X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=78d7ba7232d70289dc0ec7af6d6b64fd37d594e1;hb=83f6c6309e9705037a0853a26da74821c9d4fd12;hp=22cfd67d4e0f89fd8f1961b177b217ae04efa47b;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 22cfd67..78d7ba7 100755
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,43 +1,58 @@
 /*
-* 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
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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.jbappletgui.GCutAndPasteTransfer;
-import jalview.datamodel.*;
-import jalview.io.*;
 import java.awt.*;
 import java.awt.event.*;
 
-public class CutAndPasteTransfer extends GCutAndPasteTransfer
+import jalview.datamodel.*;
+import jalview.io.*;
+
+public class CutAndPasteTransfer
+    extends Panel implements ActionListener, MouseListener
 {
-  public CutAndPasteTransfer(boolean forImport)
+  boolean pdbImport = false;
+  boolean treeImport = false;
+  boolean annotationImport = false;
+  Sequence  seq;
+  AlignFrame alignFrame;
+
+  public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
   {
-    super();
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    this.alignFrame = alignFrame;
 
-    if(!forImport)
+    if (!forImport)
     {
       buttonPanel.setVisible(false);
     }
   }
 
-
   public String getText()
   {
     return textarea.getText();
@@ -48,34 +63,217 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     textarea.setText(text);
   }
 
+  public void setPDBImport(Sequence seq)
+  {
+    this.seq = seq;
+    accept.setLabel("Accept");
+    addSequences.setVisible(false);
+    pdbImport = true;
+  }
+
+  public void setTreeImport()
+  {
+    treeImport = true;
+    accept.setLabel("Accept");
+    addSequences.setVisible(false);
+  }
 
-  protected void ok_actionPerformed(ActionEvent e)
+  public void setAnnotationImport()
+  {
+    annotationImport = true;
+    accept.setLabel("Accept");
+    addSequences.setVisible(false);
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == accept)
+    {
+      ok(true);
+    }
+    else if (evt.getSource() == addSequences)
+    {
+      ok(false);
+    }
+    else if (evt.getSource() == cancel)
+    {
+      cancel();
+    }
+  }
+
+  protected void ok(boolean newWindow)
   {
     String text = getText();
-    SequenceI[] sequences = null;
+    int length = text.length();
+    textarea.append("\n");
+    if (textarea.getText().length() == length)
+    {
+      String warning =
+          "\n\n#################################################\n"
+          + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
+          + "\nCAN'T INPUT FULL ALIGNMENT"
+          + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
+          + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
+          + "\n#################################################\n";
+      textarea.setText(text.substring(0, text.length() - warning.length())
+                       + warning);
+
+      textarea.setCaretPosition(text.length());
+    }
+
+    if (pdbImport)
+    {
+      PDBEntry pdb = new PDBEntry();
+      pdb.setFile(text);
+
+      if ( alignFrame.alignPanel.av.applet.jmolAvailable )
+        new jalview.appletgui.AppletJmol(pdb,
+                                         new Sequence[]{seq},
+                                         null,
+                                         alignFrame.alignPanel,
+                                         AppletFormatAdapter.PASTE);
+      else
 
-    String format = IdentifyFile.Identify(text, "Paste");
-    sequences = FormatAdapter.readFile(text, "Paste", format);
+        new MCview.AppletPDBViewer(pdb,
+                                   new Sequence[]{seq},
+                                   null,
+                                   alignFrame.alignPanel,
+                                   AppletFormatAdapter.PASTE);
 
-    if (sequences != null)
+    }
+    else if (treeImport)
     {
-      AlignFrame af = new AlignFrame(new Alignment(sequences));
-      jalview.bin.JalviewLite.addFrame(af, "Cut & Paste input - " + format,
-                                       AlignFrame.NEW_WINDOW_WIDTH,
-                                       AlignFrame.NEW_WINDOW_HEIGHT);
-      af.statusBar.setText("Successfully pasted alignment file");
+      try
+      {
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea.getText(),
+            "Paste");
+
+        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 (annotationImport)
+    {
+      if (new AnnotationFile().readAnnotationFile(
+          alignFrame.viewport.alignment, textarea.getText(),
+          jalview.io.AppletFormatAdapter.PASTE))
+      {
+        alignFrame.alignPanel.fontChanged();
+        alignFrame.alignPanel.setScrollValues(0, 0);
+
+      }
+      else
+      {
+        alignFrame.parseFeaturesFile(textarea.getText(),
+                                     jalview.io.AppletFormatAdapter.PASTE);
+      }
+    }
+    else if (alignFrame != null)
+    {
+      Alignment al = null;
 
-    Frame frame = (Frame)this.getParent();
-    frame.setVisible(false);
-   }
+      String format = new IdentifyFile().Identify(text,
+                                                  AppletFormatAdapter.PASTE);
+      try
+      {
+        al = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE,
+                                                format);
+      }
+      catch (java.io.IOException ex)
+      {
+        ex.printStackTrace();
+      }
+
+      if (al != null)
+      {
+        if (newWindow)
+        {
+          AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
+                                         "Cut & Paste input - " + format,
+                                         false);
+          af.statusBar.setText("Successfully pasted alignment file");
+        }
+        else
+        {
+          alignFrame.addSequences(al.getSequencesArray());
+        }
+      }
+    }
+
+    if (this.getParent() instanceof Frame)
+    {
+      ( (Frame)this.getParent()).setVisible(false);
+    }
+    else
+    {
+      ( (Dialog)this.getParent()).setVisible(false);
+    }
+  }
 
-   protected void cancel_actionPerformed(ActionEvent e) {
-     Frame frame = (Frame)this.getParent();
-     frame.setVisible(false);
-   }
+  protected void cancel()
+  {
+    textarea.setText("");
+    if (this.getParent() instanceof Frame)
+    {
+      ( (Frame)this.getParent()).setVisible(false);
+    }
+    else
+    {
+      ( (Dialog)this.getParent()).setVisible(false);
+    }
+  }
+
+  protected TextArea textarea = new TextArea();
+  Button accept = new Button("New Window");
+  Button addSequences = new Button("Add to Current Alignment");
+  Button cancel = new Button("Close");
+
+  protected Panel buttonPanel = new Panel();
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  private void jbInit()
+      throws Exception
+  {
+    textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
+    textarea.setText("Paste your alignment file here");
+    textarea.addMouseListener(this);
+    this.setLayout(borderLayout1);
+    accept.addActionListener(this);
+    addSequences.addActionListener(this);
+    cancel.addActionListener(this);
+    this.add(buttonPanel, BorderLayout.SOUTH);
+    buttonPanel.add(accept, null);
+    buttonPanel.add(addSequences);
+    buttonPanel.add(cancel, null);
+    this.add(textarea, java.awt.BorderLayout.CENTER);
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    if (textarea.getText().startsWith("Paste your"))
+    {
+      textarea.setText("");
+    }
+  }
 
+  public void mouseReleased(MouseEvent evt)
+  {}
 
+  public void mouseClicked(MouseEvent evt)
+  {}
 
+  public void mouseEntered(MouseEvent evt)
+  {}
 
+  public void mouseExited(MouseEvent evt)
+  {}
 }