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.
23 import java.awt.BorderLayout;
24 import java.awt.Color;
25 import java.awt.Dimension;
27 import java.awt.Graphics;
29 import java.util.ArrayList;
30 import java.util.List;
33 import javax.swing.JPanel;
34 import javax.swing.JSplitPane;
35 import javax.swing.SwingUtilities;
36 import javax.swing.event.InternalFrameAdapter;
37 import javax.swing.event.InternalFrameEvent;
39 import jalview.api.AlignmentViewPanel;
40 import jalview.bin.Cache;
41 import jalview.datamodel.AlignmentI;
42 import jalview.datamodel.PDBEntry;
43 import jalview.datamodel.SequenceI;
44 import jalview.datamodel.StructureViewerModel;
45 import jalview.datamodel.StructureViewerModel.StructureData;
46 import jalview.gui.ImageExporter.ImageWriterI;
47 import jalview.gui.StructureViewer.ViewerType;
48 import jalview.structure.StructureCommand;
49 import jalview.structures.models.AAStructureBindingModel;
50 import jalview.util.BrowserLauncher;
51 import jalview.util.ImageMaker;
52 import jalview.util.MessageManager;
53 import jalview.util.Platform;
54 import jalview.ws.dbsources.Pdb;
56 public class AppJmol extends StructureViewerBase
58 // ms to wait for Jmol to load files
59 private static final int JMOL_LOAD_TIMEOUT = 20000;
61 private static final String SPACE = " ";
63 private static final String QUOTE = "\"";
71 RenderPanel renderPanel;
80 * - add the alignment panel to the list used for colouring these
83 * - add the alignment panel to the list used for aligning these
85 * @param leaveColouringToJmol
86 * - do not update the colours from any other source. Jmol is
92 public AppJmol(StructureViewerModel viewerModel, AlignmentPanel ap,
93 String sessionFile, String viewid)
95 Map<File, StructureData> pdbData = viewerModel.getFileData();
96 PDBEntry[] pdbentrys = new PDBEntry[pdbData.size()];
97 SequenceI[][] seqs = new SequenceI[pdbData.size()][];
99 for (StructureData data : pdbData.values())
101 PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null,
102 PDBEntry.Type.PDB, data.getFilePath());
103 pdbentrys[i] = pdbentry;
104 List<SequenceI> sequencesForPdb = data.getSeqList();
105 seqs[i] = sequencesForPdb
106 .toArray(new SequenceI[sequencesForPdb.size()]);
110 // TODO: check if protocol is needed to be set, and if chains are
112 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
113 pdbentrys, seqs, null);
115 jmb.setLoadingFromArchive(true);
116 addAlignmentPanel(ap);
117 if (viewerModel.isAlignWithPanel())
119 useAlignmentPanelForSuperposition(ap);
122 boolean useToColour = viewerModel.isColourWithAlignPanel();
123 boolean leaveColouringToJmol = viewerModel.isColourByViewer();
124 if (leaveColouringToJmol || !useToColour)
126 jmb.setColourBySequence(false);
127 seqColour.setSelected(false);
128 viewerColour.setSelected(true);
130 else if (useToColour)
132 useAlignmentPanelForColourbyseq(ap);
133 jmb.setColourBySequence(true);
134 seqColour.setSelected(true);
135 viewerColour.setSelected(false);
138 this.setBounds(viewerModel.getX(), viewerModel.getY(),
139 viewerModel.getWidth(), viewerModel.getHeight());
142 this.addInternalFrameListener(new InternalFrameAdapter()
145 public void internalFrameClosing(
146 InternalFrameEvent internalFrameEvent)
151 StringBuilder cmd = new StringBuilder();
152 cmd.append("load FILES ").append(QUOTE)
153 .append(Platform.escapeBackslashes(sessionFile)).append(QUOTE);
154 initJmol(cmd.toString());
158 protected void initMenus()
163 .setText(MessageManager.getString("label.colour_with_jmol"));
164 viewerColour.setToolTipText(MessageManager
165 .getString("label.let_jmol_manage_structure_colours"));
169 * display a single PDB structure in a new Jmol view
176 public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
177 final AlignmentPanel ap)
179 setProgressIndicator(ap.alignFrame);
181 openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
186 private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
187 PDBEntry[] pdbentrys,
190 setProgressIndicator(ap.alignFrame);
191 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
192 pdbentrys, seqs, null);
193 addAlignmentPanel(ap);
194 useAlignmentPanelForColourbyseq(ap);
196 alignAddedStructures = alignAdded;
197 if (pdbentrys.length > 1)
199 useAlignmentPanelForSuperposition(ap);
202 jmb.setColourBySequence(true);
203 setSize(400, 400); // probably should be a configurable/dynamic default here
205 addingStructures = false;
206 worker = new Thread(this);
209 this.addInternalFrameListener(new InternalFrameAdapter()
212 public void internalFrameClosing(
213 InternalFrameEvent internalFrameEvent)
222 * create a new Jmol containing several structures optionally superimposed
223 * using the given alignPanel.
227 * - true to superimpose
231 public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
234 openNewJmol(ap, alignAdded, pe, seqs);
238 void initJmol(String command)
240 jmb.setFinishedInit(false);
241 renderPanel = new RenderPanel();
242 // TODO: consider waiting until the structure/view is fully loaded before
244 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
245 jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
246 getBounds().width, getBounds().height);
247 if (scriptWindow == null)
249 BorderLayout bl = new BorderLayout();
252 scriptWindow = new JPanel(bl);
253 scriptWindow.setVisible(false);
256 jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
258 // jmb.newJmolPopup("Jmol");
263 jmb.executeCommand(new StructureCommand(command), false);
264 jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false);
265 jmb.setFinishedInit(true);
274 List<String> files = fetchPdbFiles();
275 if (files.size() > 0)
277 showFilesInViewer(files);
287 * Either adds the given files to a structure viewer or opens a new viewer to
291 * list of absolute paths to structure files
293 void showFilesInViewer(List<String> files)
295 long lastnotify = jmb.getLoadNotifiesHandled();
296 StringBuilder fileList = new StringBuilder();
297 for (String s : files)
299 fileList.append(SPACE).append(QUOTE)
300 .append(Platform.escapeBackslashes(s)).append(QUOTE);
302 String filesString = fileList.toString();
304 if (!addingStructures)
308 initJmol("load FILES " + filesString);
309 } catch (OutOfMemoryError oomerror)
311 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
312 Cache.log.debug("File locations are " + filesString);
313 } catch (Exception ex)
315 Cache.log.error("Couldn't open Jmol viewer!", ex);
316 ex.printStackTrace();
322 StringBuilder cmd = new StringBuilder();
323 cmd.append("loadingJalviewdata=true\nload APPEND ");
324 cmd.append(filesString);
325 cmd.append("\nloadingJalviewdata=null");
326 final StructureCommand command = new StructureCommand(cmd.toString());
327 lastnotify = jmb.getLoadNotifiesHandled();
331 jmb.executeCommand(command, false);
332 } catch (OutOfMemoryError oomerror)
334 new OOMWarning("When trying to add structures to the Jmol viewer!",
336 Cache.log.debug("File locations are " + filesString);
338 } catch (Exception ex)
340 Cache.log.error("Couldn't add files to Jmol viewer!", ex);
341 ex.printStackTrace();
346 // need to wait around until script has finished
347 int waitMax = JMOL_LOAD_TIMEOUT;
350 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
351 : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null
352 && jmb.getStructureFiles().length == files.size()))
356 Cache.log.debug("Waiting around for jmb notify.");
357 waitTotal += waitFor;
359 // Thread.sleep() throws an exception in JS
360 Thread.sleep(waitFor);
361 } catch (Exception e)
364 if (waitTotal > waitMax)
366 System.err.println("Timed out waiting for Jmol to load files after "
368 // System.err.println("finished: " + jmb.isFinishedInit()
369 // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
370 // + "; files: " + files.toString());
371 jmb.getStructureFiles();
376 // refresh the sequence colours for the new structure(s)
377 for (AlignmentViewPanel ap : _colourwith)
379 jmb.updateColours(ap);
381 // do superposition if asked to
382 if (alignAddedStructures)
384 alignAddedStructures();
386 addingStructures = false;
390 * Queues a thread to align structures with Jalview alignments
392 void alignAddedStructures()
394 javax.swing.SwingUtilities.invokeLater(new Runnable()
399 if (jmb.jmolViewer.isScriptExecuting())
401 SwingUtilities.invokeLater(this);
405 } catch (InterruptedException q)
412 alignStructsWithAllAlignPanels();
420 * Retrieves and saves as file any modelled PDB entries for which we do not
421 * already have a file saved. Returns a list of absolute paths to structure
422 * files which were either retrieved, or already stored but not modelled in
423 * the structure viewer (i.e. files to add to the viewer display).
427 List<String> fetchPdbFiles()
429 // todo - record which pdbids were successfully imported.
430 StringBuilder errormsgs = new StringBuilder();
432 List<String> files = new ArrayList<>();
436 String[] filesInViewer = jmb.getStructureFiles();
437 // TODO: replace with reference fetching/transfer code (validate PDBentry
439 Pdb pdbclient = new Pdb();
440 for (int pi = 0; pi < jmb.getPdbCount(); pi++)
442 String file = jmb.getPdbEntry(pi).getFile();
445 // todo: extract block as method and pull up (also ChimeraViewFrame)
446 // retrieve the pdb and store it locally
447 AlignmentI pdbseq = null;
448 pdbid = jmb.getPdbEntry(pi).getId();
449 long hdl = pdbid.hashCode() - System.currentTimeMillis();
450 setProgressMessage(MessageManager
451 .formatMessage("status.fetching_pdb", new String[]
455 pdbseq = pdbclient.getSequenceRecords(pdbid);
456 } catch (OutOfMemoryError oomerror)
458 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
459 } catch (Exception ex)
461 ex.printStackTrace();
462 errormsgs.append("'").append(pdbid).append("'");
466 MessageManager.getString("label.state_completed"), hdl);
470 // just transfer the file name from the first sequence's first
472 file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
473 .elementAt(0).getFile()).getAbsolutePath();
474 jmb.getPdbEntry(pi).setFile(file);
479 errormsgs.append("'").append(pdbid).append("' ");
484 if (filesInViewer != null && filesInViewer.length > 0)
486 addingStructures = true; // already files loaded.
487 for (int c = 0; c < filesInViewer.length; c++)
489 if (Platform.pathEquals(filesInViewer[c], file))
502 } catch (OutOfMemoryError oomerror)
504 new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
505 } catch (Exception ex)
507 ex.printStackTrace();
508 errormsgs.append("When retrieving pdbfiles : current was: '")
509 .append(pdbid).append("'");
511 if (errormsgs.length() > 0)
513 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
514 MessageManager.formatMessage(
515 "label.pdb_entries_couldnt_be_retrieved", new String[]
516 { errormsgs.toString() }),
517 MessageManager.getString("label.couldnt_load_file"),
518 JvOptionPane.ERROR_MESSAGE);
524 * Outputs the Jmol viewer image as an image file, after prompting the user to
525 * choose a file and (for EPS) choice of Text or Lineart character rendering
526 * (unless a preference for this is set)
531 public void makePDBImage(ImageMaker.TYPE type)
533 int width = getWidth();
534 int height = getHeight();
535 ImageWriterI writer = new ImageWriterI()
538 public void exportImage(Graphics g) throws Exception
540 jmb.jmolViewer.renderScreenImage(g, width, height);
543 String view = MessageManager.getString("action.view").toLowerCase();
544 ImageExporter exporter = new ImageExporter(writer,
545 getProgressIndicator(), type, getTitle());
546 exporter.doExport(null, this, width, height, view);
550 public void showHelp_actionPerformed()
554 BrowserLauncher // BH 2018
555 .openURL("http://wiki.jmol.org");//http://jmol.sourceforge.net/docs/JmolUserGuide/");
556 } catch (Exception ex)
558 System.err.println("Show Jmol help failed with: " + ex.getMessage());
563 public void showConsole(boolean showConsole)
567 if (splitPane == null)
569 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
570 splitPane.setTopComponent(renderPanel);
571 splitPane.setBottomComponent(scriptWindow);
572 this.getContentPane().add(splitPane, BorderLayout.CENTER);
573 splitPane.setDividerLocation(getHeight() - 200);
574 scriptWindow.setVisible(true);
575 scriptWindow.validate();
576 splitPane.validate();
582 if (splitPane != null)
584 splitPane.setVisible(false);
589 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
595 class RenderPanel extends JPanel
597 final Dimension currentSize = new Dimension();
600 public void paintComponent(Graphics g)
602 getSize(currentSize);
604 if (jmb != null && jmb.hasFileLoadingError())
606 g.setColor(Color.black);
607 g.fillRect(0, 0, currentSize.width, currentSize.height);
608 g.setColor(Color.white);
609 g.setFont(new Font("Verdana", Font.BOLD, 14));
610 g.drawString(MessageManager.getString("label.error_loading_file")
611 + "...", 20, currentSize.height / 2);
612 StringBuffer sb = new StringBuffer();
614 for (int e = 0; e < jmb.getPdbCount(); e++)
616 sb.append(jmb.getPdbEntry(e).getId());
617 if (e < jmb.getPdbCount() - 1)
622 if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
625 g.drawString(sb.toString(), 20, currentSize.height / 2
626 - lines * g.getFontMetrics().getHeight());
630 else if (jmb == null || jmb.jmolViewer == null || !jmb.isFinishedInit())
632 g.setColor(Color.black);
633 g.fillRect(0, 0, currentSize.width, currentSize.height);
634 g.setColor(Color.white);
635 g.setFont(new Font("Verdana", Font.BOLD, 14));
636 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
637 20, currentSize.height / 2);
641 jmb.jmolViewer.renderScreenImage(g, currentSize.width,
648 public AAStructureBindingModel getBinding()
654 public ViewerType getViewerType()
656 return ViewerType.JMOL;
660 protected String getViewerName()