2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
20 package jalview.appletgui;
24 import java.awt.event.*;
26 import jalview.datamodel.*;
27 import jalview.structure.*;
30 import org.jmol.api.*;
31 import org.jmol.adapter.smarter.SmarterJmolAdapter;
33 import org.jmol.popup.*;
34 import jalview.schemes.*;
37 public class AppletJmol extends Frame
38 implements StructureListener, JmolStatusListener,
39 KeyListener, ActionListener, ItemListener
42 Menu fileMenu = new Menu("File");
43 Menu viewMenu = new Menu("View");
44 Menu coloursMenu = new Menu("Colours");
45 Menu chainMenu = new Menu("Show Chain");
46 Menu helpMenu = new Menu("Help");
47 MenuItem mappingMenuItem = new MenuItem("View Mapping");
49 CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
50 MenuItem chain = new MenuItem("By Chain");
51 MenuItem charge = new MenuItem("Charge & Cysteine");
52 MenuItem zappo = new MenuItem("Zappo");
53 MenuItem taylor = new MenuItem("Taylor");
54 MenuItem hydro = new MenuItem("Hydrophobicity");
55 MenuItem helix = new MenuItem("Helix Propensity");
56 MenuItem strand = new MenuItem("Strand Propensity");
57 MenuItem turn = new MenuItem("Turn Propensity");
58 MenuItem buried = new MenuItem("Buried Index");
59 MenuItem user = new MenuItem("User Defined Colours");
61 MenuItem jmolHelp = new MenuItem("Jmol Help");
71 StructureSelectionManager ssm;
72 RenderPanel renderPanel;
74 String fileLoadingError;
77 boolean colourBySequence = true;
78 Vector atomsPicked = new Vector();
80 public AppletJmol(PDBEntry pdbentry,
89 this.pdbentry = pdbentry;
91 String alreadyMapped = StructureSelectionManager
92 .getStructureSelectionManager()
93 .alreadyMappedToFile(pdbentry.getId());
95 if (alreadyMapped != null)
97 StructureSelectionManager.getStructureSelectionManager()
98 .setMapping(seq, chains, pdbentry.getFile(), protocol);
99 //PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
100 //FOR NOW, LETS JUST OPEN A NEW WINDOW
103 renderPanel = new RenderPanel();
105 this.add(renderPanel, BorderLayout.CENTER);
106 viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter());
108 viewer.setAppletContext("jalview",
109 ap.av.applet.getDocumentBase(),
110 ap.av.applet.getCodeBase(),
113 viewer.setJmolStatusListener(this);
115 jmolpopup = JmolPopup.newJmolPopup(viewer);
117 this.addWindowListener(new WindowAdapter()
119 public void windowClosing(WindowEvent evt)
125 MenuBar menuBar = new MenuBar();
126 menuBar.add(fileMenu);
127 fileMenu.add(mappingMenuItem);
128 menuBar.add(viewMenu);
129 mappingMenuItem.addActionListener(this);
130 viewMenu.add(chainMenu);
131 menuBar.add(coloursMenu);
132 menuBar.add(helpMenu);
134 charge.addActionListener(this);
135 hydro.addActionListener(this);
136 chain.addActionListener(this);
137 seqColour.addItemListener(this);
138 zappo.addActionListener(this);
139 taylor.addActionListener(this);
140 helix.addActionListener(this);
141 strand.addActionListener(this);
142 turn.addActionListener(this);
143 buried.addActionListener(this);
144 user.addActionListener(this);
146 jmolHelp.addActionListener(this);
148 coloursMenu.add(seqColour);
149 coloursMenu.add(chain);
150 coloursMenu.add(charge);
151 coloursMenu.add(zappo);
152 coloursMenu.add(taylor);
153 coloursMenu.add(hydro);
154 coloursMenu.add(helix);
155 coloursMenu.add(strand);
156 coloursMenu.add(turn);
157 coloursMenu.add(buried);
158 coloursMenu.add(user);
160 helpMenu.add(jmolHelp);
162 this.setMenuBar(menuBar);
164 if(pdbentry.getFile()!=null)
166 if (protocol.equals(AppletFormatAdapter.PASTE))
167 loadInline(pdbentry.getFile());
169 viewer.openFile(pdbentry.getFile());
172 jalview.bin.JalviewLite.addFrame(this, "Jmol", 400,400);
175 public void loadInline(String string)
178 viewer.openStringInline(string);
182 void setChainMenuItems(Vector chains)
184 chainMenu.removeAll();
186 MenuItem menuItem = new MenuItem("All");
187 menuItem.addActionListener(this);
189 chainMenu.add(menuItem);
191 CheckboxMenuItem menuItemCB;
192 for (int c = 0; c < chains.size(); c++)
194 menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(), true);
195 menuItemCB.addItemListener(this);
196 chainMenu.add(menuItemCB);
200 boolean allChainsSelected = false;
203 StringBuffer cmd = new StringBuffer();
204 for (int i = 0; i < chainMenu.getItemCount(); i++)
206 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
208 CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
210 cmd.append(":" + item.getLabel() + " or ");
214 if (cmd.length() > 0)
215 cmd.setLength(cmd.length() - 4);
217 viewer.evalString("select *;restrict "
218 + cmd + ";cartoon;center " + cmd);
224 viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
225 viewer.evalStringQuiet("zap");
226 viewer.setJmolStatusListener(null);
229 //We'll need to find out what other
230 // listeners need to be shut down in Jmol
231 StructureSelectionManager
232 .getStructureSelectionManager()
233 .removeStructureViewerListener(this, pdbentry.getId());
235 this.setVisible(false);
238 public void actionPerformed(ActionEvent evt)
240 if(evt.getSource()==mappingMenuItem)
242 jalview.appletgui.CutAndPasteTransfer cap
243 = new jalview.appletgui.CutAndPasteTransfer(false, null);
244 Frame frame = new Frame();
247 jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 550,
250 StructureSelectionManager.getStructureSelectionManager().printMapping(
254 else if (evt.getSource() == charge)
256 colourBySequence = false;
257 seqColour.setState(false);
258 viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
259 +"select LYS,ARG;color blue;select CYS;color yellow");
262 else if (evt.getSource() == chain)
264 colourBySequence = false;
265 seqColour.setState(false);
266 viewer.evalStringQuiet("select *;color chain");
268 else if (evt.getSource() == zappo)
270 setJalviewColourScheme(new ZappoColourScheme());
272 else if (evt.getSource() == taylor)
274 setJalviewColourScheme(new TaylorColourScheme());
276 else if (evt.getSource() == hydro)
278 setJalviewColourScheme(new HydrophobicColourScheme());
280 else if (evt.getSource() == helix)
282 setJalviewColourScheme(new HelixColourScheme());
284 else if (evt.getSource() == strand)
286 setJalviewColourScheme(new StrandColourScheme());
288 else if (evt.getSource() == turn)
290 setJalviewColourScheme(new TurnColourScheme());
292 else if (evt.getSource() == buried)
294 setJalviewColourScheme(new BuriedColourScheme());
296 else if (evt.getSource() == user)
298 new UserDefinedColours(this);
300 else if(evt.getSource() == jmolHelp)
303 ap.av.applet.getAppletContext().showDocument(
304 new java.net.URL("http://jmol.sourceforge.net/docs/JmolUserGuide/"),
306 }catch(java.net.MalformedURLException ex){}
310 allChainsSelected = true;
311 for (int i = 0; i < chainMenu.getItemCount(); i++)
313 if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
314 ( (CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
317 allChainsSelected = false;
321 public void setJalviewColourScheme(ColourSchemeI cs)
323 colourBySequence = false;
324 seqColour.setState(false);
333 Enumeration en = ResidueProperties.aa3Hash.keys();
334 StringBuffer command = new StringBuffer("select *;color white;");
335 while(en.hasMoreElements())
337 res = en.nextElement().toString();
338 index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
342 col = cs.findColour(ResidueProperties.aa[index].charAt(0));
344 command.append("select "+res+";color["
346 + col.getGreen() + ","
347 + col.getBlue() + "];");
350 viewer.evalStringQuiet(command.toString());
353 public void itemStateChanged(ItemEvent evt)
355 if (evt.getSource() == seqColour)
357 colourBySequence = seqColour.getState();
358 colourBySequence(ap);
360 else if (!allChainsSelected)
364 public void keyPressed(KeyEvent evt)
366 if (evt.getKeyCode() == KeyEvent.VK_ENTER
367 && scriptWindow.isVisible())
369 viewer.evalString(inputLine.getText());
370 history.append("\n$ "+inputLine.getText());
371 inputLine.setText("");
376 public void keyTyped(KeyEvent evt)
379 public void keyReleased(KeyEvent evt){}
381 //////////////////////////////////
383 public String getPdbFile()
391 public void mouseOverStructure(int atomIndex, String strInfo)
395 int chainSeparator = strInfo.indexOf(":");
397 if(chainSeparator==-1)
398 chainSeparator = strInfo.indexOf(".");
400 pdbResNum = Integer.parseInt(
401 strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator));
405 if (strInfo.indexOf(":") > -1)
406 chainId = strInfo.substring
407 (strInfo.indexOf(":")+1, strInfo.indexOf("."));
413 if (lastMessage == null || !lastMessage.equals(strInfo))
414 ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
416 lastMessage = strInfo;
419 StringBuffer resetLastRes = new StringBuffer();
420 StringBuffer eval = new StringBuffer();
422 public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
424 if (!pdbfile.equals(pdbentry.getFile()))
427 if (resetLastRes.length() > 0)
429 viewer.evalStringQuiet(resetLastRes.toString());
433 eval.append("select " + pdbResNum);
435 resetLastRes.setLength(0);
436 resetLastRes.append("select " + pdbResNum);
438 if (!chain.equals(" "))
440 eval.append(":" + chain);
441 resetLastRes.append(":" + chain);
444 eval.append(";color gold;wireframe 100");
446 Color col = new Color(viewer.getAtomArgb(atomIndex));
448 resetLastRes.append(";color["
450 + col.getGreen() + ","
451 + col.getBlue() + "];wireframe 0");
453 viewer.evalStringQuiet(eval.toString());
457 public void updateColours(Object source)
459 colourBySequence( (AlignmentPanel) source);
462 //End StructureListener
463 ////////////////////////////
465 public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
467 if (!pdbfile.equals(pdbentry.getFile()))
470 return new Color(viewer.getAtomArgb(atomIndex));
474 public void colourBySequence(AlignmentPanel ap)
476 if(!colourBySequence)
480 StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
482 if (mapping.length < 1)
485 SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
487 boolean showFeatures = false;
488 if (ap.av.showSequenceFeatures)
493 fr = new jalview.appletgui.FeatureRenderer(ap.av);
496 fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
499 StringBuffer command = new StringBuffer();
502 for (int s = 0; s < sequence.length; s++)
504 for (int m = 0; m < mapping.length; m++)
506 if (mapping[m].getSequence() == sequence[s]
507 && ap.av.alignment.findIndex(sequence[s])>-1)
509 for (int r = 0; r < sequence[s].getLength(); r++)
511 int pos = mapping[m].getPDBResNum(
512 sequence[s].findPosition(r));
514 if (pos < 1 || pos==lastPos)
519 Color col = sr.getResidueBoxColour(sequence[s], r);
522 col = fr.findFeatureColour(col, sequence[s], r);
524 if (command.toString().endsWith(":" + mapping[m].getChain()+
527 + col.getGreen() + ","
528 + col.getBlue() + "]"))
530 command = condenseCommand(command.toString(), pos);
534 command.append(";select " + pos);
536 if (!mapping[m].getChain().equals(" "))
538 command.append(":" + mapping[m].getChain());
541 command.append(";color["
543 + col.getGreen() + ","
544 + col.getBlue() + "]");
552 viewer.evalStringQuiet(command.toString());
555 StringBuffer condenseCommand(String command, int pos)
558 StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
560 command = command.substring(sb.length());
564 if (command.indexOf("-") > -1)
566 start = command.substring(0,command.indexOf("-"));
570 start = command.substring(0, command.indexOf(":"));
573 sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
578 /////////////////////////////////
581 public String eval(String strEval)
583 // System.out.println(strEval);
584 //"# 'eval' is implemented only for the applet.";
588 public void createImage(String file, String type, int quality)
591 public void setCallbackFunction(String callbackType,
592 String callbackFunction)
595 public void notifyFileLoaded(String fullPathName, String fileName,
596 String modelName, Object clientFile,
601 fileLoadingError = errorMsg;
606 fileLoadingError = null;
608 if (fileName != null)
611 jmolpopup.updateComputedMenus();
612 viewer.evalStringQuiet(
613 "select backbone;restrict;cartoon;wireframe off;spacefill off");
615 ssm = StructureSelectionManager.getStructureSelectionManager();
620 pdb = ssm.setMapping(sequence,chains,
622 AppletFormatAdapter.PASTE);
623 pdbentry.setFile("INLINE"+pdb.id);
627 pdb = ssm.setMapping(sequence,chains,
629 AppletFormatAdapter.URL);
632 pdbentry.setId(pdb.id);
634 ssm.addStructureViewerListener(this);
636 Vector chains = new Vector();
637 for (int i = 0; i < pdb.chains.size(); i++)
639 chains.addElement( ( (MCview.PDBChain) pdb.chains.elementAt(i)).id);
641 setChainMenuItems(chains);
643 colourBySequence(ap);
645 StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
648 if (pdbentry.getProperty() != null)
650 if (pdbentry.getProperty().get("method") != null)
652 title.append(" Method: ");
653 title.append(pdbentry.getProperty().get("method"));
655 if (pdbentry.getProperty().get("chains") != null)
657 title.append(" Chain:");
658 title.append(pdbentry.getProperty().get("chains"));
662 this.setTitle(title.toString());
669 public void notifyFrameChanged(int frameNo)
671 boolean isAnimationRunning = (frameNo <= -2);
674 public void notifyScriptStart(String statusMessage, String additionalInfo)
677 public void sendConsoleEcho(String strEcho)
679 if (scriptWindow == null)
682 history.append("\n"+strEcho);
685 public void sendConsoleMessage(String strStatus)
687 if(history!=null && strStatus!=null
688 && !strStatus.equals("Script completed"))
690 history.append("\n"+strStatus);
694 public void notifyScriptTermination(String strStatus, int msWalltime)
697 public void handlePopupMenu(int x, int y)
699 jmolpopup.show(x, y);
702 public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
704 notifyAtomPicked(iatom, strMeasure);
707 public void notifyNewDefaultModeMeasurement(int count, String strInfo)
710 public void notifyAtomPicked(int atomIndex, String strInfo)
713 int chainSeparator = strInfo.indexOf(":");
715 if(chainSeparator==-1)
716 chainSeparator = strInfo.indexOf(".");
719 strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator);
722 if (strInfo.indexOf(":") > -1)
723 picked+=strInfo.substring(strInfo.indexOf(":")+1,
724 strInfo.indexOf("."));
728 if (!atomsPicked.contains(picked))
730 viewer.evalString("select "+picked+";label %n %r:%c");
731 atomsPicked.addElement(picked);
735 viewer.evalString("select "+picked+";label off");
736 atomsPicked.removeElement(picked);
740 public void notifyAtomHovered(int atomIndex, String strInfo)
742 mouseOverStructure(atomIndex, strInfo);
745 public void sendSyncScript(String script, String appletName)
748 public void showUrl(String url)
751 ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
753 }catch(java.net.MalformedURLException ex)
757 public void showConsole(boolean showConsole)
759 if (scriptWindow == null)
761 scriptWindow = new Panel(new BorderLayout());
762 inputLine = new TextField();
763 history = new TextArea(5, 40);
764 scriptWindow.add(history, BorderLayout.CENTER);
765 scriptWindow.add(inputLine, BorderLayout.SOUTH);
766 add(scriptWindow, BorderLayout.SOUTH);
767 scriptWindow.setVisible(false);
768 history.setEditable(false);
769 inputLine.addKeyListener(this);
772 scriptWindow.setVisible(!scriptWindow.isVisible());
776 public float functionXY(String functionName, int x, int y)
781 ///End JmolStatusListener
782 ///////////////////////////////
788 Dimension currentSize = new Dimension();
789 Rectangle rectClip = new Rectangle();
791 public void update(Graphics g) {
794 public void paint(Graphics g)
796 currentSize = this.getSize();
797 rectClip = g.getClipBounds();
801 g.setColor(Color.black);
802 g.fillRect(0, 0, currentSize.width, currentSize.height);
803 g.setColor(Color.white);
804 g.setFont(new Font("Verdana", Font.BOLD, 14));
805 g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
809 viewer.renderScreenImage(g, currentSize, rectClip);