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.schemes.BuriedColourScheme;
29 import jalview.schemes.HelixColourScheme;
30 import jalview.schemes.HydrophobicColourScheme;
31 import jalview.schemes.PurinePyrimidineColourScheme;
32 import jalview.schemes.StrandColourScheme;
33 import jalview.schemes.TaylorColourScheme;
34 import jalview.schemes.TurnColourScheme;
35 import jalview.schemes.UserColourScheme;
36 import jalview.schemes.ZappoColourScheme;
37 import jalview.structure.StructureSelectionManager;
38 import jalview.util.MessageManager;
40 import java.awt.BorderLayout;
41 import java.awt.CheckboxMenuItem;
42 import java.awt.Color;
43 import java.awt.Dimension;
45 import java.awt.Frame;
46 import java.awt.Graphics;
48 import java.awt.MenuBar;
49 import java.awt.MenuItem;
50 import java.awt.Panel;
51 import java.awt.TextArea;
52 import java.awt.TextField;
53 import java.awt.event.ActionEvent;
54 import java.awt.event.ActionListener;
55 import java.awt.event.ItemEvent;
56 import java.awt.event.ItemListener;
57 import java.awt.event.KeyEvent;
58 import java.awt.event.KeyListener;
59 import java.awt.event.WindowAdapter;
60 import java.awt.event.WindowEvent;
61 import java.util.ArrayList;
62 import java.util.Hashtable;
63 import java.util.Vector;
65 public class AppletJmol extends EmbmenuFrame implements
67 KeyListener, ActionListener, ItemListener
70 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
72 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
74 Menu coloursMenu = new Menu(MessageManager.getString("action.colour"));
76 Menu chainMenu = new Menu(MessageManager.getString("action.show_chain"));
78 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
80 MenuItem mappingMenuItem = new MenuItem(
81 MessageManager.getString("label.view_mapping"));
83 CheckboxMenuItem seqColour = new CheckboxMenuItem(
84 MessageManager.getString("action.by_sequence"), true);
86 CheckboxMenuItem jmolColour = new CheckboxMenuItem(
87 MessageManager.getString("action.using_jmol"), false);
89 MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
91 MenuItem charge = new MenuItem(
92 MessageManager.getString("label.charge_cysteine"));
94 MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
96 MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
98 MenuItem hydro = new MenuItem(
99 MessageManager.getString("label.hydrophobicity"));
101 MenuItem helix = new MenuItem(
102 MessageManager.getString("label.helix_propensity"));
104 MenuItem strand = new MenuItem(
105 MessageManager.getString("label.strand_propensity"));
107 MenuItem turn = new MenuItem(
108 MessageManager.getString("label.turn_propensity"));
110 MenuItem buried = new MenuItem(
111 MessageManager.getString("label.buried_index"));
113 MenuItem purinepyrimidine = new MenuItem(
114 MessageManager.getString("label.purine_pyrimidine"));
116 MenuItem user = new MenuItem(
117 MessageManager.getString("label.user_defined_colours"));
119 MenuItem jmolHelp = new MenuItem(
120 MessageManager.getString("label.jmol_help"));
128 RenderPanel renderPanel;
132 ArrayList _aps = new ArrayList();
134 String fileLoadingError;
136 boolean loadedInline;
138 // boolean colourBySequence = true;
140 FeatureRenderer fr = null;
142 AppletJmolBinding jmb;
145 * datasource protocol for access to PDBEntry
147 String protocol = null;
150 * Load a bunch of pdb entries associated with sequences in the alignment and
151 * display them - aligning them if necessary.
154 * each pdb file (at least one needed)
156 * each set of sequences for each pdb file (must match number of pdb
159 * the target pdb chain corresponding with each sequence associated
160 * with each pdb file (may be null at any level)
164 * associated alignment
166 * how to get pdb data
168 public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs,
169 String[][] boundchains, boolean align, AlignmentPanel ap,
172 throw new Error(MessageManager.getString("error.not_yet_implemented"));
175 public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
176 AlignmentPanel ap, String protocol)
179 jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
181 { pdbentry }, new SequenceI[][]
182 { seq }, new String[][]
183 { 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 MCview.PDBfile 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()
286 public void windowClosing(WindowEvent evt)
291 if (pdbentry.getProperty() == null)
293 pdbentry.setProperty(new Hashtable());
294 pdbentry.getProperty().put("protocol", protocol);
296 if (pdbentry.getFile() != null)
298 // import structure data from pdbentry.getFile based on given protocol
299 if (protocol.equals(AppletFormatAdapter.PASTE))
301 // TODO: JAL-623 : correctly record file contents for matching up later
302 // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
303 loadInline(pdbentry.getFile());
305 else if (protocol.equals(AppletFormatAdapter.FILE)
306 || protocol.equals(AppletFormatAdapter.URL))
308 jmb.viewer.openFile(pdbentry.getFile());
312 // probably CLASSLOADER based datasource..
313 // Try and get a reader on the datasource, and pass that to Jmol
316 java.io.Reader freader = null;
319 if (jalview.bin.JalviewLite.debug)
322 .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
324 // re-use the one we opened earlier
325 freader = reader.getReader();
329 if (jalview.bin.JalviewLite.debug)
332 .println("AppletJmol:Creating new PDBfile IO parser.");
334 FileParse fp = new FileParse(pdbentry.getFile(), protocol);
336 // reader = new MCview.PDBfile(fp);
337 // could set ID, etc.
338 // if (!reader.isValid())
340 // throw new Exception("Invalid datasource.
341 // "+reader.getWarningMessage());
344 freader = fp.getReader();
348 throw new Exception(MessageManager.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 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 (int c = 0; c < chains.size(); c++)
384 menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
386 menuItemCB.addItemListener(this);
387 chainMenu.add(menuItemCB);
391 boolean allChainsSelected = false;
395 Vector toshow = new Vector();
397 int mlength, p, mnum;
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 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.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 jalview.bin.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.av.isShowSequenceFeatures(), 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 ap = (AlignmentPanel) source;
579 jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
582 public void updateTitleAndMenus()
584 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
589 setChainMenuItems(jmb.chainNames);
590 jmb.colourBySequence(ap.av.isShowSequenceFeatures(), 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 (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
700 return ((AlignmentPanel) _aps.get(i));