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.bin.JalviewLite;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.ColumnSelection;
28 import jalview.datamodel.PDBEntry;
29 import jalview.datamodel.SequenceI;
30 import jalview.io.AnnotationFile;
31 import jalview.io.AppletFormatAdapter;
32 import jalview.io.FileParse;
33 import jalview.io.IdentifyFile;
34 import jalview.io.NewickFile;
35 import jalview.io.AlignFile;
36 import jalview.io.TCoffeeScoreFile;
37 import jalview.jsdev.GenericFileAdapter;
38 import jalview.schemes.ColourSchemeI;
39 import jalview.schemes.TCoffeeColourScheme;
40 import jalview.util.MessageManager;
42 import java.awt.BorderLayout;
43 import awt2swing.Button;
44 import java.awt.Dialog;
46 import awt2swing.Frame;
47 import awt2swing.Label;
48 import awt2swing.Panel;
49 import awt2swing.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);
120 public void actionPerformed(ActionEvent evt)
122 if (evt.getSource() == accept)
126 else if (evt.getSource() == addSequences)
130 else if (evt.getSource() == cancel)
136 protected void ok(boolean newWindow)
138 String text = getText();
139 int length = text.length();
140 textarea.append("\n");
141 if (textarea.getText().length() == length)
143 String warning = "\n\n#################################################\n"
144 + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
145 + "\nCAN'T INPUT FULL ALIGNMENT"
146 + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
147 + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
148 + "\n#################################################\n";
149 textarea.setText(text.substring(0, text.length() - warning.length())
152 textarea.setCaretPosition(text.length());
167 else if (annotationImport)
171 else if (alignFrame != null)
173 loadAlignment(text, newWindow, alignFrame.getAlignViewport());
176 // TODO: dialog should indicate if data was parsed correctly or not - see
178 if (this.getParent() instanceof Frame)
180 ((Frame) this.getParent()).setVisible(false);
184 ((Dialog) this.getParent()).setVisible(false);
189 * Parses text as Newick Tree format, and loads on to the alignment. Returns
190 * true if successful, else false.
192 protected boolean loadTree()
196 NewickFile fin = new NewickFile(textarea.getText(), "Paste");
199 if (fin.getTree() != null)
201 alignFrame.loadTree(fin, "Pasted tree file");
204 } catch (Exception ex)
206 // TODO: JAL-1102 - should have a warning message in dialog, not simply
207 // overwrite the broken input data with the exception
208 textarea.setText(MessageManager.formatMessage(
209 "label.could_not_parse_newick_file", new Object[]
210 { ex.getMessage() }));
217 * Parse text as an alignment file and add to the current or a new window.
222 protected void loadAlignment(String text, boolean newWindow,
223 AlignViewport viewport)
225 AlignmentI al = null;
227 String format = new IdentifyFile().Identify(text,
228 AppletFormatAdapter.PASTE);
229 AppletFormatAdapter afa = new AppletFormatAdapter(alignFrame.alignPanel);
232 al = afa.readFile(text, AppletFormatAdapter.PASTE, format);
233 source = afa.getAlignFile();
234 } catch (java.io.IOException ex)
236 ex.printStackTrace();
241 al.setDataset(null); // set dataset on alignment/sequences
244 * SplitFrame option dependent on applet parameter for now.
246 boolean allowSplitFrame = alignFrame.viewport.applet
247 .getDefaultParameter("enableSplitFrame", false);
248 if (allowSplitFrame && openSplitFrame(al, format))
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 af = new AlignFrame(al, hiddenSeqs, colSel,
266 alignFrame.viewport.applet, "Cut & Paste input - "
268 af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
273 af = new AlignFrame(al, alignFrame.viewport.applet,
274 "Cut & Paste input - " + format, false);
277 af.setStatus(MessageManager
278 .getString("label.successfully_pasted_annotation_to_alignment"));
282 alignFrame.addSequences(al.getSequencesArray());
283 alignFrame.setStatus(MessageManager
284 .getString("label.successfully_pasted_alignment_file"));
290 * Check whether the new alignment could be mapped to the current one as
291 * cDNA/protein, if so offer the option to open as split frame view. Returns
292 * true if a split frame view is opened, false if not.
297 protected boolean openSplitFrame(AlignmentI al, String format)
299 final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
300 if (thisAlignment.isNucleotide() == al.isNucleotide())
302 // both nucleotide or both protein
305 AlignmentI protein = thisAlignment.isNucleotide() ? al : thisAlignment;
306 AlignmentI dna = thisAlignment.isNucleotide() ? thisAlignment : al;
307 boolean mapped = AlignmentUtils.mapProteinToCdna(protein, dna);
314 * A mapping is possible; ask user if they want a split frame.
316 String title = MessageManager.getString("label.open_split_window");
317 final JVDialog dialog = new JVDialog((Frame) this.getParent(), title,
319 dialog.ok.setLabel(MessageManager.getString("action.yes"));
320 dialog.cancel.setLabel(MessageManager.getString("action.no"));
321 Panel question = new Panel(new BorderLayout());
322 final String text = MessageManager
323 .getString("label.open_split_window?");
324 question.add(new Label(text, Label.CENTER), BorderLayout.CENTER);
325 dialog.setMainPanel(question);
326 dialog.setVisible(true);
335 * Open SplitFrame with DNA above and protein below, including the alignment
336 * from textbox and a copy of the original.
338 final JalviewLite applet = this.alignFrame.viewport.applet;
339 AlignFrame copyFrame = new AlignFrame(
340 this.alignFrame.viewport.getAlignment(), applet,
341 alignFrame.getTitle(), false, false);
342 AlignFrame newFrame = new AlignFrame(al, alignFrame.viewport.applet,
343 "Cut & Paste input - " + format, false, false);
344 AlignFrame dnaFrame = al.isNucleotide() ? newFrame : copyFrame;
345 AlignFrame proteinFrame = al.isNucleotide() ? copyFrame
347 SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame);
348 sf.addToDisplay(false, applet);
353 * Parse the text as a TCoffee score file, if successful add scores as
354 * alignment annotations.
356 protected void loadAnnotations()
358 TCoffeeScoreFile tcf = null;
361 tcf = (TCoffeeScoreFile) GenericFileAdapter.getFile("TCoffeeScoreFile", textarea.getText(),
362 AppletFormatAdapter.PASTE);
365 if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
368 alignFrame.tcoffeeColour.setEnabled(true);
369 alignFrame.alignPanel.fontChanged();
370 alignFrame.changeColour(new TCoffeeColourScheme(
371 alignFrame.viewport.getAlignment()));
372 alignFrame.setStatus(MessageManager
373 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
377 // file valid but didn't get added to alignment for some reason
378 alignFrame.setStatus(MessageManager.formatMessage(
379 "label.failed_add_tcoffee_scores",
381 { (tcf.getWarningMessage() != null ? tcf
382 .getWarningMessage() : "") }));
389 } catch (Exception x)
395 if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
396 textarea.getText(), AppletFormatAdapter.PASTE))
398 alignFrame.alignPanel.fontChanged();
399 alignFrame.alignPanel.setScrollValues(0, 0);
400 alignFrame.setStatus(MessageManager
401 .getString("label.successfully_pasted_annotation_to_alignment"));
406 if (!alignFrame.parseFeaturesFile(textarea.getText(),
407 AppletFormatAdapter.PASTE))
409 alignFrame.setStatus(MessageManager
410 .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
417 * Open a Jmol viewer (if available), failing that the built-in PDB viewer,
418 * passing the input text as the PDB file data.
422 protected void openPdbViewer(String text)
424 PDBEntry pdb = new PDBEntry();
427 // if (alignFrame.alignPanel.av.applet.jmolAvailable)
429 new AppletJmol(pdb, new SequenceI[]
430 { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
434 // new MCview.AppletPDBViewer(pdb, new SequenceI[]
435 // { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
439 protected void cancel()
441 textarea.setText("");
442 if (this.getParent() instanceof Frame)
444 ((Frame) this.getParent()).setVisible(false);
448 ((Dialog) this.getParent()).setVisible(false);
452 protected TextArea textarea = new TextArea();
454 Button accept = new Button("New Window");
456 Button addSequences = new Button("Add to Current Alignment");
458 Button cancel = new Button("Close");
460 protected Panel buttonPanel = new Panel();
462 BorderLayout borderLayout1 = new BorderLayout();
464 private void jbInit() throws Exception
466 textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
467 textarea.setText(MessageManager
468 .getString("label.paste_your_alignment_file"));
469 textarea.addMouseListener(this);
470 this.setLayout(borderLayout1);
471 accept.addActionListener(this);
472 addSequences.addActionListener(this);
473 cancel.addActionListener(this);
474 this.add(buttonPanel, BorderLayout.SOUTH);
475 buttonPanel.add(accept, null);
476 buttonPanel.add(addSequences);
477 buttonPanel.add(cancel, null);
478 this.add(textarea, java.awt.BorderLayout.CENTER);
481 public void mousePressed(MouseEvent evt)
483 if (textarea.getText().startsWith(
484 MessageManager.getString("label.paste_your")))
486 textarea.setText("");
490 public void mouseReleased(MouseEvent evt)
494 public void mouseClicked(MouseEvent evt)
498 public void mouseEntered(MouseEvent evt)
502 public void mouseExited(MouseEvent evt)