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;
66 public class PDBViewer extends JInternalFrame implements Runnable
70 * The associated sequence in an alignment
86 public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
87 AlignmentPanel ap, String protocol)
89 this.pdbentry = pdbentry;
93 this.protocol = protocol;
98 } catch (Exception ex)
100 ex.printStackTrace();
103 StringBuffer title = new StringBuffer(seq[0].getName() + ":"
104 + pdbentry.getFile());
106 pdbcanvas = new PDBCanvas();
108 setContentPane(pdbcanvas);
110 if (pdbentry.getFile() != null)
114 tmpPDBFile = pdbentry.getFile();
115 PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
116 jalview.io.AppletFormatAdapter.FILE);
118 pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
120 } catch (java.io.IOException ex)
122 ex.printStackTrace();
127 Thread worker = new Thread(this);
131 if (pdbentry.getProperty() != null)
133 if (pdbentry.getProperty().get("method") != null)
135 title.append(" Method: ");
136 title.append(pdbentry.getProperty().get("method"));
138 if (pdbentry.getProperty().get("chains") != null)
140 title.append(" Chain:");
141 title.append(pdbentry.getProperty().get("chains"));
144 Desktop.addInternalFrame(this, title.toString(), 400, 400);
152 EBIFetchClient ebi = new EBIFetchClient();
153 String query = "pdb:" + pdbentry.getId();
154 pdbentry.setFile(ebi.fetchDataAsFile(query, "default", ".xml")
157 if (pdbentry.getFile() != null)
159 pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
161 } catch (Exception ex)
163 pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
164 ex.printStackTrace();
168 private void jbInit() throws Exception
170 this.addKeyListener(new KeyAdapter()
173 public void keyPressed(KeyEvent evt)
175 pdbcanvas.keyPressed(evt);
179 this.setJMenuBar(jMenuBar1);
180 fileMenu.setText(MessageManager.getString("action.file"));
181 coloursMenu.setText(MessageManager.getString("label.colours"));
182 saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
183 saveMenu.setText(MessageManager.getString("action.save_as"));
185 png.addActionListener(new ActionListener()
188 public void actionPerformed(ActionEvent e)
190 png_actionPerformed(e);
194 eps.addActionListener(new ActionListener()
197 public void actionPerformed(ActionEvent e)
199 eps_actionPerformed(e);
202 mapping.setText(MessageManager.getString("label.view_mapping"));
203 mapping.addActionListener(new ActionListener()
206 public void actionPerformed(ActionEvent e)
208 mapping_actionPerformed(e);
211 wire.setText(MessageManager.getString("label.wireframe"));
212 wire.addActionListener(new ActionListener()
215 public void actionPerformed(ActionEvent e)
217 wire_actionPerformed(e);
220 depth.setSelected(true);
221 depth.setText(MessageManager.getString("label.depthcue"));
222 depth.addActionListener(new ActionListener()
225 public void actionPerformed(ActionEvent e)
227 depth_actionPerformed(e);
230 zbuffer.setSelected(true);
231 zbuffer.setText(MessageManager.getString("label.z_buffering"));
232 zbuffer.addActionListener(new ActionListener()
235 public void actionPerformed(ActionEvent e)
237 zbuffer_actionPerformed(e);
240 charge.setText(MessageManager.getString("label.charge_cysteine"));
241 charge.addActionListener(new ActionListener()
244 public void actionPerformed(ActionEvent e)
246 charge_actionPerformed(e);
249 chain.setText(MessageManager.getString("action.by_chain"));
250 chain.addActionListener(new ActionListener()
253 public void actionPerformed(ActionEvent e)
255 chain_actionPerformed(e);
258 seqButton.setSelected(true);
259 seqButton.setText(MessageManager.getString("action.by_sequence"));
260 seqButton.addActionListener(new ActionListener()
263 public void actionPerformed(ActionEvent e)
265 seqButton_actionPerformed(e);
268 allchains.setSelected(true);
269 allchains.setText(MessageManager.getString("label.show_all_chains"));
270 allchains.addItemListener(new ItemListener()
273 public void itemStateChanged(ItemEvent e)
275 allchains_itemStateChanged(e);
278 zappo.setText(MessageManager.getString("label.zappo"));
279 zappo.addActionListener(new ActionListener()
282 public void actionPerformed(ActionEvent e)
284 zappo_actionPerformed(e);
287 taylor.setText(MessageManager.getString("label.taylor"));
288 taylor.addActionListener(new ActionListener()
291 public void actionPerformed(ActionEvent e)
293 taylor_actionPerformed(e);
296 hydro.setText(MessageManager.getString("label.hydrophobicity"));
297 hydro.addActionListener(new ActionListener()
300 public void actionPerformed(ActionEvent e)
302 hydro_actionPerformed(e);
305 helix.setText(MessageManager.getString("label.helix_propensity"));
306 helix.addActionListener(new ActionListener()
309 public void actionPerformed(ActionEvent e)
311 helix_actionPerformed(e);
314 strand.setText(MessageManager.getString("label.strand_propensity"));
315 strand.addActionListener(new ActionListener()
318 public void actionPerformed(ActionEvent e)
320 strand_actionPerformed(e);
323 turn.setText(MessageManager.getString("label.turn_propensity"));
324 turn.addActionListener(new ActionListener()
327 public void actionPerformed(ActionEvent e)
329 turn_actionPerformed(e);
332 buried.setText(MessageManager.getString("label.buried_index"));
333 buried.addActionListener(new ActionListener()
336 public void actionPerformed(ActionEvent e)
338 buried_actionPerformed(e);
341 user.setText(MessageManager.getString("action.user_defined"));
342 user.addActionListener(new ActionListener()
345 public void actionPerformed(ActionEvent e)
347 user_actionPerformed(e);
350 viewMenu.setText(MessageManager.getString("action.view"));
352 .setText(MessageManager.getString("action.background_colour"));
353 background.addActionListener(new ActionListener()
356 public void actionPerformed(ActionEvent e)
358 background_actionPerformed(e);
361 savePDB.setText(MessageManager.getString("label.pdb_file"));
362 savePDB.addActionListener(new ActionListener()
365 public void actionPerformed(ActionEvent e)
367 savePDB_actionPerformed(e);
370 jMenuBar1.add(fileMenu);
371 jMenuBar1.add(coloursMenu);
372 jMenuBar1.add(viewMenu);
373 fileMenu.add(saveMenu);
374 fileMenu.add(mapping);
375 saveMenu.add(savePDB);
378 coloursMenu.add(seqButton);
379 coloursMenu.add(chain);
380 coloursMenu.add(charge);
381 coloursMenu.add(zappo);
382 coloursMenu.add(taylor);
383 coloursMenu.add(hydro);
384 coloursMenu.add(helix);
385 coloursMenu.add(strand);
386 coloursMenu.add(turn);
387 coloursMenu.add(buried);
388 coloursMenu.add(user);
389 coloursMenu.add(background);
390 ButtonGroup bg = new ButtonGroup();
403 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
405 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
406 .getUserColourSchemes().keys();
408 while (userColours.hasMoreElements())
410 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
411 userColours.nextElement().toString());
412 radioItem.setName("USER_DEFINED");
413 radioItem.addMouseListener(new MouseAdapter()
416 public void mousePressed(MouseEvent evt)
418 if (evt.isPopupTrigger())
420 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
422 int option = JOptionPane.showInternalConfirmDialog(
423 jalview.gui.Desktop.desktop,
425 .getString("label.remove_from_default_list"),
427 .getString("label.remove_user_defined_colour"),
428 JOptionPane.YES_NO_OPTION);
429 if (option == JOptionPane.YES_OPTION)
431 jalview.gui.UserDefinedColours
432 .removeColourFromDefaults(radioItem.getText());
433 coloursMenu.remove(radioItem);
437 radioItem.addActionListener(new ActionListener()
440 public void actionPerformed(ActionEvent evt)
442 user_actionPerformed(evt);
449 radioItem.addActionListener(new ActionListener()
452 public void actionPerformed(ActionEvent evt)
454 user_actionPerformed(evt);
457 coloursMenu.add(radioItem);
464 viewMenu.add(zbuffer);
465 viewMenu.add(allchains);
468 JMenuBar jMenuBar1 = new JMenuBar();
470 JMenu fileMenu = new JMenu();
472 JMenu coloursMenu = new JMenu();
474 JMenu saveMenu = new JMenu();
476 JMenuItem png = new JMenuItem();
478 JMenuItem eps = new JMenuItem();
480 JMenuItem mapping = new JMenuItem();
482 JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
484 JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
486 JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
488 JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
490 JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
492 JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
494 JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
496 JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
498 JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
500 JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
502 JRadioButtonMenuItem user = new JRadioButtonMenuItem();
504 JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
506 JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
508 JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
510 JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
512 JMenu viewMenu = new JMenu();
514 JMenuItem background = new JMenuItem();
516 JMenuItem savePDB = new JMenuItem();
524 public void eps_actionPerformed(ActionEvent e)
526 makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
535 public void png_actionPerformed(ActionEvent e)
537 makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
540 void makePDBImage(jalview.util.ImageMaker.TYPE type)
542 int width = pdbcanvas.getWidth();
543 int height = pdbcanvas.getHeight();
545 jalview.util.ImageMaker im;
547 if (type == jalview.util.ImageMaker.TYPE.PNG)
549 im = new jalview.util.ImageMaker(this,
550 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
551 width, height, null, null, null, 0, false);
553 else if (type == jalview.util.ImageMaker.TYPE.EPS)
555 im = new jalview.util.ImageMaker(this,
556 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
557 width, height, null, this.getTitle(), null, 0, false);
562 im = new jalview.util.ImageMaker(this,
563 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
564 width, height, null, this.getTitle(), null, 0, false);
567 if (im.getGraphics() != null)
569 pdbcanvas.drawAll(im.getGraphics(), width, height);
574 public void charge_actionPerformed(ActionEvent e)
576 pdbcanvas.bysequence = false;
577 pdbcanvas.pdb.setChargeColours();
578 pdbcanvas.redrawneeded = true;
582 public void hydro_actionPerformed(ActionEvent e)
584 pdbcanvas.bysequence = false;
585 pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
586 pdbcanvas.redrawneeded = true;
590 public void chain_actionPerformed(ActionEvent e)
592 pdbcanvas.bysequence = false;
593 pdbcanvas.pdb.setChainColours();
594 pdbcanvas.redrawneeded = true;
598 public void zbuffer_actionPerformed(ActionEvent e)
600 pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
601 pdbcanvas.redrawneeded = true;
605 public void molecule_actionPerformed(ActionEvent e)
607 pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
608 pdbcanvas.redrawneeded = true;
612 public void depth_actionPerformed(ActionEvent e)
614 pdbcanvas.depthcue = !pdbcanvas.depthcue;
615 pdbcanvas.redrawneeded = true;
619 public void wire_actionPerformed(ActionEvent e)
621 pdbcanvas.wire = !pdbcanvas.wire;
622 pdbcanvas.redrawneeded = true;
626 public void seqButton_actionPerformed(ActionEvent e)
628 pdbcanvas.bysequence = true;
629 pdbcanvas.updateSeqColours();
632 public void mapping_actionPerformed(ActionEvent e)
634 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
637 cap.setText(pdbcanvas.mappingDetails.toString());
638 Desktop.addInternalFrame(cap,
639 MessageManager.getString("label.pdb_sequence_mapping"), 550,
641 } catch (OutOfMemoryError oom)
643 new OOMWarning("Opening sequence to structure mapping report", oom);
648 public void allchains_itemStateChanged(ItemEvent e)
650 pdbcanvas.setAllchainsVisible(allchains.getState());
653 public void zappo_actionPerformed(ActionEvent e)
655 pdbcanvas.bysequence = false;
656 pdbcanvas.pdb.setColours(new ZappoColourScheme());
657 pdbcanvas.redrawneeded = true;
661 public void taylor_actionPerformed(ActionEvent e)
663 pdbcanvas.bysequence = false;
664 pdbcanvas.pdb.setColours(new TaylorColourScheme());
665 pdbcanvas.redrawneeded = true;
669 public void helix_actionPerformed(ActionEvent e)
671 pdbcanvas.bysequence = false;
672 pdbcanvas.pdb.setColours(new HelixColourScheme());
673 pdbcanvas.redrawneeded = true;
677 public void strand_actionPerformed(ActionEvent e)
679 pdbcanvas.bysequence = false;
680 pdbcanvas.pdb.setColours(new StrandColourScheme());
681 pdbcanvas.redrawneeded = true;
685 public void turn_actionPerformed(ActionEvent e)
687 pdbcanvas.bysequence = false;
688 pdbcanvas.pdb.setColours(new TurnColourScheme());
689 pdbcanvas.redrawneeded = true;
693 public void buried_actionPerformed(ActionEvent e)
695 pdbcanvas.bysequence = false;
696 pdbcanvas.pdb.setColours(new BuriedColourScheme());
697 pdbcanvas.redrawneeded = true;
701 public void user_actionPerformed(ActionEvent e)
703 if (e.getActionCommand().equals(
704 MessageManager.getString("action.user_defined")))
706 // new UserDefinedColours(pdbcanvas, null);
710 UserColourScheme udc = (UserColourScheme) UserDefinedColours
711 .getUserColourSchemes().get(e.getActionCommand());
713 pdbcanvas.pdb.setColours(udc);
714 pdbcanvas.redrawneeded = true;
719 public void background_actionPerformed(ActionEvent e)
721 java.awt.Color col = JColorChooser.showDialog(this,
722 MessageManager.getString("label.select_backgroud_colour"),
723 pdbcanvas.backgroundColour);
727 pdbcanvas.backgroundColour = col;
728 pdbcanvas.redrawneeded = true;
733 public void savePDB_actionPerformed(ActionEvent e)
735 JalviewFileChooser chooser = new JalviewFileChooser(
736 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
738 chooser.setFileView(new JalviewFileView());
739 chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
740 chooser.setToolTipText(MessageManager.getString("action.save"));
742 int value = chooser.showSaveDialog(this);
744 if (value == JalviewFileChooser.APPROVE_OPTION)
748 BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
749 File outFile = chooser.getSelectedFile();
751 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
753 while ((data = in.readLine()) != null)
755 if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
762 } catch (Exception ex)
764 ex.printStackTrace();