2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.api.ComplexAlignFile;
26 import jalview.api.FeaturesDisplayedI;
27 import jalview.bin.Jalview;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.ColumnSelection;
30 import jalview.datamodel.SequenceI;
31 import jalview.io.FileParse;
32 import jalview.io.FormatAdapter;
33 import jalview.io.IdentifyFile;
34 import jalview.io.JalviewFileChooser;
35 import jalview.io.JalviewFileView;
36 import jalview.jbgui.GCutAndPasteTransfer;
37 import jalview.schemes.ColourSchemeI;
38 import jalview.util.MessageManager;
40 import java.awt.Toolkit;
41 import java.awt.datatransfer.Clipboard;
42 import java.awt.datatransfer.DataFlavor;
43 import java.awt.datatransfer.StringSelection;
44 import java.awt.datatransfer.Transferable;
45 import java.awt.event.ActionEvent;
46 import java.awt.event.ActionListener;
47 import java.awt.event.MouseEvent;
49 import javax.swing.JMenuItem;
50 import javax.swing.JOptionPane;
51 import javax.swing.JPopupMenu;
52 import javax.swing.SwingUtilities;
55 * Cut'n'paste files into the desktop See JAL-1105
60 public class CutAndPasteTransfer extends GCutAndPasteTransfer
63 AlignmentViewPanel alignpanel;
65 AlignViewportI viewport;
67 FileParse source = null;
68 public CutAndPasteTransfer()
70 SwingUtilities.invokeLater(new Runnable()
74 textarea.requestFocus();
83 public void setForInput(AlignmentViewPanel viewpanel)
85 this.alignpanel = viewpanel;
86 if (alignpanel != null)
88 this.viewport = alignpanel.getAlignViewport();
92 ok.setText(MessageManager.getString("action.add"));
95 getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
101 * @return DOCUMENT ME!
103 public String getText()
105 return textarea.getText();
114 public void setText(String text)
116 textarea.setText(text);
119 public void appendText(String text)
121 textarea.append(text);
124 public void save_actionPerformed(ActionEvent e)
126 JalviewFileChooser chooser = new JalviewFileChooser(
127 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
129 chooser.setAcceptAllFileFilterUsed(false);
130 chooser.setFileView(new JalviewFileView());
131 chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file"));
132 chooser.setToolTipText(MessageManager.getString("action.save"));
134 int value = chooser.showSaveDialog(this);
136 if (value == JalviewFileChooser.APPROVE_OPTION)
140 java.io.PrintWriter out = new java.io.PrintWriter(
141 new java.io.FileWriter(chooser.getSelectedFile()));
143 out.print(getText());
145 } catch (Exception ex)
147 ex.printStackTrace();
159 public void copyItem_actionPerformed(ActionEvent e)
161 textarea.getSelectedText();
162 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
163 c.setContents(new StringSelection(textarea.getSelectedText()), null);
172 public void pasteMenu_actionPerformed(ActionEvent e)
174 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
175 Transferable contents = c.getContents(this);
177 if (contents == null)
184 textarea.append((String) contents
185 .getTransferData(DataFlavor.stringFlavor));
186 } catch (Exception ex)
197 public void ok_actionPerformed(ActionEvent e)
199 String text = getText();
200 if (text.trim().length() < 1)
205 String format = new IdentifyFile().Identify(text, "Paste");
206 if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
208 System.err.println(MessageManager
209 .getString("label.null_or_unidentifiable_data"));
210 if (!Jalview.isHeadlessMode())
212 JOptionPane.showMessageDialog(null,
214 .getString("label.null_or_unidentifiable_data"),
215 MessageManager.getString("label.unidentifiable_data"),
216 JOptionPane.ERROR_MESSAGE);
221 // TODO: identify feature, annotation or tree file and parse appropriately.
222 AlignmentI al = null;
224 if (FormatAdapter.isValidFormat(format))
228 FormatAdapter fa = new FormatAdapter(alignpanel);
229 al = fa.readFile(getText(), "Paste", format);
230 source = fa.getAlignFile();
232 } catch (java.io.IOException ex)
234 JOptionPane.showInternalMessageDialog(Desktop.desktop,
235 MessageManager.formatMessage(
236 "label.couldnt_read_pasted_text", new String[]
237 { ex.toString() }), MessageManager
238 .getString("label.error_parsing_text"),
239 JOptionPane.WARNING_MESSAGE);
243 if (al != null && al.hasValidSequence())
245 String title = MessageManager.formatMessage(
246 "label.input_cut_paste_params", new String[]
248 if (viewport != null)
250 ((AlignViewport) viewport).addAlignment(al, title);
256 if (source instanceof ComplexAlignFile)
258 ColumnSelection colSel = ((ComplexAlignFile) source)
259 .getColumnSelection();
260 SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
261 .getHiddenSequences();
262 boolean showSeqFeatures = ((ComplexAlignFile) source)
263 .isShowSeqFeatures();
264 ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
265 FeaturesDisplayedI fd = ((ComplexAlignFile) source)
266 .getDisplayedFeatures();
267 af = new AlignFrame(al, hiddenSeqs, colSel,
268 AlignFrame.DEFAULT_WIDTH,
269 AlignFrame.DEFAULT_HEIGHT);
270 af.getViewport().setShowSequenceFeatures(showSeqFeatures);
271 af.getViewport().setFeaturesDisplayed(fd);
276 af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
277 AlignFrame.DEFAULT_HEIGHT);
280 af.currentFileFormat = format;
281 Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
282 AlignFrame.DEFAULT_HEIGHT);
283 af.statusBar.setText(MessageManager
284 .getString("label.successfully_pasted_alignment_file"));
288 af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
290 } catch (Exception ex)
297 System.err.println(MessageManager
298 .getString("label.null_or_invalid_alignment"));
299 if (!Jalview.isHeadlessMode())
305 .getString("label.null_or_invalid_alignment"),
307 .getString("label.unable_to_create_alignment"),
308 JOptionPane.ERROR_MESSAGE);
320 public void cancel_actionPerformed(ActionEvent e)
324 this.setClosed(true);
325 } catch (Exception ex)
330 public void textarea_mousePressed(MouseEvent e)
332 if (SwingUtilities.isRightMouseButton(e))
334 JPopupMenu popup = new JPopupMenu(
335 MessageManager.getString("action.edit"));
336 JMenuItem item = new JMenuItem(
337 MessageManager.getString("action.copy"));
338 item.addActionListener(new ActionListener()
340 public void actionPerformed(ActionEvent e)
342 copyItem_actionPerformed(e);
346 item = new JMenuItem(MessageManager.getString("action.paste"));
347 item.addActionListener(new ActionListener()
349 public void actionPerformed(ActionEvent e)
351 pasteMenu_actionPerformed(e);
355 popup.show(this, e.getX() + 10, e.getY() + textarea.getY() + 40);