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;
86 ArrayList _aps = new ArrayList();
88 String fileLoadingError;
92 // boolean colourBySequence = true;
94 FeatureRenderer fr = null;
96 AppletJmolBinding jmb;
99 * datasource protocol for access to PDBEntry
101 String protocol = null;
104 * Load a bunch of pdb entries associated with sequences in the alignment and
105 * display them - aligning them if necessary.
108 * each pdb file (at least one needed)
110 * each set of sequences for each pdb file (must match number of pdb
113 * the target pdb chain corresponding with each sequence associated
114 * with each pdb file (may be null at any level)
118 * associated alignment
120 * how to get pdb data
122 public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs,
123 String[][] boundchains, boolean align, AlignmentPanel ap,
126 throw new Error("Not yet implemented.");
129 public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
130 AlignmentPanel ap, String protocol)
133 jmb = new AppletJmolBinding(this, new PDBEntry[]
134 { pdbentry }, new SequenceI[][]
135 { seq }, new String[][]
136 { chains }, protocol);
137 jmb.setColourBySequence(true);
138 if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
140 if (protocol.equals(AppletFormatAdapter.PASTE))
142 pdbentry.setId("PASTED PDB"
143 + (chains == null ? "_" : chains.toString()));
147 pdbentry.setId(pdbentry.getFile());
151 if (jalview.bin.JalviewLite.debug)
154 .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
157 String alreadyMapped = StructureSelectionManager
158 .getStructureSelectionManager().alreadyMappedToFile(
160 MCview.PDBfile reader = null;
161 if (alreadyMapped != null)
163 reader = StructureSelectionManager.getStructureSelectionManager()
164 .setMapping(seq, chains, pdbentry.getFile(), protocol);
165 // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
166 // FOR NOW, LETS JUST OPEN A NEW WINDOW
168 MenuBar menuBar = new MenuBar();
169 menuBar.add(fileMenu);
170 fileMenu.add(mappingMenuItem);
171 menuBar.add(viewMenu);
172 mappingMenuItem.addActionListener(this);
173 viewMenu.add(chainMenu);
174 menuBar.add(coloursMenu);
175 menuBar.add(helpMenu);
177 charge.addActionListener(this);
178 hydro.addActionListener(this);
179 chain.addActionListener(this);
180 seqColour.addItemListener(this);
181 zappo.addActionListener(this);
182 taylor.addActionListener(this);
183 helix.addActionListener(this);
184 strand.addActionListener(this);
185 turn.addActionListener(this);
186 buried.addActionListener(this);
187 user.addActionListener(this);
189 jmolHelp.addActionListener(this);
191 coloursMenu.add(seqColour);
192 coloursMenu.add(chain);
193 coloursMenu.add(charge);
194 coloursMenu.add(zappo);
195 coloursMenu.add(taylor);
196 coloursMenu.add(hydro);
197 coloursMenu.add(helix);
198 coloursMenu.add(strand);
199 coloursMenu.add(turn);
200 coloursMenu.add(buried);
201 coloursMenu.add(user);
203 helpMenu.add(jmolHelp);
204 this.setLayout(new BorderLayout());
208 renderPanel = new RenderPanel();
209 embedMenuIfNeeded(renderPanel);
210 this.add(renderPanel, BorderLayout.CENTER);
211 scriptWindow = new Panel();
212 scriptWindow.setVisible(false);
213 // this.add(scriptWindow, BorderLayout.SOUTH);
217 jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
218 + "_jmol_", ap.av.applet.getDocumentBase(),
219 ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
220 } catch (Exception e)
223 .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
224 + ap.av.applet.getDocumentBase()
226 + ap.av.applet.getCodeBase());
231 jmb.newJmolPopup(true, "Jmol", true);
233 this.addWindowListener(new WindowAdapter()
235 public void windowClosing(WindowEvent evt)
240 if (pdbentry.getProperty() == null)
242 pdbentry.setProperty(new Hashtable());
243 pdbentry.getProperty().put("protocol", protocol);
245 if (pdbentry.getFile() != null)
247 // import structure data from pdbentry.getFile based on given protocol
248 if (protocol.equals(AppletFormatAdapter.PASTE))
250 // TODO: JAL-623 : correctly record file contents for matching up later
251 // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
252 loadInline(pdbentry.getFile());
254 else if (protocol.equals(AppletFormatAdapter.FILE)
255 || protocol.equals(AppletFormatAdapter.URL))
257 jmb.viewer.openFile(pdbentry.getFile());
261 // probably CLASSLOADER based datasource..
262 // Try and get a reader on the datasource, and pass that to Jmol
265 java.io.Reader freader = null;
268 if (jalview.bin.JalviewLite.debug)
271 .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
273 // re-use the one we opened earlier
274 freader = reader.getReader();
278 if (jalview.bin.JalviewLite.debug)
281 .println("AppletJmol:Creating new PDBfile IO parser.");
283 FileParse fp = new FileParse(pdbentry.getFile(), protocol);
285 // reader = new MCview.PDBfile(fp);
286 // could set ID, etc.
287 // if (!reader.isValid())
289 // throw new Exception("Invalid datasource.
290 // "+reader.getWarningMessage());
293 freader = fp.getReader();
298 "Invalid datasource. Could not obtain Reader.");
300 jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
302 } catch (Exception e)
305 System.err.println("Couldn't access pdbentry id="
306 + pdbentry.getId() + " and file=" + pdbentry.getFile()
307 + " using protocol=" + protocol);
313 jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
316 public void loadInline(String string)
319 jmb.loadInline(string);
322 void setChainMenuItems(Vector chains)
324 chainMenu.removeAll();
326 MenuItem menuItem = new MenuItem("All");
327 menuItem.addActionListener(this);
329 chainMenu.add(menuItem);
331 CheckboxMenuItem menuItemCB;
332 for (int c = 0; c < chains.size(); c++)
334 menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
336 menuItemCB.addItemListener(this);
337 chainMenu.add(menuItemCB);
341 boolean allChainsSelected = false;
345 Vector toshow = new Vector();
347 int mlength, p, mnum;
348 for (int i = 0; i < chainMenu.getItemCount(); i++)
350 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
352 CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
355 toshow.addElement(item.getLabel());
359 jmb.centerViewer(toshow);
366 this.setVisible(false);
369 public void actionPerformed(ActionEvent evt)
371 if (evt.getSource() == mappingMenuItem)
373 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
375 Frame frame = new Frame();
378 StringBuffer sb = new StringBuffer();
381 for (int s = 0; s < jmb.pdbentry.length; s++)
383 sb.append(StructureSelectionManager
384 .getStructureSelectionManager().printMapping(
385 jmb.pdbentry[s].getFile()));
388 cap.setText(sb.toString());
389 } catch (OutOfMemoryError ex)
393 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
396 jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
399 else if (evt.getSource() == charge)
402 jmb.colourByCharge();
405 else if (evt.getSource() == chain)
410 else if (evt.getSource() == zappo)
413 jmb.setJalviewColourScheme(new ZappoColourScheme());
415 else if (evt.getSource() == taylor)
418 jmb.setJalviewColourScheme(new TaylorColourScheme());
420 else if (evt.getSource() == hydro)
423 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
425 else if (evt.getSource() == helix)
428 jmb.setJalviewColourScheme(new HelixColourScheme());
430 else if (evt.getSource() == strand)
433 jmb.setJalviewColourScheme(new StrandColourScheme());
435 else if (evt.getSource() == turn)
438 jmb.setJalviewColourScheme(new TurnColourScheme());
440 else if (evt.getSource() == buried)
443 jmb.setJalviewColourScheme(new BuriedColourScheme());
445 else if (evt.getSource() == user)
448 new UserDefinedColours(this);
450 else if (evt.getSource() == jmolHelp)
454 ap.av.applet.getAppletContext().showDocument(
456 "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
458 } catch (java.net.MalformedURLException ex)
464 allChainsSelected = true;
465 for (int i = 0; i < chainMenu.getItemCount(); i++)
467 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
468 ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
472 allChainsSelected = false;
477 * tick or untick the seqColour menu entry depending upon if it was selected
482 private void setEnabled(MenuItem itm)
484 seqColour.setState(itm == seqColour);
485 jmb.setColourBySequence(itm == seqColour);
488 public void itemStateChanged(ItemEvent evt)
490 if (evt.getSource() == seqColour)
492 setEnabled(seqColour);
493 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
495 else if (!allChainsSelected)
499 public void keyPressed(KeyEvent evt)
501 if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
503 jmb.eval(inputLine.getText());
504 history.append("\n$ " + inputLine.getText());
505 inputLine.setText("");
510 public void keyTyped(KeyEvent evt)
514 public void keyReleased(KeyEvent evt)
518 public void updateColours(Object source)
520 AlignmentPanel ap = (AlignmentPanel) source;
521 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
524 public void updateTitleAndMenus()
526 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
531 setChainMenuItems(jmb.chainNames);
532 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
534 setTitle(jmb.getViewerTitle());
537 public void showUrl(String url)
541 ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
543 } catch (java.net.MalformedURLException ex)
548 Panel splitPane = null;
550 public void showConsole(boolean showConsole)
555 splitPane = new Panel();
557 splitPane.setLayout(new java.awt.GridLayout(2, 1));
558 splitPane.add(renderPanel);
559 splitPane.add(scriptWindow);
560 scriptWindow.setVisible(true);
561 this.add(splitPane, BorderLayout.CENTER);
562 splitPane.setVisible(true);
563 splitPane.validate();
567 scriptWindow.setVisible(false);
569 add(renderPanel, BorderLayout.CENTER);
575 public float[][] functionXY(String functionName, int x, int y)
580 // /End JmolStatusListener
581 // /////////////////////////////
583 class RenderPanel extends Panel
585 Dimension currentSize = new Dimension();
587 Rectangle rectClip = new Rectangle();
589 public void update(Graphics g)
594 public void paint(Graphics g)
596 currentSize = this.getSize();
597 rectClip = g.getClipBounds();
599 if (jmb.viewer == null)
601 g.setColor(Color.black);
602 g.fillRect(0, 0, currentSize.width, currentSize.height);
603 g.setColor(Color.white);
604 g.setFont(new Font("Verdana", Font.BOLD, 14));
605 g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
609 jmb.viewer.renderScreenImage(g, currentSize, rectClip);
615 * @Override public Color getColour(int atomIndex, int pdbResNum, String
616 * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
619 * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
621 * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
622 * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
627 * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
628 * jmb.mouseOverStructure(atomIndex, strInfo);
632 public void setJalviewColourScheme(UserColourScheme ucs)
634 jmb.setJalviewColourScheme(ucs);
637 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
639 for (int i=0;i<_aps.size();i++)
641 if (((AlignmentPanel)_aps.get(i)).av.getAlignment()==alignment)
643 return ((AlignmentPanel)_aps.get(i));