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.util.BrowserLauncher;
30 import jalview.util.MessageManager;
31 import jalview.util.Platform;
32 import jalview.ws.dbsources.Pdb;
34 import java.awt.BorderLayout;
35 import java.awt.Color;
36 import java.awt.Dimension;
38 import java.awt.Graphics;
39 import java.awt.Rectangle;
40 import java.awt.event.ActionEvent;
42 import java.util.ArrayList;
43 import java.util.List;
44 import java.util.Vector;
46 import javax.swing.JCheckBoxMenuItem;
47 import javax.swing.JInternalFrame;
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 BACKSLASH = "\"";
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,
93 Rectangle bounds, String viewid)
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(InternalFrameEvent internalFrameEvent)
141 initJmol(loadStatus); // pdbentry, seq, JBPCHECK!ˇ
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()
166 * add a single PDB structure to a new or existing Jmol view
173 public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
174 final AlignmentPanel ap)
176 progressBar = ap.alignFrame;
177 String pdbId = pdbentry.getId();
180 * If the PDB file is already loaded, the user may just choose to add to an
181 * existing viewer (or cancel)
183 if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
189 * Check if there are other Jmol views involving this alignment and prompt
190 * user about adding this molecule to one of them
192 if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
198 * If the options above are declined or do not apply, open a new viewer
200 openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
203 private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
206 progressBar = ap.alignFrame;
207 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
208 pdbentrys, seqs, null);
209 addAlignmentPanel(ap);
210 useAlignmentPanelForColourbyseq(ap);
212 if (pdbentrys.length > 1)
214 alignAddedStructures = true;
215 useAlignmentPanelForSuperposition(ap);
217 jmb.setColourBySequence(true);
218 setSize(400, 400); // probably should be a configurable/dynamic default here
220 addingStructures = false;
221 worker = new Thread(this);
224 this.addInternalFrameListener(new InternalFrameAdapter()
227 public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
236 * create a new Jmol containing several structures superimposed using the
243 public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
245 openNewJmol(ap, pe, seqs);
249 * Returns a list of any Jmol viewers. The list is restricted to those linked
250 * to the given alignment panel if it is not null.
253 protected List<StructureViewerBase> getViewersFor(AlignmentPanel apanel)
255 List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
256 JInternalFrame[] frames = Desktop.instance.getAllFrames();
258 for (JInternalFrame frame : frames)
260 if (frame instanceof AppJmol)
263 || ((StructureViewerBase) frame).isLinkedWith(apanel))
265 result.add((StructureViewerBase) frame);
272 void initJmol(String command)
274 jmb.setFinishedInit(false);
275 renderPanel = new RenderPanel();
276 // TODO: consider waiting until the structure/view is fully loaded before
278 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
279 jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
280 getBounds().width, getBounds().height);
281 if (scriptWindow == null)
283 BorderLayout bl = new BorderLayout();
286 scriptWindow = new JPanel(bl);
287 scriptWindow.setVisible(false);
290 jmb.allocateViewer(renderPanel, true, "", null, null, "",
292 // jmb.newJmolPopup("Jmol");
297 jmb.evalStateCommand(command);
298 jmb.evalStateCommand("set hoverDelay=0.1");
299 jmb.setFinishedInit(true);
304 boolean allChainsSelected = false;
307 void showSelectedChains()
309 Vector<String> toshow = new Vector<String>();
310 for (int i = 0; i < chainMenu.getItemCount(); i++)
312 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
314 JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
315 if (item.isSelected())
317 toshow.addElement(item.getText());
321 jmb.centerViewer(toshow);
325 public void closeViewer(boolean closeExternalViewer)
327 // Jmol does not use an external viewer
332 setAlignmentPanel(null);
336 // TODO: check for memory leaks where instance isn't finalised because jmb
337 // holds a reference to the window
347 List<String> files = fetchPdbFiles();
348 if (files.size() > 0)
350 showFilesInViewer(files);
360 * Either adds the given files to a structure viewer or opens a new viewer to
364 * list of absolute paths to structure files
366 void showFilesInViewer(List<String> files)
368 long lastnotify = jmb.getLoadNotifiesHandled();
369 StringBuilder fileList = new StringBuilder();
370 for (String s : files)
372 fileList.append(SPACE).append(BACKSLASH)
373 .append(Platform.escapeString(s)).append(BACKSLASH);
375 String filesString = fileList.toString();
377 if (!addingStructures)
381 initJmol("load FILES " + filesString);
382 } catch (OutOfMemoryError oomerror)
384 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
385 Cache.log.debug("File locations are " + filesString);
386 } catch (Exception ex)
388 Cache.log.error("Couldn't open Jmol viewer!", ex);
393 StringBuilder cmd = new StringBuilder();
394 cmd.append("loadingJalviewdata=true\nload APPEND ");
395 cmd.append(filesString);
396 cmd.append("\nloadingJalviewdata=null");
397 final String command = cmd.toString();
398 lastnotify = jmb.getLoadNotifiesHandled();
402 jmb.evalStateCommand(command);
403 } catch (OutOfMemoryError oomerror)
405 new OOMWarning("When trying to add structures to the Jmol viewer!",
407 Cache.log.debug("File locations are " + filesString);
408 } catch (Exception ex)
410 Cache.log.error("Couldn't add files to Jmol viewer!", ex);
414 // need to wait around until script has finished
415 int waitMax = JMOL_LOAD_TIMEOUT;
418 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
419 : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null && jmb
420 .getStructureFiles().length == files.size()))
424 Cache.log.debug("Waiting around for jmb notify.");
425 Thread.sleep(waitFor);
426 waitTotal += waitFor;
427 } catch (Exception e)
430 if (waitTotal > waitMax)
433 .println("Timed out waiting for Jmol to load files after "
435 // System.err.println("finished: " + jmb.isFinishedInit()
436 // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
437 // + "; files: " + files.toString());
438 jmb.getStructureFiles();
443 // refresh the sequence colours for the new structure(s)
444 for (AlignmentPanel ap : _colourwith)
446 jmb.updateColours(ap);
448 // do superposition if asked to
449 if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
451 alignAddedStructures();
453 addingStructures = false;
457 * Queues a thread to align structures with Jalview alignments
459 void alignAddedStructures()
461 javax.swing.SwingUtilities.invokeLater(new Runnable()
466 if (jmb.viewer.isScriptExecuting())
468 SwingUtilities.invokeLater(this);
472 } catch (InterruptedException q)
479 alignStructs_withAllAlignPanels();
483 alignAddedStructures = false;
487 * Retrieves and saves as file any modelled PDB entries for which we do not
488 * already have a file saved. Returns a list of absolute paths to structure
489 * files which were either retrieved, or already stored but not modelled in
490 * the structure viewer (i.e. files to add to the viewer display).
494 List<String> fetchPdbFiles()
496 // todo - record which pdbids were successfully imported.
497 StringBuilder errormsgs = new StringBuilder();
499 List<String> files = new ArrayList<String>();
503 String[] filesInViewer = jmb.getStructureFiles();
504 // TODO: replace with reference fetching/transfer code (validate PDBentry
506 Pdb pdbclient = new Pdb();
507 for (int pi = 0; pi < jmb.getPdbCount(); pi++)
509 String file = jmb.getPdbEntry(pi).getFile();
512 // retrieve the pdb and store it locally
513 AlignmentI pdbseq = null;
514 pdbid = jmb.getPdbEntry(pi).getId();
515 long hdl = pdbid.hashCode() - System.currentTimeMillis();
516 if (progressBar != null)
518 progressBar.setProgressBar(MessageManager.formatMessage(
519 "status.fetching_pdb", new String[] { pdbid }), hdl);
523 pdbseq = pdbclient.getSequenceRecords(pdbid);
524 } catch (OutOfMemoryError oomerror)
526 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
527 } catch (Exception ex)
529 ex.printStackTrace();
530 errormsgs.append("'").append(pdbid).append("'");
533 if (progressBar != null)
535 progressBar.setProgressBar(
536 MessageManager.getString("label.state_completed"),
542 // just transfer the file name from the first sequence's first
544 file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
545 .elementAt(0).getFile()).getAbsolutePath();
546 jmb.getPdbEntry(pi).setFile(file);
551 errormsgs.append("'").append(pdbid).append("' ");
556 if (filesInViewer != null && filesInViewer.length > 0)
558 addingStructures = true; // already files loaded.
559 for (int c = 0; c < filesInViewer.length; c++)
561 if (filesInViewer[c].equals(file))
574 } catch (OutOfMemoryError oomerror)
576 new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
577 } catch (Exception ex)
579 ex.printStackTrace();
580 errormsgs.append("When retrieving pdbfiles : current was: '")
581 .append(pdbid).append("'");
583 if (errormsgs.length() > 0)
585 JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
586 .formatMessage("label.pdb_entries_couldnt_be_retrieved",
587 new String[] { errormsgs.toString() }),
588 MessageManager.getString("label.couldnt_load_file"),
589 JvOptionPane.ERROR_MESSAGE);
595 public void eps_actionPerformed(ActionEvent e)
597 makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
601 public void png_actionPerformed(ActionEvent e)
603 makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
606 void makePDBImage(jalview.util.ImageMaker.TYPE type)
608 int width = getWidth();
609 int height = getHeight();
611 jalview.util.ImageMaker im;
613 if (type == jalview.util.ImageMaker.TYPE.PNG)
615 im = new jalview.util.ImageMaker(this,
616 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
617 width, height, null, null, null, 0, false);
619 else if (type == jalview.util.ImageMaker.TYPE.EPS)
621 im = new jalview.util.ImageMaker(this,
622 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
623 width, height, null, this.getTitle(), null, 0, false);
628 im = new jalview.util.ImageMaker(this,
629 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
630 width, height, null, this.getTitle(), null, 0, false);
633 if (im.getGraphics() != null)
635 jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
641 public void showHelp_actionPerformed(ActionEvent actionEvent)
646 .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
647 } catch (Exception ex)
652 public void showConsole(boolean showConsole)
657 if (splitPane == null)
659 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
660 splitPane.setTopComponent(renderPanel);
661 splitPane.setBottomComponent(scriptWindow);
662 this.getContentPane().add(splitPane, BorderLayout.CENTER);
663 splitPane.setDividerLocation(getHeight() - 200);
664 scriptWindow.setVisible(true);
665 scriptWindow.validate();
666 splitPane.validate();
672 if (splitPane != null)
674 splitPane.setVisible(false);
679 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
685 class RenderPanel extends JPanel
687 final Dimension currentSize = new Dimension();
690 public void paintComponent(Graphics g)
692 getSize(currentSize);
694 if (jmb != null && jmb.hasFileLoadingError())
696 g.setColor(Color.black);
697 g.fillRect(0, 0, currentSize.width, currentSize.height);
698 g.setColor(Color.white);
699 g.setFont(new Font("Verdana", Font.BOLD, 14));
700 g.drawString(MessageManager.getString("label.error_loading_file")
701 + "...", 20, currentSize.height / 2);
702 StringBuffer sb = new StringBuffer();
704 for (int e = 0; e < jmb.getPdbCount(); e++)
706 sb.append(jmb.getPdbEntry(e).getId());
707 if (e < jmb.getPdbCount() - 1)
712 if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
715 g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
716 * g.getFontMetrics().getHeight());
720 else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
722 g.setColor(Color.black);
723 g.fillRect(0, 0, currentSize.width, currentSize.height);
724 g.setColor(Color.white);
725 g.setFont(new Font("Verdana", Font.BOLD, 14));
726 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
727 20, currentSize.height / 2);
731 jmb.viewer.renderScreenImage(g, currentSize.width,
738 public AAStructureBindingModel getBinding()
744 public String getStateInfo()
746 return jmb == null ? null : jmb.viewer.getStateInfo();
750 public ViewerType getViewerType()
752 return ViewerType.JMOL;
756 protected String getViewerName()
762 protected AAStructureBindingModel getBindingModel()