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 jalview.bin.Cache;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.PDBEntry;
26 import jalview.datamodel.SequenceI;
27 import jalview.gui.StructureViewer.ViewerType;
28 import jalview.structures.models.AAStructureBindingModel;
29 import jalview.structures.models.AAStructureBindingModel.ColourBy;
30 import jalview.util.BrowserLauncher;
31 import jalview.util.MessageManager;
32 import jalview.util.Platform;
33 import jalview.ws.dbsources.Pdb;
35 import java.awt.BorderLayout;
36 import java.awt.Color;
37 import java.awt.Dimension;
39 import java.awt.Graphics;
40 import java.awt.Rectangle;
41 import java.awt.event.ActionEvent;
43 import java.util.ArrayList;
44 import java.util.List;
45 import java.util.Vector;
47 import javax.swing.JCheckBoxMenuItem;
48 import javax.swing.JPanel;
49 import javax.swing.JSplitPane;
50 import javax.swing.SwingUtilities;
51 import javax.swing.event.InternalFrameAdapter;
52 import javax.swing.event.InternalFrameEvent;
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.setColourBy(ColourBy.Viewer);
118 seqColour.setSelected(false);
119 viewerColour.setSelected(true);
121 else if (usetoColour)
123 useAlignmentPanelForColourbyseq(ap);
124 jmb.setColourBy(ColourBy.Sequence);
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"));
158 IProgressIndicator progressBar = null;
161 protected IProgressIndicator getIProgressIndicator()
167 * display a single PDB structure in a new Jmol view
174 public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
175 final AlignmentPanel ap)
177 progressBar = ap.alignFrame;
179 openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
184 private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
185 PDBEntry[] pdbentrys,
188 progressBar = ap.alignFrame;
189 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
190 pdbentrys, seqs, null);
191 addAlignmentPanel(ap);
192 useAlignmentPanelForColourbyseq(ap);
194 alignAddedStructures = alignAdded;
195 useAlignmentPanelForSuperposition(ap);
197 jmb.setColourBy(ColourBy.Sequence);
198 setSize(400, 400); // probably should be a configurable/dynamic default here
200 addingStructures = false;
201 worker = new Thread(this);
204 this.addInternalFrameListener(new InternalFrameAdapter()
207 public void internalFrameClosing(
208 InternalFrameEvent internalFrameEvent)
217 * create a new Jmol containing several structures optionally superimposed
218 * using the given alignPanel.
222 * - true to superimpose
226 public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
229 openNewJmol(ap, alignAdded, pe, seqs);
233 void initJmol(String command)
235 jmb.setFinishedInit(false);
236 renderPanel = new RenderPanel();
237 // TODO: consider waiting until the structure/view is fully loaded before
239 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
240 jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
241 getBounds().width, getBounds().height);
242 if (scriptWindow == null)
244 BorderLayout bl = new BorderLayout();
247 scriptWindow = new JPanel(bl);
248 scriptWindow.setVisible(false);
251 jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
253 // jmb.newJmolPopup("Jmol");
258 jmb.evalStateCommand(command);
259 jmb.evalStateCommand("set hoverDelay=0.1");
260 jmb.setFinishedInit(true);
264 void showSelectedChains()
266 Vector<String> toshow = new Vector<>();
267 for (int i = 0; i < chainMenu.getItemCount(); i++)
269 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
271 JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
272 if (item.isSelected())
274 toshow.addElement(item.getText());
278 jmb.centerViewer(toshow);
282 public void closeViewer(boolean closeExternalViewer)
284 // Jmol does not use an external viewer
289 setAlignmentPanel(null);
293 // TODO: check for memory leaks where instance isn't finalised because jmb
294 // holds a reference to the window
304 List<String> files = fetchPdbFiles();
305 if (files.size() > 0)
307 showFilesInViewer(files);
317 * Either adds the given files to a structure viewer or opens a new viewer to
321 * list of absolute paths to structure files
323 void showFilesInViewer(List<String> files)
325 long lastnotify = jmb.getLoadNotifiesHandled();
326 StringBuilder fileList = new StringBuilder();
327 for (String s : files)
329 fileList.append(SPACE).append(QUOTE)
330 .append(Platform.escapeString(s)).append(QUOTE);
332 String filesString = fileList.toString();
334 if (!addingStructures)
338 initJmol("load FILES " + filesString);
339 } catch (OutOfMemoryError oomerror)
341 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
342 Cache.log.debug("File locations are " + filesString);
343 } catch (Exception ex)
345 Cache.log.error("Couldn't open Jmol viewer!", ex);
350 StringBuilder cmd = new StringBuilder();
351 cmd.append("loadingJalviewdata=true\nload APPEND ");
352 cmd.append(filesString);
353 cmd.append("\nloadingJalviewdata=null");
354 final String command = cmd.toString();
355 lastnotify = jmb.getLoadNotifiesHandled();
359 jmb.evalStateCommand(command);
360 } catch (OutOfMemoryError oomerror)
362 new OOMWarning("When trying to add structures to the Jmol viewer!",
364 Cache.log.debug("File locations are " + filesString);
365 } catch (Exception ex)
367 Cache.log.error("Couldn't add files to Jmol viewer!", ex);
371 // need to wait around until script has finished
372 int waitMax = JMOL_LOAD_TIMEOUT;
375 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
376 : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null
377 && jmb.getStructureFiles().length == files.size()))
381 Cache.log.debug("Waiting around for jmb notify.");
382 Thread.sleep(waitFor);
383 waitTotal += waitFor;
384 } catch (Exception e)
387 if (waitTotal > waitMax)
389 System.err.println("Timed out waiting for Jmol to load files after "
391 // System.err.println("finished: " + jmb.isFinishedInit()
392 // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
393 // + "; files: " + files.toString());
394 jmb.getStructureFiles();
399 // refresh the sequence colours for the new structure(s)
400 for (AlignmentPanel ap : _colourwith)
402 jmb.updateColours(ap);
404 // do superposition if asked to
405 if (alignAddedStructures)
407 alignAddedStructures();
409 addingStructures = false;
413 * Queues a thread to align structures with Jalview alignments
415 void alignAddedStructures()
417 javax.swing.SwingUtilities.invokeLater(new Runnable()
422 if (jmb.viewer.isScriptExecuting())
424 SwingUtilities.invokeLater(this);
428 } catch (InterruptedException q)
435 alignStructs_withAllAlignPanels();
443 * Retrieves and saves as file any modelled PDB entries for which we do not
444 * already have a file saved. Returns a list of absolute paths to structure
445 * files which were either retrieved, or already stored but not modelled in
446 * the structure viewer (i.e. files to add to the viewer display).
450 List<String> fetchPdbFiles()
452 // todo - record which pdbids were successfully imported.
453 StringBuilder errormsgs = new StringBuilder();
455 List<String> files = new ArrayList<>();
459 String[] filesInViewer = jmb.getStructureFiles();
460 // TODO: replace with reference fetching/transfer code (validate PDBentry
462 Pdb pdbclient = new Pdb();
463 for (int pi = 0; pi < jmb.getPdbCount(); pi++)
465 String file = jmb.getPdbEntry(pi).getFile();
468 // todo: extract block as method and pull up (also ChimeraViewFrame)
469 // retrieve the pdb and store it locally
470 AlignmentI pdbseq = null;
471 pdbid = jmb.getPdbEntry(pi).getId();
472 long hdl = pdbid.hashCode() - System.currentTimeMillis();
473 if (progressBar != null)
475 progressBar.setProgressBar(MessageManager
476 .formatMessage("status.fetching_pdb", new String[]
481 pdbseq = pdbclient.getSequenceRecords(pdbid);
482 } catch (OutOfMemoryError oomerror)
484 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
485 } catch (Exception ex)
487 ex.printStackTrace();
488 errormsgs.append("'").append(pdbid).append("'");
491 if (progressBar != null)
493 progressBar.setProgressBar(
494 MessageManager.getString("label.state_completed"),
500 // just transfer the file name from the first sequence's first
502 file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
503 .elementAt(0).getFile()).getAbsolutePath();
504 jmb.getPdbEntry(pi).setFile(file);
509 errormsgs.append("'").append(pdbid).append("' ");
514 if (filesInViewer != null && filesInViewer.length > 0)
516 addingStructures = true; // already files loaded.
517 for (int c = 0; c < filesInViewer.length; c++)
519 if (filesInViewer[c].equals(file))
532 } catch (OutOfMemoryError oomerror)
534 new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
535 } catch (Exception ex)
537 ex.printStackTrace();
538 errormsgs.append("When retrieving pdbfiles : current was: '")
539 .append(pdbid).append("'");
541 if (errormsgs.length() > 0)
543 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
544 MessageManager.formatMessage(
545 "label.pdb_entries_couldnt_be_retrieved", new String[]
546 { errormsgs.toString() }),
547 MessageManager.getString("label.couldnt_load_file"),
548 JvOptionPane.ERROR_MESSAGE);
554 public void eps_actionPerformed(ActionEvent e)
556 makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
560 public void png_actionPerformed(ActionEvent e)
562 makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
565 void makePDBImage(jalview.util.ImageMaker.TYPE type)
567 int width = getWidth();
568 int height = getHeight();
570 jalview.util.ImageMaker im;
572 if (type == jalview.util.ImageMaker.TYPE.PNG)
574 im = new jalview.util.ImageMaker(this,
575 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
576 width, height, null, null, null, 0, false);
578 else if (type == jalview.util.ImageMaker.TYPE.EPS)
580 im = new jalview.util.ImageMaker(this,
581 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
582 width, height, null, this.getTitle(), null, 0, false);
587 im = new jalview.util.ImageMaker(this,
588 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
589 width, height, null, this.getTitle(), null, 0, false);
592 if (im.getGraphics() != null)
594 jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
600 public void showHelp_actionPerformed(ActionEvent actionEvent)
605 .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
606 } catch (Exception ex)
611 public void showConsole(boolean showConsole)
616 if (splitPane == null)
618 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
619 splitPane.setTopComponent(renderPanel);
620 splitPane.setBottomComponent(scriptWindow);
621 this.getContentPane().add(splitPane, BorderLayout.CENTER);
622 splitPane.setDividerLocation(getHeight() - 200);
623 scriptWindow.setVisible(true);
624 scriptWindow.validate();
625 splitPane.validate();
631 if (splitPane != null)
633 splitPane.setVisible(false);
638 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
644 class RenderPanel extends JPanel
646 final Dimension currentSize = new Dimension();
649 public void paintComponent(Graphics g)
651 getSize(currentSize);
653 if (jmb != null && jmb.hasFileLoadingError())
655 g.setColor(Color.black);
656 g.fillRect(0, 0, currentSize.width, currentSize.height);
657 g.setColor(Color.white);
658 g.setFont(new Font("Verdana", Font.BOLD, 14));
659 g.drawString(MessageManager.getString("label.error_loading_file")
660 + "...", 20, currentSize.height / 2);
661 StringBuffer sb = new StringBuffer();
663 for (int e = 0; e < jmb.getPdbCount(); e++)
665 sb.append(jmb.getPdbEntry(e).getId());
666 if (e < jmb.getPdbCount() - 1)
671 if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
674 g.drawString(sb.toString(), 20, currentSize.height / 2
675 - lines * g.getFontMetrics().getHeight());
679 else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
681 g.setColor(Color.black);
682 g.fillRect(0, 0, currentSize.width, currentSize.height);
683 g.setColor(Color.white);
684 g.setFont(new Font("Verdana", Font.BOLD, 14));
685 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
686 20, currentSize.height / 2);
690 jmb.viewer.renderScreenImage(g, currentSize.width,
697 public AAStructureBindingModel getBinding()
703 public String getStateInfo()
705 return jmb == null ? null : jmb.viewer.getStateInfo();
709 public ViewerType getViewerType()
711 return ViewerType.JMOL;
715 protected String getViewerName()