2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 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
21 import java.util.regex.*;
25 import javax.swing.event.*;
26 import java.awt.event.*;
29 import jalview.jbgui.GStructureViewer;
30 import jalview.datamodel.*;
32 import jalview.structure.*;
33 import jalview.datamodel.PDBEntry;
35 import jalview.schemes.*;
36 import jalview.ws.ebi.EBIFetchClient;
38 import org.jmol.api.*;
39 import org.jmol.adapter.smarter.SmarterJmolAdapter;
40 import org.jmol.popup.*;
42 public class AppJmol extends GStructureViewer implements StructureListener,
43 JmolStatusListener, Runnable
50 ScriptWindow scriptWindow;
58 StructureSelectionManager ssm;
62 RenderPanel renderPanel;
66 String fileLoadingError;
68 boolean colourBySequence = true;
70 boolean loadingFromArchive = false;
72 Vector atomsPicked = new Vector();
74 public AppJmol(String file, String id, SequenceI[] seq,
75 AlignmentPanel ap, String loadStatus, Rectangle bounds)
77 this(file, id, seq, ap, loadStatus, bounds, null);
80 public AppJmol(String file, String id, SequenceI[] seq,
81 AlignmentPanel ap, String loadStatus, Rectangle bounds,
84 loadingFromArchive = true;
85 pdbentry = new PDBEntry();
86 pdbentry.setFile(file);
91 this.setBounds(bounds);
92 colourBySequence = false;
93 seqColour.setSelected(false);
95 // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
96 // bounds.width,bounds.height);
100 this.addInternalFrameListener(new InternalFrameAdapter()
102 public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
109 public synchronized void addSequence(SequenceI[] seq)
111 Vector v = new Vector();
112 for (int i = 0; i < sequence.length; i++)
113 v.addElement(sequence[i]);
115 for (int i = 0; i < seq.length; i++)
116 if (!v.contains(seq[i]))
117 v.addElement(seq[i]);
119 SequenceI[] tmp = new SequenceI[v.size()];
124 public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
127 // ////////////////////////////////
128 // Is the pdb file already loaded?
129 String alreadyMapped = StructureSelectionManager
130 .getStructureSelectionManager().alreadyMappedToFile(
133 if (alreadyMapped != null)
135 int option = JOptionPane
136 .showInternalConfirmDialog(
139 + " is already displayed."
140 + "\nDo you want to map sequences to the visible structure?",
141 "Map Sequences to Visible Window: "
142 + pdbentry.getId(), JOptionPane.YES_NO_OPTION);
144 if (option == JOptionPane.YES_OPTION)
146 StructureSelectionManager.getStructureSelectionManager()
147 .setMapping(seq, chains, alreadyMapped,
148 AppletFormatAdapter.FILE);
149 if (ap.seqPanel.seqCanvas.fr != null)
151 ap.seqPanel.seqCanvas.fr.featuresAdded();
152 ap.paintAlignment(true);
155 // Now this AppJmol is mapped to new sequences. We must add them to
156 // the exisiting array
157 JInternalFrame[] frames = Desktop.instance.getAllFrames();
159 for (int i = 0; i < frames.length; i++)
161 if (frames[i] instanceof AppJmol)
163 AppJmol topJmol = ((AppJmol) frames[i]);
164 if (topJmol.pdbentry.getFile().equals(alreadyMapped))
166 topJmol.addSequence(seq);
175 // /////////////////////////////////
178 this.pdbentry = pdbentry;
180 this.setSize(400, 400);
181 // jalview.gui.Desktop.addInternalFrame(this, "Jmol
182 // View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId()
185 if (pdbentry.getFile() != null)
187 initJmol("load \"" + pdbentry.getFile() + "\"");
191 Thread worker = new Thread(this);
195 this.addInternalFrameListener(new InternalFrameAdapter()
197 public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
204 void initJmol(String command)
206 renderPanel = new RenderPanel();
208 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
210 StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
213 if (pdbentry.getProperty() != null)
215 if (pdbentry.getProperty().get("method") != null)
217 title.append(" Method: ");
218 title.append(pdbentry.getProperty().get("method"));
220 if (pdbentry.getProperty().get("chains") != null)
222 title.append(" Chain:");
223 title.append(pdbentry.getProperty().get("chains"));
227 this.setTitle(title.toString());
228 jalview.gui.Desktop.addInternalFrame(this, title.toString(),
229 getBounds().width, getBounds().height);
231 viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
232 new SmarterJmolAdapter());
234 viewer.setAppletContext("", null, null, "");
236 viewer.setJmolStatusListener(this);
238 jmolpopup = JmolPopup.newJmolPopup(viewer);
240 viewer.evalStringQuiet(command);
243 void setChainMenuItems(Vector chains)
245 chainMenu.removeAll();
247 JMenuItem menuItem = new JMenuItem("All");
248 menuItem.addActionListener(new ActionListener()
250 public void actionPerformed(ActionEvent evt)
252 allChainsSelected = true;
253 for (int i = 0; i < chainMenu.getItemCount(); i++)
255 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
256 ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
259 allChainsSelected = false;
263 chainMenu.add(menuItem);
265 for (int c = 0; c < chains.size(); c++)
267 menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
268 menuItem.addItemListener(new ItemListener()
270 public void itemStateChanged(ItemEvent evt)
272 if (!allChainsSelected)
277 chainMenu.add(menuItem);
281 boolean allChainsSelected = false;
285 StringBuffer cmd = new StringBuffer();
286 for (int i = 0; i < chainMenu.getItemCount(); i++)
288 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
290 JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
291 if (item.isSelected())
292 cmd.append(":" + item.getText() + " or ");
296 if (cmd.length() > 0)
297 cmd.setLength(cmd.length() - 4);
299 viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center "
305 viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
306 viewer.evalStringQuiet("zap");
307 viewer.setJmolStatusListener(null);
310 // We'll need to find out what other
311 // listeners need to be shut down in Jmol
312 StructureSelectionManager.getStructureSelectionManager()
313 .removeStructureViewerListener(this, pdbentry.getFile());
320 // TODO: replace with reference fetching/transfer code (validate PDBentry as a DBRef?)
321 jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
323 if ((pdbseq=pdbclient.getSequenceRecords(pdbentry.getId())) != null)
325 // just transfer the file name from the first seuqence's first PDBEntry
326 pdbentry.setFile(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId().elementAt(0)).getFile());
327 initJmol("load " + pdbentry.getFile());
332 .showInternalMessageDialog(
335 + " could not be retrieved. Please try downloading the file manually.",
336 "Couldn't load file", JOptionPane.ERROR_MESSAGE);
339 } catch (OutOfMemoryError oomerror)
341 new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
343 } catch (Exception ex)
345 ex.printStackTrace();
349 public void pdbFile_actionPerformed(ActionEvent actionEvent)
351 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
352 .getProperty("LAST_DIRECTORY"));
354 chooser.setFileView(new JalviewFileView());
355 chooser.setDialogTitle("Save PDB File");
356 chooser.setToolTipText("Save");
358 int value = chooser.showSaveDialog(this);
360 if (value == JalviewFileChooser.APPROVE_OPTION)
364 BufferedReader in = new BufferedReader(new FileReader(pdbentry
366 File outFile = chooser.getSelectedFile();
368 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
370 while ((data = in.readLine()) != null)
372 if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
378 } catch (Exception ex)
380 ex.printStackTrace();
385 public void viewMapping_actionPerformed(ActionEvent actionEvent)
387 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
388 jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
390 cap.setText(StructureSelectionManager.getStructureSelectionManager()
391 .printMapping(pdbentry.getFile()));
400 public void eps_actionPerformed(ActionEvent e)
402 makePDBImage(jalview.util.ImageMaker.EPS);
411 public void png_actionPerformed(ActionEvent e)
413 makePDBImage(jalview.util.ImageMaker.PNG);
416 void makePDBImage(int type)
418 int width = getWidth();
419 int height = getHeight();
421 jalview.util.ImageMaker im;
423 if (type == jalview.util.ImageMaker.PNG)
425 im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
426 "Make PNG image from view", width, height, null, null);
430 im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
431 "Make EPS file from view", width, height, null, this
435 if (im.getGraphics() != null)
437 Rectangle rect = new Rectangle(width, height);
438 viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
443 public void seqColour_actionPerformed(ActionEvent actionEvent)
446 colourBySequence = seqColour.isSelected();
447 colourBySequence(ap.alignFrame.alignPanel);
450 public void chainColour_actionPerformed(ActionEvent actionEvent)
452 colourBySequence = false;
453 seqColour.setSelected(false);
454 viewer.evalStringQuiet("select *;color chain");
457 public void chargeColour_actionPerformed(ActionEvent actionEvent)
459 colourBySequence = false;
460 seqColour.setSelected(false);
461 viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
462 + "select LYS,ARG;color blue;select CYS;color yellow");
465 public void zappoColour_actionPerformed(ActionEvent actionEvent)
467 setJalviewColourScheme(new ZappoColourScheme());
470 public void taylorColour_actionPerformed(ActionEvent actionEvent)
472 setJalviewColourScheme(new TaylorColourScheme());
475 public void hydroColour_actionPerformed(ActionEvent actionEvent)
477 setJalviewColourScheme(new HydrophobicColourScheme());
480 public void helixColour_actionPerformed(ActionEvent actionEvent)
482 setJalviewColourScheme(new HelixColourScheme());
485 public void strandColour_actionPerformed(ActionEvent actionEvent)
487 setJalviewColourScheme(new StrandColourScheme());
490 public void turnColour_actionPerformed(ActionEvent actionEvent)
492 setJalviewColourScheme(new TurnColourScheme());
495 public void buriedColour_actionPerformed(ActionEvent actionEvent)
497 setJalviewColourScheme(new BuriedColourScheme());
500 public void setJalviewColourScheme(ColourSchemeI cs)
502 colourBySequence = false;
503 seqColour.setSelected(false);
512 Enumeration en = ResidueProperties.aa3Hash.keys();
513 StringBuffer command = new StringBuffer("select *;color white;");
514 while (en.hasMoreElements())
516 res = en.nextElement().toString();
517 index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
521 col = cs.findColour(ResidueProperties.aa[index].charAt(0));
523 command.append("select " + res + ";color[" + col.getRed() + ","
524 + col.getGreen() + "," + col.getBlue() + "];");
527 viewer.evalStringQuiet(command.toString());
530 public void userColour_actionPerformed(ActionEvent actionEvent)
532 new UserDefinedColours(this, null);
535 public void backGround_actionPerformed(ActionEvent actionEvent)
537 java.awt.Color col = JColorChooser.showDialog(this,
538 "Select Background Colour", null);
542 viewer.evalStringQuiet("background [" + col.getRed() + ","
543 + col.getGreen() + "," + col.getBlue() + "];");
547 public void jmolHelp_actionPerformed(ActionEvent actionEvent)
551 jalview.util.BrowserLauncher
552 .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
553 } catch (Exception ex)
558 // ////////////////////////////////
559 // /StructureListener
560 public String getPdbFile()
562 return pdbentry.getFile();
565 Pattern pattern = Pattern
566 .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?");
570 public void mouseOverStructure(int atomIndex, String strInfo)
572 Matcher matcher = pattern.matcher(strInfo);
575 int pdbResNum = Integer.parseInt(matcher.group(2));
576 String chainId = matcher.group(3);
579 chainId = chainId.substring(1, chainId.length());
585 if (lastMessage == null || !lastMessage.equals(strInfo))
587 ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
589 lastMessage = strInfo;
592 StringBuffer resetLastRes = new StringBuffer();
594 StringBuffer eval = new StringBuffer();
596 public void highlightAtom(int atomIndex, int pdbResNum, String chain,
599 if (!pdbfile.equals(pdbentry.getFile()))
602 if (resetLastRes.length() > 0)
604 viewer.evalStringQuiet(resetLastRes.toString());
608 eval.append("select " + pdbResNum);
610 resetLastRes.setLength(0);
611 resetLastRes.append("select " + pdbResNum);
613 if (!chain.equals(" "))
615 eval.append(":" + chain);
616 resetLastRes.append(":" + chain);
619 eval.append(";wireframe 100;" + eval.toString() + ".CA;");
621 resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
622 + ".CA;spacefill 0;");
624 eval.append("spacefill 200;select none");
626 viewer.evalStringQuiet(eval.toString());
629 public Color getColour(int atomIndex, int pdbResNum, String chain,
632 if (!pdbfile.equals(pdbentry.getFile()))
635 return new Color(viewer.getAtomArgb(atomIndex));
638 public void updateColours(Object source)
640 colourBySequence((AlignmentPanel) source);
643 // End StructureListener
644 // //////////////////////////
648 FeatureRenderer fr = null;
650 public void colourBySequence(AlignmentPanel sourceap)
654 if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av)
657 StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
659 if (mapping.length < 1)
662 SequenceRenderer sr = new SequenceRenderer(ap.av);
664 boolean showFeatures = false;
666 if (ap.av.showSequenceFeatures)
671 fr = new jalview.gui.FeatureRenderer(ap);
674 fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
677 StringBuffer command = new StringBuffer();
680 for (int sp, s = 0; s < sequence.length; s++)
682 for (int m = 0; m < mapping.length; m++)
684 if (mapping[m].getSequence() == sequence[s]
685 && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
687 SequenceI asp = ap.av.alignment.getSequenceAt(sp);
688 for (int r = 0; r < asp.getLength(); r++)
690 // No mapping to gaps in sequence.
691 if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
695 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
697 if (pos < 1 || pos == lastPos)
702 Color col = sr.getResidueBoxColour(asp, r);
705 col = fr.findFeatureColour(col, asp, r);
707 if (command.toString().endsWith(
708 ":" + mapping[m].getChain() + ";color[" + col.getRed()
709 + "," + col.getGreen() + "," + col.getBlue()
712 command = condenseCommand(command, pos);
716 command.append(";select " + pos);
718 if (!mapping[m].getChain().equals(" "))
720 command.append(":" + mapping[m].getChain());
723 command.append(";color[" + col.getRed() + "," + col.getGreen()
724 + "," + col.getBlue() + "]");
732 if (lastCommand == null || !lastCommand.equals(command.toString()))
734 viewer.evalStringQuiet(command.toString());
736 lastCommand = command.toString();
739 StringBuffer condenseCommand(StringBuffer command, int pos)
741 StringBuffer sb = new StringBuffer(command.substring(0, command
742 .lastIndexOf("select") + 7));
744 command.delete(0, sb.length());
748 if (command.indexOf("-") > -1)
750 start = command.substring(0, command.indexOf("-"));
754 start = command.substring(0, command.indexOf(":"));
757 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
762 // ///////////////////////////////
763 // JmolStatusListener
765 public String eval(String strEval)
767 // System.out.println(strEval);
768 // "# 'eval' is implemented only for the applet.";
772 public void createImage(String file, String type, int quality)
774 System.out.println("JMOL CREATE IMAGE");
777 public void setCallbackFunction(String callbackType,
778 String callbackFunction)
782 public void notifyFileLoaded(String fullPathName, String fileName,
783 String modelName, Object clientFile, String errorMsg)
785 if (errorMsg != null)
787 fileLoadingError = errorMsg;
792 fileLoadingError = null;
794 if (fileName != null)
798 ssm = StructureSelectionManager.getStructureSelectionManager();
799 MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry
800 .getFile(), AppletFormatAdapter.FILE);
801 ssm.addStructureViewerListener(this);
802 Vector chains = new Vector();
803 for (int i = 0; i < pdbFile.chains.size(); i++)
806 .addElement(((MCview.PDBChain) pdbFile.chains.elementAt(i)).id);
808 setChainMenuItems(chains);
810 jmolpopup.updateComputedMenus();
812 if (!loadingFromArchive)
815 .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
817 colourBySequence(ap);
822 loadingFromArchive = false;
828 public void notifyFrameChanged(int frameNo)
830 boolean isAnimationRunning = (frameNo <= -2);
833 public void notifyScriptStart(String statusMessage, String additionalInfo)
837 public void sendConsoleEcho(String strEcho)
839 if (scriptWindow != null)
840 scriptWindow.sendConsoleEcho(strEcho);
843 public void sendConsoleMessage(String strStatus)
845 if (scriptWindow != null)
846 scriptWindow.sendConsoleMessage(strStatus);
849 public void notifyScriptTermination(String strStatus, int msWalltime)
851 if (scriptWindow != null)
852 scriptWindow.notifyScriptTermination(strStatus, msWalltime);
855 public void handlePopupMenu(int x, int y)
857 jmolpopup.show(x, y);
860 public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
862 notifyAtomPicked(iatom, strMeasure);
865 public void notifyNewDefaultModeMeasurement(int count, String strInfo)
869 public void notifyAtomPicked(int atomIndex, String strInfo)
871 Matcher matcher = pattern.matcher(strInfo);
875 String resnum = new String(matcher.group(2));
876 String chainId = matcher.group(3);
878 String picked = resnum;
881 picked += (":" + chainId.substring(1, chainId.length()));
885 if (!atomsPicked.contains(picked))
888 viewer.evalString("select " + picked + ";label %n %r:%c");
890 viewer.evalString("select " + picked + ";label %n %r");
891 atomsPicked.addElement(picked);
895 viewer.evalString("select " + picked + ";label off");
896 atomsPicked.removeElement(picked);
899 if (scriptWindow != null)
901 scriptWindow.sendConsoleMessage(strInfo);
902 scriptWindow.sendConsoleMessage("\n");
906 public void notifyAtomHovered(int atomIndex, String strInfo)
908 mouseOverStructure(atomIndex, strInfo);
911 public void sendSyncScript(String script, String appletName)
915 public void showUrl(String url)
919 public void showConsole(boolean showConsole)
921 if (scriptWindow == null)
922 scriptWindow = new ScriptWindow(this);
926 if (splitPane == null)
928 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
929 splitPane.setTopComponent(renderPanel);
930 splitPane.setBottomComponent(scriptWindow);
931 this.getContentPane().add(splitPane, BorderLayout.CENTER);
934 splitPane.setDividerLocation(getHeight() - 200);
935 splitPane.validate();
939 if (splitPane != null)
940 splitPane.setVisible(false);
944 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
950 public float functionXY(String functionName, int x, int y)
955 // /End JmolStatusListener
956 // /////////////////////////////
958 class RenderPanel extends JPanel
960 final Dimension currentSize = new Dimension();
962 final Rectangle rectClip = new Rectangle();
964 public void paintComponent(Graphics g)
966 getSize(currentSize);
967 g.getClipBounds(rectClip);
971 g.setColor(Color.black);
972 g.fillRect(0, 0, currentSize.width, currentSize.height);
973 g.setColor(Color.white);
974 g.setFont(new Font("Verdana", Font.BOLD, 14));
975 g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
977 else if (fileLoadingError != null)
979 g.setColor(Color.black);
980 g.fillRect(0, 0, currentSize.width, currentSize.height);
981 g.setColor(Color.white);
982 g.setFont(new Font("Verdana", Font.BOLD, 14));
983 g.drawString("Error loading file..." + pdbentry.getId(), 20,
984 currentSize.height / 2);
988 viewer.renderScreenImage(g, currentSize, rectClip);
993 String viewId = null;
995 public String getViewId()
999 viewId = System.currentTimeMillis() + "." + this.hashCode();