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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.gui

File CutAndPasteTransfer.java

 

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../../img/srcFileCovDistChart0.png
56% of files have more coverage

Code metrics

32
96
14
1
407
294
38
0.4
6.86
14
2.71

Classes

Class Line # Actions
CutAndPasteTransfer 69 96 38 142
0.00%
 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.gui;
22   
23    import jalview.api.AlignViewportI;
24    import jalview.api.AlignmentViewPanel;
25    import jalview.api.ComplexAlignFile;
26    import jalview.api.FeatureSettingsModelI;
27    import jalview.api.FeaturesDisplayedI;
28    import jalview.api.FeaturesSourceI;
29    import jalview.bin.Jalview;
30    import jalview.datamodel.AlignmentI;
31    import jalview.datamodel.HiddenColumns;
32    import jalview.datamodel.SequenceI;
33    import jalview.io.AlignmentFileReaderI;
34    import jalview.io.AppletFormatAdapter;
35    import jalview.io.DataSourceType;
36    import jalview.io.FileFormatException;
37    import jalview.io.FileFormatI;
38    import jalview.io.FormatAdapter;
39    import jalview.io.IdentifyFile;
40    import jalview.io.JalviewFileChooser;
41    import jalview.io.JalviewFileView;
42    import jalview.jbgui.GCutAndPasteTransfer;
43    import jalview.json.binding.biojson.v1.ColourSchemeMapper;
44    import jalview.schemes.ColourSchemeI;
45    import jalview.util.MessageManager;
46   
47    import java.awt.Toolkit;
48    import java.awt.datatransfer.Clipboard;
49    import java.awt.datatransfer.DataFlavor;
50    import java.awt.datatransfer.StringSelection;
51    import java.awt.datatransfer.Transferable;
52    import java.awt.event.ActionEvent;
53    import java.awt.event.ActionListener;
54    import java.awt.event.MouseEvent;
55    import java.io.FileWriter;
56    import java.io.IOException;
57    import java.io.PrintWriter;
58   
59    import javax.swing.JMenuItem;
60    import javax.swing.JPopupMenu;
61    import javax.swing.SwingUtilities;
62   
63    /**
64    * Cut'n'paste files into the desktop See JAL-1105
65    *
66    * @author $author$
67    * @version $Revision$
68    */
 
69    public class CutAndPasteTransfer extends GCutAndPasteTransfer
70    {
71   
72    AlignmentViewPanel alignpanel;
73   
74    AlignViewportI viewport;
75   
76    AlignmentFileReaderI source = null;
77   
 
78  0 toggle public CutAndPasteTransfer()
79    {
80  0 SwingUtilities.invokeLater(new Runnable()
81    {
 
82  0 toggle @Override
83    public void run()
84    {
85  0 textarea.requestFocus();
86    }
87    });
88   
89    }
90   
91    /**
92    * DOCUMENT ME!
93    */
 
94  0 toggle public void setForInput(AlignmentViewPanel viewpanel)
95    {
96  0 this.alignpanel = viewpanel;
97  0 if (alignpanel != null)
98    {
99  0 this.viewport = alignpanel.getAlignViewport();
100    }
101  0 if (viewport != null)
102    {
103  0 ok.setText(MessageManager.getString("action.add"));
104    }
105   
106  0 getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
107    }
108   
109    /**
110    * DOCUMENT ME!
111    *
112    * @return DOCUMENT ME!
113    */
 
114  0 toggle public String getText()
115    {
116  0 return textarea.getText();
117    }
118   
119    /**
120    * DOCUMENT ME!
121    *
122    * @param text
123    * DOCUMENT ME!
124    */
 
125  0 toggle public void setText(String text)
126    {
127  0 textarea.setText(text);
128    }
129   
 
130  0 toggle public void appendText(String text)
131    {
132  0 textarea.append(text);
133    }
134   
 
135  0 toggle @Override
136    public void save_actionPerformed(ActionEvent e)
137    {
138    // TODO: JAL-3048 JalviewFileChooser - Save option
139   
140  0 JalviewFileChooser chooser = new JalviewFileChooser(
141    jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
142   
143  0 chooser.setAcceptAllFileFilterUsed(false);
144  0 chooser.setFileView(new JalviewFileView());
145  0 chooser.setDialogTitle(
146    MessageManager.getString("label.save_text_to_file"));
147  0 chooser.setToolTipText(MessageManager.getString("action.save"));
148   
149  0 int value = chooser.showSaveDialog(this);
150   
151  0 if (value == JalviewFileChooser.APPROVE_OPTION)
152    {
153  0 try
154    {
155  0 PrintWriter out = new PrintWriter(
156    new FileWriter(chooser.getSelectedFile()));
157   
158  0 out.print(getText());
159  0 out.close();
160    } catch (Exception ex)
161    {
162  0 ex.printStackTrace();
163    }
164   
165    }
166    }
167   
168    /**
169    * DOCUMENT ME!
170    *
171    * @param e
172    * DOCUMENT ME!
173    */
 
174  0 toggle @Override
175    public void copyItem_actionPerformed(ActionEvent e)
176    {
177  0 textarea.getSelectedText();
178  0 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
179  0 c.setContents(new StringSelection(textarea.getSelectedText()), null);
180    }
181   
182    /**
183    * DOCUMENT ME!
184    *
185    * @param e
186    * DOCUMENT ME!
187    */
 
188  0 toggle @Override
189    public void pasteMenu_actionPerformed(ActionEvent e)
190    {
191  0 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
192  0 Transferable contents = c.getContents(this);
193   
194  0 if (contents == null)
195    {
196  0 return;
197    }
198   
199  0 try
200    {
201  0 textarea.append(
202    (String) contents.getTransferData(DataFlavor.stringFlavor));
203    } catch (Exception ex)
204    {
205    }
206    }
207   
208    /**
209    * DOCUMENT ME!
210    *
211    * @param e
212    * DOCUMENT ME!
213    */
 
214  0 toggle @Override
215    public void ok_actionPerformed(ActionEvent e)
216    {
217  0 String text = getText();
218  0 if (text.trim().length() < 1)
219    {
220  0 return;
221    }
222   
223  0 FileFormatI format = null;
224  0 try
225    {
226  0 format = new IdentifyFile().identify(text, DataSourceType.PASTE);
227    } catch (FileFormatException e1)
228    {
229    // leave as null
230    }
231  0 if (format == null)
232    {
233  0 System.err
234    .println(MessageManager.getString("label.couldnt_read_data"));
235  0 if (!Jalview.isHeadlessMode())
236    {
237  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
238    AppletFormatAdapter.getSupportedFormats(),
239    MessageManager.getString("label.couldnt_read_data"),
240    JvOptionPane.WARNING_MESSAGE);
241    }
242  0 return;
243    }
244   
245    // TODO: identify feature, annotation or tree file and parse appropriately.
246  0 AlignmentI al = null;
247   
248  0 try
249    {
250  0 FormatAdapter fa = new FormatAdapter(alignpanel);
251  0 al = fa.readFile(getText(), DataSourceType.PASTE, format);
252  0 source = fa.getAlignFile();
253   
254    } catch (IOException ex)
255    {
256  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
257    .formatMessage("label.couldnt_read_pasted_text", new String[]
258    { ex.toString() }),
259    MessageManager.getString("label.error_parsing_text"),
260    JvOptionPane.WARNING_MESSAGE);
261    }
262   
263  0 if (al != null && al.hasValidSequence())
264    {
265  0 String title = MessageManager
266    .formatMessage("label.input_cut_paste_params", new String[]
267    { format.getName() });
268  0 FeatureSettingsModelI proxyColourScheme = source
269    .getFeatureColourScheme();
270   
271    /*
272    * if the view panel was closed its alignment is nulled
273    * and this is an orphaned cut and paste window
274    */
275  0 if (viewport != null && viewport.getAlignment() != null)
276    {
277  0 if (proxyColourScheme != null)
278    {
279  0 viewport.applyFeaturesStyle(proxyColourScheme);
280    }
281  0 ((AlignViewport) viewport).addAlignment(al, title);
282    }
283    else
284    {
285   
286  0 AlignFrame af;
287  0 if (source instanceof ComplexAlignFile)
288    {
289  0 HiddenColumns hidden = ((ComplexAlignFile) source)
290    .getHiddenColumns();
291  0 SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
292    .getHiddenSequences();
293  0 boolean showSeqFeatures = ((ComplexAlignFile) source)
294    .isShowSeqFeatures();
295  0 String colourSchemeName = ((ComplexAlignFile) source)
296    .getGlobalColourScheme();
297  0 FeaturesDisplayedI fd = ((ComplexAlignFile) source)
298    .getDisplayedFeatures();
299  0 af = new AlignFrame(al, hiddenSeqs, hidden,
300    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
301  0 af.getViewport().setShowSequenceFeatures(showSeqFeatures);
302  0 af.getViewport().setFeaturesDisplayed(fd);
303  0 af.setMenusForViewport();
304  0 ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
305    colourSchemeName, al);
306  0 if (cs != null)
307    {
308  0 af.changeColour(cs);
309    }
310    }
311    else
312    {
313  0 af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
314    AlignFrame.DEFAULT_HEIGHT);
315  0 if (source instanceof FeaturesSourceI)
316    {
317  0 af.getViewport().setShowSequenceFeatures(true);
318    }
319    }
320  0 if (proxyColourScheme != null)
321    {
322  0 af.getViewport().applyFeaturesStyle(proxyColourScheme);
323    }
324  0 af.currentFileFormat = format;
325  0 Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
326    AlignFrame.DEFAULT_HEIGHT);
327  0 af.setStatus(MessageManager
328    .getString("label.successfully_pasted_alignment_file"));
329   
330  0 try
331    {
332  0 af.setMaximum(
333    jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
334    } catch (Exception ex)
335    {
336    }
337    }
338    }
339    else
340    {
341  0 System.err
342    .println(MessageManager.getString("label.couldnt_read_data"));
343  0 if (!Jalview.isHeadlessMode())
344    {
345  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
346    AppletFormatAdapter.getSupportedFormats(),
347    MessageManager.getString("label.couldnt_read_data"),
348    JvOptionPane.WARNING_MESSAGE);
349    }
350    }
351    }
352   
353    /**
354    * DOCUMENT ME!
355    *
356    * @param e
357    * DOCUMENT ME!
358    */
 
359  0 toggle @Override
360    public void cancel_actionPerformed(ActionEvent e)
361    {
362  0 try
363    {
364  0 this.setClosed(true);
365    } catch (Exception ex)
366    {
367    }
368    }
369   
 
370  0 toggle @Override
371    public void textarea_mousePressed(MouseEvent e)
372    {
373    /*
374    * isPopupTrigger is checked in mousePressed on Mac,
375    * in mouseReleased on Windows
376    */
377  0 if (e.isPopupTrigger())
378    {
379  0 JPopupMenu popup = new JPopupMenu(
380    MessageManager.getString("action.edit"));
381  0 JMenuItem item = new JMenuItem(
382    MessageManager.getString("action.copy"));
383  0 item.addActionListener(new ActionListener()
384    {
 
385  0 toggle @Override
386    public void actionPerformed(ActionEvent e)
387    {
388  0 copyItem_actionPerformed(e);
389    }
390    });
391  0 popup.add(item);
392  0 item = new JMenuItem(MessageManager.getString("action.paste"));
393  0 item.addActionListener(new ActionListener()
394    {
 
395  0 toggle @Override
396    public void actionPerformed(ActionEvent e)
397    {
398  0 pasteMenu_actionPerformed(e);
399    }
400    });
401  0 popup.add(item);
402  0 popup.show(this, e.getX() + 10, e.getY() + textarea.getY() + 40);
403   
404    }
405    }
406   
407    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.