2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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;
25 import java.awt.event.*;
27 import jalview.api.SequenceStructureBinding;
28 import jalview.datamodel.*;
29 import jalview.structure.*;
32 import jalview.schemes.*;
33 import jalview.util.MessageManager;
35 public class AppletJmol extends EmbmenuFrame implements
37 KeyListener, ActionListener, ItemListener, SequenceStructureBinding
40 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
42 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
44 Menu coloursMenu = new Menu(MessageManager.getString("action.colour"));
46 Menu chainMenu = new Menu(MessageManager.getString("action.show_chain"));
48 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
50 MenuItem mappingMenuItem = new MenuItem(MessageManager.getString("label.view_mapping"));
52 CheckboxMenuItem seqColour = new CheckboxMenuItem(MessageManager.getString("action.by_sequence"), true);
54 CheckboxMenuItem jmolColour = new CheckboxMenuItem(MessageManager.getString("action.using_jmol"), false);
56 MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
58 MenuItem charge = new MenuItem(MessageManager.getString("label.charge_cysteine"));
60 MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
62 MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
64 MenuItem hydro = new MenuItem(MessageManager.getString("label.hydrophobicity"));
66 MenuItem helix = new MenuItem(MessageManager.getString("label.helix_propensity"));
68 MenuItem strand = new MenuItem(MessageManager.getString("label.strand_propensity"));
70 MenuItem turn = new MenuItem(MessageManager.getString("label.turn_propensity"));
72 MenuItem buried = new MenuItem(MessageManager.getString("label.buried_index"));
74 MenuItem purinepyrimidine = new MenuItem(MessageManager.getString("label.purine_pyrimidine"));
76 MenuItem user = new MenuItem(MessageManager.getString("label.user_defined_colours"));
78 MenuItem jmolHelp = new MenuItem(MessageManager.getString("label.jmol_help"));
86 RenderPanel renderPanel;
90 ArrayList _aps = new ArrayList();
92 String fileLoadingError;
96 // boolean colourBySequence = true;
98 FeatureRenderer fr = null;
100 AppletJmolBinding jmb;
103 * datasource protocol for access to PDBEntry
105 String protocol = null;
108 * Load a bunch of pdb entries associated with sequences in the alignment and
109 * display them - aligning them if necessary.
112 * each pdb file (at least one needed)
114 * each set of sequences for each pdb file (must match number of pdb
117 * the target pdb chain corresponding with each sequence associated
118 * with each pdb file (may be null at any level)
122 * associated alignment
124 * how to get pdb data
126 public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs,
127 String[][] boundchains, boolean align, AlignmentPanel ap,
130 throw new Error("Not yet implemented.");
133 public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
134 AlignmentPanel ap, String protocol)
137 jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
139 { pdbentry }, new SequenceI[][]
140 { seq }, new String[][]
141 { chains }, protocol);
142 jmb.setColourBySequence(true);
143 if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
145 if (protocol.equals(AppletFormatAdapter.PASTE))
147 pdbentry.setId("PASTED PDB"
148 + (chains == null ? "_" : chains.toString()));
152 pdbentry.setId(pdbentry.getFile());
156 if (jalview.bin.JalviewLite.debug)
159 .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
162 String alreadyMapped = StructureSelectionManager
163 .getStructureSelectionManager(ap.av.applet)
164 .alreadyMappedToFile(pdbentry.getId());
165 MCview.PDBfile reader = null;
166 if (alreadyMapped != null)
168 reader = StructureSelectionManager.getStructureSelectionManager(
169 ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
171 // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
172 // FOR NOW, LETS JUST OPEN A NEW WINDOW
174 MenuBar menuBar = new MenuBar();
175 menuBar.add(fileMenu);
176 fileMenu.add(mappingMenuItem);
177 menuBar.add(viewMenu);
178 mappingMenuItem.addActionListener(this);
179 viewMenu.add(chainMenu);
180 menuBar.add(coloursMenu);
181 menuBar.add(helpMenu);
183 charge.addActionListener(this);
184 hydro.addActionListener(this);
185 chain.addActionListener(this);
186 seqColour.addItemListener(this);
187 jmolColour.addItemListener(this);
188 zappo.addActionListener(this);
189 taylor.addActionListener(this);
190 helix.addActionListener(this);
191 strand.addActionListener(this);
192 turn.addActionListener(this);
193 buried.addActionListener(this);
194 purinepyrimidine.addActionListener(this);
195 user.addActionListener(this);
197 jmolHelp.addActionListener(this);
199 coloursMenu.add(seqColour);
200 coloursMenu.add(chain);
201 coloursMenu.add(charge);
202 coloursMenu.add(zappo);
203 coloursMenu.add(taylor);
204 coloursMenu.add(hydro);
205 coloursMenu.add(helix);
206 coloursMenu.add(strand);
207 coloursMenu.add(turn);
208 coloursMenu.add(buried);
209 coloursMenu.add(purinepyrimidine);
210 coloursMenu.add(user);
211 coloursMenu.add(jmolColour);
212 helpMenu.add(jmolHelp);
213 this.setLayout(new BorderLayout());
217 renderPanel = new RenderPanel();
218 embedMenuIfNeeded(renderPanel);
219 this.add(renderPanel, BorderLayout.CENTER);
220 scriptWindow = new Panel();
221 scriptWindow.setVisible(false);
222 // this.add(scriptWindow, BorderLayout.SOUTH);
226 jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
227 + "_jmol_", ap.av.applet.getDocumentBase(),
228 ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
229 } catch (Exception e)
232 .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
233 + ap.av.applet.getDocumentBase()
235 + ap.av.applet.getCodeBase());
240 jmb.newJmolPopup(true, "Jmol", true);
242 this.addWindowListener(new WindowAdapter()
244 public void windowClosing(WindowEvent evt)
249 if (pdbentry.getProperty() == null)
251 pdbentry.setProperty(new Hashtable());
252 pdbentry.getProperty().put("protocol", protocol);
254 if (pdbentry.getFile() != null)
256 // import structure data from pdbentry.getFile based on given protocol
257 if (protocol.equals(AppletFormatAdapter.PASTE))
259 // TODO: JAL-623 : correctly record file contents for matching up later
260 // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
261 loadInline(pdbentry.getFile());
263 else if (protocol.equals(AppletFormatAdapter.FILE)
264 || protocol.equals(AppletFormatAdapter.URL))
266 jmb.viewer.openFile(pdbentry.getFile());
270 // probably CLASSLOADER based datasource..
271 // Try and get a reader on the datasource, and pass that to Jmol
274 java.io.Reader freader = null;
277 if (jalview.bin.JalviewLite.debug)
280 .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
282 // re-use the one we opened earlier
283 freader = reader.getReader();
287 if (jalview.bin.JalviewLite.debug)
290 .println("AppletJmol:Creating new PDBfile IO parser.");
292 FileParse fp = new FileParse(pdbentry.getFile(), protocol);
294 // reader = new MCview.PDBfile(fp);
295 // could set ID, etc.
296 // if (!reader.isValid())
298 // throw new Exception("Invalid datasource.
299 // "+reader.getWarningMessage());
302 freader = fp.getReader();
307 "Invalid datasource. Could not obtain Reader.");
309 jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
311 } catch (Exception e)
314 System.err.println("Couldn't access pdbentry id="
315 + pdbentry.getId() + " and file=" + pdbentry.getFile()
316 + " using protocol=" + protocol);
322 jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
325 public void loadInline(String string)
328 jmb.loadInline(string);
331 void setChainMenuItems(Vector chains)
333 chainMenu.removeAll();
335 MenuItem menuItem = new MenuItem(MessageManager.getString("label.all"));
336 menuItem.addActionListener(this);
338 chainMenu.add(menuItem);
340 CheckboxMenuItem menuItemCB;
341 for (int c = 0; c < chains.size(); c++)
343 menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
345 menuItemCB.addItemListener(this);
346 chainMenu.add(menuItemCB);
350 boolean allChainsSelected = false;
354 Vector toshow = new Vector();
356 int mlength, p, mnum;
357 for (int i = 0; i < chainMenu.getItemCount(); i++)
359 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
361 CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
364 toshow.addElement(item.getLabel());
368 jmb.centerViewer(toshow);
375 this.setVisible(false);
378 public void actionPerformed(ActionEvent evt)
380 if (evt.getSource() == mappingMenuItem)
382 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
384 Frame frame = new Frame();
387 StringBuffer sb = new StringBuffer();
390 for (int s = 0; s < jmb.pdbentry.length; s++)
392 sb.append(jmb.printMapping(jmb.pdbentry[s].getFile()));
395 cap.setText(sb.toString());
396 } catch (OutOfMemoryError ex)
400 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
403 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pdb_sequence_mapping"),
406 else if (evt.getSource() == charge)
409 jmb.colourByCharge();
412 else if (evt.getSource() == chain)
417 else if (evt.getSource() == zappo)
420 jmb.setJalviewColourScheme(new ZappoColourScheme());
422 else if (evt.getSource() == taylor)
425 jmb.setJalviewColourScheme(new TaylorColourScheme());
427 else if (evt.getSource() == hydro)
430 jmb.setJalviewColourScheme(new HydrophobicColourScheme());
432 else if (evt.getSource() == helix)
435 jmb.setJalviewColourScheme(new HelixColourScheme());
437 else if (evt.getSource() == strand)
440 jmb.setJalviewColourScheme(new StrandColourScheme());
442 else if (evt.getSource() == turn)
445 jmb.setJalviewColourScheme(new TurnColourScheme());
447 else if (evt.getSource() == buried)
450 jmb.setJalviewColourScheme(new BuriedColourScheme());
452 else if (evt.getSource() == purinepyrimidine)
454 jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
456 else if (evt.getSource() == user)
459 new UserDefinedColours(this);
461 else if (evt.getSource() == jmolHelp)
465 ap.av.applet.getAppletContext().showDocument(
467 "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
469 } catch (java.net.MalformedURLException ex)
475 allChainsSelected = true;
476 for (int i = 0; i < chainMenu.getItemCount(); i++)
478 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
479 ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
483 allChainsSelected = false;
488 * tick or untick the seqColour menu entry or jmoColour entry depending upon
489 * if it was selected or not.
493 private void setEnabled(MenuItem itm)
495 jmolColour.setState(itm == jmolColour);
496 seqColour.setState(itm == seqColour);
497 jmb.setColourBySequence(itm == seqColour);
500 public void itemStateChanged(ItemEvent evt)
502 if (evt.getSource() == jmolColour)
504 setEnabled(jmolColour);
505 jmb.setColourBySequence(false);
507 else if (evt.getSource() == seqColour)
509 setEnabled(seqColour);
510 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
512 else if (!allChainsSelected)
516 public void keyPressed(KeyEvent evt)
518 if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
520 jmb.eval(inputLine.getText());
521 history.append("\n$ " + inputLine.getText());
522 inputLine.setText("");
527 public void keyTyped(KeyEvent evt)
531 public void keyReleased(KeyEvent evt)
535 public void updateColours(Object source)
537 AlignmentPanel ap = (AlignmentPanel) source;
538 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
541 public void updateTitleAndMenus()
543 if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
548 setChainMenuItems(jmb.chainNames);
549 jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
551 setTitle(jmb.getViewerTitle());
554 public void showUrl(String url)
558 ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
560 } catch (java.net.MalformedURLException ex)
565 Panel splitPane = null;
567 public void showConsole(boolean showConsole)
572 splitPane = new Panel();
574 splitPane.setLayout(new java.awt.GridLayout(2, 1));
575 splitPane.add(renderPanel);
576 splitPane.add(scriptWindow);
577 scriptWindow.setVisible(true);
578 this.add(splitPane, BorderLayout.CENTER);
579 splitPane.setVisible(true);
580 splitPane.validate();
584 scriptWindow.setVisible(false);
586 add(renderPanel, BorderLayout.CENTER);
592 public float[][] functionXY(String functionName, int x, int y)
597 // /End JmolStatusListener
598 // /////////////////////////////
600 class RenderPanel extends Panel
602 Dimension currentSize = new Dimension();
604 Rectangle rectClip = new Rectangle();
606 public void update(Graphics g)
611 public void paint(Graphics g)
613 currentSize = this.getSize();
614 rectClip = g.getClipBounds();
616 if (jmb.viewer == null)
618 g.setColor(Color.black);
619 g.fillRect(0, 0, currentSize.width, currentSize.height);
620 g.setColor(Color.white);
621 g.setFont(new Font("Verdana", Font.BOLD, 14));
622 g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
626 jmb.viewer.renderScreenImage(g, currentSize, rectClip);
632 * @Override public Color getColour(int atomIndex, int pdbResNum, String
633 * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
636 * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
638 * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
639 * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
644 * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
645 * jmb.mouseOverStructure(atomIndex, strInfo);
649 public void setJalviewColourScheme(UserColourScheme ucs)
651 jmb.setJalviewColourScheme(ucs);
654 public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
656 for (int i = 0; i < _aps.size(); i++)
658 if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
660 return ((AlignmentPanel) _aps.get(i));