2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, 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 MenuItem chain = new MenuItem("By Chain");
57 MenuItem charge = new MenuItem("Charge & Cysteine");
59 MenuItem zappo = new MenuItem("Zappo");
61 MenuItem taylor = new MenuItem("Taylor");
63 MenuItem hydro = new MenuItem("Hydrophobicity");
65 MenuItem helix = new MenuItem("Helix Propensity");
67 MenuItem strand = new MenuItem("Strand Propensity");
69 MenuItem turn = new MenuItem("Turn Propensity");
71 MenuItem buried = new MenuItem("Buried Index");
73 MenuItem user = new MenuItem("User Defined Colours");
75 MenuItem jmolHelp = new MenuItem("Jmol Help");
83 RenderPanel renderPanel;
87 String fileLoadingError;
91 // boolean colourBySequence = true;
93 FeatureRenderer fr = null;
95 AppletJmolBinding jmb;
98 * datasource protocol for access to PDBEntry
100 String protocol = null;
102 public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
103 AlignmentPanel ap, String protocol)
106 jmb = new AppletJmolBinding(this, new PDBEntry[]
107 { pdbentry }, seq, chains, protocol);
108 jmb.setColourBySequence(true);
109 if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
111 if (protocol.equals(AppletFormatAdapter.PASTE))
113 pdbentry.setId("PASTED PDB"
114 + (chains == null ? "_" : chains.toString()));
118 pdbentry.setId(pdbentry.getFile());
122 if (jalview.bin.JalviewLite.debug)
125 .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
128 String alreadyMapped = StructureSelectionManager
129 .getStructureSelectionManager().alreadyMappedToFile(
131 MCview.PDBfile reader = null;
132 if (alreadyMapped != null)
134 reader = StructureSelectionManager.getStructureSelectionManager()
135 .setMapping(seq, chains, pdbentry.getFile(), protocol);
136 // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
137 // FOR NOW, LETS JUST OPEN A NEW WINDOW
139 MenuBar menuBar = new MenuBar();
140 menuBar.add(fileMenu);
141 fileMenu.add(mappingMenuItem);
142 menuBar.add(viewMenu);
143 mappingMenuItem.addActionListener(this);
144 viewMenu.add(chainMenu);
145 menuBar.add(coloursMenu);
146 menuBar.add(helpMenu);
148 charge.addActionListener(this);
149 hydro.addActionListener(this);
150 chain.addActionListener(this);
151 seqColour.addItemListener(this);
152 zappo.addActionListener(this);
153 taylor.addActionListener(this);
154 helix.addActionListener(this);
155 strand.addActionListener(this);
156 turn.addActionListener(this);
157 buried.addActionListener(this);
158 user.addActionListener(this);
160 jmolHelp.addActionListener(this);
162 coloursMenu.add(seqColour);
163 coloursMenu.add(chain);
164 coloursMenu.add(charge);
165 coloursMenu.add(zappo);
166 coloursMenu.add(taylor);
167 coloursMenu.add(hydro);
168 coloursMenu.add(helix);
169 coloursMenu.add(strand);
170 coloursMenu.add(turn);
171 coloursMenu.add(buried);
172 coloursMenu.add(user);
174 helpMenu.add(jmolHelp);
178 renderPanel = new RenderPanel();
179 embedMenuIfNeeded(renderPanel);
180 this.add(renderPanel, BorderLayout.CENTER);
183 jmb.allocateViewer(renderPanel, "jalviewJmol",
184 ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(),
186 } catch (Exception e)
189 .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
190 + ap.av.applet.getDocumentBase()
192 + ap.av.applet.getCodeBase());
197 jmb.newJmolPopup(true, "Jmol", true);
199 this.addWindowListener(new WindowAdapter()
201 public void windowClosing(WindowEvent evt)
207 if (pdbentry.getFile() != null)
209 // import structure data from pdbentry.getFile based on given protocol
210 if (protocol.equals(AppletFormatAdapter.PASTE))
212 loadInline(pdbentry.getFile());
214 else if (protocol.equals(AppletFormatAdapter.FILE)
215 || protocol.equals(AppletFormatAdapter.URL))
217 jmb.viewer.openFile(pdbentry.getFile());
221 // probably CLASSLOADER based datasource..
222 // Try and get a reader on the datasource, and pass that to Jmol
225 java.io.Reader freader = null;
228 if (jalview.bin.JalviewLite.debug)
231 .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
233 // re-use the one we opened earlier
234 freader = reader.getReader();
238 if (jalview.bin.JalviewLite.debug)
241 .println("AppletJmol:Creating new PDBfile IO parser.");
243 FileParse fp = new FileParse(pdbentry.getFile(), protocol);
245 // reader = new MCview.PDBfile(fp);
246 // could set ID, etc.
247 // if (!reader.isValid())
249 // throw new Exception("Invalid datasource.
250 // "+reader.getWarningMessage());
253 freader = fp.getReader();
258 "Invalid datasource. Could not obtain Reader.");
260 jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
262 } catch (Exception e)
265 System.err.println("Couldn't access pdbentry id="
266 + pdbentry.getId() + " and file=" + pdbentry.getFile()
267 + " using protocol=" + protocol);
273 jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
276 public void loadInline(String string)
279 jmb.viewer.openStringInline(string);
282 void setChainMenuItems(Vector chains)
284 chainMenu.removeAll();
286 MenuItem menuItem = new MenuItem("All");
287 menuItem.addActionListener(this);
289 chainMenu.add(menuItem);
291 CheckboxMenuItem menuItemCB;
292 for (int c = 0; c < chains.size(); c++)
294 menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
296 menuItemCB.addItemListener(this);
297 chainMenu.add(menuItemCB);
301 boolean allChainsSelected = false;
305 Vector toshow = new Vector();
307 int mlength, p, mnum;
308 for (int i = 0; i < chainMenu.getItemCount(); i++)
310 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
312 CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
315 toshow.addElement(item.getLabel());
319 jmb.centerViewer(toshow);
326 this.setVisible(false);
329 public void actionPerformed(ActionEvent evt)
331 if (evt.getSource() == mappingMenuItem)
333 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
335 Frame frame = new Frame();
338 StringBuffer sb = new StringBuffer();
340 for (int s = 0; s < jmb.pdbentry.length; s++)
342 sb.append(StructureSelectionManager.getStructureSelectionManager()
343 .printMapping(jmb.pdbentry[s].getFile()));
346 cap.setText(sb.toString());
348 catch (OutOfMemoryError ex)
351 System.err.println("Out of memory when trying to create dialog box with sequence-structure mapping.");
354 jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
357 else if (evt.getSource() == charge)
360 jmb.colourByCharge();
363 else if (evt.getSource() == chain)
368 else if (evt.getSource() == zappo)
371 jmb.setJalviewColourScheme(new ZappoColourScheme());
373 else if (evt.getSource() == taylor)
376 jmb.setJalviewColourScheme(new TaylorColourScheme());
378 else if (evt.getSource() == hydro)
381 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
383 else if (evt.getSource() == helix)
386 jmb.setJalviewColourScheme(new HelixColourScheme());
388 else if (evt.getSource() == strand)
391 jmb.setJalviewColourScheme(new StrandColourScheme());
393 else if (evt.getSource() == turn)
396 jmb.setJalviewColourScheme(new TurnColourScheme());
398 else if (evt.getSource() == buried)
401 jmb.setJalviewColourScheme(new BuriedColourScheme());
403 else if (evt.getSource() == user)
406 new UserDefinedColours(this);
408 else if (evt.getSource() == jmolHelp)
412 ap.av.applet.getAppletContext().showDocument(
414 "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
416 } catch (java.net.MalformedURLException ex)
422 allChainsSelected = true;
423 for (int i = 0; i < chainMenu.getItemCount(); i++)
425 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
426 ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
430 allChainsSelected = false;
435 * tick or untick the seqColour menu entry depending upon if it was selected
440 private void setEnabled(MenuItem itm)
442 seqColour.setState(itm == seqColour);
443 jmb.setColourBySequence(itm == seqColour);
446 public void itemStateChanged(ItemEvent evt)
448 if (evt.getSource() == seqColour)
450 setEnabled(seqColour);
451 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
453 else if (!allChainsSelected)
457 public void keyPressed(KeyEvent evt)
459 if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
461 jmb.eval(inputLine.getText());
462 history.append("\n$ " + inputLine.getText());
463 inputLine.setText("");
468 public void keyTyped(KeyEvent evt)
472 public void keyReleased(KeyEvent evt)
476 public void updateColours(Object source)
478 AlignmentPanel ap = (AlignmentPanel) source;
479 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
482 public void updateTitleAndMenus()
484 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
489 setChainMenuItems(jmb.chainNames);
490 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
492 setTitle(jmb.getViewerTitle());
495 public void showUrl(String url)
499 ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
501 } catch (java.net.MalformedURLException ex)
506 public void showConsole(boolean showConsole)
508 if (scriptWindow == null)
510 scriptWindow = new Panel(new BorderLayout());
511 inputLine = new TextField();
512 history = new TextArea(5, 40);
513 scriptWindow.add(history, BorderLayout.CENTER);
514 scriptWindow.add(inputLine, BorderLayout.SOUTH);
515 add(scriptWindow, BorderLayout.SOUTH);
516 scriptWindow.setVisible(false);
517 history.setEditable(false);
518 inputLine.addKeyListener(this);
521 scriptWindow.setVisible(!scriptWindow.isVisible());
525 public float[][] functionXY(String functionName, int x, int y)
530 // /End JmolStatusListener
531 // /////////////////////////////
533 class RenderPanel extends Panel
535 Dimension currentSize = new Dimension();
537 Rectangle rectClip = new Rectangle();
539 public void update(Graphics g)
544 public void paint(Graphics g)
546 currentSize = this.getSize();
547 rectClip = g.getClipBounds();
549 if (jmb.viewer == null)
551 g.setColor(Color.black);
552 g.fillRect(0, 0, currentSize.width, currentSize.height);
553 g.setColor(Color.white);
554 g.setFont(new Font("Verdana", Font.BOLD, 14));
555 g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
559 jmb.viewer.renderScreenImage(g, currentSize, rectClip);
565 * @Override public Color getColour(int atomIndex, int pdbResNum, String
566 * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
569 * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
571 * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
572 * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
577 * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
578 * jmb.mouseOverStructure(atomIndex, strInfo);
582 public void setJalviewColourScheme(UserColourScheme ucs)
584 jmb.setJalviewColourScheme(ucs);