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()
151 .setText(MessageManager.getString("label.colour_with_jmol"));
152 viewerColour.setToolTipText(MessageManager
153 .getString("label.let_jmol_manage_structure_colours"));
157 * display a single PDB structure in a new Jmol view
164 public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
165 final AlignmentPanel ap)
167 setProgressIndicator(ap.alignFrame);
169 openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
174 private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
175 PDBEntry[] pdbentrys,
178 setProgressIndicator(ap.alignFrame);
179 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
180 pdbentrys, seqs, null);
181 addAlignmentPanel(ap);
182 useAlignmentPanelForColourbyseq(ap);
184 alignAddedStructures = alignAdded;
185 if (pdbentrys.length > 1)
187 useAlignmentPanelForSuperposition(ap);
190 jmb.setColourBySequence(true);
191 setSize(400, 400); // probably should be a configurable/dynamic default here
193 addingStructures = false;
194 worker = new Thread(this);
197 this.addInternalFrameListener(new InternalFrameAdapter()
200 public void internalFrameClosing(
201 InternalFrameEvent internalFrameEvent)
210 * create a new Jmol containing several structures optionally superimposed
211 * using the given alignPanel.
215 * - true to superimpose
219 public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
222 openNewJmol(ap, alignAdded, pe, seqs);
226 void initJmol(String command)
228 jmb.setFinishedInit(false);
229 renderPanel = new RenderPanel();
230 // TODO: consider waiting until the structure/view is fully loaded before
232 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
233 jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
234 getBounds().width, getBounds().height);
235 if (scriptWindow == null)
237 BorderLayout bl = new BorderLayout();
240 scriptWindow = new JPanel(bl);
241 scriptWindow.setVisible(false);
244 jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
246 // jmb.newJmolPopup("Jmol");
251 jmb.executeCommand(new StructureCommand(command), false);
252 jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false);
253 jmb.setFinishedInit(true);
262 List<String> files = fetchPdbFiles();
263 if (files.size() > 0)
265 showFilesInViewer(files);
275 * Either adds the given files to a structure viewer or opens a new viewer to
279 * list of absolute paths to structure files
281 void showFilesInViewer(List<String> files)
283 long lastnotify = jmb.getLoadNotifiesHandled();
284 StringBuilder fileList = new StringBuilder();
285 for (String s : files)
287 fileList.append(SPACE).append(QUOTE)
288 .append(Platform.escapeBackslashes(s)).append(QUOTE);
290 String filesString = fileList.toString();
292 if (!addingStructures)
296 initJmol("load FILES " + filesString);
297 } catch (OutOfMemoryError oomerror)
299 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
300 Cache.log.debug("File locations are " + filesString);
301 } catch (Exception ex)
303 Cache.log.error("Couldn't open Jmol viewer!", ex);
304 ex.printStackTrace();
310 StringBuilder cmd = new StringBuilder();
311 cmd.append("loadingJalviewdata=true\nload APPEND ");
312 cmd.append(filesString);
313 cmd.append("\nloadingJalviewdata=null");
314 final StructureCommand command = new StructureCommand(cmd.toString());
315 lastnotify = jmb.getLoadNotifiesHandled();
319 jmb.executeCommand(command, false);
320 } catch (OutOfMemoryError oomerror)
322 new OOMWarning("When trying to add structures to the Jmol viewer!",
324 Cache.log.debug("File locations are " + filesString);
326 } catch (Exception ex)
328 Cache.log.error("Couldn't add files to Jmol viewer!", ex);
329 ex.printStackTrace();
334 // need to wait around until script has finished
335 int waitMax = JMOL_LOAD_TIMEOUT;
338 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
339 : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null
340 && jmb.getStructureFiles().length == files.size()))
344 Cache.log.debug("Waiting around for jmb notify.");
345 waitTotal += waitFor;
347 // Thread.sleep() throws an exception in JS
348 Thread.sleep(waitFor);
349 } catch (Exception e)
352 if (waitTotal > waitMax)
354 System.err.println("Timed out waiting for Jmol to load files after "
356 // System.err.println("finished: " + jmb.isFinishedInit()
357 // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
358 // + "; files: " + files.toString());
359 jmb.getStructureFiles();
364 // refresh the sequence colours for the new structure(s)
365 for (AlignmentViewPanel ap : _colourwith)
367 jmb.updateColours(ap);
369 // do superposition if asked to
370 if (alignAddedStructures)
372 alignAddedStructures();
374 addingStructures = false;
378 * Queues a thread to align structures with Jalview alignments
380 void alignAddedStructures()
382 javax.swing.SwingUtilities.invokeLater(new Runnable()
387 if (jmb.jmolViewer.isScriptExecuting())
389 SwingUtilities.invokeLater(this);
393 } catch (InterruptedException q)
400 alignStructsWithAllAlignPanels();
408 * Retrieves and saves as file any modelled PDB entries for which we do not
409 * already have a file saved. Returns a list of absolute paths to structure
410 * files which were either retrieved, or already stored but not modelled in
411 * the structure viewer (i.e. files to add to the viewer display).
415 List<String> fetchPdbFiles()
417 // todo - record which pdbids were successfully imported.
418 StringBuilder errormsgs = new StringBuilder();
420 List<String> files = new ArrayList<>();
424 String[] filesInViewer = jmb.getStructureFiles();
425 // TODO: replace with reference fetching/transfer code (validate PDBentry
427 Pdb pdbclient = new Pdb();
428 for (int pi = 0; pi < jmb.getPdbCount(); pi++)
430 String file = jmb.getPdbEntry(pi).getFile();
433 // todo: extract block as method and pull up (also ChimeraViewFrame)
434 // retrieve the pdb and store it locally
435 AlignmentI pdbseq = null;
436 pdbid = jmb.getPdbEntry(pi).getId();
437 long hdl = pdbid.hashCode() - System.currentTimeMillis();
438 setProgressMessage(MessageManager
439 .formatMessage("status.fetching_pdb", new String[]
443 pdbseq = pdbclient.getSequenceRecords(pdbid);
444 } catch (OutOfMemoryError oomerror)
446 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
447 } catch (Exception ex)
449 ex.printStackTrace();
450 errormsgs.append("'").append(pdbid).append("'");
454 MessageManager.getString("label.state_completed"), hdl);
458 // just transfer the file name from the first sequence's first
460 file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
461 .elementAt(0).getFile()).getAbsolutePath();
462 jmb.getPdbEntry(pi).setFile(file);
467 errormsgs.append("'").append(pdbid).append("' ");
472 if (filesInViewer != null && filesInViewer.length > 0)
474 addingStructures = true; // already files loaded.
475 for (int c = 0; c < filesInViewer.length; c++)
477 if (Platform.pathEquals(filesInViewer[c], file))
490 } catch (OutOfMemoryError oomerror)
492 new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
493 } catch (Exception ex)
495 ex.printStackTrace();
496 errormsgs.append("When retrieving pdbfiles : current was: '")
497 .append(pdbid).append("'");
499 if (errormsgs.length() > 0)
501 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
502 MessageManager.formatMessage(
503 "label.pdb_entries_couldnt_be_retrieved", new String[]
504 { errormsgs.toString() }),
505 MessageManager.getString("label.couldnt_load_file"),
506 JvOptionPane.ERROR_MESSAGE);
512 * Outputs the Jmol viewer image as an image file, after prompting the user to
513 * choose a file and (for EPS) choice of Text or Lineart character rendering
514 * (unless a preference for this is set)
519 public void makePDBImage(ImageMaker.TYPE type)
521 int width = getWidth();
522 int height = getHeight();
523 ImageWriterI writer = new ImageWriterI()
526 public void exportImage(Graphics g) throws Exception
528 jmb.jmolViewer.renderScreenImage(g, width, height);
531 String view = MessageManager.getString("action.view").toLowerCase();
532 ImageExporter exporter = new ImageExporter(writer,
533 getProgressIndicator(), type, getTitle());
534 exporter.doExport(null, this, width, height, view);
538 public void showHelp_actionPerformed()
542 BrowserLauncher // BH 2018
543 .openURL("http://wiki.jmol.org");//http://jmol.sourceforge.net/docs/JmolUserGuide/");
544 } catch (Exception ex)
546 System.err.println("Show Jmol help failed with: " + ex.getMessage());
551 public void showConsole(boolean showConsole)
555 if (splitPane == null)
557 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
558 splitPane.setTopComponent(renderPanel);
559 splitPane.setBottomComponent(scriptWindow);
560 this.getContentPane().add(splitPane, BorderLayout.CENTER);
561 splitPane.setDividerLocation(getHeight() - 200);
562 scriptWindow.setVisible(true);
563 scriptWindow.validate();
564 splitPane.validate();
570 if (splitPane != null)
572 splitPane.setVisible(false);
577 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
583 class RenderPanel extends JPanel
585 final Dimension currentSize = new Dimension();
588 public void paintComponent(Graphics g)
590 getSize(currentSize);
592 if (jmb != null && jmb.hasFileLoadingError())
594 g.setColor(Color.black);
595 g.fillRect(0, 0, currentSize.width, currentSize.height);
596 g.setColor(Color.white);
597 g.setFont(new Font("Verdana", Font.BOLD, 14));
598 g.drawString(MessageManager.getString("label.error_loading_file")
599 + "...", 20, currentSize.height / 2);
600 StringBuffer sb = new StringBuffer();
602 for (int e = 0; e < jmb.getPdbCount(); e++)
604 sb.append(jmb.getPdbEntry(e).getId());
605 if (e < jmb.getPdbCount() - 1)
610 if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
613 g.drawString(sb.toString(), 20, currentSize.height / 2
614 - lines * g.getFontMetrics().getHeight());
618 else if (jmb == null || jmb.jmolViewer == null || !jmb.isFinishedInit())
620 g.setColor(Color.black);
621 g.fillRect(0, 0, currentSize.width, currentSize.height);
622 g.setColor(Color.white);
623 g.setFont(new Font("Verdana", Font.BOLD, 14));
624 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
625 20, currentSize.height / 2);
629 jmb.jmolViewer.renderScreenImage(g, currentSize.width,
636 public AAStructureBindingModel getBinding()
642 public ViewerType getViewerType()
644 return ViewerType.JMOL;
648 protected String getViewerName()