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.
21 package jalview.appletgui;
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.ColumnSelection;
29 import jalview.datamodel.PDBEntry;
30 import jalview.datamodel.SequenceI;
31 import jalview.io.AnnotationFile;
32 import jalview.io.AppletFormatAdapter;
33 import jalview.io.FileParse;
34 import jalview.io.IdentifyFile;
35 import jalview.io.NewickFile;
36 import jalview.io.TCoffeeScoreFile;
37 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
38 import jalview.schemes.ColourSchemeI;
39 import jalview.schemes.TCoffeeColourScheme;
40 import jalview.util.MessageManager;
42 import java.awt.BorderLayout;
43 import java.awt.Button;
44 import java.awt.Dialog;
46 import java.awt.Frame;
47 import java.awt.Label;
48 import java.awt.Panel;
49 import java.awt.TextArea;
50 import java.awt.event.ActionEvent;
51 import java.awt.event.ActionListener;
52 import java.awt.event.MouseEvent;
53 import java.awt.event.MouseListener;
55 public class CutAndPasteTransfer extends Panel implements ActionListener,
58 boolean pdbImport = false;
60 boolean treeImport = false;
62 boolean annotationImport = false;
66 AlignFrame alignFrame;
68 FileParse source = null;
70 public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
80 this.alignFrame = alignFrame;
84 buttonPanel.setVisible(false);
88 public String getText()
90 return textarea.getText();
93 public void setText(String text)
95 textarea.setText(text);
98 public void setPDBImport(SequenceI seq)
101 accept.setLabel(MessageManager.getString("action.accept"));
102 addSequences.setVisible(false);
106 public void setTreeImport()
109 accept.setLabel(MessageManager.getString("action.accept"));
110 addSequences.setVisible(false);
113 public void setAnnotationImport()
115 annotationImport = true;
116 accept.setLabel(MessageManager.getString("action.accept"));
117 addSequences.setVisible(false);
121 public void actionPerformed(ActionEvent evt)
123 if (evt.getSource() == accept)
127 else if (evt.getSource() == addSequences)
131 else if (evt.getSource() == cancel)
137 protected void ok(boolean newWindow)
139 String text = getText();
140 int length = text.length();
141 textarea.append("\n");
142 if (textarea.getText().length() == length)
144 String warning = "\n\n#################################################\n"
145 + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
146 + "\nCAN'T INPUT FULL ALIGNMENT"
147 + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
148 + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
149 + "\n#################################################\n";
150 textarea.setText(text.substring(0, text.length() - warning.length())
153 textarea.setCaretPosition(text.length());
168 else if (annotationImport)
172 else if (alignFrame != null)
174 loadAlignment(text, newWindow, alignFrame.getAlignViewport());
177 // TODO: dialog should indicate if data was parsed correctly or not - see
179 if (this.getParent() instanceof Frame)
181 ((Frame) this.getParent()).setVisible(false);
185 ((Dialog) this.getParent()).setVisible(false);
190 * Parses text as Newick Tree format, and loads on to the alignment. Returns
191 * true if successful, else false.
193 protected boolean loadTree()
197 NewickFile fin = new NewickFile(textarea.getText(), "Paste");
200 if (fin.getTree() != null)
202 alignFrame.loadTree(fin, "Pasted tree file");
205 } catch (Exception ex)
207 // TODO: JAL-1102 - should have a warning message in dialog, not simply
208 // overwrite the broken input data with the exception
209 textarea.setText(MessageManager.formatMessage(
210 "label.could_not_parse_newick_file",
211 new Object[] { ex.getMessage() }));
218 * Parse text as an alignment file and add to the current or a new window.
223 protected void loadAlignment(String text, boolean newWindow,
224 AlignViewport viewport)
226 AlignmentI al = null;
228 String format = new IdentifyFile().identify(text,
229 AppletFormatAdapter.PASTE);
230 AppletFormatAdapter afa = new AppletFormatAdapter(alignFrame.alignPanel);
233 al = afa.readFile(text, AppletFormatAdapter.PASTE, format);
234 source = afa.getAlignFile();
235 } catch (java.io.IOException ex)
237 ex.printStackTrace();
242 al.setDataset(null); // set dataset on alignment/sequences
245 * SplitFrame option dependent on applet parameter for now.
247 boolean allowSplitFrame = alignFrame.viewport.applet
248 .getDefaultParameter("enableSplitFrame", false);
249 if (allowSplitFrame && openSplitFrame(al, format))
257 if (source instanceof ComplexAlignFile)
259 ColumnSelection colSel = ((ComplexAlignFile) source)
260 .getColumnSelection();
261 SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
262 .getHiddenSequences();
263 boolean showSeqFeatures = ((ComplexAlignFile) source)
264 .isShowSeqFeatures();
265 String colourSchemeName = ((ComplexAlignFile) source)
266 .getGlobalColourScheme();
267 af = new AlignFrame(al, hiddenSeqs, colSel,
268 alignFrame.viewport.applet, "Cut & Paste input - "
270 af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
271 ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
272 colourSchemeName, al);
280 af = new AlignFrame(al, alignFrame.viewport.applet,
281 "Cut & Paste input - " + format, false);
282 if (source instanceof FeaturesSourceI)
284 af.getAlignViewport().setShowSequenceFeatures(true);
289 .setText(MessageManager
290 .getString("label.successfully_pasted_annotation_to_alignment"));
294 alignFrame.addSequences(al.getSequencesArray());
295 alignFrame.statusBar.setText(MessageManager
296 .getString("label.successfully_pasted_alignment_file"));
302 * Check whether the new alignment could be mapped to the current one as
303 * cDNA/protein, if so offer the option to open as split frame view. Returns
304 * true if a split frame view is opened, false if not.
309 protected boolean openSplitFrame(AlignmentI al, String format)
311 final AlignmentI thisAlignment = this.alignFrame.getAlignViewport()
313 if (thisAlignment.isNucleotide() == al.isNucleotide())
315 // both nucleotide or both protein
318 AlignmentI protein = thisAlignment.isNucleotide() ? al : thisAlignment;
319 AlignmentI dna = thisAlignment.isNucleotide() ? thisAlignment : al;
320 boolean mapped = AlignmentUtils.mapProteinAlignmentToCdna(protein, dna);
327 * A mapping is possible; ask user if they want a split frame.
329 String title = MessageManager.getString("label.open_split_window");
330 final JVDialog dialog = new JVDialog((Frame) this.getParent(), title,
332 dialog.ok.setLabel(MessageManager.getString("action.yes"));
333 dialog.cancel.setLabel(MessageManager.getString("action.no"));
334 Panel question = new Panel(new BorderLayout());
335 final String text = MessageManager
336 .getString("label.open_split_window?");
337 question.add(new Label(text, Label.CENTER), BorderLayout.CENTER);
338 dialog.setMainPanel(question);
339 dialog.setVisible(true);
348 * 'align' the added alignment to match the current one
350 al.alignAs(thisAlignment);
353 * Open SplitFrame with DNA above and protein below, including the alignment
354 * from textbox and a copy of the original.
356 final JalviewLite applet = this.alignFrame.viewport.applet;
357 AlignFrame copyFrame = new AlignFrame(
358 this.alignFrame.viewport.getAlignment(), applet,
359 alignFrame.getTitle(), false, false);
360 AlignFrame newFrame = new AlignFrame(al, alignFrame.viewport.applet,
361 "Cut & Paste input - " + format, false, false);
362 AlignFrame dnaFrame = al.isNucleotide() ? newFrame : copyFrame;
363 AlignFrame proteinFrame = al.isNucleotide() ? copyFrame : newFrame;
364 SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame);
365 sf.addToDisplay(false, applet);
370 * Parse the text as a TCoffee score file, if successful add scores as
371 * alignment annotations.
373 protected void loadAnnotations()
375 TCoffeeScoreFile tcf = null;
378 tcf = new TCoffeeScoreFile(textarea.getText(),
379 jalview.io.AppletFormatAdapter.PASTE);
382 if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), true))
384 alignFrame.tcoffeeColour.setEnabled(true);
385 alignFrame.alignPanel.fontChanged();
386 alignFrame.changeColour(new TCoffeeColourScheme(
387 alignFrame.viewport.getAlignment()));
389 .setText(MessageManager
390 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
394 // file valid but didn't get added to alignment for some reason
395 alignFrame.statusBar.setText(MessageManager.formatMessage(
396 "label.failed_add_tcoffee_scores",
397 new Object[] { (tcf.getWarningMessage() != null ? tcf
398 .getWarningMessage() : "") }));
405 } catch (Exception x)
411 if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
412 textarea.getText(), jalview.io.AppletFormatAdapter.PASTE))
414 alignFrame.alignPanel.fontChanged();
415 alignFrame.alignPanel.setScrollValues(0, 0);
417 .setText(MessageManager
418 .getString("label.successfully_pasted_annotation_to_alignment"));
423 if (!alignFrame.parseFeaturesFile(textarea.getText(),
424 jalview.io.AppletFormatAdapter.PASTE))
427 .setText(MessageManager
428 .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
435 * Open a Jmol viewer (if available), failing that the built-in PDB viewer,
436 * passing the input text as the PDB file data.
440 protected void openPdbViewer(String text)
442 PDBEntry pdb = new PDBEntry();
445 if (alignFrame.alignPanel.av.applet.jmolAvailable)
447 new jalview.appletgui.AppletJmol(pdb, new SequenceI[] { seq }, null,
448 alignFrame.alignPanel, AppletFormatAdapter.PASTE);
452 new MCview.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
453 alignFrame.alignPanel, AppletFormatAdapter.PASTE);
457 protected void cancel()
459 textarea.setText("");
460 if (this.getParent() instanceof Frame)
462 ((Frame) this.getParent()).setVisible(false);
466 ((Dialog) this.getParent()).setVisible(false);
470 protected TextArea textarea = new TextArea();
472 Button accept = new Button("New Window");
474 Button addSequences = new Button("Add to Current Alignment");
476 Button cancel = new Button("Close");
478 protected Panel buttonPanel = new Panel();
480 BorderLayout borderLayout1 = new BorderLayout();
482 private void jbInit() throws Exception
484 textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
485 textarea.setText(MessageManager
486 .getString("label.paste_your_alignment_file"));
487 textarea.addMouseListener(this);
488 this.setLayout(borderLayout1);
489 accept.addActionListener(this);
490 addSequences.addActionListener(this);
491 cancel.addActionListener(this);
492 this.add(buttonPanel, BorderLayout.SOUTH);
493 buttonPanel.add(accept, null);
494 buttonPanel.add(addSequences);
495 buttonPanel.add(cancel, null);
496 this.add(textarea, java.awt.BorderLayout.CENTER);
500 public void mousePressed(MouseEvent evt)
502 if (textarea.getText().startsWith(
503 MessageManager.getString("label.paste_your")))
505 textarea.setText("");
510 public void mouseReleased(MouseEvent evt)
515 public void mouseClicked(MouseEvent evt)
520 public void mouseEntered(MouseEvent evt)
525 public void mouseExited(MouseEvent evt)