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.FileParse;
28 import jalview.io.DataSourceType;
29 import jalview.io.StructureFile;
30 import jalview.schemes.BuriedColourScheme;
31 import jalview.schemes.HelixColourScheme;
32 import jalview.schemes.HydrophobicColourScheme;
33 import jalview.schemes.PurinePyrimidineColourScheme;
34 import jalview.schemes.StrandColourScheme;
35 import jalview.schemes.TaylorColourScheme;
36 import jalview.schemes.TurnColourScheme;
37 import jalview.schemes.UserColourScheme;
38 import jalview.schemes.ZappoColourScheme;
39 import jalview.structure.StructureSelectionManager;
40 import jalview.util.MessageManager;
42 import java.awt.BorderLayout;
43 import java.awt.CheckboxMenuItem;
44 import java.awt.Color;
45 import java.awt.Dimension;
47 import java.awt.Frame;
48 import java.awt.Graphics;
50 import java.awt.MenuBar;
51 import java.awt.MenuItem;
52 import java.awt.Panel;
53 import java.awt.TextArea;
54 import java.awt.TextField;
55 import java.awt.event.ActionEvent;
56 import java.awt.event.ActionListener;
57 import java.awt.event.ItemEvent;
58 import java.awt.event.ItemListener;
59 import java.awt.event.KeyEvent;
60 import java.awt.event.KeyListener;
61 import java.awt.event.WindowAdapter;
62 import java.awt.event.WindowEvent;
63 import java.util.ArrayList;
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, DataSourceType protocol)
182 jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
183 new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
185 jmb.setColourBySequence(true);
186 if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
188 if (protocol == DataSourceType.PASTE)
190 pdbentry.setId("PASTED PDB"
191 + (chains == null ? "_" : chains.toString()));
195 pdbentry.setId(pdbentry.getFile());
199 if (JalviewLite.debug)
202 .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
205 String alreadyMapped = StructureSelectionManager
206 .getStructureSelectionManager(ap.av.applet)
207 .alreadyMappedToFile(pdbentry.getId());
208 StructureFile reader = null;
209 if (alreadyMapped != null)
211 reader = StructureSelectionManager.getStructureSelectionManager(
212 ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
214 // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
215 // FOR NOW, LETS JUST OPEN A NEW WINDOW
217 MenuBar menuBar = new MenuBar();
218 menuBar.add(fileMenu);
219 fileMenu.add(mappingMenuItem);
220 menuBar.add(viewMenu);
221 mappingMenuItem.addActionListener(this);
222 viewMenu.add(chainMenu);
223 menuBar.add(coloursMenu);
224 menuBar.add(helpMenu);
226 charge.addActionListener(this);
227 hydro.addActionListener(this);
228 chain.addActionListener(this);
229 seqColour.addItemListener(this);
230 jmolColour.addItemListener(this);
231 zappo.addActionListener(this);
232 taylor.addActionListener(this);
233 helix.addActionListener(this);
234 strand.addActionListener(this);
235 turn.addActionListener(this);
236 buried.addActionListener(this);
237 purinepyrimidine.addActionListener(this);
238 user.addActionListener(this);
240 jmolHelp.addActionListener(this);
242 coloursMenu.add(seqColour);
243 coloursMenu.add(chain);
244 coloursMenu.add(charge);
245 coloursMenu.add(zappo);
246 coloursMenu.add(taylor);
247 coloursMenu.add(hydro);
248 coloursMenu.add(helix);
249 coloursMenu.add(strand);
250 coloursMenu.add(turn);
251 coloursMenu.add(buried);
252 coloursMenu.add(purinepyrimidine);
253 coloursMenu.add(user);
254 coloursMenu.add(jmolColour);
255 helpMenu.add(jmolHelp);
256 this.setLayout(new BorderLayout());
260 renderPanel = new RenderPanel();
261 embedMenuIfNeeded(renderPanel);
262 this.add(renderPanel, BorderLayout.CENTER);
263 scriptWindow = new Panel();
264 scriptWindow.setVisible(false);
265 // this.add(scriptWindow, BorderLayout.SOUTH);
269 jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
270 + "_jmol_", ap.av.applet.getDocumentBase(),
271 ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
272 } catch (Exception e)
275 .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
276 + ap.av.applet.getDocumentBase()
278 + ap.av.applet.getCodeBase());
283 // jmb.newJmolPopup(true, "Jmol", true);
285 this.addWindowListener(new WindowAdapter()
288 public void windowClosing(WindowEvent evt)
293 pdbentry.setProperty("protocol", protocol);
294 if (pdbentry.getFile() != null)
297 // import structure data from pdbentry.getFile based on given protocol
298 if (protocol == DataSourceType.PASTE)
300 // TODO: JAL-623 : correctly record file contents for matching up later
301 // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
302 loadInline(pdbentry.getFile());
304 else if (protocol == DataSourceType.FILE
305 || protocol == DataSourceType.URL)
307 jmb.viewer.openFile(pdbentry.getFile());
311 // probably CLASSLOADER based datasource..
312 // Try and get a reader on the datasource, and pass that to Jmol
315 java.io.Reader freader = null;
318 if (jalview.bin.JalviewLite.debug)
321 .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
323 // re-use the one we opened earlier
324 freader = reader.getReader();
328 if (jalview.bin.JalviewLite.debug)
331 .println("AppletJmol:Creating new PDBfile IO parser.");
333 FileParse fp = new FileParse(pdbentry.getFile(), protocol);
335 // reader = new MCview.PDBfile(fp);
336 // could set ID, etc.
337 // if (!reader.isValid())
339 // throw new Exception("Invalid datasource.
340 // "+reader.getWarningMessage());
343 freader = fp.getReader();
349 .getString("exception.invalid_datasource_couldnt_obtain_reader"));
351 jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
353 } catch (Exception e)
356 System.err.println("Couldn't access pdbentry id="
357 + pdbentry.getId() + " and file=" + pdbentry.getFile()
358 + " using protocol=" + protocol);
364 jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
367 public void loadInline(String string)
370 jmb.loadInline(string);
373 void setChainMenuItems(List<String> chains)
375 chainMenu.removeAll();
377 MenuItem menuItem = new MenuItem(MessageManager.getString("label.all"));
378 menuItem.addActionListener(this);
380 chainMenu.add(menuItem);
382 CheckboxMenuItem menuItemCB;
383 for (String ch : chains)
385 menuItemCB = new CheckboxMenuItem(ch, true);
386 menuItemCB.addItemListener(this);
387 chainMenu.add(menuItemCB);
391 boolean allChainsSelected = false;
395 Vector<String> toshow = new Vector<String>();
396 for (int i = 0; i < chainMenu.getItemCount(); i++)
398 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
400 CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
403 toshow.addElement(item.getLabel());
407 jmb.centerViewer(toshow);
414 this.setVisible(false);
418 public void actionPerformed(ActionEvent evt)
420 if (evt.getSource() == mappingMenuItem)
422 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
424 Frame frame = new Frame();
427 StringBuffer sb = new StringBuffer();
430 cap.setText(jmb.printMappings());
431 } catch (OutOfMemoryError ex)
435 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
438 jalview.bin.JalviewLite.addFrame(frame,
439 MessageManager.getString("label.pdb_sequence_mapping"), 550,
442 else if (evt.getSource() == charge)
445 jmb.colourByCharge();
448 else if (evt.getSource() == chain)
453 else if (evt.getSource() == zappo)
456 jmb.setJalviewColourScheme(new ZappoColourScheme());
458 else if (evt.getSource() == taylor)
461 jmb.setJalviewColourScheme(new TaylorColourScheme());
463 else if (evt.getSource() == hydro)
466 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
468 else if (evt.getSource() == helix)
471 jmb.setJalviewColourScheme(new HelixColourScheme());
473 else if (evt.getSource() == strand)
476 jmb.setJalviewColourScheme(new StrandColourScheme());
478 else if (evt.getSource() == turn)
481 jmb.setJalviewColourScheme(new TurnColourScheme());
483 else if (evt.getSource() == buried)
486 jmb.setJalviewColourScheme(new BuriedColourScheme());
488 else if (evt.getSource() == purinepyrimidine)
490 jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
492 else if (evt.getSource() == user)
495 new UserDefinedColours(this);
497 else if (evt.getSource() == jmolHelp)
501 ap.av.applet.getAppletContext().showDocument(
503 "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
505 } catch (java.net.MalformedURLException ex)
511 allChainsSelected = true;
512 for (int i = 0; i < chainMenu.getItemCount(); i++)
514 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
516 ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
521 allChainsSelected = false;
526 * tick or untick the seqColour menu entry or jmoColour entry depending upon
527 * if it was selected or not.
531 private void setEnabled(MenuItem itm)
533 jmolColour.setState(itm == jmolColour);
534 seqColour.setState(itm == seqColour);
535 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)
558 public void keyPressed(KeyEvent evt)
560 if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
562 jmb.eval(inputLine.getText());
563 addToHistory("$ " + inputLine.getText());
564 inputLine.setText("");
570 public void keyTyped(KeyEvent evt)
575 public void keyReleased(KeyEvent evt)
579 public void updateColours(Object source)
581 AlignmentPanel panel = (AlignmentPanel) source;
582 jmb.colourBySequence(panel);
585 public void updateTitleAndMenus()
587 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
592 setChainMenuItems(jmb.getChainNames());
593 jmb.colourBySequence(ap);
595 setTitle(jmb.getViewerTitle());
598 public void showUrl(String url)
602 ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
604 } catch (java.net.MalformedURLException ex)
609 Panel splitPane = null;
611 public void showConsole(boolean showConsole)
616 splitPane = new Panel();
618 splitPane.setLayout(new java.awt.GridLayout(2, 1));
619 splitPane.add(renderPanel);
620 splitPane.add(scriptWindow);
621 scriptWindow.setVisible(true);
622 this.add(splitPane, BorderLayout.CENTER);
623 splitPane.setVisible(true);
624 splitPane.validate();
628 scriptWindow.setVisible(false);
630 add(renderPanel, BorderLayout.CENTER);
636 public float[][] functionXY(String functionName, int x, int y)
641 // /End JmolStatusListener
642 // /////////////////////////////
644 class RenderPanel extends Panel
646 Dimension currentSize = new Dimension();
649 public void update(Graphics g)
655 public void paint(Graphics g)
657 currentSize = this.getSize();
659 if (jmb.viewer == null)
661 g.setColor(Color.black);
662 g.fillRect(0, 0, currentSize.width, currentSize.height);
663 g.setColor(Color.white);
664 g.setFont(new Font("Verdana", Font.BOLD, 14));
665 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
666 20, currentSize.height / 2);
670 jmb.viewer.renderScreenImage(g, currentSize.width,
677 * @Override public Color getColour(int atomIndex, int pdbResNum, String
678 * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
681 * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
683 * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
684 * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
689 * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
690 * jmb.mouseOverStructure(atomIndex, strInfo);
694 public void setJalviewColourScheme(UserColourScheme ucs)
696 jmb.setJalviewColourScheme(ucs);
699 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
701 for (int i = 0; i < _aps.size(); i++)
703 if (_aps.get(i).av.getAlignment() == alignment)
705 return (_aps.get(i));
712 * Append the given text to the history object
716 public void addToHistory(String text)
718 // actually currently never initialised
721 history.append("\n" + text);