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 org.jmol.api.*;
31 import org.jmol.popup.*;
32 import org.jmol.viewer.JmolConstants;
34 import jalview.schemes.*;
36 public class AppletJmol extends EmbmenuFrame implements
38 KeyListener, ActionListener, ItemListener, SequenceStructureBinding
41 Menu fileMenu = new Menu("File");
43 Menu viewMenu = new Menu("View");
45 Menu coloursMenu = new Menu("Colours");
47 Menu chainMenu = new Menu("Show Chain");
49 Menu helpMenu = new Menu("Help");
51 MenuItem mappingMenuItem = new MenuItem("View Mapping");
53 CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
55 CheckboxMenuItem jmolColour = new CheckboxMenuItem("Using Jmol", false);
57 MenuItem chain = new MenuItem("By Chain");
59 MenuItem charge = new MenuItem("Charge & Cysteine");
61 MenuItem zappo = new MenuItem("Zappo");
63 MenuItem taylor = new MenuItem("Taylor");
65 MenuItem hydro = new MenuItem("Hydrophobicity");
67 MenuItem helix = new MenuItem("Helix Propensity");
69 MenuItem strand = new MenuItem("Strand Propensity");
71 MenuItem turn = new MenuItem("Turn Propensity");
73 MenuItem buried = new MenuItem("Buried Index");
75 MenuItem purinepyrimidine = new MenuItem("Purine/Pyrimidine");
77 MenuItem user = new MenuItem("User Defined Colours");
79 MenuItem jmolHelp = new MenuItem("Jmol Help");
87 RenderPanel renderPanel;
91 ArrayList _aps = new ArrayList();
93 String fileLoadingError;
97 // boolean colourBySequence = true;
99 FeatureRenderer fr = null;
101 AppletJmolBinding jmb;
104 * datasource protocol for access to PDBEntry
106 String protocol = null;
109 * Load a bunch of pdb entries associated with sequences in the alignment and
110 * display them - aligning them if necessary.
113 * each pdb file (at least one needed)
115 * each set of sequences for each pdb file (must match number of pdb
118 * the target pdb chain corresponding with each sequence associated
119 * with each pdb file (may be null at any level)
123 * associated alignment
125 * how to get pdb data
127 public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs,
128 String[][] boundchains, boolean align, AlignmentPanel ap,
131 throw new Error("Not yet implemented.");
134 public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
135 AlignmentPanel ap, String protocol)
138 jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
140 { pdbentry }, new SequenceI[][]
141 { seq }, new String[][]
142 { chains }, protocol);
143 jmb.setColourBySequence(true);
144 if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
146 if (protocol.equals(AppletFormatAdapter.PASTE))
148 pdbentry.setId("PASTED PDB"
149 + (chains == null ? "_" : chains.toString()));
153 pdbentry.setId(pdbentry.getFile());
157 if (jalview.bin.JalviewLite.debug)
160 .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
163 String alreadyMapped = StructureSelectionManager
164 .getStructureSelectionManager(ap.av.applet)
165 .alreadyMappedToFile(pdbentry.getId());
166 MCview.PDBfile reader = null;
167 if (alreadyMapped != null)
169 reader = StructureSelectionManager.getStructureSelectionManager(
170 ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
172 // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
173 // FOR NOW, LETS JUST OPEN A NEW WINDOW
175 MenuBar menuBar = new MenuBar();
176 menuBar.add(fileMenu);
177 fileMenu.add(mappingMenuItem);
178 menuBar.add(viewMenu);
179 mappingMenuItem.addActionListener(this);
180 viewMenu.add(chainMenu);
181 menuBar.add(coloursMenu);
182 menuBar.add(helpMenu);
184 charge.addActionListener(this);
185 hydro.addActionListener(this);
186 chain.addActionListener(this);
187 seqColour.addItemListener(this);
188 jmolColour.addItemListener(this);
189 zappo.addActionListener(this);
190 taylor.addActionListener(this);
191 helix.addActionListener(this);
192 strand.addActionListener(this);
193 turn.addActionListener(this);
194 buried.addActionListener(this);
195 purinepyrimidine.addActionListener(this);
196 user.addActionListener(this);
198 jmolHelp.addActionListener(this);
200 coloursMenu.add(seqColour);
201 coloursMenu.add(chain);
202 coloursMenu.add(charge);
203 coloursMenu.add(zappo);
204 coloursMenu.add(taylor);
205 coloursMenu.add(hydro);
206 coloursMenu.add(helix);
207 coloursMenu.add(strand);
208 coloursMenu.add(turn);
209 coloursMenu.add(buried);
210 coloursMenu.add(purinepyrimidine);
211 coloursMenu.add(user);
212 coloursMenu.add(jmolColour);
213 helpMenu.add(jmolHelp);
214 this.setLayout(new BorderLayout());
218 renderPanel = new RenderPanel();
219 embedMenuIfNeeded(renderPanel);
220 this.add(renderPanel, BorderLayout.CENTER);
221 scriptWindow = new Panel();
222 scriptWindow.setVisible(false);
223 // this.add(scriptWindow, BorderLayout.SOUTH);
227 jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
228 + "_jmol_", ap.av.applet.getDocumentBase(),
229 ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
230 } catch (Exception e)
233 .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
234 + ap.av.applet.getDocumentBase()
236 + ap.av.applet.getCodeBase());
241 jmb.newJmolPopup(true, "Jmol", true);
243 this.addWindowListener(new WindowAdapter()
245 public void windowClosing(WindowEvent evt)
250 if (pdbentry.getProperty() == null)
252 pdbentry.setProperty(new Hashtable());
253 pdbentry.getProperty().put("protocol", protocol);
255 if (pdbentry.getFile() != null)
257 // import structure data from pdbentry.getFile based on given protocol
258 if (protocol.equals(AppletFormatAdapter.PASTE))
260 // TODO: JAL-623 : correctly record file contents for matching up later
261 // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
262 loadInline(pdbentry.getFile());
264 else if (protocol.equals(AppletFormatAdapter.FILE)
265 || protocol.equals(AppletFormatAdapter.URL))
267 jmb.viewer.openFile(pdbentry.getFile());
271 // probably CLASSLOADER based datasource..
272 // Try and get a reader on the datasource, and pass that to Jmol
275 java.io.Reader freader = null;
278 if (jalview.bin.JalviewLite.debug)
281 .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
283 // re-use the one we opened earlier
284 freader = reader.getReader();
288 if (jalview.bin.JalviewLite.debug)
291 .println("AppletJmol:Creating new PDBfile IO parser.");
293 FileParse fp = new FileParse(pdbentry.getFile(), protocol);
295 // reader = new MCview.PDBfile(fp);
296 // could set ID, etc.
297 // if (!reader.isValid())
299 // throw new Exception("Invalid datasource.
300 // "+reader.getWarningMessage());
303 freader = fp.getReader();
308 "Invalid datasource. Could not obtain Reader.");
310 jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
312 } catch (Exception e)
315 System.err.println("Couldn't access pdbentry id="
316 + pdbentry.getId() + " and file=" + pdbentry.getFile()
317 + " using protocol=" + protocol);
323 jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
326 public void loadInline(String string)
329 jmb.loadInline(string);
332 void setChainMenuItems(Vector chains)
334 chainMenu.removeAll();
336 MenuItem menuItem = new MenuItem("All");
337 menuItem.addActionListener(this);
339 chainMenu.add(menuItem);
341 CheckboxMenuItem menuItemCB;
342 for (int c = 0; c < chains.size(); c++)
344 menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
346 menuItemCB.addItemListener(this);
347 chainMenu.add(menuItemCB);
351 boolean allChainsSelected = false;
355 Vector toshow = new Vector();
357 int mlength, p, mnum;
358 for (int i = 0; i < chainMenu.getItemCount(); i++)
360 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
362 CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
365 toshow.addElement(item.getLabel());
369 jmb.centerViewer(toshow);
376 this.setVisible(false);
379 public void actionPerformed(ActionEvent evt)
381 if (evt.getSource() == mappingMenuItem)
383 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
385 Frame frame = new Frame();
388 StringBuffer sb = new StringBuffer();
391 for (int s = 0; s < jmb.pdbentry.length; s++)
393 sb.append(jmb.printMapping(jmb.pdbentry[s].getFile()));
396 cap.setText(sb.toString());
397 } catch (OutOfMemoryError ex)
401 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
404 jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
407 else if (evt.getSource() == charge)
410 jmb.colourByCharge();
413 else if (evt.getSource() == chain)
418 else if (evt.getSource() == zappo)
421 jmb.setJalviewColourScheme(new ZappoColourScheme());
423 else if (evt.getSource() == taylor)
426 jmb.setJalviewColourScheme(new TaylorColourScheme());
428 else if (evt.getSource() == hydro)
431 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
433 else if (evt.getSource() == helix)
436 jmb.setJalviewColourScheme(new HelixColourScheme());
438 else if (evt.getSource() == strand)
441 jmb.setJalviewColourScheme(new StrandColourScheme());
443 else if (evt.getSource() == turn)
446 jmb.setJalviewColourScheme(new TurnColourScheme());
448 else if (evt.getSource() == buried)
451 jmb.setJalviewColourScheme(new BuriedColourScheme());
453 else if (evt.getSource() == purinepyrimidine)
455 jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
457 else if (evt.getSource() == user)
460 new UserDefinedColours(this);
462 else if (evt.getSource() == jmolHelp)
466 ap.av.applet.getAppletContext().showDocument(
468 "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
470 } catch (java.net.MalformedURLException ex)
476 allChainsSelected = true;
477 for (int i = 0; i < chainMenu.getItemCount(); i++)
479 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
480 ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
484 allChainsSelected = false;
489 * tick or untick the seqColour menu entry or jmoColour entry depending upon
490 * if it was selected or not.
494 private void setEnabled(MenuItem itm)
496 jmolColour.setState(itm == jmolColour);
497 seqColour.setState(itm == seqColour);
498 jmb.setColourBySequence(itm == seqColour);
501 public void itemStateChanged(ItemEvent evt)
503 if (evt.getSource() == jmolColour)
505 setEnabled(jmolColour);
506 jmb.setColourBySequence(false);
508 else if (evt.getSource() == seqColour)
510 setEnabled(seqColour);
511 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
513 else if (!allChainsSelected)
517 public void keyPressed(KeyEvent evt)
519 if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
521 jmb.eval(inputLine.getText());
522 history.append("\n$ " + inputLine.getText());
523 inputLine.setText("");
528 public void keyTyped(KeyEvent evt)
532 public void keyReleased(KeyEvent evt)
536 public void updateColours(Object source)
538 AlignmentPanel ap = (AlignmentPanel) source;
539 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
542 public void updateTitleAndMenus()
544 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
549 setChainMenuItems(jmb.chainNames);
550 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
552 setTitle(jmb.getViewerTitle());
555 public void showUrl(String url)
559 ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
561 } catch (java.net.MalformedURLException ex)
566 Panel splitPane = null;
568 public void showConsole(boolean showConsole)
573 splitPane = new Panel();
575 splitPane.setLayout(new java.awt.GridLayout(2, 1));
576 splitPane.add(renderPanel);
577 splitPane.add(scriptWindow);
578 scriptWindow.setVisible(true);
579 this.add(splitPane, BorderLayout.CENTER);
580 splitPane.setVisible(true);
581 splitPane.validate();
585 scriptWindow.setVisible(false);
587 add(renderPanel, BorderLayout.CENTER);
593 public float[][] functionXY(String functionName, int x, int y)
598 // /End JmolStatusListener
599 // /////////////////////////////
601 class RenderPanel extends Panel
603 Dimension currentSize = new Dimension();
605 Rectangle rectClip = new Rectangle();
607 public void update(Graphics g)
612 public void paint(Graphics g)
614 currentSize = this.getSize();
615 rectClip = g.getClipBounds();
617 if (jmb.viewer == null)
619 g.setColor(Color.black);
620 g.fillRect(0, 0, currentSize.width, currentSize.height);
621 g.setColor(Color.white);
622 g.setFont(new Font("Verdana", Font.BOLD, 14));
623 g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
627 jmb.viewer.renderScreenImage(g, currentSize, rectClip);
633 * @Override public Color getColour(int atomIndex, int pdbResNum, String
634 * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
637 * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
639 * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
640 * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
645 * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
646 * jmb.mouseOverStructure(atomIndex, strInfo);
650 public void setJalviewColourScheme(UserColourScheme ucs)
652 jmb.setJalviewColourScheme(ucs);
655 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
657 for (int i = 0; i < _aps.size(); i++)
659 if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
661 return ((AlignmentPanel) _aps.get(i));