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.JvOptionPane;
28 import jalview.gui.OOMWarning;
29 import jalview.gui.UserDefinedColours;
30 import jalview.io.DataSourceType;
31 import jalview.io.JalviewFileChooser;
32 import jalview.io.JalviewFileView;
33 import jalview.schemes.BuriedColourScheme;
34 import jalview.schemes.HelixColourScheme;
35 import jalview.schemes.HydrophobicColourScheme;
36 import jalview.schemes.StrandColourScheme;
37 import jalview.schemes.TaylorColourScheme;
38 import jalview.schemes.TurnColourScheme;
39 import jalview.schemes.UserColourScheme;
40 import jalview.schemes.ZappoColourScheme;
41 import jalview.util.MessageManager;
42 import jalview.ws.ebi.EBIFetchClient;
44 import java.awt.Color;
45 import java.awt.event.ActionEvent;
46 import java.awt.event.ActionListener;
47 import java.awt.event.ItemEvent;
48 import java.awt.event.ItemListener;
49 import java.awt.event.KeyAdapter;
50 import java.awt.event.KeyEvent;
51 import java.awt.event.MouseAdapter;
52 import java.awt.event.MouseEvent;
53 import java.io.BufferedReader;
55 import java.io.FileOutputStream;
56 import java.io.FileReader;
57 import java.io.PrintWriter;
60 import javax.swing.ButtonGroup;
61 import javax.swing.JCheckBoxMenuItem;
62 import javax.swing.JColorChooser;
63 import javax.swing.JInternalFrame;
64 import javax.swing.JMenu;
65 import javax.swing.JMenuBar;
66 import javax.swing.JMenuItem;
67 import javax.swing.JRadioButtonMenuItem;
69 public class PDBViewer extends JInternalFrame implements Runnable
73 * The associated sequence in an alignment
85 DataSourceType protocol;
89 public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
90 AlignmentPanel ap, DataSourceType protocol)
92 this.pdbentry = pdbentry;
96 this.protocol = protocol;
101 } catch (Exception ex)
103 ex.printStackTrace();
106 StringBuffer title = new StringBuffer(seq[0].getName() + ":"
107 + pdbentry.getFile());
109 pdbcanvas = new PDBCanvas();
111 setContentPane(pdbcanvas);
113 if (pdbentry.getFile() != null)
117 tmpPDBFile = pdbentry.getFile();
118 PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
119 DataSourceType.FILE);
121 pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
123 } catch (java.io.IOException ex)
125 ex.printStackTrace();
130 Thread worker = new Thread(this);
134 String method = (String) pdbentry.getProperty("method");
137 title.append(" Method: ");
138 title.append(method);
140 String ch = (String) pdbentry.getProperty("chains");
143 title.append(" Chain:");
146 Desktop.addInternalFrame(this, title.toString(), 400, 400);
154 EBIFetchClient ebi = new EBIFetchClient();
155 String query = "pdb:" + pdbentry.getId();
156 pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "xml")
159 if (pdbentry.getFile() != null)
161 pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
163 } catch (Exception ex)
165 pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
166 ex.printStackTrace();
170 private void jbInit() throws Exception
172 this.addKeyListener(new KeyAdapter()
175 public void keyPressed(KeyEvent evt)
177 pdbcanvas.keyPressed(evt);
181 this.setJMenuBar(jMenuBar1);
182 fileMenu.setText(MessageManager.getString("action.file"));
183 coloursMenu.setText(MessageManager.getString("label.colours"));
184 saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
185 saveMenu.setText(MessageManager.getString("action.save_as"));
187 png.addActionListener(new ActionListener()
190 public void actionPerformed(ActionEvent e)
192 png_actionPerformed(e);
196 eps.addActionListener(new ActionListener()
199 public void actionPerformed(ActionEvent e)
201 eps_actionPerformed(e);
204 mapping.setText(MessageManager.getString("label.view_mapping"));
205 mapping.addActionListener(new ActionListener()
208 public void actionPerformed(ActionEvent e)
210 mapping_actionPerformed(e);
213 wire.setText(MessageManager.getString("label.wireframe"));
214 wire.addActionListener(new ActionListener()
217 public void actionPerformed(ActionEvent e)
219 wire_actionPerformed(e);
222 depth.setSelected(true);
223 depth.setText(MessageManager.getString("label.depthcue"));
224 depth.addActionListener(new ActionListener()
227 public void actionPerformed(ActionEvent e)
229 depth_actionPerformed(e);
232 zbuffer.setSelected(true);
233 zbuffer.setText(MessageManager.getString("label.z_buffering"));
234 zbuffer.addActionListener(new ActionListener()
237 public void actionPerformed(ActionEvent e)
239 zbuffer_actionPerformed(e);
242 charge.setText(MessageManager.getString("label.charge_cysteine"));
243 charge.addActionListener(new ActionListener()
246 public void actionPerformed(ActionEvent e)
248 charge_actionPerformed(e);
251 chain.setText(MessageManager.getString("action.by_chain"));
252 chain.addActionListener(new ActionListener()
255 public void actionPerformed(ActionEvent e)
257 chain_actionPerformed(e);
260 seqButton.setSelected(true);
261 seqButton.setText(MessageManager.getString("action.by_sequence"));
262 seqButton.addActionListener(new ActionListener()
265 public void actionPerformed(ActionEvent e)
267 seqButton_actionPerformed(e);
270 allchains.setSelected(true);
271 allchains.setText(MessageManager.getString("label.show_all_chains"));
272 allchains.addItemListener(new ItemListener()
275 public void itemStateChanged(ItemEvent e)
277 allchains_itemStateChanged(e);
280 zappo.setText(MessageManager.getString("label.zappo"));
281 zappo.addActionListener(new ActionListener()
284 public void actionPerformed(ActionEvent e)
286 zappo_actionPerformed(e);
289 taylor.setText(MessageManager.getString("label.taylor"));
290 taylor.addActionListener(new ActionListener()
293 public void actionPerformed(ActionEvent e)
295 taylor_actionPerformed(e);
298 hydro.setText(MessageManager.getString("label.hydrophobicity"));
299 hydro.addActionListener(new ActionListener()
302 public void actionPerformed(ActionEvent e)
304 hydro_actionPerformed(e);
307 helix.setText(MessageManager.getString("label.helix_propensity"));
308 helix.addActionListener(new ActionListener()
311 public void actionPerformed(ActionEvent e)
313 helix_actionPerformed(e);
316 strand.setText(MessageManager.getString("label.strand_propensity"));
317 strand.addActionListener(new ActionListener()
320 public void actionPerformed(ActionEvent e)
322 strand_actionPerformed(e);
325 turn.setText(MessageManager.getString("label.turn_propensity"));
326 turn.addActionListener(new ActionListener()
329 public void actionPerformed(ActionEvent e)
331 turn_actionPerformed(e);
334 buried.setText(MessageManager.getString("label.buried_index"));
335 buried.addActionListener(new ActionListener()
338 public void actionPerformed(ActionEvent e)
340 buried_actionPerformed(e);
343 user.setText(MessageManager.getString("action.user_defined"));
344 user.addActionListener(new ActionListener()
347 public void actionPerformed(ActionEvent e)
349 user_actionPerformed(e);
352 viewMenu.setText(MessageManager.getString("action.view"));
354 .setText(MessageManager.getString("action.background_colour"));
355 background.addActionListener(new ActionListener()
358 public void actionPerformed(ActionEvent e)
360 background_actionPerformed(e);
363 savePDB.setText(MessageManager.getString("label.pdb_file"));
364 savePDB.addActionListener(new ActionListener()
367 public void actionPerformed(ActionEvent e)
369 savePDB_actionPerformed(e);
372 jMenuBar1.add(fileMenu);
373 jMenuBar1.add(coloursMenu);
374 jMenuBar1.add(viewMenu);
375 fileMenu.add(saveMenu);
376 fileMenu.add(mapping);
377 saveMenu.add(savePDB);
380 coloursMenu.add(seqButton);
381 coloursMenu.add(chain);
382 coloursMenu.add(charge);
383 coloursMenu.add(zappo);
384 coloursMenu.add(taylor);
385 coloursMenu.add(hydro);
386 coloursMenu.add(helix);
387 coloursMenu.add(strand);
388 coloursMenu.add(turn);
389 coloursMenu.add(buried);
390 coloursMenu.add(user);
391 coloursMenu.add(background);
392 ButtonGroup bg = new ButtonGroup();
405 Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
406 .getUserColourSchemes();
407 if (userColourSchemes != null)
409 for (String userColour : userColourSchemes.keySet())
411 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
413 radioItem.setName("USER_DEFINED");
414 radioItem.addMouseListener(new MouseAdapter()
417 public void mousePressed(MouseEvent evt)
419 if (evt.isPopupTrigger()) // Mac
421 offerRemoval(radioItem);
426 public void mouseReleased(MouseEvent evt)
428 if (evt.isPopupTrigger()) // Windows
430 offerRemoval(radioItem);
437 void offerRemoval(final JRadioButtonMenuItem radioItem)
439 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
441 int option = JvOptionPane.showInternalConfirmDialog(
442 jalview.gui.Desktop.desktop, MessageManager
443 .getString("label.remove_from_default_list"),
445 .getString("label.remove_user_defined_colour"),
446 JvOptionPane.YES_NO_OPTION);
447 if (option == JvOptionPane.YES_OPTION)
449 jalview.gui.UserDefinedColours
450 .removeColourFromDefaults(radioItem.getText());
451 coloursMenu.remove(radioItem);
455 radioItem.addActionListener(new ActionListener()
458 public void actionPerformed(ActionEvent evt)
460 user_actionPerformed(evt);
466 radioItem.addActionListener(new ActionListener()
469 public void actionPerformed(ActionEvent evt)
471 user_actionPerformed(evt);
474 coloursMenu.add(radioItem);
481 viewMenu.add(zbuffer);
482 viewMenu.add(allchains);
485 JMenuBar jMenuBar1 = new JMenuBar();
487 JMenu fileMenu = new JMenu();
489 JMenu coloursMenu = new JMenu();
491 JMenu saveMenu = new JMenu();
493 JMenuItem png = new JMenuItem();
495 JMenuItem eps = new JMenuItem();
497 JMenuItem mapping = new JMenuItem();
499 JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
501 JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
503 JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
505 JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
507 JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
509 JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
511 JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
513 JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
515 JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
517 JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
519 JRadioButtonMenuItem user = new JRadioButtonMenuItem();
521 JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
523 JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
525 JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
527 JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
529 JMenu viewMenu = new JMenu();
531 JMenuItem background = new JMenuItem();
533 JMenuItem savePDB = new JMenuItem();
541 public void eps_actionPerformed(ActionEvent e)
543 makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
552 public void png_actionPerformed(ActionEvent e)
554 makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
557 void makePDBImage(jalview.util.ImageMaker.TYPE type)
559 int width = pdbcanvas.getWidth();
560 int height = pdbcanvas.getHeight();
562 jalview.util.ImageMaker im;
564 if (type == jalview.util.ImageMaker.TYPE.PNG)
566 im = new jalview.util.ImageMaker(this,
567 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
568 width, height, null, null, null, 0, false);
570 else if (type == jalview.util.ImageMaker.TYPE.EPS)
572 im = new jalview.util.ImageMaker(this,
573 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
574 width, height, null, this.getTitle(), null, 0, false);
579 im = new jalview.util.ImageMaker(this,
580 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
581 width, height, null, this.getTitle(), null, 0, false);
584 if (im.getGraphics() != null)
586 pdbcanvas.drawAll(im.getGraphics(), width, height);
591 public void charge_actionPerformed(ActionEvent e)
593 pdbcanvas.bysequence = false;
594 pdbcanvas.pdb.setChargeColours();
595 pdbcanvas.redrawneeded = true;
599 public void hydro_actionPerformed(ActionEvent e)
601 pdbcanvas.bysequence = false;
602 pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
603 pdbcanvas.redrawneeded = true;
607 public void chain_actionPerformed(ActionEvent e)
609 pdbcanvas.bysequence = false;
610 pdbcanvas.pdb.setChainColours();
611 pdbcanvas.redrawneeded = true;
615 public void zbuffer_actionPerformed(ActionEvent e)
617 pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
618 pdbcanvas.redrawneeded = true;
622 public void molecule_actionPerformed(ActionEvent e)
624 pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
625 pdbcanvas.redrawneeded = true;
629 public void depth_actionPerformed(ActionEvent e)
631 pdbcanvas.depthcue = !pdbcanvas.depthcue;
632 pdbcanvas.redrawneeded = true;
636 public void wire_actionPerformed(ActionEvent e)
638 pdbcanvas.wire = !pdbcanvas.wire;
639 pdbcanvas.redrawneeded = true;
643 public void seqButton_actionPerformed(ActionEvent e)
645 pdbcanvas.bysequence = true;
646 pdbcanvas.updateSeqColours();
649 public void mapping_actionPerformed(ActionEvent e)
651 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
654 cap.setText(pdbcanvas.mappingDetails.toString());
655 Desktop.addInternalFrame(cap,
656 MessageManager.getString("label.pdb_sequence_mapping"), 550,
658 } catch (OutOfMemoryError oom)
660 new OOMWarning("Opening sequence to structure mapping report", oom);
665 public void allchains_itemStateChanged(ItemEvent e)
667 pdbcanvas.setAllchainsVisible(allchains.getState());
670 public void zappo_actionPerformed(ActionEvent e)
672 pdbcanvas.bysequence = false;
673 pdbcanvas.pdb.setColours(new ZappoColourScheme());
674 pdbcanvas.redrawneeded = true;
678 public void taylor_actionPerformed(ActionEvent e)
680 pdbcanvas.bysequence = false;
681 pdbcanvas.pdb.setColours(new TaylorColourScheme());
682 pdbcanvas.redrawneeded = true;
686 public void helix_actionPerformed(ActionEvent e)
688 pdbcanvas.bysequence = false;
689 pdbcanvas.pdb.setColours(new HelixColourScheme());
690 pdbcanvas.redrawneeded = true;
694 public void strand_actionPerformed(ActionEvent e)
696 pdbcanvas.bysequence = false;
697 pdbcanvas.pdb.setColours(new StrandColourScheme());
698 pdbcanvas.redrawneeded = true;
702 public void turn_actionPerformed(ActionEvent e)
704 pdbcanvas.bysequence = false;
705 pdbcanvas.pdb.setColours(new TurnColourScheme());
706 pdbcanvas.redrawneeded = true;
710 public void buried_actionPerformed(ActionEvent e)
712 pdbcanvas.bysequence = false;
713 pdbcanvas.pdb.setColours(new BuriedColourScheme());
714 pdbcanvas.redrawneeded = true;
718 public void user_actionPerformed(ActionEvent e)
720 if (e.getActionCommand().equals(
721 MessageManager.getString("action.user_defined")))
723 // new UserDefinedColours(pdbcanvas, null);
727 UserColourScheme udc = UserDefinedColours
728 .getUserColourSchemes().get(e.getActionCommand());
730 pdbcanvas.pdb.setColours(udc);
731 pdbcanvas.redrawneeded = true;
736 public void background_actionPerformed(ActionEvent e)
738 Color col = JColorChooser.showDialog(this,
739 MessageManager.getString("label.select_background_colour"),
740 pdbcanvas.backgroundColour);
744 pdbcanvas.backgroundColour = col;
745 pdbcanvas.redrawneeded = true;
750 public void savePDB_actionPerformed(ActionEvent e)
752 JalviewFileChooser chooser = new JalviewFileChooser(
753 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
755 chooser.setFileView(new JalviewFileView());
756 chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
757 chooser.setToolTipText(MessageManager.getString("action.save"));
759 int value = chooser.showSaveDialog(this);
761 if (value == JalviewFileChooser.APPROVE_OPTION)
765 BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
766 File outFile = chooser.getSelectedFile();
768 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
770 while ((data = in.readLine()) != null)
772 if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
779 } catch (Exception ex)
781 ex.printStackTrace();