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.JPanel;
48 import javax.swing.JSplitPane;
49 import javax.swing.SwingUtilities;
50 import javax.swing.event.InternalFrameAdapter;
51 import javax.swing.event.InternalFrameEvent;
53 public class AppJmol extends StructureViewerBase
55 // ms to wait for Jmol to load files
56 private static final int JMOL_LOAD_TIMEOUT = 20000;
58 private static final String SPACE = " ";
60 private static final String QUOTE = "\"";
68 RenderPanel renderPanel;
77 * - add the alignment panel to the list used for colouring these
80 * - add the alignment panel to the list used for aligning these
82 * @param leaveColouringToJmol
83 * - do not update the colours from any other source. Jmol is
89 public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
90 AlignmentPanel ap, boolean usetoColour, boolean useToAlign,
91 boolean leaveColouringToJmol, String loadStatus, Rectangle bounds,
94 PDBEntry[] pdbentrys = new PDBEntry[files.length];
95 for (int i = 0; i < pdbentrys.length; i++)
97 // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
98 PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB,
100 pdbentrys[i] = pdbentry;
102 // / TODO: check if protocol is needed to be set, and if chains are
104 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
105 pdbentrys, seqs, null);
107 jmb.setLoadingFromArchive(true);
108 addAlignmentPanel(ap);
111 useAlignmentPanelForSuperposition(ap);
114 if (leaveColouringToJmol || !usetoColour)
116 jmb.setColourBySequence(false);
117 seqColour.setSelected(false);
118 viewerColour.setSelected(true);
120 else if (usetoColour)
122 useAlignmentPanelForColourbyseq(ap);
123 jmb.setColourBySequence(true);
124 seqColour.setSelected(true);
125 viewerColour.setSelected(false);
127 this.setBounds(bounds);
129 // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
130 // bounds.width,bounds.height);
132 this.addInternalFrameListener(new InternalFrameAdapter()
135 public void internalFrameClosing(
136 InternalFrameEvent internalFrameEvent)
141 initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
145 protected void initMenus()
149 viewerActionMenu.setText(MessageManager.getString("label.jmol"));
152 .setText(MessageManager.getString("label.colour_with_jmol"));
153 viewerColour.setToolTipText(MessageManager
154 .getString("label.let_jmol_manage_structure_colours"));
157 IProgressIndicator progressBar = null;
160 protected IProgressIndicator getIProgressIndicator()
166 * display a single PDB structure in a new Jmol view
173 public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
174 final AlignmentPanel ap)
176 progressBar = ap.alignFrame;
178 openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
183 private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
184 PDBEntry[] pdbentrys,
187 progressBar = ap.alignFrame;
188 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
189 pdbentrys, seqs, null);
190 addAlignmentPanel(ap);
191 useAlignmentPanelForColourbyseq(ap);
193 alignAddedStructures = alignAdded;
194 useAlignmentPanelForSuperposition(ap);
196 jmb.setColourBySequence(true);
197 setSize(400, 400); // probably should be a configurable/dynamic default here
199 addingStructures = false;
200 worker = new Thread(this);
203 this.addInternalFrameListener(new InternalFrameAdapter()
206 public void internalFrameClosing(
207 InternalFrameEvent internalFrameEvent)
216 * create a new Jmol containing several structures optionally superimposed
217 * using the given alignPanel.
221 * - true to superimpose
225 public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
228 openNewJmol(ap, alignAdded, pe, seqs);
232 void initJmol(String command)
234 jmb.setFinishedInit(false);
235 renderPanel = new RenderPanel();
236 // TODO: consider waiting until the structure/view is fully loaded before
238 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
239 jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
240 getBounds().width, getBounds().height);
241 if (scriptWindow == null)
243 BorderLayout bl = new BorderLayout();
246 scriptWindow = new JPanel(bl);
247 scriptWindow.setVisible(false);
250 jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
252 // jmb.newJmolPopup("Jmol");
257 jmb.evalStateCommand(command);
258 jmb.evalStateCommand("set hoverDelay=0.1");
259 jmb.setFinishedInit(true);
263 void showSelectedChains()
265 Vector<String> toshow = new Vector<>();
266 for (int i = 0; i < chainMenu.getItemCount(); i++)
268 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
270 JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
271 if (item.isSelected())
273 toshow.addElement(item.getText());
277 jmb.centerViewer(toshow);
281 public void closeViewer(boolean closeExternalViewer)
283 // Jmol does not use an external viewer
288 setAlignmentPanel(null);
292 // TODO: check for memory leaks where instance isn't finalised because jmb
293 // holds a reference to the window
303 List<String> files = fetchPdbFiles();
304 if (files.size() > 0)
306 showFilesInViewer(files);
316 * Either adds the given files to a structure viewer or opens a new viewer to
320 * list of absolute paths to structure files
322 void showFilesInViewer(List<String> files)
324 long lastnotify = jmb.getLoadNotifiesHandled();
325 StringBuilder fileList = new StringBuilder();
326 for (String s : files)
328 fileList.append(SPACE).append(QUOTE)
329 .append(Platform.escapeBackslashes(s)).append(QUOTE);
331 String filesString = fileList.toString();
333 if (!addingStructures)
337 initJmol("load FILES " + filesString);
338 } catch (OutOfMemoryError oomerror)
340 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
341 Cache.log.debug("File locations are " + filesString);
342 } catch (Exception ex)
344 Cache.log.error("Couldn't open Jmol viewer!", ex);
349 StringBuilder cmd = new StringBuilder();
350 cmd.append("loadingJalviewdata=true\nload APPEND ");
351 cmd.append(filesString);
352 cmd.append("\nloadingJalviewdata=null");
353 final String command = cmd.toString();
354 lastnotify = jmb.getLoadNotifiesHandled();
358 jmb.evalStateCommand(command);
359 } catch (OutOfMemoryError oomerror)
361 new OOMWarning("When trying to add structures to the Jmol viewer!",
363 Cache.log.debug("File locations are " + filesString);
364 } catch (Exception ex)
366 Cache.log.error("Couldn't add files to Jmol viewer!", ex);
370 // need to wait around until script has finished
371 int waitMax = JMOL_LOAD_TIMEOUT;
374 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
375 : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null
376 && jmb.getStructureFiles().length == files.size()))
380 Cache.log.debug("Waiting around for jmb notify.");
381 Thread.sleep(waitFor);
382 waitTotal += waitFor;
383 } catch (Exception e)
386 if (waitTotal > waitMax)
388 System.err.println("Timed out waiting for Jmol to load files after "
390 // System.err.println("finished: " + jmb.isFinishedInit()
391 // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
392 // + "; files: " + files.toString());
393 jmb.getStructureFiles();
398 // refresh the sequence colours for the new structure(s)
399 for (AlignmentPanel ap : _colourwith)
401 jmb.updateColours(ap);
403 // do superposition if asked to
404 if (alignAddedStructures)
406 alignAddedStructures();
408 addingStructures = false;
412 * Queues a thread to align structures with Jalview alignments
414 void alignAddedStructures()
416 javax.swing.SwingUtilities.invokeLater(new Runnable()
421 if (jmb.viewer.isScriptExecuting())
423 SwingUtilities.invokeLater(this);
427 } catch (InterruptedException q)
434 alignStructs_withAllAlignPanels();
442 * Retrieves and saves as file any modelled PDB entries for which we do not
443 * already have a file saved. Returns a list of absolute paths to structure
444 * files which were either retrieved, or already stored but not modelled in
445 * the structure viewer (i.e. files to add to the viewer display).
449 List<String> fetchPdbFiles()
451 // todo - record which pdbids were successfully imported.
452 StringBuilder errormsgs = new StringBuilder();
454 List<String> files = new ArrayList<>();
458 String[] filesInViewer = jmb.getStructureFiles();
459 // TODO: replace with reference fetching/transfer code (validate PDBentry
461 Pdb pdbclient = new Pdb();
462 for (int pi = 0; pi < jmb.getPdbCount(); pi++)
464 String file = jmb.getPdbEntry(pi).getFile();
467 // todo: extract block as method and pull up (also ChimeraViewFrame)
468 // retrieve the pdb and store it locally
469 AlignmentI pdbseq = null;
470 pdbid = jmb.getPdbEntry(pi).getId();
471 long hdl = pdbid.hashCode() - System.currentTimeMillis();
472 if (progressBar != null)
474 progressBar.setProgressBar(MessageManager
475 .formatMessage("status.fetching_pdb", new String[]
480 pdbseq = pdbclient.getSequenceRecords(pdbid);
481 } catch (OutOfMemoryError oomerror)
483 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
484 } catch (Exception ex)
486 ex.printStackTrace();
487 errormsgs.append("'").append(pdbid).append("'");
490 if (progressBar != null)
492 progressBar.setProgressBar(
493 MessageManager.getString("label.state_completed"),
499 // just transfer the file name from the first sequence's first
501 file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
502 .elementAt(0).getFile()).getAbsolutePath();
503 jmb.getPdbEntry(pi).setFile(file);
508 errormsgs.append("'").append(pdbid).append("' ");
513 if (filesInViewer != null && filesInViewer.length > 0)
515 addingStructures = true; // already files loaded.
516 for (int c = 0; c < filesInViewer.length; c++)
518 if (Platform.pathEquals(filesInViewer[c], file))
531 } catch (OutOfMemoryError oomerror)
533 new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
534 } catch (Exception ex)
536 ex.printStackTrace();
537 errormsgs.append("When retrieving pdbfiles : current was: '")
538 .append(pdbid).append("'");
540 if (errormsgs.length() > 0)
542 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
543 MessageManager.formatMessage(
544 "label.pdb_entries_couldnt_be_retrieved", new String[]
545 { errormsgs.toString() }),
546 MessageManager.getString("label.couldnt_load_file"),
547 JvOptionPane.ERROR_MESSAGE);
553 public void eps_actionPerformed(ActionEvent e)
555 makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
559 public void png_actionPerformed(ActionEvent e)
561 makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
564 void makePDBImage(jalview.util.ImageMaker.TYPE type)
566 int width = getWidth();
567 int height = getHeight();
569 jalview.util.ImageMaker im;
571 if (type == jalview.util.ImageMaker.TYPE.PNG)
573 im = new jalview.util.ImageMaker(this,
574 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
575 width, height, null, null, null, 0, false);
577 else if (type == jalview.util.ImageMaker.TYPE.EPS)
579 im = new jalview.util.ImageMaker(this,
580 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
581 width, height, null, this.getTitle(), null, 0, false);
586 im = new jalview.util.ImageMaker(this,
587 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
588 width, height, null, this.getTitle(), null, 0, false);
591 if (im.getGraphics() != null)
593 jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
599 public void showHelp_actionPerformed(ActionEvent actionEvent)
604 .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
605 } catch (Exception ex)
610 public void showConsole(boolean showConsole)
615 if (splitPane == null)
617 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
618 splitPane.setTopComponent(renderPanel);
619 splitPane.setBottomComponent(scriptWindow);
620 this.getContentPane().add(splitPane, BorderLayout.CENTER);
621 splitPane.setDividerLocation(getHeight() - 200);
622 scriptWindow.setVisible(true);
623 scriptWindow.validate();
624 splitPane.validate();
630 if (splitPane != null)
632 splitPane.setVisible(false);
637 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
643 class RenderPanel extends JPanel
645 final Dimension currentSize = new Dimension();
648 public void paintComponent(Graphics g)
650 getSize(currentSize);
652 if (jmb != null && jmb.hasFileLoadingError())
654 g.setColor(Color.black);
655 g.fillRect(0, 0, currentSize.width, currentSize.height);
656 g.setColor(Color.white);
657 g.setFont(new Font("Verdana", Font.BOLD, 14));
658 g.drawString(MessageManager.getString("label.error_loading_file")
659 + "...", 20, currentSize.height / 2);
660 StringBuffer sb = new StringBuffer();
662 for (int e = 0; e < jmb.getPdbCount(); e++)
664 sb.append(jmb.getPdbEntry(e).getId());
665 if (e < jmb.getPdbCount() - 1)
670 if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
673 g.drawString(sb.toString(), 20, currentSize.height / 2
674 - lines * g.getFontMetrics().getHeight());
678 else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
680 g.setColor(Color.black);
681 g.fillRect(0, 0, currentSize.width, currentSize.height);
682 g.setColor(Color.white);
683 g.setFont(new Font("Verdana", Font.BOLD, 14));
684 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
685 20, currentSize.height / 2);
689 jmb.viewer.renderScreenImage(g, currentSize.width,
696 public AAStructureBindingModel getBinding()
702 public String getStateInfo()
704 return jmb == null ? null : jmb.viewer.getStateInfo();
708 public ViewerType getViewerType()
710 return ViewerType.JMOL;
714 protected String getViewerName()