RepresentGroup count items

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

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 90bd343..d908f20 100755 (executable)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -24,16 +24,23 @@ import java.awt.event.*;
 \r
 import jalview.datamodel.*;\r
 import jalview.io.*;\r
-import jalview.jbappletgui.*;\r
 \r
-public class CutAndPasteTransfer\r
-    extends GCutAndPasteTransfer\r
+public class CutAndPasteTransfer extends Panel implements ActionListener, MouseListener\r
 {\r
-  jalview.bin.JalviewLite applet;\r
-  public CutAndPasteTransfer(boolean forImport, jalview.bin.JalviewLite mainApplet)\r
+  boolean pdbImport = false;\r
+  boolean treeImport = false;\r
+  Sequence seq;\r
+  AlignFrame alignFrame;\r
+\r
+  public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)\r
   {\r
-    super();\r
-    applet = mainApplet;\r
+    try {\r
+        jbInit();\r
+    } catch (Exception e) {\r
+        e.printStackTrace();\r
+    }\r
+\r
+    this.alignFrame = alignFrame;\r
 \r
     if (!forImport)\r
     {\r
@@ -51,7 +58,22 @@ public class CutAndPasteTransfer
     textarea.setText(text);\r
   }\r
 \r
-  protected void ok_actionPerformed(ActionEvent e)\r
+  public void setPDBImport(Sequence seq)\r
+  {\r
+    this.seq = seq;\r
+    pdbImport = true;\r
+  }\r
+\r
+\r
+  public void actionPerformed(ActionEvent evt)\r
+  {\r
+    if(evt.getSource()==ok)\r
+      ok_actionPerformed();\r
+    else if(evt.getSource()==cancel)\r
+      cancel_actionPerformed();\r
+  }\r
+\r
+  protected void ok_actionPerformed()\r
   {\r
     String text = getText();\r
     int length = text.length();\r
@@ -68,31 +90,95 @@ public class CutAndPasteTransfer
           +warning);\r
 \r
       textarea.setCaretPosition(text.length());\r
-      return;\r
     }\r
 \r
-    SequenceI[] sequences = null;\r
+    if(pdbImport)\r
+    {\r
+      new MCview.AppletPDBViewer(text, AppletFormatAdapter.PASTE,\r
+                                 seq,\r
+                                 alignFrame.getSeqcanvas());\r
+    }\r
+    else if(treeImport)\r
+    {\r
+      try{\r
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea.getText(),\r
+            "Paste");\r
 \r
-    String format = IdentifyFile.Identify(text, "Paste");\r
-    sequences = new FormatAdapter().readFile(text, "Paste", format);\r
+        fin.parse();\r
+        if(fin.getTree()!=null)\r
+          alignFrame.loadTree(fin, "Pasted tree file");\r
 \r
-    if (sequences != null)\r
+      }\r
+      catch (Exception ex)\r
+      {\r
+        textarea.setText("Could not parse Newick file!\n" + ex);\r
+        return;\r
+      }\r
+    }\r
+    else if(alignFrame!=null)\r
     {\r
-      AlignFrame af = new AlignFrame(new Alignment(sequences), applet);\r
-      jalview.bin.JalviewLite.addFrame(af, "Cut & Paste input - " + format,\r
-                                       AlignFrame.NEW_WINDOW_WIDTH,\r
-                                       AlignFrame.NEW_WINDOW_HEIGHT);\r
-      af.statusBar.setText("Successfully pasted alignment file");\r
+      SequenceI[] sequences = null;\r
+\r
+      String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);\r
+      try{\r
+        sequences = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE, format);\r
+      }catch(java.io.IOException ex)\r
+      {\r
+        ex.printStackTrace();\r
+      }\r
+      if (sequences != null)\r
+      {\r
+        AlignFrame af = new AlignFrame(new Alignment(sequences), alignFrame.viewport.applet,\r
+                                       "Cut & Paste input - " + format,\r
+                                       false);\r
+        af.statusBar.setText("Successfully pasted alignment file");\r
+      }\r
     }\r
 \r
-    Frame frame = (Frame)this.getParent();\r
-    frame.setVisible(false);\r
+   if(this.getParent() instanceof Frame)\r
+    ((Frame)this.getParent()).setVisible(false);\r
+   else\r
+     ((Dialog)this.getParent()).setVisible(false);\r
   }\r
 \r
-  protected void cancel_actionPerformed(ActionEvent e)\r
+  protected void cancel_actionPerformed()\r
   {\r
-    Frame frame = (Frame)this.getParent();\r
-    frame.setVisible(false);\r
+    textarea.setText("");\r
+    if(this.getParent() instanceof Frame)\r
+     ((Frame)this.getParent()).setVisible(false);\r
+    else\r
+     ((Dialog)this.getParent()).setVisible(false);\r
   }\r
 \r
+  protected TextArea textarea = new TextArea();\r
+  Button ok = new Button();\r
+  Button cancel = new Button();\r
+  protected Panel buttonPanel = new Panel();\r
+  BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+\r
+  private void jbInit() throws Exception {\r
+      textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));\r
+      textarea.setText("Paste your alignment file here");\r
+      textarea.addMouseListener(this);\r
+      this.setLayout(borderLayout1);\r
+      ok.setLabel("OK");\r
+      ok.addActionListener(this);\r
+      cancel.setLabel("Cancel");\r
+      cancel.addActionListener(this);\r
+      this.add(buttonPanel, BorderLayout.SOUTH);\r
+      buttonPanel.add(ok, null);\r
+      buttonPanel.add(cancel, null);\r
+      this.add(textarea, java.awt.BorderLayout.CENTER);\r
+  }\r
+\r
+  public void mousePressed(MouseEvent evt) {\r
+      if (textarea.getText().startsWith("Paste your")) {\r
+          textarea.setText("");\r
+     }\r
+  }\r
+  public void mouseReleased(MouseEvent evt){}\r
+  public void mouseClicked(MouseEvent evt){}\r
+  public void mouseEntered(MouseEvent evt){}\r
+  public void mouseExited(MouseEvent evt){}\r
 }\r