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;
28 import java.awt.Rectangle;
30 import java.util.ArrayList;
31 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.gui.ImageExporter.ImageWriterI;
45 import jalview.gui.StructureViewer.ViewerType;
46 import jalview.structure.StructureCommand;
47 import jalview.structures.models.AAStructureBindingModel;
48 import jalview.util.BrowserLauncher;
49 import jalview.util.ImageMaker;
50 import jalview.util.MessageManager;
51 import jalview.util.Platform;
52 import jalview.ws.dbsources.Pdb;
54 public class AppJmol extends StructureViewerBase
56 // ms to wait for Jmol to load files
57 private static final int JMOL_LOAD_TIMEOUT = 20000;
59 private static final String SPACE = " ";
61 private static final String QUOTE = "\"";
69 RenderPanel renderPanel;
78 * - add the alignment panel to the list used for colouring these
81 * - add the alignment panel to the list used for aligning these
83 * @param leaveColouringToJmol
84 * - do not update the colours from any other source. Jmol is
90 public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
91 AlignmentPanel ap, boolean usetoColour, boolean useToAlign,
92 boolean leaveColouringToJmol, String loadStatus, Rectangle bounds,
95 PDBEntry[] pdbentrys = new PDBEntry[files.length];
96 for (int i = 0; i < pdbentrys.length; i++)
98 // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
99 PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB,
101 pdbentrys[i] = pdbentry;
103 // / TODO: check if protocol is needed to be set, and if chains are
105 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
106 pdbentrys, seqs, null);
108 jmb.setLoadingFromArchive(true);
109 addAlignmentPanel(ap);
112 useAlignmentPanelForSuperposition(ap);
115 if (leaveColouringToJmol || !usetoColour)
117 jmb.setColourBySequence(false);
118 seqColour.setSelected(false);
119 viewerColour.setSelected(true);
121 else if (usetoColour)
123 useAlignmentPanelForColourbyseq(ap);
124 jmb.setColourBySequence(true);
125 seqColour.setSelected(true);
126 viewerColour.setSelected(false);
128 this.setBounds(bounds);
130 // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
131 // bounds.width,bounds.height);
133 this.addInternalFrameListener(new InternalFrameAdapter()
136 public void internalFrameClosing(
137 InternalFrameEvent internalFrameEvent)
142 initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
146 protected void initMenus()
150 viewerActionMenu.setText(MessageManager.getString("label.jmol"));
153 .setText(MessageManager.getString("label.colour_with_jmol"));
154 viewerColour.setToolTipText(MessageManager
155 .getString("label.let_jmol_manage_structure_colours"));
159 * display a single PDB structure in a new Jmol view
166 public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
167 final AlignmentPanel ap)
169 setProgressIndicator(ap.alignFrame);
171 openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
176 private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
177 PDBEntry[] pdbentrys,
180 setProgressIndicator(ap.alignFrame);
181 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
182 pdbentrys, seqs, null);
183 addAlignmentPanel(ap);
184 useAlignmentPanelForColourbyseq(ap);
186 alignAddedStructures = alignAdded;
187 if (pdbentrys.length > 1)
189 useAlignmentPanelForSuperposition(ap);
192 jmb.setColourBySequence(true);
193 setSize(400, 400); // probably should be a configurable/dynamic default here
195 addingStructures = false;
196 worker = new Thread(this);
199 this.addInternalFrameListener(new InternalFrameAdapter()
202 public void internalFrameClosing(
203 InternalFrameEvent internalFrameEvent)
212 * create a new Jmol containing several structures optionally superimposed
213 * using the given alignPanel.
217 * - true to superimpose
221 public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
224 openNewJmol(ap, alignAdded, pe, seqs);
228 void initJmol(String command)
230 jmb.setFinishedInit(false);
231 renderPanel = new RenderPanel();
232 // TODO: consider waiting until the structure/view is fully loaded before
234 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
235 jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
236 getBounds().width, getBounds().height);
237 if (scriptWindow == null)
239 BorderLayout bl = new BorderLayout();
242 scriptWindow = new JPanel(bl);
243 scriptWindow.setVisible(false);
246 jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
248 // jmb.newJmolPopup("Jmol");
253 jmb.executeCommand(new StructureCommand(command), false);
254 jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false);
255 jmb.setFinishedInit(true);
264 List<String> files = fetchPdbFiles();
265 if (files.size() > 0)
267 showFilesInViewer(files);
277 * Either adds the given files to a structure viewer or opens a new viewer to
281 * list of absolute paths to structure files
283 void showFilesInViewer(List<String> files)
285 long lastnotify = jmb.getLoadNotifiesHandled();
286 StringBuilder fileList = new StringBuilder();
287 for (String s : files)
289 fileList.append(SPACE).append(QUOTE)
290 .append(Platform.escapeBackslashes(s)).append(QUOTE);
292 String filesString = fileList.toString();
294 if (!addingStructures)
298 initJmol("load FILES " + filesString);
299 } catch (OutOfMemoryError oomerror)
301 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
302 Cache.log.debug("File locations are " + filesString);
303 } catch (Exception ex)
305 Cache.log.error("Couldn't open Jmol viewer!", ex);
306 ex.printStackTrace();
312 StringBuilder cmd = new StringBuilder();
313 cmd.append("loadingJalviewdata=true\nload APPEND ");
314 cmd.append(filesString);
315 cmd.append("\nloadingJalviewdata=null");
316 final StructureCommand command = new StructureCommand(cmd.toString());
317 lastnotify = jmb.getLoadNotifiesHandled();
321 jmb.executeCommand(command, false);
322 } catch (OutOfMemoryError oomerror)
324 new OOMWarning("When trying to add structures to the Jmol viewer!",
326 Cache.log.debug("File locations are " + filesString);
328 } catch (Exception ex)
330 Cache.log.error("Couldn't add files to Jmol viewer!", ex);
331 ex.printStackTrace();
336 // need to wait around until script has finished
337 int waitMax = JMOL_LOAD_TIMEOUT;
340 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
341 : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null
342 && jmb.getStructureFiles().length == files.size()))
346 Cache.log.debug("Waiting around for jmb notify.");
347 waitTotal += waitFor;
349 // Thread.sleep() throws an exception in JS
350 Thread.sleep(waitFor);
351 } catch (Exception e)
354 if (waitTotal > waitMax)
356 System.err.println("Timed out waiting for Jmol to load files after "
358 // System.err.println("finished: " + jmb.isFinishedInit()
359 // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
360 // + "; files: " + files.toString());
361 jmb.getStructureFiles();
366 // refresh the sequence colours for the new structure(s)
367 for (AlignmentViewPanel ap : _colourwith)
369 jmb.updateColours(ap);
371 // do superposition if asked to
372 if (alignAddedStructures)
374 alignAddedStructures();
376 addingStructures = false;
380 * Queues a thread to align structures with Jalview alignments
382 void alignAddedStructures()
384 javax.swing.SwingUtilities.invokeLater(new Runnable()
389 if (jmb.jmolViewer.isScriptExecuting())
391 SwingUtilities.invokeLater(this);
395 } catch (InterruptedException q)
402 alignStructsWithAllAlignPanels();
410 * Retrieves and saves as file any modelled PDB entries for which we do not
411 * already have a file saved. Returns a list of absolute paths to structure
412 * files which were either retrieved, or already stored but not modelled in
413 * the structure viewer (i.e. files to add to the viewer display).
417 List<String> fetchPdbFiles()
419 // todo - record which pdbids were successfully imported.
420 StringBuilder errormsgs = new StringBuilder();
422 List<String> files = new ArrayList<>();
426 String[] filesInViewer = jmb.getStructureFiles();
427 // TODO: replace with reference fetching/transfer code (validate PDBentry
429 Pdb pdbclient = new Pdb();
430 for (int pi = 0; pi < jmb.getPdbCount(); pi++)
432 String file = jmb.getPdbEntry(pi).getFile();
435 // todo: extract block as method and pull up (also ChimeraViewFrame)
436 // retrieve the pdb and store it locally
437 AlignmentI pdbseq = null;
438 pdbid = jmb.getPdbEntry(pi).getId();
439 long hdl = pdbid.hashCode() - System.currentTimeMillis();
440 setProgressMessage(MessageManager
441 .formatMessage("status.fetching_pdb", new String[]
445 pdbseq = pdbclient.getSequenceRecords(pdbid);
446 } catch (OutOfMemoryError oomerror)
448 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
449 } catch (Exception ex)
451 ex.printStackTrace();
452 errormsgs.append("'").append(pdbid).append("'");
456 MessageManager.getString("label.state_completed"), hdl);
460 // just transfer the file name from the first sequence's first
462 file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
463 .elementAt(0).getFile()).getAbsolutePath();
464 jmb.getPdbEntry(pi).setFile(file);
469 errormsgs.append("'").append(pdbid).append("' ");
474 if (filesInViewer != null && filesInViewer.length > 0)
476 addingStructures = true; // already files loaded.
477 for (int c = 0; c < filesInViewer.length; c++)
479 if (Platform.pathEquals(filesInViewer[c], file))
492 } catch (OutOfMemoryError oomerror)
494 new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
495 } catch (Exception ex)
497 ex.printStackTrace();
498 errormsgs.append("When retrieving pdbfiles : current was: '")
499 .append(pdbid).append("'");
501 if (errormsgs.length() > 0)
503 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
504 MessageManager.formatMessage(
505 "label.pdb_entries_couldnt_be_retrieved", new String[]
506 { errormsgs.toString() }),
507 MessageManager.getString("label.couldnt_load_file"),
508 JvOptionPane.ERROR_MESSAGE);
514 * Outputs the Jmol viewer image as an image file, after prompting the user to
515 * choose a file and (for EPS) choice of Text or Lineart character rendering
516 * (unless a preference for this is set)
521 public void makePDBImage(ImageMaker.TYPE type)
523 int width = getWidth();
524 int height = getHeight();
525 ImageWriterI writer = new ImageWriterI()
528 public void exportImage(Graphics g) throws Exception
530 jmb.jmolViewer.renderScreenImage(g, width, height);
533 String view = MessageManager.getString("action.view").toLowerCase();
534 ImageExporter exporter = new ImageExporter(writer,
535 getProgressIndicator(), type, getTitle());
536 exporter.doExport(null, this, width, height, view);
540 public void showHelp_actionPerformed()
544 BrowserLauncher // BH 2018
545 .openURL("http://wiki.jmol.org");//http://jmol.sourceforge.net/docs/JmolUserGuide/");
546 } catch (Exception ex)
548 System.err.println("Show Jmol help failed with: " + ex.getMessage());
553 public void showConsole(boolean showConsole)
557 if (splitPane == null)
559 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
560 splitPane.setTopComponent(renderPanel);
561 splitPane.setBottomComponent(scriptWindow);
562 this.getContentPane().add(splitPane, BorderLayout.CENTER);
563 splitPane.setDividerLocation(getHeight() - 200);
564 scriptWindow.setVisible(true);
565 scriptWindow.validate();
566 splitPane.validate();
572 if (splitPane != null)
574 splitPane.setVisible(false);
579 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
585 class RenderPanel extends JPanel
587 final Dimension currentSize = new Dimension();
590 public void paintComponent(Graphics g)
592 getSize(currentSize);
594 if (jmb != null && jmb.hasFileLoadingError())
596 g.setColor(Color.black);
597 g.fillRect(0, 0, currentSize.width, currentSize.height);
598 g.setColor(Color.white);
599 g.setFont(new Font("Verdana", Font.BOLD, 14));
600 g.drawString(MessageManager.getString("label.error_loading_file")
601 + "...", 20, currentSize.height / 2);
602 StringBuffer sb = new StringBuffer();
604 for (int e = 0; e < jmb.getPdbCount(); e++)
606 sb.append(jmb.getPdbEntry(e).getId());
607 if (e < jmb.getPdbCount() - 1)
612 if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
615 g.drawString(sb.toString(), 20, currentSize.height / 2
616 - lines * g.getFontMetrics().getHeight());
620 else if (jmb == null || jmb.jmolViewer == null || !jmb.isFinishedInit())
622 g.setColor(Color.black);
623 g.fillRect(0, 0, currentSize.width, currentSize.height);
624 g.setColor(Color.white);
625 g.setFont(new Font("Verdana", Font.BOLD, 14));
626 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
627 20, currentSize.height / 2);
631 jmb.jmolViewer.renderScreenImage(g, currentSize.width,
638 public AAStructureBindingModel getBinding()
644 public ViewerType getViewerType()
646 return ViewerType.JMOL;
650 protected String getViewerName()