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Coverage Report

  1. Project Clover database Wed Nov 12 2025 09:00:47 GMT
  2. Package jalview.appletgui

File CutAndPasteTransfer.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

68
153
20
1
530
411
59
0.39
7.65
20
2.95

Classes

Class Line # Actions
CutAndPasteTransfer 58 153 59
0.00%
 

Contributing tests

No tests hitting this source file were found.

Source view

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.appletgui;
22   
23    import jalview.analysis.AlignmentUtils;
24    import jalview.api.ComplexAlignFile;
25    import jalview.api.FeaturesSourceI;
26    import jalview.bin.JalviewLite;
27    import jalview.datamodel.AlignmentI;
28    import jalview.datamodel.HiddenColumns;
29    import jalview.datamodel.PDBEntry;
30    import jalview.datamodel.SequenceI;
31    import jalview.io.AlignmentFileReaderI;
32    import jalview.io.AnnotationFile;
33    import jalview.io.AppletFormatAdapter;
34    import jalview.io.DataSourceType;
35    import jalview.io.FileFormatI;
36    import jalview.io.IdentifyFile;
37    import jalview.io.NewickFile;
38    import jalview.io.TCoffeeScoreFile;
39    import jalview.json.binding.biojson.v1.ColourSchemeMapper;
40    import jalview.schemes.ColourSchemeI;
41    import jalview.schemes.TCoffeeColourScheme;
42    import jalview.util.MessageManager;
43   
44    import java.awt.BorderLayout;
45    import java.awt.Button;
46    import java.awt.Dialog;
47    import java.awt.Font;
48    import java.awt.Frame;
49    import java.awt.Label;
50    import java.awt.Panel;
51    import java.awt.TextArea;
52    import java.awt.event.ActionEvent;
53    import java.awt.event.ActionListener;
54    import java.awt.event.MouseEvent;
55    import java.awt.event.MouseListener;
56    import java.io.IOException;
57   
 
58    public class CutAndPasteTransfer extends Panel
59    implements ActionListener, MouseListener
60    {
61    boolean pdbImport = false;
62   
63    boolean treeImport = false;
64   
65    boolean annotationImport = false;
66   
67    SequenceI seq;
68   
69    AlignFrame alignFrame;
70   
71    AlignmentFileReaderI source = null;
72   
 
73  0 toggle public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
74    {
75  0 try
76    {
77  0 jbInit();
78    } catch (Exception e)
79    {
80  0 e.printStackTrace();
81    }
82   
83  0 this.alignFrame = alignFrame;
84   
85  0 if (!forImport)
86    {
87  0 buttonPanel.setVisible(false);
88    }
89    }
90   
 
91  0 toggle public String getText()
92    {
93  0 return textarea.getText();
94    }
95   
 
96  0 toggle public void setText(String text)
97    {
98  0 textarea.setText(text);
99    }
100   
 
101  0 toggle public void setPDBImport(SequenceI seq)
102    {
103  0 this.seq = seq;
104  0 accept.setLabel(MessageManager.getString("action.accept"));
105  0 addSequences.setVisible(false);
106  0 pdbImport = true;
107    }
108   
 
109  0 toggle public void setTreeImport()
110    {
111  0 treeImport = true;
112  0 accept.setLabel(MessageManager.getString("action.accept"));
113  0 addSequences.setVisible(false);
114    }
115   
 
116  0 toggle public void setAnnotationImport()
117    {
118  0 annotationImport = true;
119  0 accept.setLabel(MessageManager.getString("action.accept"));
120  0 addSequences.setVisible(false);
121    }
122   
 
123  0 toggle @Override
124    public void actionPerformed(ActionEvent evt)
125    {
126  0 if (evt.getSource() == accept)
127    {
128  0 ok(true);
129    }
130  0 else if (evt.getSource() == addSequences)
131    {
132  0 ok(false);
133    }
134  0 else if (evt.getSource() == cancel)
135    {
136  0 cancel();
137    }
138    }
139   
 
140  0 toggle protected void ok(boolean newWindow)
141    {
142  0 String text = getText();
143  0 int length = text.length();
144  0 textarea.append("\n");
145  0 if (textarea.getText().length() == length)
146    {
147  0 String warning = "\n\n#################################################\n"
148    + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
149    + "\nCAN'T INPUT FULL ALIGNMENT"
150    + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
151    + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
152    + "\n#################################################\n";
153  0 textarea.setText(text.substring(0, text.length() - warning.length())
154    + warning);
155   
156  0 textarea.setCaretPosition(text.length());
157    }
158   
159  0 if (pdbImport)
160    {
161  0 openPdbViewer(text);
162   
163    }
164  0 else if (treeImport)
165    {
166  0 if (!loadTree())
167    {
168  0 return;
169    }
170    }
171  0 else if (annotationImport)
172    {
173  0 loadAnnotations();
174    }
175  0 else if (alignFrame != null)
176    {
177  0 loadAlignment(text, newWindow, alignFrame.getAlignViewport());
178    }
179   
180    // TODO: dialog should indicate if data was parsed correctly or not - see
181    // JAL-1102
182  0 if (this.getParent() instanceof Frame)
183    {
184  0 ((Frame) this.getParent()).setVisible(false);
185    }
186    else
187    {
188  0 ((Dialog) this.getParent()).setVisible(false);
189    }
190    }
191   
192    /**
193    * Parses text as Newick Tree format, and loads on to the alignment. Returns
194    * true if successful, else false.
195    */
 
196  0 toggle protected boolean loadTree()
197    {
198  0 try
199    {
200  0 NewickFile fin = new NewickFile(textarea.getText(),
201    DataSourceType.PASTE);
202   
203  0 fin.parse();
204  0 if (fin.getTree() != null)
205    {
206  0 alignFrame.loadTree(fin, "Pasted tree file");
207  0 return true;
208    }
209    } catch (Exception ex)
210    {
211    // TODO: JAL-1102 - should have a warning message in dialog, not simply
212    // overwrite the broken input data with the exception
213  0 textarea.setText(MessageManager.formatMessage(
214    "label.could_not_parse_newick_file", new Object[]
215    { ex.getMessage() }));
216  0 return false;
217    }
218  0 return false;
219    }
220   
221    /**
222    * Parse text as an alignment file and add to the current or a new window.
223    *
224    * @param text
225    * @param newWindow
226    */
 
227  0 toggle protected void loadAlignment(String text, boolean newWindow,
228    AlignViewport viewport)
229    {
230  0 AlignmentI al = null;
231   
232  0 try
233    {
234  0 FileFormatI format = new IdentifyFile().identify(text,
235    DataSourceType.PASTE);
236  0 AppletFormatAdapter afa = new AppletFormatAdapter(
237    alignFrame.alignPanel);
238  0 al = afa.readFile(text, DataSourceType.PASTE, format);
239  0 source = afa.getAlignFile();
240   
241  0 if (al != null)
242    {
243  0 al.setDataset(null); // set dataset on alignment/sequences
244   
245    /*
246    * SplitFrame option dependent on applet parameter for now.
247    */
248  0 boolean allowSplitFrame = alignFrame.viewport.applet
249    .getDefaultParameter("enableSplitFrame", false);
250  0 if (allowSplitFrame && openSplitFrame(al, format))
251    {
252  0 return;
253    }
254  0 if (newWindow)
255    {
256  0 AlignFrame af;
257   
258  0 if (source instanceof ComplexAlignFile)
259    {
260  0 HiddenColumns colSel = ((ComplexAlignFile) source)
261    .getHiddenColumns();
262  0 SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
263    .getHiddenSequences();
264  0 boolean showSeqFeatures = ((ComplexAlignFile) source)
265    .isShowSeqFeatures();
266  0 String colourSchemeName = ((ComplexAlignFile) source)
267    .getGlobalColourScheme();
268  0 af = new AlignFrame(al, hiddenSeqs, colSel,
269    alignFrame.viewport.applet,
270    "Cut & Paste input - " + format, false);
271  0 af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
272  0 ColourSchemeI cs = ColourSchemeMapper
273    .getJalviewColourScheme(colourSchemeName, al);
274  0 if (cs != null)
275    {
276  0 af.changeColour(cs);
277    }
278    }
279    else
280    {
281  0 af = new AlignFrame(al, alignFrame.viewport.applet,
282    "Cut & Paste input - " + format, false);
283  0 if (source instanceof FeaturesSourceI)
284    {
285  0 af.getAlignViewport().setShowSequenceFeatures(true);
286    }
287    }
288   
289  0 af.statusBar.setText(MessageManager.getString(
290    "label.successfully_pasted_annotation_to_alignment"));
291    }
292    else
293    {
294  0 alignFrame.addSequences(al.getSequencesArray());
295  0 alignFrame.statusBar.setText(MessageManager
296    .getString("label.successfully_pasted_alignment_file"));
297    }
298    }
299    } catch (IOException ex)
300    {
301  0 ex.printStackTrace();
302    }
303    }
304   
305    /**
306    * Check whether the new alignment could be mapped to the current one as
307    * cDNA/protein, if so offer the option to open as split frame view. Returns
308    * true if a split frame view is opened, false if not.
309    *
310    * @param al
311    * @return
312    */
 
313  0 toggle protected boolean openSplitFrame(AlignmentI al, FileFormatI format)
314    {
315  0 final AlignmentI thisAlignment = this.alignFrame.getAlignViewport()
316    .getAlignment();
317  0 if (thisAlignment.isNucleotide() == al.isNucleotide())
318    {
319    // both nucleotide or both protein
320  0 return false;
321    }
322  0 AlignmentI protein = thisAlignment.isNucleotide() ? al : thisAlignment;
323  0 AlignmentI dna = thisAlignment.isNucleotide() ? thisAlignment : al;
324  0 boolean mapped = AlignmentUtils.mapProteinAlignmentToCdna(protein, dna);
325  0 if (!mapped)
326    {
327  0 return false;
328    }
329   
330    /*
331    * A mapping is possible; ask user if they want a split frame.
332    */
333  0 String title = MessageManager.getString("label.open_split_window");
334  0 final JVDialog dialog = new JVDialog((Frame) this.getParent(), title,
335    true, 100, 400);
336  0 dialog.ok.setLabel(MessageManager.getString("action.yes"));
337  0 dialog.cancel.setLabel(MessageManager.getString("action.no"));
338  0 Panel question = new Panel(new BorderLayout());
339  0 final String text = MessageManager
340    .getString("label.open_split_window?");
341  0 question.add(new Label(text, Label.CENTER), BorderLayout.CENTER);
342  0 dialog.setMainPanel(question);
343  0 dialog.setVisible(true);
344  0 dialog.toFront();
345   
346  0 if (!dialog.accept)
347    {
348  0 return false;
349    }
350   
351    /*
352    * 'align' the added alignment to match the current one
353    */
354  0 al.alignAs(thisAlignment);
355   
356    /*
357    * Open SplitFrame with DNA above and protein below, including the alignment
358    * from textbox and a copy of the original.
359    */
360  0 final JalviewLite applet = this.alignFrame.viewport.applet;
361  0 AlignFrame copyFrame = new AlignFrame(
362    this.alignFrame.viewport.getAlignment(), applet,
363    alignFrame.getTitle(), false, false);
364  0 AlignFrame newFrame = new AlignFrame(al, alignFrame.viewport.applet,
365    "Cut & Paste input - " + format, false, false);
366  0 AlignFrame dnaFrame = al.isNucleotide() ? newFrame : copyFrame;
367  0 AlignFrame proteinFrame = al.isNucleotide() ? copyFrame : newFrame;
368  0 SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame);
369  0 sf.addToDisplay(false, applet);
370  0 return true;
371    }
372   
373    /**
374    * Parse the text as a TCoffee score file, if successful add scores as
375    * alignment annotations.
376    */
 
377  0 toggle protected void loadAnnotations()
378    {
379  0 TCoffeeScoreFile tcf = null;
380  0 try
381    {
382  0 tcf = new TCoffeeScoreFile(textarea.getText(),
383    jalview.io.DataSourceType.PASTE);
384  0 if (tcf.isValid())
385    {
386  0 if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), true))
387    {
388  0 alignFrame.tcoffeeColour.setEnabled(true);
389  0 alignFrame.alignPanel.fontChanged();
390  0 alignFrame.changeColour(new TCoffeeColourScheme(
391    alignFrame.viewport.getAlignment()));
392  0 alignFrame.statusBar.setText(MessageManager.getString(
393    "label.successfully_pasted_tcoffee_scores_to_alignment"));
394    }
395    else
396    {
397    // file valid but didn't get added to alignment for some reason
398  0 alignFrame.statusBar.setText(MessageManager.formatMessage(
399    "label.failed_add_tcoffee_scores", new Object[]
400  0 { (tcf.getWarningMessage() != null
401    ? tcf.getWarningMessage()
402    : "") }));
403    }
404    }
405    else
406    {
407  0 tcf = null;
408    }
409    } catch (Exception x)
410    {
411  0 tcf = null;
412    }
413  0 if (tcf == null)
414    {
415  0 if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
416    textarea.getText(), jalview.io.DataSourceType.PASTE))
417    {
418  0 alignFrame.alignPanel.fontChanged();
419  0 alignFrame.alignPanel.setScrollValues(0, 0);
420  0 alignFrame.statusBar.setText(MessageManager.getString(
421    "label.successfully_pasted_annotation_to_alignment"));
422   
423    }
424    else
425    {
426  0 if (!alignFrame.parseFeaturesFile(textarea.getText(),
427    jalview.io.DataSourceType.PASTE))
428    {
429  0 alignFrame.statusBar.setText(MessageManager.getString(
430    "label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
431    }
432    }
433    }
434    }
435   
436    /**
437    * Open a Jmol viewer (if available), failing that the built-in PDB viewer,
438    * passing the input text as the PDB file data.
439    *
440    * @param text
441    */
 
442  0 toggle protected void openPdbViewer(String text)
443    {
444  0 PDBEntry pdb = new PDBEntry();
445  0 pdb.setFile(text);
446   
447  0 if (alignFrame.alignPanel.av.applet.jmolAvailable)
448    {
449  0 new jalview.appletgui.AppletJmol(pdb, new SequenceI[] { seq }, null,
450    alignFrame.alignPanel, DataSourceType.PASTE);
451    }
452    else
453    {
454  0 new mc_view.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
455    alignFrame.alignPanel, DataSourceType.PASTE);
456    }
457    }
458   
 
459  0 toggle protected void cancel()
460    {
461  0 textarea.setText("");
462  0 if (this.getParent() instanceof Frame)
463    {
464  0 ((Frame) this.getParent()).setVisible(false);
465    }
466    else
467    {
468  0 ((Dialog) this.getParent()).setVisible(false);
469    }
470    }
471   
472    protected TextArea textarea = new TextArea();
473   
474    Button accept = new Button("New Window");
475   
476    Button addSequences = new Button("Add to Current Alignment");
477   
478    Button cancel = new Button("Close");
479   
480    protected Panel buttonPanel = new Panel();
481   
482    BorderLayout borderLayout1 = new BorderLayout();
483   
 
484  0 toggle private void jbInit() throws Exception
485    {
486  0 textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
487  0 textarea.setText(
488    MessageManager.getString("label.paste_your_alignment_file"));
489  0 textarea.addMouseListener(this);
490  0 this.setLayout(borderLayout1);
491  0 accept.addActionListener(this);
492  0 addSequences.addActionListener(this);
493  0 cancel.addActionListener(this);
494  0 this.add(buttonPanel, BorderLayout.SOUTH);
495  0 buttonPanel.add(accept, null);
496  0 buttonPanel.add(addSequences);
497  0 buttonPanel.add(cancel, null);
498  0 this.add(textarea, java.awt.BorderLayout.CENTER);
499    }
500   
 
501  0 toggle @Override
502    public void mousePressed(MouseEvent evt)
503    {
504  0 if (textarea.getText()
505    .startsWith(MessageManager.getString("label.paste_your")))
506    {
507  0 textarea.setText("");
508    }
509    }
510   
 
511  0 toggle @Override
512    public void mouseReleased(MouseEvent evt)
513    {
514    }
515   
 
516  0 toggle @Override
517    public void mouseClicked(MouseEvent evt)
518    {
519    }
520   
 
521  0 toggle @Override
522    public void mouseEntered(MouseEvent evt)
523    {
524    }
525   
 
526  0 toggle @Override
527    public void mouseExited(MouseEvent evt)
528    {
529    }
530    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 12 2025 09:10:40 GMT using coverage data from Wed Nov 12 2025 09:10:27 GMT.
  • OpenClover is free and open-source software.