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.bin.JalviewLite;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.PDBEntry;
26 import jalview.datamodel.SequenceI;
27 import jalview.io.AppletFormatAdapter;
28 import jalview.io.FileParse;
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.Hashtable;
64 import java.util.List;
65 import java.util.Vector;
67 public class AppletJmol extends EmbmenuFrame implements
69 KeyListener, ActionListener, ItemListener
72 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
74 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
76 Menu coloursMenu = new Menu(MessageManager.getString("action.colour"));
78 Menu chainMenu = new Menu(MessageManager.getString("action.show_chain"));
80 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
82 MenuItem mappingMenuItem = new MenuItem(
83 MessageManager.getString("label.view_mapping"));
85 CheckboxMenuItem seqColour = new CheckboxMenuItem(
86 MessageManager.getString("action.by_sequence"), true);
88 CheckboxMenuItem jmolColour = new CheckboxMenuItem(
89 MessageManager.getString("action.using_jmol"), false);
91 MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
93 MenuItem charge = new MenuItem(
94 MessageManager.getString("label.charge_cysteine"));
96 MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
98 MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
100 MenuItem hydro = new MenuItem(
101 MessageManager.getString("label.hydrophobicity"));
103 MenuItem helix = new MenuItem(
104 MessageManager.getString("label.helix_propensity"));
106 MenuItem strand = new MenuItem(
107 MessageManager.getString("label.strand_propensity"));
109 MenuItem turn = new MenuItem(
110 MessageManager.getString("label.turn_propensity"));
112 MenuItem buried = new MenuItem(
113 MessageManager.getString("label.buried_index"));
115 MenuItem purinepyrimidine = new MenuItem(
116 MessageManager.getString("label.purine_pyrimidine"));
118 MenuItem user = new MenuItem(
119 MessageManager.getString("label.user_defined_colours"));
121 MenuItem jmolHelp = new MenuItem(
122 MessageManager.getString("label.jmol_help"));
130 RenderPanel renderPanel;
134 List<AlignmentPanel> _aps = new ArrayList<AlignmentPanel>(); // remove? never
137 String fileLoadingError;
139 boolean loadedInline;
141 // boolean colourBySequence = true;
143 FeatureRenderer fr = null;
145 AppletJmolBinding jmb;
148 * datasource protocol for access to PDBEntry
150 String protocol = null;
153 * Load a bunch of pdb entries associated with sequences in the alignment and
154 * display them - aligning them if necessary.
157 * each pdb file (at least one needed)
159 * each set of sequences for each pdb file (must match number of pdb
162 * the target pdb chain corresponding with each sequence associated
163 * with each pdb file (may be null at any level)
167 * associated alignment
169 * how to get pdb data
171 public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs,
172 String[][] boundchains, boolean align, AlignmentPanel ap,
175 throw new Error(MessageManager.getString("error.not_yet_implemented"));
178 public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
179 AlignmentPanel ap, String protocol)
182 jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
184 { pdbentry }, new SequenceI[][]
185 { seq }, new String[][]
186 { chains }, protocol);
187 jmb.setColourBySequence(true);
188 if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
190 if (protocol.equals(AppletFormatAdapter.PASTE))
192 pdbentry.setId("PASTED PDB"
193 + (chains == null ? "_" : chains.toString()));
197 pdbentry.setId(pdbentry.getFile());
201 if (JalviewLite.debug)
204 .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
207 String alreadyMapped = StructureSelectionManager
208 .getStructureSelectionManager(ap.av.applet)
209 .alreadyMappedToFile(pdbentry.getId());
210 MCview.PDBfile reader = null;
211 if (alreadyMapped != null)
213 reader = StructureSelectionManager.getStructureSelectionManager(
214 ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
216 // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
217 // FOR NOW, LETS JUST OPEN A NEW WINDOW
219 MenuBar menuBar = new MenuBar();
220 menuBar.add(fileMenu);
221 fileMenu.add(mappingMenuItem);
222 menuBar.add(viewMenu);
223 mappingMenuItem.addActionListener(this);
224 viewMenu.add(chainMenu);
225 menuBar.add(coloursMenu);
226 menuBar.add(helpMenu);
228 charge.addActionListener(this);
229 hydro.addActionListener(this);
230 chain.addActionListener(this);
231 seqColour.addItemListener(this);
232 jmolColour.addItemListener(this);
233 zappo.addActionListener(this);
234 taylor.addActionListener(this);
235 helix.addActionListener(this);
236 strand.addActionListener(this);
237 turn.addActionListener(this);
238 buried.addActionListener(this);
239 purinepyrimidine.addActionListener(this);
240 user.addActionListener(this);
242 jmolHelp.addActionListener(this);
244 coloursMenu.add(seqColour);
245 coloursMenu.add(chain);
246 coloursMenu.add(charge);
247 coloursMenu.add(zappo);
248 coloursMenu.add(taylor);
249 coloursMenu.add(hydro);
250 coloursMenu.add(helix);
251 coloursMenu.add(strand);
252 coloursMenu.add(turn);
253 coloursMenu.add(buried);
254 coloursMenu.add(purinepyrimidine);
255 coloursMenu.add(user);
256 coloursMenu.add(jmolColour);
257 helpMenu.add(jmolHelp);
258 this.setLayout(new BorderLayout());
262 renderPanel = new RenderPanel();
263 embedMenuIfNeeded(renderPanel);
264 this.add(renderPanel, BorderLayout.CENTER);
265 scriptWindow = new Panel();
266 scriptWindow.setVisible(false);
267 // this.add(scriptWindow, BorderLayout.SOUTH);
271 jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
272 + "_jmol_", ap.av.applet.getDocumentBase(),
273 ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
274 } catch (Exception e)
277 .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
278 + ap.av.applet.getDocumentBase()
280 + ap.av.applet.getCodeBase());
285 // jmb.newJmolPopup(true, "Jmol", true);
287 this.addWindowListener(new WindowAdapter()
289 public void windowClosing(WindowEvent evt)
294 if (pdbentry.getProperty() == null)
296 pdbentry.setProperty(new Hashtable());
297 pdbentry.getProperty().put("protocol", protocol);
299 if (pdbentry.getFile() != null)
301 // import structure data from pdbentry.getFile based on given protocol
302 if (protocol.equals(AppletFormatAdapter.PASTE))
304 // TODO: JAL-623 : correctly record file contents for matching up later
305 // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
306 loadInline(pdbentry.getFile());
308 else if (protocol.equals(AppletFormatAdapter.FILE)
309 || protocol.equals(AppletFormatAdapter.URL))
311 jmb.viewer.openFile(pdbentry.getFile());
315 // probably CLASSLOADER based datasource..
316 // Try and get a reader on the datasource, and pass that to Jmol
319 java.io.Reader freader = null;
322 if (JalviewLite.debug)
325 .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
327 // re-use the one we opened earlier
328 freader = reader.getReader();
332 if (JalviewLite.debug)
335 .println("AppletJmol:Creating new PDBfile IO parser.");
337 FileParse fp = new FileParse(pdbentry.getFile(), protocol);
339 // reader = new MCview.PDBfile(fp);
340 // could set ID, etc.
341 // if (!reader.isValid())
343 // throw new Exception("Invalid datasource.
344 // "+reader.getWarningMessage());
347 freader = fp.getReader();
351 throw new Exception(MessageManager.getString("exception.invalid_datasource_couldnt_obtain_reader"));
353 jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
355 } catch (Exception e)
358 System.err.println("Couldn't access pdbentry id="
359 + pdbentry.getId() + " and file=" + pdbentry.getFile()
360 + " using protocol=" + protocol);
366 JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
369 public void loadInline(String string)
372 jmb.loadInline(string);
375 void setChainMenuItems(Vector<String> chains)
377 chainMenu.removeAll();
379 MenuItem menuItem = new MenuItem(MessageManager.getString("label.all"));
380 menuItem.addActionListener(this);
382 chainMenu.add(menuItem);
384 CheckboxMenuItem menuItemCB;
385 for (String ch : chains)
387 menuItemCB = new CheckboxMenuItem(ch, true);
388 menuItemCB.addItemListener(this);
389 chainMenu.add(menuItemCB);
393 boolean allChainsSelected = false;
397 Vector<String> toshow = new Vector<String>();
398 for (int i = 0; i < chainMenu.getItemCount(); i++)
400 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
402 CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
405 toshow.addElement(item.getLabel());
409 jmb.centerViewer(toshow);
416 this.setVisible(false);
419 public void actionPerformed(ActionEvent evt)
421 if (evt.getSource() == mappingMenuItem)
423 CutAndPasteTransfer cap = new CutAndPasteTransfer(
425 Frame frame = new Frame();
428 StringBuffer sb = new StringBuffer();
431 cap.setText(jmb.printMappings());
432 } catch (OutOfMemoryError ex)
436 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
439 JalviewLite.addFrame(frame,
440 MessageManager.getString("label.pdb_sequence_mapping"), 550,
443 else if (evt.getSource() == charge)
446 jmb.colourByCharge();
449 else if (evt.getSource() == chain)
454 else if (evt.getSource() == zappo)
457 jmb.setJalviewColourScheme(new ZappoColourScheme());
459 else if (evt.getSource() == taylor)
462 jmb.setJalviewColourScheme(new TaylorColourScheme());
464 else if (evt.getSource() == hydro)
467 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
469 else if (evt.getSource() == helix)
472 jmb.setJalviewColourScheme(new HelixColourScheme());
474 else if (evt.getSource() == strand)
477 jmb.setJalviewColourScheme(new StrandColourScheme());
479 else if (evt.getSource() == turn)
482 jmb.setJalviewColourScheme(new TurnColourScheme());
484 else if (evt.getSource() == buried)
487 jmb.setJalviewColourScheme(new BuriedColourScheme());
489 else if (evt.getSource() == purinepyrimidine)
491 jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
493 else if (evt.getSource() == user)
496 new UserDefinedColours(this);
498 else if (evt.getSource() == jmolHelp)
502 ap.av.applet.getAppletContext().showDocument(
504 "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
506 } catch (java.net.MalformedURLException ex)
512 allChainsSelected = true;
513 for (int i = 0; i < chainMenu.getItemCount(); i++)
515 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
517 ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
522 allChainsSelected = false;
527 * tick or untick the seqColour menu entry or jmoColour entry depending upon
528 * if it was selected or not.
532 private void setEnabled(MenuItem itm)
534 jmolColour.setState(itm == jmolColour);
535 seqColour.setState(itm == seqColour);
536 jmb.setColourBySequence(itm == seqColour);
539 public void itemStateChanged(ItemEvent evt)
541 if (evt.getSource() == jmolColour)
543 setEnabled(jmolColour);
544 jmb.setColourBySequence(false);
546 else if (evt.getSource() == seqColour)
548 setEnabled(seqColour);
549 jmb.colourBySequence(ap);
551 else if (!allChainsSelected)
557 public void keyPressed(KeyEvent evt)
559 if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
561 jmb.eval(inputLine.getText());
562 history.append("\n$ " + inputLine.getText());
563 inputLine.setText("");
568 public void keyTyped(KeyEvent evt)
572 public void keyReleased(KeyEvent evt)
576 public void updateColours(Object source)
578 AlignmentPanel panel = (AlignmentPanel) source;
579 jmb.colourBySequence(panel);
582 public void updateTitleAndMenus()
584 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
589 setChainMenuItems(jmb.chainNames);
590 jmb.colourBySequence(ap);
592 setTitle(jmb.getViewerTitle());
595 public void showUrl(String url)
599 ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
601 } catch (java.net.MalformedURLException ex)
606 Panel splitPane = null;
608 public void showConsole(boolean showConsole)
613 splitPane = new Panel();
615 splitPane.setLayout(new java.awt.GridLayout(2, 1));
616 splitPane.add(renderPanel);
617 splitPane.add(scriptWindow);
618 scriptWindow.setVisible(true);
619 this.add(splitPane, BorderLayout.CENTER);
620 splitPane.setVisible(true);
621 splitPane.validate();
625 scriptWindow.setVisible(false);
627 add(renderPanel, BorderLayout.CENTER);
633 public float[][] functionXY(String functionName, int x, int y)
638 // /End JmolStatusListener
639 // /////////////////////////////
641 class RenderPanel extends Panel
643 Dimension currentSize = new Dimension();
645 public void update(Graphics g)
650 public void paint(Graphics g)
652 currentSize = this.getSize();
654 if (jmb.viewer == null)
656 g.setColor(Color.black);
657 g.fillRect(0, 0, currentSize.width, currentSize.height);
658 g.setColor(Color.white);
659 g.setFont(new Font("Verdana", Font.BOLD, 14));
660 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
661 20, currentSize.height / 2);
665 jmb.viewer.renderScreenImage(g, currentSize.width,
672 * @Override public Color getColour(int atomIndex, int pdbResNum, String
673 * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
676 * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
678 * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
679 * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
684 * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
685 * jmb.mouseOverStructure(atomIndex, strInfo);
689 public void setJalviewColourScheme(UserColourScheme ucs)
691 jmb.setJalviewColourScheme(ucs);
694 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
696 for (int i = 0; i < _aps.size(); i++)
698 if (_aps.get(i).av.getAlignment() == alignment)
700 return (_aps.get(i));