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 java.awt.BorderLayout;
24 import java.awt.CheckboxMenuItem;
25 import java.awt.Color;
26 import java.awt.Dimension;
28 import java.awt.Frame;
29 import java.awt.Graphics;
31 import java.awt.MenuBar;
32 import java.awt.MenuItem;
33 import java.awt.Panel;
34 import java.awt.Rectangle;
35 import java.awt.TextArea;
36 import java.awt.TextField;
37 import java.awt.event.ActionEvent;
38 import java.awt.event.ActionListener;
39 import java.awt.event.ItemEvent;
40 import java.awt.event.ItemListener;
41 import java.awt.event.KeyEvent;
42 import java.awt.event.KeyListener;
43 import java.awt.event.WindowAdapter;
44 import java.awt.event.WindowEvent;
45 import java.util.ArrayList;
46 import java.util.Hashtable;
47 import java.util.Vector;
49 import jalview.datamodel.AlignmentI;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.SequenceI;
52 import jalview.io.AppletFormatAdapter;
53 import jalview.io.FileParse;
54 import jalview.schemes.BuriedColourScheme;
55 import jalview.schemes.HelixColourScheme;
56 import jalview.schemes.HydrophobicColourScheme;
57 import jalview.schemes.PurinePyrimidineColourScheme;
58 import jalview.schemes.StrandColourScheme;
59 import jalview.schemes.TaylorColourScheme;
60 import jalview.schemes.TurnColourScheme;
61 import jalview.schemes.UserColourScheme;
62 import jalview.schemes.ZappoColourScheme;
63 import jalview.structure.StructureSelectionManager;
64 import jalview.util.MessageManager;
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 ArrayList _aps = new ArrayList();
135 String fileLoadingError;
137 boolean loadedInline;
139 // boolean colourBySequence = true;
141 FeatureRenderer fr = null;
143 AppletJmolBinding jmb;
146 * datasource protocol for access to PDBEntry
148 String protocol = null;
151 * Load a bunch of pdb entries associated with sequences in the alignment and
152 * display them - aligning them if necessary.
155 * each pdb file (at least one needed)
157 * each set of sequences for each pdb file (must match number of pdb
160 * the target pdb chain corresponding with each sequence associated
161 * with each pdb file (may be null at any level)
165 * associated alignment
167 * how to get pdb data
169 public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs,
170 String[][] boundchains, boolean align, AlignmentPanel ap,
173 throw new Error(MessageManager.getString("error.not_yet_implemented"));
176 public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
177 AlignmentPanel ap, String protocol)
180 jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
182 { pdbentry }, new SequenceI[][]
183 { seq }, new String[][]
184 { chains }, protocol);
185 jmb.setColourBySequence(true);
186 if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
188 if (protocol.equals(AppletFormatAdapter.PASTE))
190 pdbentry.setId("PASTED PDB"
191 + (chains == null ? "_" : chains.toString()));
195 pdbentry.setId(pdbentry.getFile());
199 if (jalview.bin.JalviewLite.debug)
202 .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
205 String alreadyMapped = StructureSelectionManager
206 .getStructureSelectionManager(ap.av.applet)
207 .alreadyMappedToFile(pdbentry.getId());
208 MCview.PDBfile 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()
287 public void windowClosing(WindowEvent evt)
292 if (pdbentry.getProperty() == null)
294 pdbentry.setProperty(new Hashtable());
295 pdbentry.getProperty().put("protocol", protocol);
297 if (pdbentry.getFile() != null)
299 // import structure data from pdbentry.getFile based on given protocol
300 if (protocol.equals(AppletFormatAdapter.PASTE))
302 // TODO: JAL-623 : correctly record file contents for matching up later
303 // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
304 loadInline(pdbentry.getFile());
306 else if (protocol.equals(AppletFormatAdapter.FILE)
307 || protocol.equals(AppletFormatAdapter.URL))
309 jmb.viewer.openFile(pdbentry.getFile());
313 // probably CLASSLOADER based datasource..
314 // Try and get a reader on the datasource, and pass that to Jmol
317 java.io.Reader freader = null;
320 if (jalview.bin.JalviewLite.debug)
323 .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
325 // re-use the one we opened earlier
326 freader = reader.getReader();
330 if (jalview.bin.JalviewLite.debug)
333 .println("AppletJmol:Creating new PDBfile IO parser.");
335 FileParse fp = new FileParse(pdbentry.getFile(), protocol);
337 // reader = new MCview.PDBfile(fp);
338 // could set ID, etc.
339 // if (!reader.isValid())
341 // throw new Exception("Invalid datasource.
342 // "+reader.getWarningMessage());
345 freader = fp.getReader();
349 throw new Exception(MessageManager.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(Vector 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 (int c = 0; c < chains.size(); c++)
385 menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
387 menuItemCB.addItemListener(this);
388 chainMenu.add(menuItemCB);
392 boolean allChainsSelected = false;
396 Vector toshow = new Vector();
398 int mlength, p, mnum;
399 for (int i = 0; i < chainMenu.getItemCount(); i++)
401 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
403 CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
406 toshow.addElement(item.getLabel());
410 jmb.centerViewer(toshow);
417 this.setVisible(false);
420 public void actionPerformed(ActionEvent evt)
422 if (evt.getSource() == mappingMenuItem)
424 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
426 Frame frame = new Frame();
429 StringBuffer sb = new StringBuffer();
432 cap.setText(jmb.printMappings());
433 } catch (OutOfMemoryError ex)
437 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
440 jalview.bin.JalviewLite.addFrame(frame,
441 MessageManager.getString("label.pdb_sequence_mapping"), 550,
444 else if (evt.getSource() == charge)
447 jmb.colourByCharge();
450 else if (evt.getSource() == chain)
455 else if (evt.getSource() == zappo)
458 jmb.setJalviewColourScheme(new ZappoColourScheme());
460 else if (evt.getSource() == taylor)
463 jmb.setJalviewColourScheme(new TaylorColourScheme());
465 else if (evt.getSource() == hydro)
468 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
470 else if (evt.getSource() == helix)
473 jmb.setJalviewColourScheme(new HelixColourScheme());
475 else if (evt.getSource() == strand)
478 jmb.setJalviewColourScheme(new StrandColourScheme());
480 else if (evt.getSource() == turn)
483 jmb.setJalviewColourScheme(new TurnColourScheme());
485 else if (evt.getSource() == buried)
488 jmb.setJalviewColourScheme(new BuriedColourScheme());
490 else if (evt.getSource() == purinepyrimidine)
492 jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
494 else if (evt.getSource() == user)
497 new UserDefinedColours(this);
499 else if (evt.getSource() == jmolHelp)
503 ap.av.applet.getAppletContext().showDocument(
505 "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
507 } catch (java.net.MalformedURLException ex)
513 allChainsSelected = true;
514 for (int i = 0; i < chainMenu.getItemCount(); i++)
516 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
518 ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
523 allChainsSelected = false;
528 * tick or untick the seqColour menu entry or jmoColour entry depending upon
529 * if it was selected or not.
533 private void setEnabled(MenuItem itm)
535 jmolColour.setState(itm == jmolColour);
536 seqColour.setState(itm == seqColour);
537 jmb.setColourBySequence(itm == seqColour);
540 public void itemStateChanged(ItemEvent evt)
542 if (evt.getSource() == jmolColour)
544 setEnabled(jmolColour);
545 jmb.setColourBySequence(false);
547 else if (evt.getSource() == seqColour)
549 setEnabled(seqColour);
550 jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
552 else if (!allChainsSelected)
558 public void keyPressed(KeyEvent evt)
560 if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
562 jmb.eval(inputLine.getText());
563 history.append("\n$ " + inputLine.getText());
564 inputLine.setText("");
569 public void keyTyped(KeyEvent evt)
573 public void keyReleased(KeyEvent evt)
577 public void updateColours(Object source)
579 AlignmentPanel ap = (AlignmentPanel) source;
580 jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
583 public void updateTitleAndMenus()
585 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
590 setChainMenuItems(jmb.chainNames);
591 jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
593 setTitle(jmb.getViewerTitle());
596 public void showUrl(String url)
600 ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
602 } catch (java.net.MalformedURLException ex)
607 Panel splitPane = null;
609 public void showConsole(boolean showConsole)
614 splitPane = new Panel();
616 splitPane.setLayout(new java.awt.GridLayout(2, 1));
617 splitPane.add(renderPanel);
618 splitPane.add(scriptWindow);
619 scriptWindow.setVisible(true);
620 this.add(splitPane, BorderLayout.CENTER);
621 splitPane.setVisible(true);
622 splitPane.validate();
626 scriptWindow.setVisible(false);
628 add(renderPanel, BorderLayout.CENTER);
634 public float[][] functionXY(String functionName, int x, int y)
639 // /End JmolStatusListener
640 // /////////////////////////////
642 class RenderPanel extends Panel
644 Dimension currentSize = new Dimension();
646 Rectangle rectClip = new Rectangle();
648 public void update(Graphics g)
653 public void paint(Graphics g)
655 currentSize = this.getSize();
656 rectClip = g.getClipBounds();
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, rectClip);
675 * @Override public Color getColour(int atomIndex, int pdbResNum, String
676 * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
679 * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
681 * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
682 * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
687 * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
688 * jmb.mouseOverStructure(atomIndex, strInfo);
692 public void setJalviewColourScheme(UserColourScheme ucs)
694 jmb.setJalviewColourScheme(ucs);
697 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
699 for (int i = 0; i < _aps.size(); i++)
701 if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
703 return ((AlignmentPanel) _aps.get(i));