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, 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"));
158 IProgressIndicator progressBar = null;
161 * add a single PDB structure to a new or existing Jmol view
168 public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
169 final AlignmentPanel ap)
171 progressBar = ap.alignFrame;
172 String pdbId = pdbentry.getId();
175 * If the PDB file is already loaded, the user may just choose to add to an
176 * existing viewer (or cancel)
178 if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
184 * Check if there are other Jmol views involving this alignment and prompt
185 * user about adding this molecule to one of them
187 if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
193 * If the options above are declined or do not apply, open a new viewer
195 openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
198 private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
201 progressBar = ap.alignFrame;
202 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
203 pdbentrys, seqs, null);
204 addAlignmentPanel(ap);
205 useAlignmentPanelForColourbyseq(ap);
207 if (pdbentrys.length > 1)
209 alignAddedStructures = true;
210 useAlignmentPanelForSuperposition(ap);
212 jmb.setColourBySequence(true);
213 setSize(400, 400); // probably should be a configurable/dynamic default here
215 addingStructures = false;
216 worker = new Thread(this);
219 this.addInternalFrameListener(new InternalFrameAdapter()
222 public void internalFrameClosing(
223 InternalFrameEvent internalFrameEvent)
232 * create a new Jmol containing several structures superimposed using the
239 public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
241 openNewJmol(ap, pe, seqs);
245 * Returns a list of any Jmol viewers. The list is restricted to those linked
246 * to the given alignment panel if it is not null.
249 protected List<StructureViewerBase> getViewersFor(AlignmentPanel apanel)
251 List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
252 JInternalFrame[] frames = Desktop.instance.getAllFrames();
254 for (JInternalFrame frame : frames)
256 if (frame instanceof AppJmol)
259 || ((StructureViewerBase) frame).isLinkedWith(apanel))
261 result.add((StructureViewerBase) frame);
268 void initJmol(String command)
270 jmb.setFinishedInit(false);
271 renderPanel = new RenderPanel();
272 // TODO: consider waiting until the structure/view is fully loaded before
274 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
275 jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
276 getBounds().width, getBounds().height);
277 if (scriptWindow == null)
279 BorderLayout bl = new BorderLayout();
282 scriptWindow = new JPanel(bl);
283 scriptWindow.setVisible(false);
286 jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
288 // jmb.newJmolPopup("Jmol");
293 jmb.evalStateCommand(command);
294 jmb.evalStateCommand("set hoverDelay=0.1");
295 jmb.setFinishedInit(true);
298 boolean allChainsSelected = false;
301 void showSelectedChains()
303 Vector<String> toshow = new Vector<String>();
304 for (int i = 0; i < chainMenu.getItemCount(); i++)
306 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
308 JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
309 if (item.isSelected())
311 toshow.addElement(item.getText());
315 jmb.centerViewer(toshow);
319 public void closeViewer(boolean closeExternalViewer)
321 // Jmol does not use an external viewer
326 setAlignmentPanel(null);
330 // TODO: check for memory leaks where instance isn't finalised because jmb
331 // holds a reference to the window
341 List<String> files = fetchPdbFiles();
342 if (files.size() > 0)
344 showFilesInViewer(files);
354 * Either adds the given files to a structure viewer or opens a new viewer to
358 * list of absolute paths to structure files
360 void showFilesInViewer(List<String> files)
362 long lastnotify = jmb.getLoadNotifiesHandled();
363 StringBuilder fileList = new StringBuilder();
364 for (String s : files)
366 fileList.append(SPACE).append(BACKSLASH)
367 .append(Platform.escapeString(s)).append(BACKSLASH);
369 String filesString = fileList.toString();
371 if (!addingStructures)
375 initJmol("load FILES " + filesString);
376 } catch (OutOfMemoryError oomerror)
378 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
379 Cache.log.debug("File locations are " + filesString);
380 } catch (Exception ex)
382 Cache.log.error("Couldn't open Jmol viewer!", ex);
387 StringBuilder cmd = new StringBuilder();
388 cmd.append("loadingJalviewdata=true\nload APPEND ");
389 cmd.append(filesString);
390 cmd.append("\nloadingJalviewdata=null");
391 final String command = cmd.toString();
392 lastnotify = jmb.getLoadNotifiesHandled();
396 jmb.evalStateCommand(command);
397 } catch (OutOfMemoryError oomerror)
399 new OOMWarning("When trying to add structures to the Jmol viewer!",
401 Cache.log.debug("File locations are " + filesString);
402 } catch (Exception ex)
404 Cache.log.error("Couldn't add files to Jmol viewer!", ex);
408 // need to wait around until script has finished
409 int waitMax = JMOL_LOAD_TIMEOUT;
412 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
413 : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null
414 && jmb.getStructureFiles().length == files.size()))
418 Cache.log.debug("Waiting around for jmb notify.");
419 Thread.sleep(waitFor);
420 waitTotal += waitFor;
421 } catch (Exception e)
424 if (waitTotal > waitMax)
426 System.err.println("Timed out waiting for Jmol to load files after "
428 // System.err.println("finished: " + jmb.isFinishedInit()
429 // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
430 // + "; files: " + files.toString());
431 jmb.getStructureFiles();
436 // refresh the sequence colours for the new structure(s)
437 for (AlignmentPanel ap : _colourwith)
439 jmb.updateColours(ap);
441 // do superposition if asked to
442 if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
444 alignAddedStructures();
446 addingStructures = false;
450 * Queues a thread to align structures with Jalview alignments
452 void alignAddedStructures()
454 javax.swing.SwingUtilities.invokeLater(new Runnable()
459 if (jmb.viewer.isScriptExecuting())
461 SwingUtilities.invokeLater(this);
465 } catch (InterruptedException q)
472 alignStructs_withAllAlignPanels();
476 alignAddedStructures = false;
480 * Retrieves and saves as file any modelled PDB entries for which we do not
481 * already have a file saved. Returns a list of absolute paths to structure
482 * files which were either retrieved, or already stored but not modelled in
483 * the structure viewer (i.e. files to add to the viewer display).
487 List<String> fetchPdbFiles()
489 // todo - record which pdbids were successfully imported.
490 StringBuilder errormsgs = new StringBuilder();
492 List<String> files = new ArrayList<String>();
496 String[] filesInViewer = jmb.getStructureFiles();
497 // TODO: replace with reference fetching/transfer code (validate PDBentry
499 Pdb pdbclient = new Pdb();
500 for (int pi = 0; pi < jmb.getPdbCount(); pi++)
502 String file = jmb.getPdbEntry(pi).getFile();
505 // retrieve the pdb and store it locally
506 AlignmentI pdbseq = null;
507 pdbid = jmb.getPdbEntry(pi).getId();
508 long hdl = pdbid.hashCode() - System.currentTimeMillis();
509 if (progressBar != null)
511 progressBar.setProgressBar(MessageManager
512 .formatMessage("status.fetching_pdb", new String[]
517 pdbseq = pdbclient.getSequenceRecords(pdbid);
518 } catch (OutOfMemoryError oomerror)
520 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
521 } catch (Exception ex)
523 ex.printStackTrace();
524 errormsgs.append("'").append(pdbid).append("'");
527 if (progressBar != null)
529 progressBar.setProgressBar(
530 MessageManager.getString("label.state_completed"),
536 // just transfer the file name from the first sequence's first
538 file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
539 .elementAt(0).getFile()).getAbsolutePath();
540 jmb.getPdbEntry(pi).setFile(file);
545 errormsgs.append("'").append(pdbid).append("' ");
550 if (filesInViewer != null && filesInViewer.length > 0)
552 addingStructures = true; // already files loaded.
553 for (int c = 0; c < filesInViewer.length; c++)
555 if (filesInViewer[c].equals(file))
568 } catch (OutOfMemoryError oomerror)
570 new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
571 } catch (Exception ex)
573 ex.printStackTrace();
574 errormsgs.append("When retrieving pdbfiles : current was: '")
575 .append(pdbid).append("'");
577 if (errormsgs.length() > 0)
579 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
580 MessageManager.formatMessage(
581 "label.pdb_entries_couldnt_be_retrieved", new String[]
582 { errormsgs.toString() }),
583 MessageManager.getString("label.couldnt_load_file"),
584 JvOptionPane.ERROR_MESSAGE);
590 public void eps_actionPerformed(ActionEvent e)
592 makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
596 public void png_actionPerformed(ActionEvent e)
598 makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
601 void makePDBImage(jalview.util.ImageMaker.TYPE type)
603 int width = getWidth();
604 int height = getHeight();
606 jalview.util.ImageMaker im;
608 if (type == jalview.util.ImageMaker.TYPE.PNG)
610 im = new jalview.util.ImageMaker(this,
611 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
612 width, height, null, null, null, 0, false);
614 else if (type == jalview.util.ImageMaker.TYPE.EPS)
616 im = new jalview.util.ImageMaker(this,
617 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
618 width, height, null, this.getTitle(), null, 0, false);
623 im = new jalview.util.ImageMaker(this,
624 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
625 width, height, null, this.getTitle(), null, 0, false);
628 if (im.getGraphics() != null)
630 jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
636 public void showHelp_actionPerformed(ActionEvent actionEvent)
641 .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
642 } catch (Exception ex)
647 public void showConsole(boolean showConsole)
652 if (splitPane == null)
654 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
655 splitPane.setTopComponent(renderPanel);
656 splitPane.setBottomComponent(scriptWindow);
657 this.getContentPane().add(splitPane, BorderLayout.CENTER);
658 splitPane.setDividerLocation(getHeight() - 200);
659 scriptWindow.setVisible(true);
660 scriptWindow.validate();
661 splitPane.validate();
667 if (splitPane != null)
669 splitPane.setVisible(false);
674 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
680 class RenderPanel extends JPanel
682 final Dimension currentSize = new Dimension();
685 public void paintComponent(Graphics g)
687 getSize(currentSize);
689 if (jmb != null && jmb.hasFileLoadingError())
691 g.setColor(Color.black);
692 g.fillRect(0, 0, currentSize.width, currentSize.height);
693 g.setColor(Color.white);
694 g.setFont(new Font("Verdana", Font.BOLD, 14));
695 g.drawString(MessageManager.getString("label.error_loading_file")
696 + "...", 20, currentSize.height / 2);
697 StringBuffer sb = new StringBuffer();
699 for (int e = 0; e < jmb.getPdbCount(); e++)
701 sb.append(jmb.getPdbEntry(e).getId());
702 if (e < jmb.getPdbCount() - 1)
707 if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
710 g.drawString(sb.toString(), 20, currentSize.height / 2
711 - lines * g.getFontMetrics().getHeight());
715 else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
717 g.setColor(Color.black);
718 g.fillRect(0, 0, currentSize.width, currentSize.height);
719 g.setColor(Color.white);
720 g.setFont(new Font("Verdana", Font.BOLD, 14));
721 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
722 20, currentSize.height / 2);
726 jmb.viewer.renderScreenImage(g, currentSize.width,
733 public AAStructureBindingModel getBinding()
739 public String getStateInfo()
741 return jmb == null ? null : jmb.viewer.getStateInfo();
745 public ViewerType getViewerType()
747 return ViewerType.JMOL;
751 protected String getViewerName()