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 * Load a bunch of pdb entries associated with sequences in the alignment and display them - aligning them if necessary.
103 * @param pdbentries each pdb file (at least one needed)
104 * @param boundseqs each set of sequences for each pdb file (must match number of pdb files)
105 * @param boundchains the target pdb chain corresponding with each sequence associated with each pdb file (may be null at any level)
106 * @param align true/false
107 * @param ap associated alignment
108 * @param protocol how to get pdb data
110 public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs, String[][] boundchains, boolean align, AlignmentPanel ap, String protocol)
112 throw new Error("Not yet implemented.");
114 public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
115 AlignmentPanel ap, String protocol)
118 jmb = new AppletJmolBinding(this, new PDBEntry[]
119 { pdbentry }, new SequenceI[][]{seq}, new String[][]{ chains }, protocol);
120 jmb.setColourBySequence(true);
121 if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
123 if (protocol.equals(AppletFormatAdapter.PASTE))
125 pdbentry.setId("PASTED PDB"
126 + (chains == null ? "_" : chains.toString()));
130 pdbentry.setId(pdbentry.getFile());
134 if (jalview.bin.JalviewLite.debug)
137 .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
140 String alreadyMapped = StructureSelectionManager
141 .getStructureSelectionManager().alreadyMappedToFile(
143 MCview.PDBfile reader = null;
144 if (alreadyMapped != null)
146 reader = StructureSelectionManager.getStructureSelectionManager()
147 .setMapping(seq, chains, pdbentry.getFile(), protocol);
148 // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
149 // FOR NOW, LETS JUST OPEN A NEW WINDOW
151 MenuBar menuBar = new MenuBar();
152 menuBar.add(fileMenu);
153 fileMenu.add(mappingMenuItem);
154 menuBar.add(viewMenu);
155 mappingMenuItem.addActionListener(this);
156 viewMenu.add(chainMenu);
157 menuBar.add(coloursMenu);
158 menuBar.add(helpMenu);
160 charge.addActionListener(this);
161 hydro.addActionListener(this);
162 chain.addActionListener(this);
163 seqColour.addItemListener(this);
164 zappo.addActionListener(this);
165 taylor.addActionListener(this);
166 helix.addActionListener(this);
167 strand.addActionListener(this);
168 turn.addActionListener(this);
169 buried.addActionListener(this);
170 user.addActionListener(this);
172 jmolHelp.addActionListener(this);
174 coloursMenu.add(seqColour);
175 coloursMenu.add(chain);
176 coloursMenu.add(charge);
177 coloursMenu.add(zappo);
178 coloursMenu.add(taylor);
179 coloursMenu.add(hydro);
180 coloursMenu.add(helix);
181 coloursMenu.add(strand);
182 coloursMenu.add(turn);
183 coloursMenu.add(buried);
184 coloursMenu.add(user);
186 helpMenu.add(jmolHelp);
190 renderPanel = new RenderPanel();
191 embedMenuIfNeeded(renderPanel);
192 this.add(renderPanel, BorderLayout.CENTER);
195 jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()+"_jmol_",
196 ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(),
198 } catch (Exception e)
201 .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
202 + ap.av.applet.getDocumentBase()
204 + ap.av.applet.getCodeBase());
209 jmb.newJmolPopup(true, "Jmol", true);
211 this.addWindowListener(new WindowAdapter()
213 public void windowClosing(WindowEvent evt)
218 if (pdbentry.getProperty()==null)
220 pdbentry.setProperty(new Hashtable());
221 pdbentry.getProperty().put("protocol", protocol);
223 if (pdbentry.getFile() != null)
225 // import structure data from pdbentry.getFile based on given protocol
226 if (protocol.equals(AppletFormatAdapter.PASTE))
228 // TODO: JAL-623 : correctly record file contents for matching up later
229 // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
230 loadInline(pdbentry.getFile());
232 else if (protocol.equals(AppletFormatAdapter.FILE)
233 || protocol.equals(AppletFormatAdapter.URL))
235 jmb.viewer.openFile(pdbentry.getFile());
239 // probably CLASSLOADER based datasource..
240 // Try and get a reader on the datasource, and pass that to Jmol
243 java.io.Reader freader = null;
246 if (jalview.bin.JalviewLite.debug)
249 .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
251 // re-use the one we opened earlier
252 freader = reader.getReader();
256 if (jalview.bin.JalviewLite.debug)
259 .println("AppletJmol:Creating new PDBfile IO parser.");
261 FileParse fp = new FileParse(pdbentry.getFile(), protocol);
263 // reader = new MCview.PDBfile(fp);
264 // could set ID, etc.
265 // if (!reader.isValid())
267 // throw new Exception("Invalid datasource.
268 // "+reader.getWarningMessage());
271 freader = fp.getReader();
276 "Invalid datasource. Could not obtain Reader.");
278 jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
280 } catch (Exception e)
283 System.err.println("Couldn't access pdbentry id="
284 + pdbentry.getId() + " and file=" + pdbentry.getFile()
285 + " using protocol=" + protocol);
291 jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
294 public void loadInline(String string)
297 jmb.loadInline(string);
300 void setChainMenuItems(Vector chains)
302 chainMenu.removeAll();
304 MenuItem menuItem = new MenuItem("All");
305 menuItem.addActionListener(this);
307 chainMenu.add(menuItem);
309 CheckboxMenuItem menuItemCB;
310 for (int c = 0; c < chains.size(); c++)
312 menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
314 menuItemCB.addItemListener(this);
315 chainMenu.add(menuItemCB);
319 boolean allChainsSelected = false;
323 Vector toshow = new Vector();
325 int mlength, p, mnum;
326 for (int i = 0; i < chainMenu.getItemCount(); i++)
328 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
330 CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
333 toshow.addElement(item.getLabel());
337 jmb.centerViewer(toshow);
344 this.setVisible(false);
347 public void actionPerformed(ActionEvent evt)
349 if (evt.getSource() == mappingMenuItem)
351 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
353 Frame frame = new Frame();
356 StringBuffer sb = new StringBuffer();
358 for (int s = 0; s < jmb.pdbentry.length; s++)
360 sb.append(StructureSelectionManager.getStructureSelectionManager()
361 .printMapping(jmb.pdbentry[s].getFile()));
364 cap.setText(sb.toString());
366 catch (OutOfMemoryError ex)
369 System.err.println("Out of memory when trying to create dialog box with sequence-structure mapping.");
372 jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
375 else if (evt.getSource() == charge)
378 jmb.colourByCharge();
381 else if (evt.getSource() == chain)
386 else if (evt.getSource() == zappo)
389 jmb.setJalviewColourScheme(new ZappoColourScheme());
391 else if (evt.getSource() == taylor)
394 jmb.setJalviewColourScheme(new TaylorColourScheme());
396 else if (evt.getSource() == hydro)
399 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
401 else if (evt.getSource() == helix)
404 jmb.setJalviewColourScheme(new HelixColourScheme());
406 else if (evt.getSource() == strand)
409 jmb.setJalviewColourScheme(new StrandColourScheme());
411 else if (evt.getSource() == turn)
414 jmb.setJalviewColourScheme(new TurnColourScheme());
416 else if (evt.getSource() == buried)
419 jmb.setJalviewColourScheme(new BuriedColourScheme());
421 else if (evt.getSource() == user)
424 new UserDefinedColours(this);
426 else if (evt.getSource() == jmolHelp)
430 ap.av.applet.getAppletContext().showDocument(
432 "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
434 } catch (java.net.MalformedURLException ex)
440 allChainsSelected = true;
441 for (int i = 0; i < chainMenu.getItemCount(); i++)
443 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
444 ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
448 allChainsSelected = false;
453 * tick or untick the seqColour menu entry depending upon if it was selected
458 private void setEnabled(MenuItem itm)
460 seqColour.setState(itm == seqColour);
461 jmb.setColourBySequence(itm == seqColour);
464 public void itemStateChanged(ItemEvent evt)
466 if (evt.getSource() == seqColour)
468 setEnabled(seqColour);
469 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
471 else if (!allChainsSelected)
475 public void keyPressed(KeyEvent evt)
477 if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
479 jmb.eval(inputLine.getText());
480 history.append("\n$ " + inputLine.getText());
481 inputLine.setText("");
486 public void keyTyped(KeyEvent evt)
490 public void keyReleased(KeyEvent evt)
494 public void updateColours(Object source)
496 AlignmentPanel ap = (AlignmentPanel) source;
497 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
500 public void updateTitleAndMenus()
502 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
507 setChainMenuItems(jmb.chainNames);
508 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
510 setTitle(jmb.getViewerTitle());
513 public void showUrl(String url)
517 ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
519 } catch (java.net.MalformedURLException ex)
524 public void showConsole(boolean showConsole)
526 if (scriptWindow == null)
528 scriptWindow = new Panel(new BorderLayout());
529 inputLine = new TextField();
530 history = new TextArea(5, 40);
531 scriptWindow.add(history, BorderLayout.CENTER);
532 scriptWindow.add(inputLine, BorderLayout.SOUTH);
533 add(scriptWindow, BorderLayout.SOUTH);
534 scriptWindow.setVisible(false);
535 history.setEditable(false);
536 inputLine.addKeyListener(this);
539 scriptWindow.setVisible(!scriptWindow.isVisible());
543 public float[][] functionXY(String functionName, int x, int y)
548 // /End JmolStatusListener
549 // /////////////////////////////
551 class RenderPanel extends Panel
553 Dimension currentSize = new Dimension();
555 Rectangle rectClip = new Rectangle();
557 public void update(Graphics g)
562 public void paint(Graphics g)
564 currentSize = this.getSize();
565 rectClip = g.getClipBounds();
567 if (jmb.viewer == null)
569 g.setColor(Color.black);
570 g.fillRect(0, 0, currentSize.width, currentSize.height);
571 g.setColor(Color.white);
572 g.setFont(new Font("Verdana", Font.BOLD, 14));
573 g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
577 jmb.viewer.renderScreenImage(g, currentSize, rectClip);
583 * @Override public Color getColour(int atomIndex, int pdbResNum, String
584 * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
587 * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
589 * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
590 * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
595 * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
596 * jmb.mouseOverStructure(atomIndex, strInfo);
600 public void setJalviewColourScheme(UserColourScheme ucs)
602 jmb.setJalviewColourScheme(ucs);