2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
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;
103 * Load a bunch of pdb entries associated with sequences in the alignment and
104 * display them - aligning them if necessary.
107 * each pdb file (at least one needed)
109 * each set of sequences for each pdb file (must match number of pdb
112 * the target pdb chain corresponding with each sequence associated
113 * with each pdb file (may be null at any level)
117 * associated alignment
119 * how to get pdb data
121 public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs,
122 String[][] boundchains, boolean align, AlignmentPanel ap,
125 throw new Error("Not yet implemented.");
128 public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
129 AlignmentPanel ap, String protocol)
132 jmb = new AppletJmolBinding(this, new PDBEntry[]
133 { pdbentry }, new SequenceI[][]
134 { seq }, new String[][]
135 { chains }, protocol);
136 jmb.setColourBySequence(true);
137 if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
139 if (protocol.equals(AppletFormatAdapter.PASTE))
141 pdbentry.setId("PASTED PDB"
142 + (chains == null ? "_" : chains.toString()));
146 pdbentry.setId(pdbentry.getFile());
150 if (jalview.bin.JalviewLite.debug)
153 .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
156 String alreadyMapped = StructureSelectionManager
157 .getStructureSelectionManager().alreadyMappedToFile(
159 MCview.PDBfile reader = null;
160 if (alreadyMapped != null)
162 reader = StructureSelectionManager.getStructureSelectionManager()
163 .setMapping(seq, chains, pdbentry.getFile(), protocol);
164 // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
165 // FOR NOW, LETS JUST OPEN A NEW WINDOW
167 MenuBar menuBar = new MenuBar();
168 menuBar.add(fileMenu);
169 fileMenu.add(mappingMenuItem);
170 menuBar.add(viewMenu);
171 mappingMenuItem.addActionListener(this);
172 viewMenu.add(chainMenu);
173 menuBar.add(coloursMenu);
174 menuBar.add(helpMenu);
176 charge.addActionListener(this);
177 hydro.addActionListener(this);
178 chain.addActionListener(this);
179 seqColour.addItemListener(this);
180 zappo.addActionListener(this);
181 taylor.addActionListener(this);
182 helix.addActionListener(this);
183 strand.addActionListener(this);
184 turn.addActionListener(this);
185 buried.addActionListener(this);
186 user.addActionListener(this);
188 jmolHelp.addActionListener(this);
190 coloursMenu.add(seqColour);
191 coloursMenu.add(chain);
192 coloursMenu.add(charge);
193 coloursMenu.add(zappo);
194 coloursMenu.add(taylor);
195 coloursMenu.add(hydro);
196 coloursMenu.add(helix);
197 coloursMenu.add(strand);
198 coloursMenu.add(turn);
199 coloursMenu.add(buried);
200 coloursMenu.add(user);
202 helpMenu.add(jmolHelp);
203 this.setLayout(new BorderLayout());
207 renderPanel = new RenderPanel();
208 embedMenuIfNeeded(renderPanel);
209 this.add(renderPanel, BorderLayout.CENTER);
210 scriptWindow = new Panel();
211 scriptWindow.setVisible(false);
212 // this.add(scriptWindow, BorderLayout.SOUTH);
216 jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
217 + "_jmol_", ap.av.applet.getDocumentBase(),
218 ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
219 } catch (Exception e)
222 .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
223 + ap.av.applet.getDocumentBase()
225 + ap.av.applet.getCodeBase());
230 jmb.newJmolPopup(true, "Jmol", true);
232 this.addWindowListener(new WindowAdapter()
234 public void windowClosing(WindowEvent evt)
239 if (pdbentry.getProperty() == null)
241 pdbentry.setProperty(new Hashtable());
242 pdbentry.getProperty().put("protocol", protocol);
244 if (pdbentry.getFile() != null)
246 // import structure data from pdbentry.getFile based on given protocol
247 if (protocol.equals(AppletFormatAdapter.PASTE))
249 // TODO: JAL-623 : correctly record file contents for matching up later
250 // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
251 loadInline(pdbentry.getFile());
253 else if (protocol.equals(AppletFormatAdapter.FILE)
254 || protocol.equals(AppletFormatAdapter.URL))
256 jmb.viewer.openFile(pdbentry.getFile());
260 // probably CLASSLOADER based datasource..
261 // Try and get a reader on the datasource, and pass that to Jmol
264 java.io.Reader freader = null;
267 if (jalview.bin.JalviewLite.debug)
270 .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
272 // re-use the one we opened earlier
273 freader = reader.getReader();
277 if (jalview.bin.JalviewLite.debug)
280 .println("AppletJmol:Creating new PDBfile IO parser.");
282 FileParse fp = new FileParse(pdbentry.getFile(), protocol);
284 // reader = new MCview.PDBfile(fp);
285 // could set ID, etc.
286 // if (!reader.isValid())
288 // throw new Exception("Invalid datasource.
289 // "+reader.getWarningMessage());
292 freader = fp.getReader();
297 "Invalid datasource. Could not obtain Reader.");
299 jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
301 } catch (Exception e)
304 System.err.println("Couldn't access pdbentry id="
305 + pdbentry.getId() + " and file=" + pdbentry.getFile()
306 + " using protocol=" + protocol);
312 jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
315 public void loadInline(String string)
318 jmb.loadInline(string);
321 void setChainMenuItems(Vector chains)
323 chainMenu.removeAll();
325 MenuItem menuItem = new MenuItem("All");
326 menuItem.addActionListener(this);
328 chainMenu.add(menuItem);
330 CheckboxMenuItem menuItemCB;
331 for (int c = 0; c < chains.size(); c++)
333 menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
335 menuItemCB.addItemListener(this);
336 chainMenu.add(menuItemCB);
340 boolean allChainsSelected = false;
344 Vector toshow = new Vector();
346 int mlength, p, mnum;
347 for (int i = 0; i < chainMenu.getItemCount(); i++)
349 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
351 CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
354 toshow.addElement(item.getLabel());
358 jmb.centerViewer(toshow);
365 this.setVisible(false);
368 public void actionPerformed(ActionEvent evt)
370 if (evt.getSource() == mappingMenuItem)
372 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
374 Frame frame = new Frame();
377 StringBuffer sb = new StringBuffer();
380 for (int s = 0; s < jmb.pdbentry.length; s++)
382 sb.append(StructureSelectionManager
383 .getStructureSelectionManager().printMapping(
384 jmb.pdbentry[s].getFile()));
387 cap.setText(sb.toString());
388 } catch (OutOfMemoryError ex)
392 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
395 jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
398 else if (evt.getSource() == charge)
401 jmb.colourByCharge();
404 else if (evt.getSource() == chain)
409 else if (evt.getSource() == zappo)
412 jmb.setJalviewColourScheme(new ZappoColourScheme());
414 else if (evt.getSource() == taylor)
417 jmb.setJalviewColourScheme(new TaylorColourScheme());
419 else if (evt.getSource() == hydro)
422 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
424 else if (evt.getSource() == helix)
427 jmb.setJalviewColourScheme(new HelixColourScheme());
429 else if (evt.getSource() == strand)
432 jmb.setJalviewColourScheme(new StrandColourScheme());
434 else if (evt.getSource() == turn)
437 jmb.setJalviewColourScheme(new TurnColourScheme());
439 else if (evt.getSource() == buried)
442 jmb.setJalviewColourScheme(new BuriedColourScheme());
444 else if (evt.getSource() == user)
447 new UserDefinedColours(this);
449 else if (evt.getSource() == jmolHelp)
453 ap.av.applet.getAppletContext().showDocument(
455 "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
457 } catch (java.net.MalformedURLException ex)
463 allChainsSelected = true;
464 for (int i = 0; i < chainMenu.getItemCount(); i++)
466 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
467 ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
471 allChainsSelected = false;
476 * tick or untick the seqColour menu entry depending upon if it was selected
481 private void setEnabled(MenuItem itm)
483 seqColour.setState(itm == seqColour);
484 jmb.setColourBySequence(itm == seqColour);
487 public void itemStateChanged(ItemEvent evt)
489 if (evt.getSource() == seqColour)
491 setEnabled(seqColour);
492 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
494 else if (!allChainsSelected)
498 public void keyPressed(KeyEvent evt)
500 if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
502 jmb.eval(inputLine.getText());
503 history.append("\n$ " + inputLine.getText());
504 inputLine.setText("");
509 public void keyTyped(KeyEvent evt)
513 public void keyReleased(KeyEvent evt)
517 public void updateColours(Object source)
519 AlignmentPanel ap = (AlignmentPanel) source;
520 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
523 public void updateTitleAndMenus()
525 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
530 setChainMenuItems(jmb.chainNames);
531 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
533 setTitle(jmb.getViewerTitle());
536 public void showUrl(String url)
540 ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
542 } catch (java.net.MalformedURLException ex)
547 Panel splitPane = null;
549 public void showConsole(boolean showConsole)
554 splitPane = new Panel();
556 splitPane.setLayout(new java.awt.GridLayout(2, 1));
557 splitPane.add(renderPanel);
558 splitPane.add(scriptWindow);
559 scriptWindow.setVisible(true);
560 this.add(splitPane, BorderLayout.CENTER);
561 splitPane.setVisible(true);
562 splitPane.validate();
566 scriptWindow.setVisible(false);
568 add(renderPanel, BorderLayout.CENTER);
574 public float[][] functionXY(String functionName, int x, int y)
579 // /End JmolStatusListener
580 // /////////////////////////////
582 class RenderPanel extends Panel
584 Dimension currentSize = new Dimension();
586 Rectangle rectClip = new Rectangle();
588 public void update(Graphics g)
593 public void paint(Graphics g)
595 currentSize = this.getSize();
596 rectClip = g.getClipBounds();
598 if (jmb.viewer == null)
600 g.setColor(Color.black);
601 g.fillRect(0, 0, currentSize.width, currentSize.height);
602 g.setColor(Color.white);
603 g.setFont(new Font("Verdana", Font.BOLD, 14));
604 g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
608 jmb.viewer.renderScreenImage(g, currentSize, rectClip);
614 * @Override public Color getColour(int atomIndex, int pdbResNum, String
615 * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
618 * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
620 * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
621 * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
626 * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
627 * jmb.mouseOverStructure(atomIndex, strInfo);
631 public void setJalviewColourScheme(UserColourScheme ucs)
633 jmb.setJalviewColourScheme(ucs);