2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import java.util.regex.*;
24 import javax.swing.event.*;
25 import java.awt.event.*;
28 import jalview.jbgui.GStructureViewer;
29 import jalview.bin.Cache;
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.*;
41 import org.jmol.viewer.JmolConstants;
43 public class AppJmol extends GStructureViewer implements StructureListener,
44 JmolStatusListener, Runnable
51 ScriptWindow scriptWindow;
59 StructureSelectionManager ssm;
63 RenderPanel renderPanel;
67 String fileLoadingError;
69 boolean colourBySequence = true;
71 boolean loadingFromArchive = false;
73 Vector atomsPicked = new Vector();
75 public AppJmol(String file, String id, SequenceI[] seq,
76 AlignmentPanel ap, String loadStatus, Rectangle bounds)
78 this(file, id, seq, ap, loadStatus, bounds, null);
81 public AppJmol(String file, String id, SequenceI[] seq,
82 AlignmentPanel ap, String loadStatus, Rectangle bounds,
85 loadingFromArchive = true;
86 pdbentry = new PDBEntry();
87 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);
230 // * OK, but safer to assign htmlName, URL bases, comandOptions, and
231 // statusListener now.
233 viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
234 new SmarterJmolAdapter(), "", null, null, "", this);
236 jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
238 viewer.evalStringQuiet(command);
241 void setChainMenuItems(Vector chains)
243 chainMenu.removeAll();
245 JMenuItem menuItem = new JMenuItem("All");
246 menuItem.addActionListener(new ActionListener()
248 public void actionPerformed(ActionEvent evt)
250 allChainsSelected = true;
251 for (int i = 0; i < chainMenu.getItemCount(); i++)
253 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
254 ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
257 allChainsSelected = false;
261 chainMenu.add(menuItem);
263 for (int c = 0; c < chains.size(); c++)
265 menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
266 menuItem.addItemListener(new ItemListener()
268 public void itemStateChanged(ItemEvent evt)
270 if (!allChainsSelected)
275 chainMenu.add(menuItem);
279 boolean allChainsSelected = false;
283 StringBuffer cmd = new StringBuffer();
284 for (int i = 0; i < chainMenu.getItemCount(); i++)
286 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
288 JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
289 if (item.isSelected())
290 cmd.append(":" + item.getText() + " or ");
294 if (cmd.length() > 0)
295 cmd.setLength(cmd.length() - 4);
297 viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center "
303 viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
304 viewer.evalStringQuiet("zap");
305 viewer.setJmolStatusListener(null);
308 // We'll need to find out what other
309 // listeners need to be shut down in Jmol
310 StructureSelectionManager.getStructureSelectionManager()
311 .removeStructureViewerListener(this, pdbentry.getFile());
318 // TODO: replace with reference fetching/transfer code (validate PDBentry
320 jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
322 if ((pdbseq = pdbclient.getSequenceRecords(pdbentry.getId())) != null)
324 // just transfer the file name from the first seuqence's first PDBEntry
325 pdbentry.setFile(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
326 .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 // TODO: rna: remove CA dependency in select string
600 if (!pdbfile.equals(pdbentry.getFile()))
603 if (resetLastRes.length() > 0)
605 viewer.evalStringQuiet(resetLastRes.toString());
609 eval.append("select " + pdbResNum);
611 resetLastRes.setLength(0);
612 resetLastRes.append("select " + pdbResNum);
615 resetLastRes.append(":");
616 if (!chain.equals(" "))
619 resetLastRes.append(chain);
622 eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); // ".*;");
624 resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
625 // + ".*;spacefill 0;");
626 + " and not hetero;spacefill 0;");
628 eval.append("spacefill 200;select none");
629 // System.out.println("jmol:\n"+eval+"\n");
630 viewer.evalStringQuiet(eval.toString());
633 public Color getColour(int atomIndex, int pdbResNum, String chain,
636 if (!pdbfile.equals(pdbentry.getFile()))
639 return new Color(viewer.getAtomArgb(atomIndex));
642 public void updateColours(Object source)
644 colourBySequence((AlignmentPanel) source);
647 // End StructureListener
648 // //////////////////////////
652 FeatureRenderer fr = null;
654 public void colourBySequence(AlignmentPanel sourceap)
658 if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av)
661 StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
663 if (mapping.length < 1)
666 SequenceRenderer sr = new SequenceRenderer(ap.av);
668 boolean showFeatures = false;
670 if (ap.av.showSequenceFeatures)
675 fr = new jalview.gui.FeatureRenderer(ap);
678 fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
681 StringBuffer command = new StringBuffer();
684 for (int sp, s = 0; s < sequence.length; s++)
686 for (int m = 0; m < mapping.length; m++)
688 if (mapping[m].getSequence() == sequence[s]
689 && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
691 SequenceI asp = ap.av.alignment.getSequenceAt(sp);
692 for (int r = 0; r < asp.getLength(); r++)
694 // No mapping to gaps in sequence.
695 if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
699 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
701 if (pos < 1 || pos == lastPos)
706 Color col = sr.getResidueBoxColour(asp, r);
709 col = fr.findFeatureColour(col, asp, r);
711 if (command.toString().endsWith(
712 ":" + mapping[m].getChain() + ";color[" + col.getRed()
713 + "," + col.getGreen() + "," + col.getBlue()
716 command = condenseCommand(command, pos);
720 command.append(";select " + pos);
722 if (!mapping[m].getChain().equals(" "))
724 command.append(":" + mapping[m].getChain());
727 command.append(";color[" + col.getRed() + "," + col.getGreen()
728 + "," + col.getBlue() + "]");
736 if (lastCommand == null || !lastCommand.equals(command.toString()))
738 viewer.evalStringQuiet(command.toString());
740 lastCommand = command.toString();
743 StringBuffer condenseCommand(StringBuffer command, int pos)
745 StringBuffer sb = new StringBuffer(command.substring(0, command
746 .lastIndexOf("select") + 7));
748 command.delete(0, sb.length());
752 if (command.indexOf("-") > -1)
754 start = command.substring(0, command.indexOf("-"));
758 start = command.substring(0, command.indexOf(":"));
761 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
766 // ///////////////////////////////
767 // JmolStatusListener
769 public String eval(String strEval)
771 // System.out.println(strEval);
772 // "# 'eval' is implemented only for the applet.";
776 public void createImage(String file, String type, int quality)
778 System.out.println("JMOL CREATE IMAGE");
781 public void notifyFileLoaded(String fullPathName, String fileName,
782 String modelName, String errorMsg, int modelParts)
784 if (errorMsg != null)
786 fileLoadingError = errorMsg;
791 fileLoadingError = null;
793 if (fileName != null)
795 // TODO: do some checking using the modelPts number of parts against our own estimate of the number of chains
797 ssm = StructureSelectionManager.getStructureSelectionManager();
798 MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry
799 .getFile(), AppletFormatAdapter.FILE);
800 ssm.addStructureViewerListener(this);
801 Vector chains = new Vector();
802 for (int i = 0; i < pdbFile.chains.size(); i++)
805 .addElement(((MCview.PDBChain) pdbFile.chains.elementAt(i)).id);
807 setChainMenuItems(chains);
809 jmolpopup.updateComputedMenus();
811 if (!loadingFromArchive)
814 .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
816 colourBySequence(ap);
821 loadingFromArchive = false;
827 public void sendConsoleEcho(String strEcho)
829 if (scriptWindow != null)
830 scriptWindow.sendConsoleEcho(strEcho);
833 public void sendConsoleMessage(String strStatus)
835 if (scriptWindow != null)
836 scriptWindow.sendConsoleMessage(strStatus);
839 public void notifyScriptTermination(String strStatus, int msWalltime)
841 if (scriptWindow != null)
842 scriptWindow.notifyScriptTermination(strStatus, msWalltime);
845 public void handlePopupMenu(int x, int y)
847 jmolpopup.show(x, y);
850 public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
852 notifyAtomPicked(iatom, strMeasure, null);
855 public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
859 Cache.log.info("Non null pick data string: "+strData+" (other info: '"+strInfo+"' pos "+atomIndex+")");
861 Matcher matcher = pattern.matcher(strInfo);
865 String resnum = new String(matcher.group(2));
866 String chainId = matcher.group(3);
868 String picked = resnum;
871 picked += (":" + chainId.substring(1, chainId.length()));
873 picked = "(("+picked+".CA" + ")|("+picked+".P"+"))";
875 if (!atomsPicked.contains(picked))
878 viewer.evalString("select " + picked + ";label %n %r:%c");
880 viewer.evalString("select " + picked + ";label %n %r");
881 atomsPicked.addElement(picked);
885 viewer.evalString("select " + picked + ";label off");
886 atomsPicked.removeElement(picked);
889 if (scriptWindow != null)
891 scriptWindow.sendConsoleMessage(strInfo);
892 scriptWindow.sendConsoleMessage("\n");
896 public void notifyAtomHovered(int atomIndex, String strInfo, String data)
900 Cache.log.info("Non null hover data string: "+data+" (other info: '"+strInfo+"' pos "+atomIndex+")");
902 mouseOverStructure(atomIndex, strInfo);
906 public void showUrl(String url)
909 jalview.util.BrowserLauncher.openURL(url);
910 } catch (IOException e)
912 Cache.log.error("Failed to launch Jmol-associated url "+url,e);
913 // TODO: 2.6 : warn user if browser was not configured.
917 public void showConsole(boolean showConsole)
919 if (scriptWindow == null)
920 scriptWindow = new ScriptWindow(this);
924 if (splitPane == null)
926 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
927 splitPane.setTopComponent(renderPanel);
928 splitPane.setBottomComponent(scriptWindow);
929 this.getContentPane().add(splitPane, BorderLayout.CENTER);
932 splitPane.setDividerLocation(getHeight() - 200);
933 splitPane.validate();
937 if (splitPane != null)
938 splitPane.setVisible(false);
942 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
948 public float[][] functionXY(String functionName, int x, int y)
953 // /End JmolStatusListener
954 // /////////////////////////////
956 class RenderPanel extends JPanel
958 final Dimension currentSize = new Dimension();
960 final Rectangle rectClip = new Rectangle();
962 public void paintComponent(Graphics g)
964 getSize(currentSize);
965 g.getClipBounds(rectClip);
969 g.setColor(Color.black);
970 g.fillRect(0, 0, currentSize.width, currentSize.height);
971 g.setColor(Color.white);
972 g.setFont(new Font("Verdana", Font.BOLD, 14));
973 g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
975 else if (fileLoadingError != null)
977 g.setColor(Color.black);
978 g.fillRect(0, 0, currentSize.width, currentSize.height);
979 g.setColor(Color.white);
980 g.setFont(new Font("Verdana", Font.BOLD, 14));
981 g.drawString("Error loading file..." + pdbentry.getId(), 20,
982 currentSize.height / 2);
986 viewer.renderScreenImage(g, currentSize, rectClip);
991 String viewId = null;
993 public String getViewId()
997 viewId = System.currentTimeMillis() + "." + this.hashCode();
1003 public String createImage(String fileName, String type,
1004 Object textOrBytes, int quality)
1006 // TODO Auto-generated method stub
1011 public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
1013 // TODO Auto-generated method stub
1018 public Hashtable getRegistryInfo()
1020 // TODO Auto-generated method stub
1025 public void notifyCallback(int type, Object[] data)
1030 case JmolConstants.CALLBACK_LOADSTRUCT:
1031 notifyFileLoaded((String) data[1], (String) data[2],
1032 (String) data[3], (String) data[4], ((Integer) data[5]).intValue());
1035 case JmolConstants.CALLBACK_PICK:
1036 notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]);
1037 // also highlight in alignment
1038 case JmolConstants.CALLBACK_HOVER:
1039 notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]);
1041 case JmolConstants.CALLBACK_SCRIPT:
1042 notifyScriptTermination((String)data[2], ((Integer)data[3]).intValue());
1044 case JmolConstants.CALLBACK_ECHO:
1045 sendConsoleEcho((String)data[1]);
1047 case JmolConstants.CALLBACK_MESSAGE:
1048 sendConsoleMessage((data==null) ? ((String) null) : (String)data[1]);
1050 case JmolConstants.CALLBACK_MEASURE:
1051 case JmolConstants.CALLBACK_CLICK:
1053 System.err.println("Unhandled callback "+type+" "+data);
1059 Cache.log.warn("Squashed Jmol callback handler error: ",e);
1064 public boolean notifyEnabled(int callbackPick)
1066 switch (callbackPick)
1068 case JmolConstants.CALLBACK_ECHO:
1069 case JmolConstants.CALLBACK_LOADSTRUCT:
1070 case JmolConstants.CALLBACK_MEASURE:
1071 case JmolConstants.CALLBACK_MESSAGE:
1072 case JmolConstants.CALLBACK_PICK:
1073 case JmolConstants.CALLBACK_SCRIPT:
1074 case JmolConstants.CALLBACK_HOVER:
1075 case JmolConstants.CALLBACK_ERROR:
1077 case JmolConstants.CALLBACK_CLICK:
1078 case JmolConstants.CALLBACK_ANIMFRAME:
1079 case JmolConstants.CALLBACK_MINIMIZATION:
1080 case JmolConstants.CALLBACK_RESIZE:
1081 case JmolConstants.CALLBACK_SYNC:
1087 public void setCallbackFunction(String callbackType,
1088 String callbackFunction)
1090 Cache.log.debug("Ignoring set-callback request to associate "+callbackType+" with function "+callbackFunction);