-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
package jalview.gui;
-import jalview.jbgui.GCutAndPasteTransfer;
import java.awt.*;
-import java.awt.event.ActionEvent;
import java.awt.datatransfer.*;
-import jalview.datamodel.Alignment;
-import jalview.io.FormatAdapter;
-import jalview.datamodel.SequenceI;
-import javax.swing.JOptionPane;
-import jalview.io.IdentifyFile;
+import java.awt.event.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
public class CutAndPasteTransfer extends GCutAndPasteTransfer
{
- public void setForInput()
+
+ AlignViewport viewport;
+
+ public CutAndPasteTransfer()
{
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ textarea.requestFocus();
+ }
+ });
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setForInput(AlignViewport viewport)
+ {
+ this.viewport = viewport;
+ if (viewport != null)
+ {
+ ok.setText("Add");
+ }
+
getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
public String getText()
{
return textarea.getText();
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param text
+ * DOCUMENT ME!
+ */
public void setText(String text)
{
textarea.setText(text);
}
+ public void appendText(String text)
+ {
+ textarea.append(text);
+ }
+
+ public void save_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setAcceptAllFileFilterUsed(false);
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save Text to File");
+ chooser.setToolTipText("Save");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ try
+ {
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(chooser.getSelectedFile()));
+
+ out.print(getText());
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
public void copyItem_actionPerformed(ActionEvent e)
{
+ textarea.getSelectedText();
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- c.setContents( new StringSelection( textarea.getText()) , null ) ;
+ c.setContents(new StringSelection(textarea.getSelectedText()), null);
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
public void pasteMenu_actionPerformed(ActionEvent e)
{
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
Transferable contents = c.getContents(this);
+
if (contents == null)
+ {
return;
- try{
- textarea.setText( (String) contents.getTransferData(DataFlavor.
- stringFlavor));
- }catch(Exception ex){}
+ }
+
+ try
+ {
+ textarea.append((String) contents
+ .getTransferData(DataFlavor.stringFlavor));
+ } catch (Exception ex)
+ {
+ }
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
public void ok_actionPerformed(ActionEvent e)
{
- String format = IdentifyFile.Identify(getText(), "Paste");
- SequenceI [] sequences = null;
+ String format = new IdentifyFile().Identify(getText(), "Paste");
+ // TODO: identify feature, annotation or tree file and parse appropriately.
+ Alignment al = null;
- if (FormatAdapter.formats.contains( format ))
- sequences = FormatAdapter.readFile(getText(), "Paste", format);
+ if (FormatAdapter.isValidFormat(format))
+ {
+ try
+ {
+ al = new FormatAdapter().readFile(getText(), "Paste", format);
+ } catch (java.io.IOException ex)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Couldn't read the pasted text.\n" + ex.toString(),
+ "Error parsing text", JOptionPane.WARNING_MESSAGE);
+ }
+ }
-
- if(sequences!=null)
+ if (al != null)
+ {
+ if (viewport != null)
+ {
+ for (int i = 0; i < al.getHeight(); i++)
{
- AlignFrame af = new AlignFrame(new Alignment(sequences));
- af.currentFileFormat = format;
- Desktop.addInternalFrame(af, "Cut & Paste input - "+format,
- AlignFrame.NEW_WINDOW_WIDTH,
- AlignFrame.NEW_WINDOW_HEIGHT);
- af.statusBar.setText("Successfully pasted alignment file");
+ viewport.getAlignment().addSequence(al.getSequenceAt(i));
}
- else
- JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"
- +"Formats currently supported are\n"
- +"Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",
- "Error parsing text", JOptionPane.WARNING_MESSAGE);
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
+ }
+ else
+ {
+ AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ af.currentFileFormat = format;
+ Desktop.addInternalFrame(af, "Cut & Paste input - " + format,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ af.statusBar.setText("Successfully pasted alignment file");
+
+ try
+ {
+ af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+ false));
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
public void cancel_actionPerformed(ActionEvent e)
{
- try{
+ try
+ {
this.setClosed(true);
- }catch(Exception ex){}
+ } catch (Exception ex)
+ {
+ }
}
+ public void textarea_mousePressed(MouseEvent e)
+ {
+ if (SwingUtilities.isRightMouseButton(e))
+ {
+ JPopupMenu popup = new JPopupMenu("Edit");
+ JMenuItem item = new JMenuItem("Copy");
+ item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ copyItem_actionPerformed(e);
+ }
+ });
+ popup.add(item);
+ item = new JMenuItem("Paste");
+ item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pasteMenu_actionPerformed(e);
+ }
+ });
+ popup.add(item);
+ popup.show(this, e.getX() + 10, e.getY() + textarea.getY() + 40);
+
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff