2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
22 import java.awt.event.*;
25 import jalview.datamodel.*;
28 import jalview.schemes.*;
29 import jalview.ws.ebi.EBIFetchClient;
31 public class PDBViewer extends JInternalFrame implements Runnable
35 * The associated sequence in an alignment
51 public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
52 AlignmentPanel ap, String protocol)
54 this.pdbentry = pdbentry;
58 this.protocol = protocol;
63 } catch (Exception ex)
68 StringBuffer title = new StringBuffer(seq[0].getName() + ":"
69 + pdbentry.getFile());
71 pdbcanvas = new PDBCanvas();
73 setContentPane(pdbcanvas);
75 if (pdbentry.getFile() != null)
79 tmpPDBFile = pdbentry.getFile();
80 PDBfile pdbfile = new PDBfile(tmpPDBFile,
81 jalview.io.AppletFormatAdapter.FILE);
83 pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
85 } catch (java.io.IOException ex)
92 Thread worker = new Thread(this);
96 if (pdbentry.getProperty() != null)
98 if (pdbentry.getProperty().get("method") != null)
100 title.append(" Method: ");
101 title.append(pdbentry.getProperty().get("method"));
103 if (pdbentry.getProperty().get("chains") != null)
105 title.append(" Chain:");
106 title.append(pdbentry.getProperty().get("chains"));
109 Desktop.addInternalFrame(this, title.toString(), 400, 400);
116 EBIFetchClient ebi = new EBIFetchClient();
117 String query = "pdb:" + pdbentry.getId();
118 pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
121 if (pdbentry.getFile() != null)
122 pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
123 } catch (Exception ex)
125 pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
126 ex.printStackTrace();
130 private void jbInit() throws Exception
132 this.addKeyListener(new KeyAdapter()
134 public void keyPressed(KeyEvent evt)
136 pdbcanvas.keyPressed(evt);
140 this.setJMenuBar(jMenuBar1);
141 fileMenu.setText("File");
142 coloursMenu.setText("Colours");
143 saveMenu.setActionCommand("Save Image");
144 saveMenu.setText("Save As");
146 png.addActionListener(new ActionListener()
148 public void actionPerformed(ActionEvent e)
150 png_actionPerformed(e);
154 eps.addActionListener(new ActionListener()
156 public void actionPerformed(ActionEvent e)
158 eps_actionPerformed(e);
161 mapping.setText("View Mapping");
162 mapping.addActionListener(new ActionListener()
164 public void actionPerformed(ActionEvent e)
166 mapping_actionPerformed(e);
169 wire.setText("Wireframe");
170 wire.addActionListener(new ActionListener()
172 public void actionPerformed(ActionEvent e)
174 wire_actionPerformed(e);
177 depth.setSelected(true);
178 depth.setText("Depthcue");
179 depth.addActionListener(new ActionListener()
181 public void actionPerformed(ActionEvent e)
183 depth_actionPerformed(e);
186 zbuffer.setSelected(true);
187 zbuffer.setText("Z Buffering");
188 zbuffer.addActionListener(new ActionListener()
190 public void actionPerformed(ActionEvent e)
192 zbuffer_actionPerformed(e);
195 charge.setText("Charge & Cysteine");
196 charge.addActionListener(new ActionListener()
198 public void actionPerformed(ActionEvent e)
200 charge_actionPerformed(e);
203 chain.setText("By Chain");
204 chain.addActionListener(new ActionListener()
206 public void actionPerformed(ActionEvent e)
208 chain_actionPerformed(e);
211 seqButton.setSelected(true);
212 seqButton.setText("By Sequence");
213 seqButton.addActionListener(new ActionListener()
215 public void actionPerformed(ActionEvent e)
217 seqButton_actionPerformed(e);
220 allchains.setSelected(true);
221 allchains.setText("Show All Chains");
222 allchains.addItemListener(new ItemListener()
224 public void itemStateChanged(ItemEvent e)
226 allchains_itemStateChanged(e);
229 zappo.setText("Zappo");
230 zappo.addActionListener(new ActionListener()
232 public void actionPerformed(ActionEvent e)
234 zappo_actionPerformed(e);
237 taylor.setText("Taylor");
238 taylor.addActionListener(new ActionListener()
240 public void actionPerformed(ActionEvent e)
242 taylor_actionPerformed(e);
245 hydro.setText("Hydro");
246 hydro.addActionListener(new ActionListener()
248 public void actionPerformed(ActionEvent e)
250 hydro_actionPerformed(e);
253 helix.setText("Helix");
254 helix.addActionListener(new ActionListener()
256 public void actionPerformed(ActionEvent e)
258 helix_actionPerformed(e);
261 strand.setText("Strand");
262 strand.addActionListener(new ActionListener()
264 public void actionPerformed(ActionEvent e)
266 strand_actionPerformed(e);
269 turn.setText("Turn");
270 turn.addActionListener(new ActionListener()
272 public void actionPerformed(ActionEvent e)
274 turn_actionPerformed(e);
277 buried.setText("Buried");
278 buried.addActionListener(new ActionListener()
280 public void actionPerformed(ActionEvent e)
282 buried_actionPerformed(e);
285 user.setText("User Defined...");
286 user.addActionListener(new ActionListener()
288 public void actionPerformed(ActionEvent e)
290 user_actionPerformed(e);
293 viewMenu.setText("View");
294 background.setText("Background Colour...");
295 background.addActionListener(new ActionListener()
297 public void actionPerformed(ActionEvent e)
299 background_actionPerformed(e);
302 savePDB.setText("PDB File");
303 savePDB.addActionListener(new ActionListener()
305 public void actionPerformed(ActionEvent e)
307 savePDB_actionPerformed(e);
310 jMenuBar1.add(fileMenu);
311 jMenuBar1.add(coloursMenu);
312 jMenuBar1.add(viewMenu);
313 fileMenu.add(saveMenu);
314 fileMenu.add(mapping);
315 saveMenu.add(savePDB);
318 coloursMenu.add(seqButton);
319 coloursMenu.add(chain);
320 coloursMenu.add(charge);
321 coloursMenu.add(zappo);
322 coloursMenu.add(taylor);
323 coloursMenu.add(hydro);
324 coloursMenu.add(helix);
325 coloursMenu.add(strand);
326 coloursMenu.add(turn);
327 coloursMenu.add(buried);
328 coloursMenu.add(user);
329 coloursMenu.add(background);
330 ButtonGroup bg = new ButtonGroup();
343 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
345 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
346 .getUserColourSchemes().keys();
348 while (userColours.hasMoreElements())
350 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
351 userColours.nextElement().toString());
352 radioItem.setName("USER_DEFINED");
353 radioItem.addMouseListener(new MouseAdapter()
355 public void mousePressed(MouseEvent evt)
357 if (evt.isControlDown()
358 || SwingUtilities.isRightMouseButton(evt))
360 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
362 int option = JOptionPane.showInternalConfirmDialog(
363 jalview.gui.Desktop.desktop,
364 "Remove from default list?",
365 "Remove user defined colour",
366 JOptionPane.YES_NO_OPTION);
367 if (option == JOptionPane.YES_OPTION)
369 jalview.gui.UserDefinedColours
370 .removeColourFromDefaults(radioItem.getText());
371 coloursMenu.remove(radioItem);
375 radioItem.addActionListener(new ActionListener()
377 public void actionPerformed(ActionEvent evt)
379 user_actionPerformed(evt);
386 radioItem.addActionListener(new ActionListener()
388 public void actionPerformed(ActionEvent evt)
390 user_actionPerformed(evt);
393 coloursMenu.add(radioItem);
400 viewMenu.add(zbuffer);
401 viewMenu.add(allchains);
404 JMenuBar jMenuBar1 = new JMenuBar();
406 JMenu fileMenu = new JMenu();
408 JMenu coloursMenu = new JMenu();
410 JMenu saveMenu = new JMenu();
412 JMenuItem png = new JMenuItem();
414 JMenuItem eps = new JMenuItem();
416 JMenuItem mapping = new JMenuItem();
418 JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
420 JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
422 JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
424 JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
426 JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
428 JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
430 JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
432 JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
434 JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
436 JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
438 JRadioButtonMenuItem user = new JRadioButtonMenuItem();
440 JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
442 JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
444 JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
446 JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
448 JMenu viewMenu = new JMenu();
450 JMenuItem background = new JMenuItem();
452 JMenuItem savePDB = new JMenuItem();
460 public void eps_actionPerformed(ActionEvent e)
462 makePDBImage(jalview.util.ImageMaker.EPS);
471 public void png_actionPerformed(ActionEvent e)
473 makePDBImage(jalview.util.ImageMaker.PNG);
476 void makePDBImage(int type)
478 int width = pdbcanvas.getWidth();
479 int height = pdbcanvas.getHeight();
481 jalview.util.ImageMaker im;
483 if (type == jalview.util.ImageMaker.PNG)
485 im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
486 "Make PNG image from view", width, height, null, null);
490 im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
491 "Make EPS file from view", width, height, null,
495 if (im.getGraphics() != null)
497 pdbcanvas.drawAll(im.getGraphics(), width, height);
502 public void charge_actionPerformed(ActionEvent e)
504 pdbcanvas.bysequence = false;
505 pdbcanvas.pdb.setChargeColours();
506 pdbcanvas.redrawneeded = true;
510 public void hydro_actionPerformed(ActionEvent e)
512 pdbcanvas.bysequence = false;
513 pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
514 pdbcanvas.redrawneeded = true;
518 public void chain_actionPerformed(ActionEvent e)
520 pdbcanvas.bysequence = false;
521 pdbcanvas.pdb.setChainColours();
522 pdbcanvas.redrawneeded = true;
526 public void zbuffer_actionPerformed(ActionEvent e)
528 pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
529 pdbcanvas.redrawneeded = true;
533 public void molecule_actionPerformed(ActionEvent e)
535 pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
536 pdbcanvas.redrawneeded = true;
540 public void depth_actionPerformed(ActionEvent e)
542 pdbcanvas.depthcue = !pdbcanvas.depthcue;
543 pdbcanvas.redrawneeded = true;
547 public void wire_actionPerformed(ActionEvent e)
549 pdbcanvas.wire = !pdbcanvas.wire;
550 pdbcanvas.redrawneeded = true;
554 public void seqButton_actionPerformed(ActionEvent e)
556 pdbcanvas.bysequence = true;
557 pdbcanvas.updateSeqColours();
560 public void mapping_actionPerformed(ActionEvent e)
562 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
565 cap.setText(pdbcanvas.mappingDetails.toString());
566 Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
567 } catch (OutOfMemoryError oom)
569 new OOMWarning("Opening sequence to structure mapping report", oom);
574 public void allchains_itemStateChanged(ItemEvent e)
576 pdbcanvas.setAllchainsVisible(allchains.getState());
579 public void zappo_actionPerformed(ActionEvent e)
581 pdbcanvas.bysequence = false;
582 pdbcanvas.pdb.setColours(new ZappoColourScheme());
583 pdbcanvas.redrawneeded = true;
587 public void taylor_actionPerformed(ActionEvent e)
589 pdbcanvas.bysequence = false;
590 pdbcanvas.pdb.setColours(new TaylorColourScheme());
591 pdbcanvas.redrawneeded = true;
595 public void helix_actionPerformed(ActionEvent e)
597 pdbcanvas.bysequence = false;
598 pdbcanvas.pdb.setColours(new HelixColourScheme());
599 pdbcanvas.redrawneeded = true;
603 public void strand_actionPerformed(ActionEvent e)
605 pdbcanvas.bysequence = false;
606 pdbcanvas.pdb.setColours(new StrandColourScheme());
607 pdbcanvas.redrawneeded = true;
611 public void turn_actionPerformed(ActionEvent e)
613 pdbcanvas.bysequence = false;
614 pdbcanvas.pdb.setColours(new TurnColourScheme());
615 pdbcanvas.redrawneeded = true;
619 public void buried_actionPerformed(ActionEvent e)
621 pdbcanvas.bysequence = false;
622 pdbcanvas.pdb.setColours(new BuriedColourScheme());
623 pdbcanvas.redrawneeded = true;
627 public void user_actionPerformed(ActionEvent e)
629 if (e.getActionCommand().equals("User Defined..."))
631 // new UserDefinedColours(pdbcanvas, null);
635 UserColourScheme udc = (UserColourScheme) UserDefinedColours
636 .getUserColourSchemes().get(e.getActionCommand());
638 pdbcanvas.pdb.setColours(udc);
639 pdbcanvas.redrawneeded = true;
644 public void background_actionPerformed(ActionEvent e)
646 java.awt.Color col = JColorChooser.showDialog(this,
647 "Select Background Colour", pdbcanvas.backgroundColour);
651 pdbcanvas.backgroundColour = col;
652 pdbcanvas.redrawneeded = true;
657 public void savePDB_actionPerformed(ActionEvent e)
659 JalviewFileChooser chooser = new JalviewFileChooser(
660 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
662 chooser.setFileView(new JalviewFileView());
663 chooser.setDialogTitle("Save PDB File");
664 chooser.setToolTipText("Save");
666 int value = chooser.showSaveDialog(this);
668 if (value == JalviewFileChooser.APPROVE_OPTION)
672 BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
673 File outFile = chooser.getSelectedFile();
675 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
677 while ((data = in.readLine()) != null)
679 if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
686 } catch (Exception ex)
688 ex.printStackTrace();