X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=d908f20ac83f5a15b1da961aa7ded68468b78d47;hb=e6879a932d0144d64a5ab703ae311aed0eeb83e5;hp=4fb8ec1dcc1ef3f1d3f2e7e2dcce058dd009c0ab;hpb=de468b0bf50850a89c6a8a7acfa4ff5b689ffed1;p=jalview.git

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 4fb8ec1..d908f20 100755
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.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
@@ -27,13 +27,12 @@ import jalview.io.*;
 
 public class CutAndPasteTransfer extends Panel implements ActionListener, MouseListener
 {
-  jalview.bin.JalviewLite applet;
-
   boolean pdbImport = false;
+  boolean treeImport = false;
   Sequence seq;
-  SeqCanvas seqcanvas;
+  AlignFrame alignFrame;
 
-  public CutAndPasteTransfer(boolean forImport, jalview.bin.JalviewLite mainApplet)
+  public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
   {
     try {
         jbInit();
@@ -41,7 +40,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
         e.printStackTrace();
     }
 
-    applet = mainApplet;
+    this.alignFrame = alignFrame;
 
     if (!forImport)
     {
@@ -49,14 +48,6 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
     }
   }
 
-  public void setPDBImport(Sequence seq, SeqCanvas seqcanvas)
-  {
-    this.seq = seq;
-    this.seqcanvas = seqcanvas;
-    pdbImport = true;
-  }
-
-
   public String getText()
   {
     return textarea.getText();
@@ -67,6 +58,13 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
     textarea.setText(text);
   }
 
+  public void setPDBImport(Sequence seq)
+  {
+    this.seq = seq;
+    pdbImport = true;
+  }
+
+
   public void actionPerformed(ActionEvent evt)
   {
     if(evt.getSource()==ok)
@@ -96,29 +94,60 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
 
     if(pdbImport)
     {
-      new MCview.AppletPDBViewer(text, "Paste", seq, seqcanvas);
+      new MCview.AppletPDBViewer(text, AppletFormatAdapter.PASTE,
+                                 seq,
+                                 alignFrame.getSeqcanvas());
     }
-    else
+    else if(treeImport)
     {
-      SequenceI[] sequences = null;
+      try{
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea.getText(),
+            "Paste");
 
-      String format = IdentifyFile.Identify(text, "Paste");
-      sequences = new AppletFormatAdapter().readFile(text, "Paste", format);
+        fin.parse();
+        if(fin.getTree()!=null)
+          alignFrame.loadTree(fin, "Pasted tree file");
 
+      }
+      catch (Exception ex)
+      {
+        textarea.setText("Could not parse Newick file!\n" + ex);
+        return;
+      }
+    }
+    else if(alignFrame!=null)
+    {
+      SequenceI[] sequences = null;
+
+      String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
+      try{
+        sequences = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE, format);
+      }catch(java.io.IOException ex)
+      {
+        ex.printStackTrace();
+      }
       if (sequences != null)
       {
-        AlignFrame af = new AlignFrame(new Alignment(sequences), applet,
-                                       "Cut & Paste input - " + format);
+        AlignFrame af = new AlignFrame(new Alignment(sequences), alignFrame.viewport.applet,
+                                       "Cut & Paste input - " + format,
+                                       false);
         af.statusBar.setText("Successfully pasted alignment file");
       }
     }
 
+   if(this.getParent() instanceof Frame)
     ((Frame)this.getParent()).setVisible(false);
+   else
+     ((Dialog)this.getParent()).setVisible(false);
   }
 
   protected void cancel_actionPerformed()
   {
-    ((Frame)this.getParent()).setVisible(false);
+    textarea.setText("");
+    if(this.getParent() instanceof Frame)
+     ((Frame)this.getParent()).setVisible(false);
+    else
+     ((Dialog)this.getParent()).setVisible(false);
   }
 
   protected TextArea textarea = new TextArea();