2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 import java.awt.event.*;
26 import jalview.datamodel.*;
29 import jalview.schemes.*;
31 public class PDBViewer
32 extends JInternalFrame implements Runnable
36 * The associated sequence in an alignment
42 public PDBViewer(PDBEntry entry,
61 pdbcanvas = new PDBCanvas(seqcanvas, sequence);
63 if (pdb.getFile() != null)
67 tmpPDBFile = pdb.getFile();
68 PDBfile pdbfile = new PDBfile(tmpPDBFile,
69 jalview.io.AppletFormatAdapter.FILE);
70 pdbcanvas.setPDBFile(pdbfile);
73 catch (java.io.IOException ex)
80 Thread worker = new Thread(this);
84 setContentPane(pdbcanvas);
85 StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
86 if (pdb.getProperty() != null)
88 if (pdb.getProperty().get("method") != null)
90 title.append(" Method: ");
91 title.append(pdb.getProperty().get("method"));
93 if (pdb.getProperty().get("chains") != null)
95 title.append(" Chain:");
96 title.append(pdb.getProperty().get("chains"));
99 Desktop.addInternalFrame(this, title.toString(), 400, 400);
106 EBIFetchClient ebi = new EBIFetchClient();
107 String query = "pdb:" + pdb.getId();
108 tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
109 if (tmpPDBFile != null)
111 PDBfile pdbfile = new PDBfile(tmpPDBFile,
112 jalview.io.AppletFormatAdapter.FILE);
113 pdbcanvas.setPDBFile(pdbfile);
117 throw new Exception("Empty result for WSDbFetch Query: " + query);
122 ex.printStackTrace();
123 showErrorMessage("Failed to retrieve PDB structure.");
128 private void jbInit()
131 this.addKeyListener(new KeyAdapter()
133 public void keyPressed(KeyEvent evt)
135 pdbcanvas.keyPressed(evt);
139 this.setJMenuBar(jMenuBar1);
140 fileMenu.setText("File");
141 coloursMenu.setText("Colours");
142 saveMenu.setActionCommand("Save Image");
143 saveMenu.setText("Save As");
145 png.addActionListener(new ActionListener()
147 public void actionPerformed(ActionEvent e)
149 png_actionPerformed(e);
153 eps.addActionListener(new ActionListener()
155 public void actionPerformed(ActionEvent e)
157 eps_actionPerformed(e);
160 mapping.setText("View Mapping");
161 mapping.addActionListener(new ActionListener()
163 public void actionPerformed(ActionEvent e)
165 mapping_actionPerformed(e);
168 wire.setText("Wireframe");
169 wire.addActionListener(new ActionListener()
171 public void actionPerformed(ActionEvent e)
173 wire_actionPerformed(e);
176 depth.setSelected(true);
177 depth.setText("Depthcue");
178 depth.addActionListener(new ActionListener()
180 public void actionPerformed(ActionEvent e)
182 depth_actionPerformed(e);
185 zbuffer.setSelected(true);
186 zbuffer.setText("Z Buffering");
187 zbuffer.addActionListener(new ActionListener()
189 public void actionPerformed(ActionEvent e)
191 zbuffer_actionPerformed(e);
194 charge.setText("Charge & Cysteine");
195 charge.addActionListener(new ActionListener()
197 public void actionPerformed(ActionEvent e)
199 charge_actionPerformed(e);
202 chain.setText("By Chain");
203 chain.addActionListener(new ActionListener()
205 public void actionPerformed(ActionEvent e)
207 chain_actionPerformed(e);
210 seqButton.setSelected(true);
211 seqButton.setText("By Sequence");
212 seqButton.addActionListener(new ActionListener()
214 public void actionPerformed(ActionEvent e)
216 seqButton_actionPerformed(e);
219 allchains.setSelected(true);
220 allchains.setText("Show All Chains");
221 allchains.addItemListener(new ItemListener()
223 public void itemStateChanged(ItemEvent e)
225 allchains_itemStateChanged(e);
228 zappo.setText("Zappo");
229 zappo.addActionListener(new ActionListener()
231 public void actionPerformed(ActionEvent e)
233 zappo_actionPerformed(e);
236 taylor.setText("Taylor");
237 taylor.addActionListener(new ActionListener()
239 public void actionPerformed(ActionEvent e)
241 taylor_actionPerformed(e);
244 hydro.setText("Hydro");
245 hydro.addActionListener(new ActionListener()
247 public void actionPerformed(ActionEvent e)
249 hydro_actionPerformed(e);
252 helix.setText("Helix");
253 helix.addActionListener(new ActionListener()
255 public void actionPerformed(ActionEvent e)
257 helix_actionPerformed(e);
260 strand.setText("Strand");
261 strand.addActionListener(new ActionListener()
263 public void actionPerformed(ActionEvent e)
265 strand_actionPerformed(e);
268 turn.setText("Turn");
269 turn.addActionListener(new ActionListener()
271 public void actionPerformed(ActionEvent e)
273 turn_actionPerformed(e);
276 buried.setText("Buried");
277 buried.addActionListener(new ActionListener()
279 public void actionPerformed(ActionEvent e)
281 buried_actionPerformed(e);
284 user.setText("User Defined...");
285 user.addActionListener(new ActionListener()
287 public void actionPerformed(ActionEvent e)
289 user_actionPerformed(e);
292 viewMenu.setText("View");
293 background.setText("Background Colour...");
294 background.addActionListener(new ActionListener()
296 public void actionPerformed(ActionEvent e)
298 background_actionPerformed(e);
301 savePDB.setText("PDB File");
302 savePDB.addActionListener(new ActionListener()
304 public void actionPerformed(ActionEvent e)
306 savePDB_actionPerformed(e);
309 jMenuBar1.add(fileMenu);
310 jMenuBar1.add(coloursMenu);
311 jMenuBar1.add(viewMenu);
312 fileMenu.add(saveMenu);
313 fileMenu.add(mapping);
314 saveMenu.add(savePDB);
317 coloursMenu.add(seqButton);
318 coloursMenu.add(chain);
319 coloursMenu.add(charge);
320 coloursMenu.add(zappo);
321 coloursMenu.add(taylor);
322 coloursMenu.add(hydro);
323 coloursMenu.add(helix);
324 coloursMenu.add(strand);
325 coloursMenu.add(turn);
326 coloursMenu.add(buried);
327 coloursMenu.add(user);
328 coloursMenu.add(background);
329 ButtonGroup bg = new ButtonGroup();
342 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
344 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
345 getUserColourSchemes().keys();
347 while (userColours.hasMoreElements())
349 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
351 nextElement().toString());
352 radioItem.setName("USER_DEFINED");
353 radioItem.addMouseListener(new MouseAdapter()
355 public void mousePressed(MouseEvent evt)
357 if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
359 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
361 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
363 "Remove from default list?",
364 "Remove user defined colour",
365 JOptionPane.YES_NO_OPTION);
366 if (option == JOptionPane.YES_OPTION)
368 jalview.gui.UserDefinedColours.removeColourFromDefaults(
369 radioItem.getText());
370 coloursMenu.remove(radioItem);
374 radioItem.addActionListener(new ActionListener()
376 public void actionPerformed(ActionEvent evt)
378 user_actionPerformed(evt);
385 radioItem.addActionListener(new ActionListener()
387 public void actionPerformed(ActionEvent evt)
389 user_actionPerformed(evt);
392 coloursMenu.add(radioItem);
399 viewMenu.add(zbuffer);
400 viewMenu.add(allchains);
403 JMenuBar jMenuBar1 = new JMenuBar();
404 JMenu fileMenu = new JMenu();
405 JMenu coloursMenu = new JMenu();
406 JMenu saveMenu = new JMenu();
407 JMenuItem png = new JMenuItem();
408 JMenuItem eps = new JMenuItem();
409 JMenuItem mapping = new JMenuItem();
410 JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
411 JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
412 JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
413 JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
415 JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
416 JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
417 JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
418 JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
419 JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
420 JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
421 JRadioButtonMenuItem user = new JRadioButtonMenuItem();
422 JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
423 JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
424 JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
425 JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
426 JMenu viewMenu = new JMenu();
427 JMenuItem background = new JMenuItem();
428 JMenuItem savePDB = new JMenuItem();
433 * @param e DOCUMENT ME!
435 public void eps_actionPerformed(ActionEvent e)
437 makePDBImage(jalview.util.ImageMaker.EPS);
443 * @param e DOCUMENT ME!
445 public void png_actionPerformed(ActionEvent e)
447 makePDBImage(jalview.util.ImageMaker.PNG);
450 void makePDBImage(int type)
452 int width = pdbcanvas.getWidth();
453 int height = pdbcanvas.getHeight();
455 jalview.util.ImageMaker im;
457 if (type == jalview.util.ImageMaker.PNG)
459 im = new jalview.util.ImageMaker(this,
460 jalview.util.ImageMaker.PNG,
461 "Make PNG image from view",
467 im = new jalview.util.ImageMaker(this,
468 jalview.util.ImageMaker.EPS,
469 "Make EPS file from view",
471 null, this.getTitle());
474 if (im.getGraphics() != null)
476 pdbcanvas.drawAll(im.getGraphics(), width, height);
481 public void charge_actionPerformed(ActionEvent e)
483 pdbcanvas.bysequence = false;
484 pdbcanvas.pdb.setChargeColours();
485 pdbcanvas.redrawneeded = true;
489 public void hydro_actionPerformed(ActionEvent e)
491 pdbcanvas.bysequence = false;
492 pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
493 pdbcanvas.redrawneeded = true;
497 public void chain_actionPerformed(ActionEvent e)
499 pdbcanvas.bysequence = false;
500 pdbcanvas.pdb.setChainColours();
501 pdbcanvas.redrawneeded = true;
505 public void zbuffer_actionPerformed(ActionEvent e)
507 pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
508 pdbcanvas.redrawneeded = true;
512 public void molecule_actionPerformed(ActionEvent e)
514 pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
515 pdbcanvas.redrawneeded = true;
519 public void depth_actionPerformed(ActionEvent e)
521 pdbcanvas.depthcue = !pdbcanvas.depthcue;
522 pdbcanvas.redrawneeded = true;
526 public void wire_actionPerformed(ActionEvent e)
528 pdbcanvas.wire = !pdbcanvas.wire;
529 pdbcanvas.redrawneeded = true;
533 public void seqButton_actionPerformed(ActionEvent e)
535 pdbcanvas.bysequence = true;
536 pdbcanvas.updateSeqColours();
539 public void mapping_actionPerformed(ActionEvent e)
541 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
542 Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
543 cap.setText(pdbcanvas.mappingDetails.toString());
546 public void allchains_itemStateChanged(ItemEvent e)
548 pdbcanvas.setAllchainsVisible(allchains.getState());
551 void showErrorMessage(String error)
553 JOptionPane.showInternalMessageDialog(Desktop.desktop,
554 error, "PDB Viewer Error",
555 JOptionPane.WARNING_MESSAGE);
558 public void zappo_actionPerformed(ActionEvent e)
560 pdbcanvas.bysequence = false;
561 pdbcanvas.pdb.setColours(new ZappoColourScheme());
562 pdbcanvas.redrawneeded = true;
566 public void taylor_actionPerformed(ActionEvent e)
568 pdbcanvas.bysequence = false;
569 pdbcanvas.pdb.setColours(new TaylorColourScheme());
570 pdbcanvas.redrawneeded = true;
574 public void helix_actionPerformed(ActionEvent e)
576 pdbcanvas.bysequence = false;
577 pdbcanvas.pdb.setColours(new HelixColourScheme());
578 pdbcanvas.redrawneeded = true;
582 public void strand_actionPerformed(ActionEvent e)
584 pdbcanvas.bysequence = false;
585 pdbcanvas.pdb.setColours(new StrandColourScheme());
586 pdbcanvas.redrawneeded = true;
590 public void turn_actionPerformed(ActionEvent e)
592 pdbcanvas.bysequence = false;
593 pdbcanvas.pdb.setColours(new TurnColourScheme());
594 pdbcanvas.redrawneeded = true;
598 public void buried_actionPerformed(ActionEvent e)
600 pdbcanvas.bysequence = false;
601 pdbcanvas.pdb.setColours(new BuriedColourScheme());
602 pdbcanvas.redrawneeded = true;
606 public void user_actionPerformed(ActionEvent e)
608 if (e.getActionCommand().equals("User Defined..."))
610 new UserDefinedColours(pdbcanvas, null);
614 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
615 getUserColourSchemes().get(e.getActionCommand());
617 pdbcanvas.pdb.setColours(udc);
618 pdbcanvas.redrawneeded = true;
623 public void background_actionPerformed(ActionEvent e)
625 java.awt.Color col = JColorChooser.showDialog(this,
626 "Select Background Colour",
627 pdbcanvas.backgroundColour);
631 pdbcanvas.backgroundColour = col;
632 pdbcanvas.redrawneeded = true;
637 public void savePDB_actionPerformed(ActionEvent e)
639 JalviewFileChooser chooser = new JalviewFileChooser(
640 jalview.bin.Cache.getProperty(
643 chooser.setFileView(new JalviewFileView());
644 chooser.setDialogTitle("Save PDB File");
645 chooser.setToolTipText("Save");
647 int value = chooser.showSaveDialog(this);
649 if (value == JalviewFileChooser.APPROVE_OPTION)
653 BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
654 File outFile = chooser.getSelectedFile();
656 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
658 while ( (data = in.readLine()) != null)
661 ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
671 ex.printStackTrace();