e0912ce20d2f0b3b86be0e6e;hb=174230b4233d9ce80f94527768d2cd2f76da11ab;hp=19ed987760d6fe3a1ed9008c8126190cdd7dac58;hpb=e33cdacd2ac2836504375c538574a0f1cafec7e3;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 19ed987..103c96b 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -116,9 +116,36 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 
   }
 
+  void showOriginalData()
+  {
+    // decide if av alignment is sufficiently different to original data to warrant a new window to be created
+    // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+    // or create a selection box around columns in alignment view
+    // test Alignment(SeqCigar[])
+    if(tree.seqData!=null)
+    {
+      Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
+          getGapCharacter());
+
+      if (alAndColsel != null && alAndColsel[0] != null)
+      {
+        Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
+        AlignFrame af = new AlignFrame(al,
+                                       av.applet,
+                                       "Original Data for Tree",
+                                       false);
+
+        af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);
+      }
+    }
+    else
+      System.out.println("Original Tree Data not available");
+  }
+
   class TreeLoader extends Thread
   {
     NewickFile newtree;
+    jalview.datamodel.AlignmentView odata=null;
 
     public TreeLoader(NewickFile newtree)
     {
@@ -127,19 +154,20 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 
     public void run()
     {
-      if (newtree != null)
-        tree = new NJTree(av.alignment.getSequencesArray(),
-                          newtree);
-      else
+      if(newtree!=null)
+      {
+        if (odata == null)
+          tree = new NJTree(av.alignment.getSequencesArray(),
+                            newtree);
+        else
+          tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+
+        }
+        else
         {
           int start, end;
           SequenceI [] seqs;
-          CigarArray seqStrings = null;
-       //   if (av.hasHiddenColumns)
-          {
-        //    seqStrings = av.getSelectionAsString();
-          }
-
+          AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
           if(av.getSelectionGroup()==null)
           {
             start = 0;
@@ -181,6 +209,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       newickOutput_actionPerformed();
     else if(evt.getSource()==fontSize)
       fontSize_actionPerformed();
+    else if(evt.getSource()==inputData)
+      showOriginalData();
   }
 
   public void itemStateChanged(ItemEvent evt)
@@ -245,6 +275,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
   protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
   Menu fileMenu = new Menu();
   MenuItem newickOutput = new MenuItem();
+  MenuItem inputData = new MenuItem();
 
   private void jbInit() throws Exception {
       setLayout(borderLayout1);
@@ -265,6 +296,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       fileMenu.setLabel("File");
       newickOutput.setLabel("Newick Format");
       newickOutput.addActionListener(this);
+    inputData.setLabel("Input Data...");
 
     add(scrollPane, BorderLayout.CENTER);
       jMenuBar1.add(fileMenu);
@@ -275,6 +307,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       jMenu2.add(bootstrapMenu);
       jMenu2.add(placeholdersMenu);
     fileMenu.add(newickOutput);
+    fileMenu.add(inputData);
+    inputData.addActionListener(this);
   }
 
 }