2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.datamodel.AlignmentI;
24 import jalview.datamodel.PDBEntry;
25 import jalview.datamodel.SequenceI;
26 import jalview.io.AppletFormatAdapter;
27 import jalview.io.FileParse;
28 import jalview.io.StructureFile;
29 import jalview.schemes.BuriedColourScheme;
30 import jalview.schemes.HelixColourScheme;
31 import jalview.schemes.HydrophobicColourScheme;
32 import jalview.schemes.PurinePyrimidineColourScheme;
33 import jalview.schemes.StrandColourScheme;
34 import jalview.schemes.TaylorColourScheme;
35 import jalview.schemes.TurnColourScheme;
36 import jalview.schemes.UserColourScheme;
37 import jalview.schemes.ZappoColourScheme;
38 import jalview.structure.StructureSelectionManager;
39 import jalview.util.MessageManager;
41 import java.awt.BorderLayout;
42 import java.awt.CheckboxMenuItem;
43 import java.awt.Color;
44 import java.awt.Dimension;
46 import java.awt.Frame;
47 import java.awt.Graphics;
49 import java.awt.MenuBar;
50 import java.awt.MenuItem;
51 import java.awt.Panel;
52 import java.awt.TextArea;
53 import java.awt.TextField;
54 import java.awt.event.ActionEvent;
55 import java.awt.event.ActionListener;
56 import java.awt.event.ItemEvent;
57 import java.awt.event.ItemListener;
58 import java.awt.event.KeyEvent;
59 import java.awt.event.KeyListener;
60 import java.awt.event.WindowAdapter;
61 import java.awt.event.WindowEvent;
62 import java.util.ArrayList;
63 import java.util.List;
64 import java.util.Vector;
66 public class AppletJmol extends EmbmenuFrame implements
68 KeyListener, ActionListener, ItemListener
71 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
73 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
75 Menu coloursMenu = new Menu(MessageManager.getString("action.colour"));
77 Menu chainMenu = new Menu(MessageManager.getString("action.show_chain"));
79 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
81 MenuItem mappingMenuItem = new MenuItem(
82 MessageManager.getString("label.view_mapping"));
84 CheckboxMenuItem seqColour = new CheckboxMenuItem(
85 MessageManager.getString("action.by_sequence"), true);
87 CheckboxMenuItem jmolColour = new CheckboxMenuItem(
88 MessageManager.getString("action.using_jmol"), false);
90 MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
92 MenuItem charge = new MenuItem(
93 MessageManager.getString("label.charge_cysteine"));
95 MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
97 MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
99 MenuItem hydro = new MenuItem(
100 MessageManager.getString("label.hydrophobicity"));
102 MenuItem helix = new MenuItem(
103 MessageManager.getString("label.helix_propensity"));
105 MenuItem strand = new MenuItem(
106 MessageManager.getString("label.strand_propensity"));
108 MenuItem turn = new MenuItem(
109 MessageManager.getString("label.turn_propensity"));
111 MenuItem buried = new MenuItem(
112 MessageManager.getString("label.buried_index"));
114 MenuItem purinepyrimidine = new MenuItem(
115 MessageManager.getString("label.purine_pyrimidine"));
117 MenuItem user = new MenuItem(
118 MessageManager.getString("label.user_defined_colours"));
120 MenuItem jmolHelp = new MenuItem(
121 MessageManager.getString("label.jmol_help"));
129 RenderPanel renderPanel;
133 List<AlignmentPanel> _aps = new ArrayList<AlignmentPanel>(); // remove? never
136 String fileLoadingError;
138 boolean loadedInline;
140 // boolean colourBySequence = true;
142 FeatureRenderer fr = null;
144 AppletJmolBinding jmb;
147 * datasource protocol for access to PDBEntry
149 String protocol = null;
152 * Load a bunch of pdb entries associated with sequences in the alignment and
153 * display them - aligning them if necessary.
156 * each pdb file (at least one needed)
158 * each set of sequences for each pdb file (must match number of pdb
161 * the target pdb chain corresponding with each sequence associated
162 * with each pdb file (may be null at any level)
166 * associated alignment
168 * how to get pdb data
170 public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs,
171 String[][] boundchains, boolean align, AlignmentPanel ap,
174 throw new Error(MessageManager.getString("error.not_yet_implemented"));
177 public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
178 AlignmentPanel ap, String protocol)
181 jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
182 new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
183 new String[][] { chains }, protocol);
184 jmb.setColourBySequence(true);
185 if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
187 if (protocol.equals(AppletFormatAdapter.PASTE))
189 pdbentry.setId("PASTED PDB"
190 + (chains == null ? "_" : chains.toString()));
194 pdbentry.setId(pdbentry.getFile());
198 if (jalview.bin.JalviewLite.debug)
201 .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
204 String alreadyMapped = StructureSelectionManager
205 .getStructureSelectionManager(ap.av.applet)
206 .alreadyMappedToFile(pdbentry.getId());
207 StructureFile reader = null;
208 if (alreadyMapped != null)
210 reader = StructureSelectionManager.getStructureSelectionManager(
211 ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
213 // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
214 // FOR NOW, LETS JUST OPEN A NEW WINDOW
216 MenuBar menuBar = new MenuBar();
217 menuBar.add(fileMenu);
218 fileMenu.add(mappingMenuItem);
219 menuBar.add(viewMenu);
220 mappingMenuItem.addActionListener(this);
221 viewMenu.add(chainMenu);
222 menuBar.add(coloursMenu);
223 menuBar.add(helpMenu);
225 charge.addActionListener(this);
226 hydro.addActionListener(this);
227 chain.addActionListener(this);
228 seqColour.addItemListener(this);
229 jmolColour.addItemListener(this);
230 zappo.addActionListener(this);
231 taylor.addActionListener(this);
232 helix.addActionListener(this);
233 strand.addActionListener(this);
234 turn.addActionListener(this);
235 buried.addActionListener(this);
236 purinepyrimidine.addActionListener(this);
237 user.addActionListener(this);
239 jmolHelp.addActionListener(this);
241 coloursMenu.add(seqColour);
242 coloursMenu.add(chain);
243 coloursMenu.add(charge);
244 coloursMenu.add(zappo);
245 coloursMenu.add(taylor);
246 coloursMenu.add(hydro);
247 coloursMenu.add(helix);
248 coloursMenu.add(strand);
249 coloursMenu.add(turn);
250 coloursMenu.add(buried);
251 coloursMenu.add(purinepyrimidine);
252 coloursMenu.add(user);
253 coloursMenu.add(jmolColour);
254 helpMenu.add(jmolHelp);
255 this.setLayout(new BorderLayout());
259 renderPanel = new RenderPanel();
260 embedMenuIfNeeded(renderPanel);
261 this.add(renderPanel, BorderLayout.CENTER);
262 scriptWindow = new Panel();
263 scriptWindow.setVisible(false);
264 // this.add(scriptWindow, BorderLayout.SOUTH);
268 jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
269 + "_jmol_", ap.av.applet.getDocumentBase(),
270 ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
271 } catch (Exception e)
274 .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
275 + ap.av.applet.getDocumentBase()
277 + ap.av.applet.getCodeBase());
282 // jmb.newJmolPopup(true, "Jmol", true);
284 this.addWindowListener(new WindowAdapter()
287 public void windowClosing(WindowEvent evt)
292 pdbentry.setProperty("protocol", protocol);
294 if (pdbentry.getFile() != null)
296 // import structure data from pdbentry.getFile based on given protocol
297 if (protocol.equals(AppletFormatAdapter.PASTE))
299 // TODO: JAL-623 : correctly record file contents for matching up later
300 // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
301 loadInline(pdbentry.getFile());
303 else if (protocol.equals(AppletFormatAdapter.FILE)
304 || protocol.equals(AppletFormatAdapter.URL))
306 jmb.viewer.openFile(pdbentry.getFile());
310 // probably CLASSLOADER based datasource..
311 // Try and get a reader on the datasource, and pass that to Jmol
314 java.io.Reader freader = null;
317 if (jalview.bin.JalviewLite.debug)
320 .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
322 // re-use the one we opened earlier
323 freader = reader.getReader();
327 if (jalview.bin.JalviewLite.debug)
330 .println("AppletJmol:Creating new PDBfile IO parser.");
332 FileParse fp = new FileParse(pdbentry.getFile(), protocol);
334 // reader = new MCview.PDBfile(fp);
335 // could set ID, etc.
336 // if (!reader.isValid())
338 // throw new Exception("Invalid datasource.
339 // "+reader.getWarningMessage());
342 freader = fp.getReader();
348 .getString("exception.invalid_datasource_couldnt_obtain_reader"));
350 jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
352 } catch (Exception e)
355 System.err.println("Couldn't access pdbentry id="
356 + pdbentry.getId() + " and file=" + pdbentry.getFile()
357 + " using protocol=" + protocol);
363 jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
366 public void loadInline(String string)
369 jmb.loadInline(string);
372 void setChainMenuItems(Vector<String> chains)
374 chainMenu.removeAll();
376 MenuItem menuItem = new MenuItem(MessageManager.getString("label.all"));
377 menuItem.addActionListener(this);
379 chainMenu.add(menuItem);
381 CheckboxMenuItem menuItemCB;
382 for (String ch : chains)
384 menuItemCB = new CheckboxMenuItem(ch, true);
385 menuItemCB.addItemListener(this);
386 chainMenu.add(menuItemCB);
390 boolean allChainsSelected = false;
394 Vector<String> toshow = new Vector<String>();
395 for (int i = 0; i < chainMenu.getItemCount(); i++)
397 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
399 CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
402 toshow.addElement(item.getLabel());
406 jmb.centerViewer(toshow);
413 this.setVisible(false);
417 public void actionPerformed(ActionEvent evt)
419 if (evt.getSource() == mappingMenuItem)
421 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
423 Frame frame = new Frame();
426 StringBuffer sb = new StringBuffer();
429 cap.setText(jmb.printMappings());
430 } catch (OutOfMemoryError ex)
434 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
437 jalview.bin.JalviewLite.addFrame(frame,
438 MessageManager.getString("label.pdb_sequence_mapping"), 550,
441 else if (evt.getSource() == charge)
444 jmb.colourByCharge();
447 else if (evt.getSource() == chain)
452 else if (evt.getSource() == zappo)
455 jmb.setJalviewColourScheme(new ZappoColourScheme());
457 else if (evt.getSource() == taylor)
460 jmb.setJalviewColourScheme(new TaylorColourScheme());
462 else if (evt.getSource() == hydro)
465 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
467 else if (evt.getSource() == helix)
470 jmb.setJalviewColourScheme(new HelixColourScheme());
472 else if (evt.getSource() == strand)
475 jmb.setJalviewColourScheme(new StrandColourScheme());
477 else if (evt.getSource() == turn)
480 jmb.setJalviewColourScheme(new TurnColourScheme());
482 else if (evt.getSource() == buried)
485 jmb.setJalviewColourScheme(new BuriedColourScheme());
487 else if (evt.getSource() == purinepyrimidine)
489 jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
491 else if (evt.getSource() == user)
494 new UserDefinedColours(this);
496 else if (evt.getSource() == jmolHelp)
500 ap.av.applet.getAppletContext().showDocument(
502 "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
504 } catch (java.net.MalformedURLException ex)
510 allChainsSelected = true;
511 for (int i = 0; i < chainMenu.getItemCount(); i++)
513 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
515 ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
520 allChainsSelected = false;
525 * tick or untick the seqColour menu entry or jmoColour entry depending upon
526 * if it was selected or not.
530 private void setEnabled(MenuItem itm)
532 jmolColour.setState(itm == jmolColour);
533 seqColour.setState(itm == seqColour);
534 jmb.setColourBySequence(itm == seqColour);
538 public void itemStateChanged(ItemEvent evt)
540 if (evt.getSource() == jmolColour)
542 setEnabled(jmolColour);
543 jmb.setColourBySequence(false);
545 else if (evt.getSource() == seqColour)
547 setEnabled(seqColour);
548 jmb.colourBySequence(ap);
550 else if (!allChainsSelected)
557 public void keyPressed(KeyEvent evt)
559 if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
561 jmb.eval(inputLine.getText());
562 addToHistory("$ " + inputLine.getText());
563 inputLine.setText("");
569 public void keyTyped(KeyEvent evt)
574 public void keyReleased(KeyEvent evt)
578 public void updateColours(Object source)
580 AlignmentPanel panel = (AlignmentPanel) source;
581 jmb.colourBySequence(panel);
584 public void updateTitleAndMenus()
586 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
591 setChainMenuItems(jmb.chainNames);
592 jmb.colourBySequence(ap);
594 setTitle(jmb.getViewerTitle());
597 public void showUrl(String url)
601 ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
603 } catch (java.net.MalformedURLException ex)
608 Panel splitPane = null;
610 public void showConsole(boolean showConsole)
615 splitPane = new Panel();
617 splitPane.setLayout(new java.awt.GridLayout(2, 1));
618 splitPane.add(renderPanel);
619 splitPane.add(scriptWindow);
620 scriptWindow.setVisible(true);
621 this.add(splitPane, BorderLayout.CENTER);
622 splitPane.setVisible(true);
623 splitPane.validate();
627 scriptWindow.setVisible(false);
629 add(renderPanel, BorderLayout.CENTER);
635 public float[][] functionXY(String functionName, int x, int y)
640 // /End JmolStatusListener
641 // /////////////////////////////
643 class RenderPanel extends Panel
645 Dimension currentSize = new Dimension();
648 public void update(Graphics g)
654 public void paint(Graphics g)
656 currentSize = this.getSize();
658 if (jmb.viewer == null)
660 g.setColor(Color.black);
661 g.fillRect(0, 0, currentSize.width, currentSize.height);
662 g.setColor(Color.white);
663 g.setFont(new Font("Verdana", Font.BOLD, 14));
664 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
665 20, currentSize.height / 2);
669 jmb.viewer.renderScreenImage(g, currentSize.width,
676 * @Override public Color getColour(int atomIndex, int pdbResNum, String
677 * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
680 * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
682 * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
683 * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
688 * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
689 * jmb.mouseOverStructure(atomIndex, strInfo);
693 public void setJalviewColourScheme(UserColourScheme ucs)
695 jmb.setJalviewColourScheme(ucs);
698 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
700 for (int i = 0; i < _aps.size(); i++)
702 if (_aps.get(i).av.getAlignment() == alignment)
704 return (_aps.get(i));
711 * Append the given text to the history object
715 public void addToHistory(String text)
717 // actually currently never initialised
720 history.append("\n" + text);