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/>.
18 package jalview.appletgui;
22 import java.awt.event.*;
24 import jalview.api.SequenceStructureBinding;
25 import jalview.datamodel.*;
26 import jalview.structure.*;
29 import jalview.schemes.*;
30 import jalview.util.MessageManager;
32 public class AppletJmol extends EmbmenuFrame implements
34 KeyListener, ActionListener, ItemListener, SequenceStructureBinding
37 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
39 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
41 Menu coloursMenu = new Menu(MessageManager.getString("action.colour"));
43 Menu chainMenu = new Menu(MessageManager.getString("action.show_chain"));
45 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
47 MenuItem mappingMenuItem = new MenuItem(MessageManager.getString("label.view_mapping"));
49 CheckboxMenuItem seqColour = new CheckboxMenuItem(MessageManager.getString("action.by_sequence"), true);
51 CheckboxMenuItem jmolColour = new CheckboxMenuItem(MessageManager.getString("action.using_jmol"), false);
53 MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
55 MenuItem charge = new MenuItem(MessageManager.getString("label.charge_cysteine"));
57 MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
59 MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
61 MenuItem hydro = new MenuItem(MessageManager.getString("label.hydrophobicity"));
63 MenuItem helix = new MenuItem(MessageManager.getString("label.helix_propensity"));
65 MenuItem strand = new MenuItem(MessageManager.getString("label.strand_propensity"));
67 MenuItem turn = new MenuItem(MessageManager.getString("label.turn_propensity"));
69 MenuItem buried = new MenuItem(MessageManager.getString("label.buried_index"));
71 MenuItem purinepyrimidine = new MenuItem(MessageManager.getString("label.purine_pyrimidine"));
73 MenuItem user = new MenuItem(MessageManager.getString("label.user_defined_colours"));
75 MenuItem jmolHelp = new MenuItem(MessageManager.getString("label.jmol_help"));
83 RenderPanel renderPanel;
87 ArrayList _aps = new ArrayList();
89 String fileLoadingError;
93 // boolean colourBySequence = true;
95 FeatureRenderer fr = null;
97 AppletJmolBinding jmb;
100 * datasource protocol for access to PDBEntry
102 String protocol = null;
105 * Load a bunch of pdb entries associated with sequences in the alignment and
106 * display them - aligning them if necessary.
109 * each pdb file (at least one needed)
111 * each set of sequences for each pdb file (must match number of pdb
114 * the target pdb chain corresponding with each sequence associated
115 * with each pdb file (may be null at any level)
119 * associated alignment
121 * how to get pdb data
123 public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs,
124 String[][] boundchains, boolean align, AlignmentPanel ap,
127 throw new Error("Not yet implemented.");
130 public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
131 AlignmentPanel ap, String protocol)
134 jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
136 { pdbentry }, new SequenceI[][]
137 { seq }, new String[][]
138 { chains }, protocol);
139 jmb.setColourBySequence(true);
140 if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
142 if (protocol.equals(AppletFormatAdapter.PASTE))
144 pdbentry.setId("PASTED PDB"
145 + (chains == null ? "_" : chains.toString()));
149 pdbentry.setId(pdbentry.getFile());
153 if (jalview.bin.JalviewLite.debug)
156 .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
159 String alreadyMapped = StructureSelectionManager
160 .getStructureSelectionManager(ap.av.applet)
161 .alreadyMappedToFile(pdbentry.getId());
162 MCview.PDBfile reader = null;
163 if (alreadyMapped != null)
165 reader = StructureSelectionManager.getStructureSelectionManager(
166 ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
168 // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
169 // FOR NOW, LETS JUST OPEN A NEW WINDOW
171 MenuBar menuBar = new MenuBar();
172 menuBar.add(fileMenu);
173 fileMenu.add(mappingMenuItem);
174 menuBar.add(viewMenu);
175 mappingMenuItem.addActionListener(this);
176 viewMenu.add(chainMenu);
177 menuBar.add(coloursMenu);
178 menuBar.add(helpMenu);
180 charge.addActionListener(this);
181 hydro.addActionListener(this);
182 chain.addActionListener(this);
183 seqColour.addItemListener(this);
184 jmolColour.addItemListener(this);
185 zappo.addActionListener(this);
186 taylor.addActionListener(this);
187 helix.addActionListener(this);
188 strand.addActionListener(this);
189 turn.addActionListener(this);
190 buried.addActionListener(this);
191 purinepyrimidine.addActionListener(this);
192 user.addActionListener(this);
194 jmolHelp.addActionListener(this);
196 coloursMenu.add(seqColour);
197 coloursMenu.add(chain);
198 coloursMenu.add(charge);
199 coloursMenu.add(zappo);
200 coloursMenu.add(taylor);
201 coloursMenu.add(hydro);
202 coloursMenu.add(helix);
203 coloursMenu.add(strand);
204 coloursMenu.add(turn);
205 coloursMenu.add(buried);
206 coloursMenu.add(purinepyrimidine);
207 coloursMenu.add(user);
208 coloursMenu.add(jmolColour);
209 helpMenu.add(jmolHelp);
210 this.setLayout(new BorderLayout());
214 renderPanel = new RenderPanel();
215 embedMenuIfNeeded(renderPanel);
216 this.add(renderPanel, BorderLayout.CENTER);
217 scriptWindow = new Panel();
218 scriptWindow.setVisible(false);
219 // this.add(scriptWindow, BorderLayout.SOUTH);
223 jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
224 + "_jmol_", ap.av.applet.getDocumentBase(),
225 ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
226 } catch (Exception e)
229 .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
230 + ap.av.applet.getDocumentBase()
232 + ap.av.applet.getCodeBase());
237 jmb.newJmolPopup(true, "Jmol", true);
239 this.addWindowListener(new WindowAdapter()
241 public void windowClosing(WindowEvent evt)
246 if (pdbentry.getProperty() == null)
248 pdbentry.setProperty(new Hashtable());
249 pdbentry.getProperty().put("protocol", protocol);
251 if (pdbentry.getFile() != null)
253 // import structure data from pdbentry.getFile based on given protocol
254 if (protocol.equals(AppletFormatAdapter.PASTE))
256 // TODO: JAL-623 : correctly record file contents for matching up later
257 // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
258 loadInline(pdbentry.getFile());
260 else if (protocol.equals(AppletFormatAdapter.FILE)
261 || protocol.equals(AppletFormatAdapter.URL))
263 jmb.viewer.openFile(pdbentry.getFile());
267 // probably CLASSLOADER based datasource..
268 // Try and get a reader on the datasource, and pass that to Jmol
271 java.io.Reader freader = null;
274 if (jalview.bin.JalviewLite.debug)
277 .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
279 // re-use the one we opened earlier
280 freader = reader.getReader();
284 if (jalview.bin.JalviewLite.debug)
287 .println("AppletJmol:Creating new PDBfile IO parser.");
289 FileParse fp = new FileParse(pdbentry.getFile(), protocol);
291 // reader = new MCview.PDBfile(fp);
292 // could set ID, etc.
293 // if (!reader.isValid())
295 // throw new Exception("Invalid datasource.
296 // "+reader.getWarningMessage());
299 freader = fp.getReader();
304 "Invalid datasource. Could not obtain Reader.");
306 jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
308 } catch (Exception e)
311 System.err.println("Couldn't access pdbentry id="
312 + pdbentry.getId() + " and file=" + pdbentry.getFile()
313 + " using protocol=" + protocol);
319 jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
322 public void loadInline(String string)
325 jmb.loadInline(string);
328 void setChainMenuItems(Vector chains)
330 chainMenu.removeAll();
332 MenuItem menuItem = new MenuItem(MessageManager.getString("label.all"));
333 menuItem.addActionListener(this);
335 chainMenu.add(menuItem);
337 CheckboxMenuItem menuItemCB;
338 for (int c = 0; c < chains.size(); c++)
340 menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
342 menuItemCB.addItemListener(this);
343 chainMenu.add(menuItemCB);
347 boolean allChainsSelected = false;
351 Vector toshow = new Vector();
353 int mlength, p, mnum;
354 for (int i = 0; i < chainMenu.getItemCount(); i++)
356 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
358 CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
361 toshow.addElement(item.getLabel());
365 jmb.centerViewer(toshow);
372 this.setVisible(false);
375 public void actionPerformed(ActionEvent evt)
377 if (evt.getSource() == mappingMenuItem)
379 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
381 Frame frame = new Frame();
384 StringBuffer sb = new StringBuffer();
387 for (int s = 0; s < jmb.pdbentry.length; s++)
389 sb.append(jmb.printMapping(jmb.pdbentry[s].getFile()));
392 cap.setText(sb.toString());
393 } catch (OutOfMemoryError ex)
397 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
400 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pdb_sequence_mapping"),
403 else if (evt.getSource() == charge)
406 jmb.colourByCharge();
409 else if (evt.getSource() == chain)
414 else if (evt.getSource() == zappo)
417 jmb.setJalviewColourScheme(new ZappoColourScheme());
419 else if (evt.getSource() == taylor)
422 jmb.setJalviewColourScheme(new TaylorColourScheme());
424 else if (evt.getSource() == hydro)
427 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
429 else if (evt.getSource() == helix)
432 jmb.setJalviewColourScheme(new HelixColourScheme());
434 else if (evt.getSource() == strand)
437 jmb.setJalviewColourScheme(new StrandColourScheme());
439 else if (evt.getSource() == turn)
442 jmb.setJalviewColourScheme(new TurnColourScheme());
444 else if (evt.getSource() == buried)
447 jmb.setJalviewColourScheme(new BuriedColourScheme());
449 else if (evt.getSource() == purinepyrimidine)
451 jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
453 else if (evt.getSource() == user)
456 new UserDefinedColours(this);
458 else if (evt.getSource() == jmolHelp)
462 ap.av.applet.getAppletContext().showDocument(
464 "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
466 } catch (java.net.MalformedURLException ex)
472 allChainsSelected = true;
473 for (int i = 0; i < chainMenu.getItemCount(); i++)
475 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
476 ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
480 allChainsSelected = false;
485 * tick or untick the seqColour menu entry or jmoColour entry depending upon
486 * if it was selected or not.
490 private void setEnabled(MenuItem itm)
492 jmolColour.setState(itm == jmolColour);
493 seqColour.setState(itm == seqColour);
494 jmb.setColourBySequence(itm == seqColour);
497 public void itemStateChanged(ItemEvent evt)
499 if (evt.getSource() == jmolColour)
501 setEnabled(jmolColour);
502 jmb.setColourBySequence(false);
504 else if (evt.getSource() == seqColour)
506 setEnabled(seqColour);
507 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
509 else if (!allChainsSelected)
513 public void keyPressed(KeyEvent evt)
515 if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
517 jmb.eval(inputLine.getText());
518 history.append("\n$ " + inputLine.getText());
519 inputLine.setText("");
524 public void keyTyped(KeyEvent evt)
528 public void keyReleased(KeyEvent evt)
532 public void updateColours(Object source)
534 AlignmentPanel ap = (AlignmentPanel) source;
535 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
538 public void updateTitleAndMenus()
540 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
545 setChainMenuItems(jmb.chainNames);
546 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
548 setTitle(jmb.getViewerTitle());
551 public void showUrl(String url)
555 ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
557 } catch (java.net.MalformedURLException ex)
562 Panel splitPane = null;
564 public void showConsole(boolean showConsole)
569 splitPane = new Panel();
571 splitPane.setLayout(new java.awt.GridLayout(2, 1));
572 splitPane.add(renderPanel);
573 splitPane.add(scriptWindow);
574 scriptWindow.setVisible(true);
575 this.add(splitPane, BorderLayout.CENTER);
576 splitPane.setVisible(true);
577 splitPane.validate();
581 scriptWindow.setVisible(false);
583 add(renderPanel, BorderLayout.CENTER);
589 public float[][] functionXY(String functionName, int x, int y)
594 // /End JmolStatusListener
595 // /////////////////////////////
597 class RenderPanel extends Panel
599 Dimension currentSize = new Dimension();
601 Rectangle rectClip = new Rectangle();
603 public void update(Graphics g)
608 public void paint(Graphics g)
610 currentSize = this.getSize();
611 rectClip = g.getClipBounds();
613 if (jmb.viewer == null)
615 g.setColor(Color.black);
616 g.fillRect(0, 0, currentSize.width, currentSize.height);
617 g.setColor(Color.white);
618 g.setFont(new Font("Verdana", Font.BOLD, 14));
619 g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
623 jmb.viewer.renderScreenImage(g, currentSize, rectClip);
629 * @Override public Color getColour(int atomIndex, int pdbResNum, String
630 * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
633 * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
635 * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
636 * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
641 * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
642 * jmb.mouseOverStructure(atomIndex, strInfo);
646 public void setJalviewColourScheme(UserColourScheme ucs)
648 jmb.setJalviewColourScheme(ucs);
651 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
653 for (int i = 0; i < _aps.size(); i++)
655 if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
657 return ((AlignmentPanel) _aps.get(i));