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.datamodel.PDBEntry;
24 import jalview.datamodel.SequenceI;
25 import jalview.gui.AlignmentPanel;
26 import jalview.gui.Desktop;
27 import jalview.gui.OOMWarning;
28 import jalview.gui.UserDefinedColours;
29 import jalview.io.JalviewFileChooser;
30 import jalview.io.JalviewFileView;
31 import jalview.schemes.BuriedColourScheme;
32 import jalview.schemes.HelixColourScheme;
33 import jalview.schemes.HydrophobicColourScheme;
34 import jalview.schemes.StrandColourScheme;
35 import jalview.schemes.TaylorColourScheme;
36 import jalview.schemes.TurnColourScheme;
37 import jalview.schemes.UserColourScheme;
38 import jalview.schemes.ZappoColourScheme;
39 import jalview.util.MessageManager;
40 import jalview.ws.ebi.EBIFetchClient;
42 import java.awt.event.ActionEvent;
43 import java.awt.event.ActionListener;
44 import java.awt.event.ItemEvent;
45 import java.awt.event.ItemListener;
46 import java.awt.event.KeyAdapter;
47 import java.awt.event.KeyEvent;
48 import java.awt.event.MouseAdapter;
49 import java.awt.event.MouseEvent;
50 import java.io.BufferedReader;
52 import java.io.FileOutputStream;
53 import java.io.FileReader;
54 import java.io.PrintWriter;
56 import javax.swing.ButtonGroup;
57 import javax.swing.JCheckBoxMenuItem;
58 import javax.swing.JColorChooser;
59 import javax.swing.JInternalFrame;
60 import javax.swing.JMenu;
61 import javax.swing.JMenuBar;
62 import javax.swing.JMenuItem;
63 import javax.swing.JOptionPane;
64 import javax.swing.JRadioButtonMenuItem;
65 import javax.swing.SwingUtilities;
67 public class PDBViewer extends JInternalFrame implements Runnable
71 * The associated sequence in an alignment
87 public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
88 AlignmentPanel ap, String protocol)
90 this.pdbentry = pdbentry;
94 this.protocol = protocol;
99 } catch (Exception ex)
101 ex.printStackTrace();
104 StringBuffer title = new StringBuffer(seq[0].getName() + ":"
105 + pdbentry.getFile());
107 pdbcanvas = new PDBCanvas();
109 setContentPane(pdbcanvas);
111 if (pdbentry.getFile() != null)
115 tmpPDBFile = pdbentry.getFile();
116 PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
117 jalview.io.AppletFormatAdapter.FILE);
119 pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
121 } catch (java.io.IOException ex)
123 ex.printStackTrace();
128 Thread worker = new Thread(this);
132 if (pdbentry.getProperty() != null)
134 if (pdbentry.getProperty().get("method") != null)
136 title.append(" Method: ");
137 title.append(pdbentry.getProperty().get("method"));
139 if (pdbentry.getProperty().get("chains") != null)
141 title.append(" Chain:");
142 title.append(pdbentry.getProperty().get("chains"));
145 Desktop.addInternalFrame(this, title.toString(), 400, 400);
153 EBIFetchClient ebi = new EBIFetchClient();
154 String query = "pdb:" + pdbentry.getId();
155 pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
158 if (pdbentry.getFile() != null)
160 pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
162 } catch (Exception ex)
164 pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
165 ex.printStackTrace();
169 private void jbInit() throws Exception
171 this.addKeyListener(new KeyAdapter()
174 public void keyPressed(KeyEvent evt)
176 pdbcanvas.keyPressed(evt);
180 this.setJMenuBar(jMenuBar1);
181 fileMenu.setText(MessageManager.getString("action.file"));
182 coloursMenu.setText(MessageManager.getString("label.colours"));
183 saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
184 saveMenu.setText(MessageManager.getString("action.save_as"));
186 png.addActionListener(new ActionListener()
189 public void actionPerformed(ActionEvent e)
191 png_actionPerformed(e);
195 eps.addActionListener(new ActionListener()
198 public void actionPerformed(ActionEvent e)
200 eps_actionPerformed(e);
203 mapping.setText(MessageManager.getString("label.view_mapping"));
204 mapping.addActionListener(new ActionListener()
207 public void actionPerformed(ActionEvent e)
209 mapping_actionPerformed(e);
212 wire.setText(MessageManager.getString("label.wireframe"));
213 wire.addActionListener(new ActionListener()
216 public void actionPerformed(ActionEvent e)
218 wire_actionPerformed(e);
221 depth.setSelected(true);
222 depth.setText(MessageManager.getString("label.depthcue"));
223 depth.addActionListener(new ActionListener()
226 public void actionPerformed(ActionEvent e)
228 depth_actionPerformed(e);
231 zbuffer.setSelected(true);
232 zbuffer.setText(MessageManager.getString("label.z_buffering"));
233 zbuffer.addActionListener(new ActionListener()
236 public void actionPerformed(ActionEvent e)
238 zbuffer_actionPerformed(e);
241 charge.setText(MessageManager.getString("label.charge_cysteine"));
242 charge.addActionListener(new ActionListener()
245 public void actionPerformed(ActionEvent e)
247 charge_actionPerformed(e);
250 chain.setText(MessageManager.getString("action.by_chain"));
251 chain.addActionListener(new ActionListener()
254 public void actionPerformed(ActionEvent e)
256 chain_actionPerformed(e);
259 seqButton.setSelected(true);
260 seqButton.setText(MessageManager.getString("action.by_sequence"));
261 seqButton.addActionListener(new ActionListener()
264 public void actionPerformed(ActionEvent e)
266 seqButton_actionPerformed(e);
269 allchains.setSelected(true);
270 allchains.setText(MessageManager.getString("label.show_all_chains"));
271 allchains.addItemListener(new ItemListener()
274 public void itemStateChanged(ItemEvent e)
276 allchains_itemStateChanged(e);
279 zappo.setText(MessageManager.getString("label.zappo"));
280 zappo.addActionListener(new ActionListener()
283 public void actionPerformed(ActionEvent e)
285 zappo_actionPerformed(e);
288 taylor.setText(MessageManager.getString("label.taylor"));
289 taylor.addActionListener(new ActionListener()
292 public void actionPerformed(ActionEvent e)
294 taylor_actionPerformed(e);
297 hydro.setText(MessageManager.getString("label.hydrophobicity"));
298 hydro.addActionListener(new ActionListener()
301 public void actionPerformed(ActionEvent e)
303 hydro_actionPerformed(e);
306 helix.setText(MessageManager.getString("label.helix_propensity"));
307 helix.addActionListener(new ActionListener()
310 public void actionPerformed(ActionEvent e)
312 helix_actionPerformed(e);
315 strand.setText(MessageManager.getString("label.strand_propensity"));
316 strand.addActionListener(new ActionListener()
319 public void actionPerformed(ActionEvent e)
321 strand_actionPerformed(e);
324 turn.setText(MessageManager.getString("label.turn_propensity"));
325 turn.addActionListener(new ActionListener()
328 public void actionPerformed(ActionEvent e)
330 turn_actionPerformed(e);
333 buried.setText(MessageManager.getString("label.buried_index"));
334 buried.addActionListener(new ActionListener()
337 public void actionPerformed(ActionEvent e)
339 buried_actionPerformed(e);
342 user.setText(MessageManager.getString("action.user_defined"));
343 user.addActionListener(new ActionListener()
346 public void actionPerformed(ActionEvent e)
348 user_actionPerformed(e);
351 viewMenu.setText(MessageManager.getString("action.view"));
353 .setText(MessageManager.getString("action.background_colour"));
354 background.addActionListener(new ActionListener()
357 public void actionPerformed(ActionEvent e)
359 background_actionPerformed(e);
362 savePDB.setText(MessageManager.getString("label.pdb_file"));
363 savePDB.addActionListener(new ActionListener()
366 public void actionPerformed(ActionEvent e)
368 savePDB_actionPerformed(e);
371 jMenuBar1.add(fileMenu);
372 jMenuBar1.add(coloursMenu);
373 jMenuBar1.add(viewMenu);
374 fileMenu.add(saveMenu);
375 fileMenu.add(mapping);
376 saveMenu.add(savePDB);
379 coloursMenu.add(seqButton);
380 coloursMenu.add(chain);
381 coloursMenu.add(charge);
382 coloursMenu.add(zappo);
383 coloursMenu.add(taylor);
384 coloursMenu.add(hydro);
385 coloursMenu.add(helix);
386 coloursMenu.add(strand);
387 coloursMenu.add(turn);
388 coloursMenu.add(buried);
389 coloursMenu.add(user);
390 coloursMenu.add(background);
391 ButtonGroup bg = new ButtonGroup();
404 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
406 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
407 .getUserColourSchemes().keys();
409 while (userColours.hasMoreElements())
411 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
412 userColours.nextElement().toString());
413 radioItem.setName("USER_DEFINED");
414 radioItem.addMouseListener(new MouseAdapter()
417 public void mousePressed(MouseEvent evt)
419 if (evt.isControlDown()
420 || SwingUtilities.isRightMouseButton(evt))
422 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
424 int option = JOptionPane.showInternalConfirmDialog(
425 jalview.gui.Desktop.desktop,
427 .getString("label.remove_from_default_list"),
429 .getString("label.remove_user_defined_colour"),
430 JOptionPane.YES_NO_OPTION);
431 if (option == JOptionPane.YES_OPTION)
433 jalview.gui.UserDefinedColours
434 .removeColourFromDefaults(radioItem.getText());
435 coloursMenu.remove(radioItem);
439 radioItem.addActionListener(new ActionListener()
442 public void actionPerformed(ActionEvent evt)
444 user_actionPerformed(evt);
451 radioItem.addActionListener(new ActionListener()
454 public void actionPerformed(ActionEvent evt)
456 user_actionPerformed(evt);
459 coloursMenu.add(radioItem);
466 viewMenu.add(zbuffer);
467 viewMenu.add(allchains);
470 JMenuBar jMenuBar1 = new JMenuBar();
472 JMenu fileMenu = new JMenu();
474 JMenu coloursMenu = new JMenu();
476 JMenu saveMenu = new JMenu();
478 JMenuItem png = new JMenuItem();
480 JMenuItem eps = new JMenuItem();
482 JMenuItem mapping = new JMenuItem();
484 JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
486 JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
488 JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
490 JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
492 JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
494 JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
496 JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
498 JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
500 JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
502 JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
504 JRadioButtonMenuItem user = new JRadioButtonMenuItem();
506 JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
508 JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
510 JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
512 JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
514 JMenu viewMenu = new JMenu();
516 JMenuItem background = new JMenuItem();
518 JMenuItem savePDB = new JMenuItem();
526 public void eps_actionPerformed(ActionEvent e)
528 makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
537 public void png_actionPerformed(ActionEvent e)
539 makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
542 void makePDBImage(jalview.util.ImageMaker.TYPE type)
544 int width = pdbcanvas.getWidth();
545 int height = pdbcanvas.getHeight();
547 jalview.util.ImageMaker im;
549 if (type == jalview.util.ImageMaker.TYPE.PNG)
551 im = new jalview.util.ImageMaker(this,
552 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
553 width, height, null, null, null, 0, false);
555 else if (type == jalview.util.ImageMaker.TYPE.EPS)
557 im = new jalview.util.ImageMaker(this,
558 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
559 width, height, null, this.getTitle(), null, 0, false);
564 im = new jalview.util.ImageMaker(this,
565 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
566 width, height, null, this.getTitle(), null, 0, false);
569 if (im.getGraphics() != null)
571 pdbcanvas.drawAll(im.getGraphics(), width, height);
576 public void charge_actionPerformed(ActionEvent e)
578 pdbcanvas.bysequence = false;
579 pdbcanvas.pdb.setChargeColours();
580 pdbcanvas.redrawneeded = true;
584 public void hydro_actionPerformed(ActionEvent e)
586 pdbcanvas.bysequence = false;
587 pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
588 pdbcanvas.redrawneeded = true;
592 public void chain_actionPerformed(ActionEvent e)
594 pdbcanvas.bysequence = false;
595 pdbcanvas.pdb.setChainColours();
596 pdbcanvas.redrawneeded = true;
600 public void zbuffer_actionPerformed(ActionEvent e)
602 pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
603 pdbcanvas.redrawneeded = true;
607 public void molecule_actionPerformed(ActionEvent e)
609 pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
610 pdbcanvas.redrawneeded = true;
614 public void depth_actionPerformed(ActionEvent e)
616 pdbcanvas.depthcue = !pdbcanvas.depthcue;
617 pdbcanvas.redrawneeded = true;
621 public void wire_actionPerformed(ActionEvent e)
623 pdbcanvas.wire = !pdbcanvas.wire;
624 pdbcanvas.redrawneeded = true;
628 public void seqButton_actionPerformed(ActionEvent e)
630 pdbcanvas.bysequence = true;
631 pdbcanvas.updateSeqColours();
634 public void mapping_actionPerformed(ActionEvent e)
636 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
639 cap.setText(pdbcanvas.mappingDetails.toString());
640 Desktop.addInternalFrame(cap,
641 MessageManager.getString("label.pdb_sequence_mapping"), 550,
643 } catch (OutOfMemoryError oom)
645 new OOMWarning("Opening sequence to structure mapping report", oom);
650 public void allchains_itemStateChanged(ItemEvent e)
652 pdbcanvas.setAllchainsVisible(allchains.getState());
655 public void zappo_actionPerformed(ActionEvent e)
657 pdbcanvas.bysequence = false;
658 pdbcanvas.pdb.setColours(new ZappoColourScheme());
659 pdbcanvas.redrawneeded = true;
663 public void taylor_actionPerformed(ActionEvent e)
665 pdbcanvas.bysequence = false;
666 pdbcanvas.pdb.setColours(new TaylorColourScheme());
667 pdbcanvas.redrawneeded = true;
671 public void helix_actionPerformed(ActionEvent e)
673 pdbcanvas.bysequence = false;
674 pdbcanvas.pdb.setColours(new HelixColourScheme());
675 pdbcanvas.redrawneeded = true;
679 public void strand_actionPerformed(ActionEvent e)
681 pdbcanvas.bysequence = false;
682 pdbcanvas.pdb.setColours(new StrandColourScheme());
683 pdbcanvas.redrawneeded = true;
687 public void turn_actionPerformed(ActionEvent e)
689 pdbcanvas.bysequence = false;
690 pdbcanvas.pdb.setColours(new TurnColourScheme());
691 pdbcanvas.redrawneeded = true;
695 public void buried_actionPerformed(ActionEvent e)
697 pdbcanvas.bysequence = false;
698 pdbcanvas.pdb.setColours(new BuriedColourScheme());
699 pdbcanvas.redrawneeded = true;
703 public void user_actionPerformed(ActionEvent e)
705 if (e.getActionCommand().equals(
706 MessageManager.getString("action.user_defined")))
708 // new UserDefinedColours(pdbcanvas, null);
712 UserColourScheme udc = (UserColourScheme) UserDefinedColours
713 .getUserColourSchemes().get(e.getActionCommand());
715 pdbcanvas.pdb.setColours(udc);
716 pdbcanvas.redrawneeded = true;
721 public void background_actionPerformed(ActionEvent e)
723 java.awt.Color col = JColorChooser.showDialog(this,
724 MessageManager.getString("label.select_backgroud_colour"),
725 pdbcanvas.backgroundColour);
729 pdbcanvas.backgroundColour = col;
730 pdbcanvas.redrawneeded = true;
735 public void savePDB_actionPerformed(ActionEvent e)
737 JalviewFileChooser chooser = new JalviewFileChooser(
738 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
740 chooser.setFileView(new JalviewFileView());
741 chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
742 chooser.setToolTipText(MessageManager.getString("action.save"));
744 int value = chooser.showSaveDialog(this);
746 if (value == JalviewFileChooser.APPROVE_OPTION)
750 BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
751 File outFile = chooser.getSelectedFile();
753 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
755 while ((data = in.readLine()) != null)
757 if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
764 } catch (Exception ex)
766 ex.printStackTrace();