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.api.AlignmentViewPanel;
24 import jalview.api.FeatureRenderer;
25 import jalview.bin.Cache;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.PDBEntry;
28 import jalview.datamodel.SequenceI;
29 import jalview.ext.rbvi.chimera.ChimeraCommands;
30 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
31 import jalview.gui.StructureViewer.ViewerType;
32 import jalview.io.DataSourceType;
33 import jalview.io.StructureFile;
34 import jalview.structures.models.AAStructureBindingModel;
35 import jalview.util.BrowserLauncher;
36 import jalview.util.MessageManager;
37 import jalview.util.Platform;
38 import jalview.ws.dbsources.Pdb;
40 import java.awt.event.ActionEvent;
41 import java.awt.event.ActionListener;
42 import java.awt.event.MouseAdapter;
43 import java.awt.event.MouseEvent;
45 import java.io.FileInputStream;
46 import java.io.IOException;
47 import java.io.InputStream;
48 import java.util.ArrayList;
49 import java.util.Collections;
50 import java.util.List;
51 import java.util.Random;
53 import javax.swing.JInternalFrame;
54 import javax.swing.JMenu;
55 import javax.swing.JMenuItem;
56 import javax.swing.event.InternalFrameAdapter;
57 import javax.swing.event.InternalFrameEvent;
60 * GUI elements for handling an external chimera display
65 public class ChimeraViewFrame extends StructureViewerBase
67 private JalviewChimeraBinding jmb;
69 private IProgressIndicator progressBar = null;
72 * Path to Chimera session file. This is set when an open Jalview/Chimera
73 * session is saved, or on restore from a Jalview project (if it holds the
74 * filename of any saved Chimera sessions).
76 private String chimeraSessionFile = null;
78 private Random random = new Random();
80 private int myWidth = 500;
82 private int myHeight = 150;
85 * Initialise menu options.
88 protected void initMenus()
92 viewerActionMenu.setText(MessageManager.getString("label.chimera"));
95 .setText(MessageManager.getString("label.colour_with_chimera"));
96 viewerColour.setToolTipText(MessageManager
97 .getString("label.let_chimera_manage_structure_colours"));
99 helpItem.setText(MessageManager.getString("label.chimera_help"));
100 savemenu.setVisible(false); // not yet implemented
101 viewMenu.add(fitToWindow);
103 JMenuItem writeFeatures = new JMenuItem(
104 MessageManager.getString("label.create_chimera_attributes"));
105 writeFeatures.setToolTipText(MessageManager
106 .getString("label.create_chimera_attributes_tip"));
107 writeFeatures.addActionListener(new ActionListener()
110 public void actionPerformed(ActionEvent e)
112 sendFeaturesToChimera();
115 viewerActionMenu.add(writeFeatures);
117 final JMenu fetchAttributes = new JMenu(
118 MessageManager.getString("label.fetch_chimera_attributes"));
119 fetchAttributes.setToolTipText(
120 MessageManager.getString("label.fetch_chimera_attributes_tip"));
121 fetchAttributes.addMouseListener(new MouseAdapter()
125 public void mouseEntered(MouseEvent e)
127 buildAttributesMenu(fetchAttributes);
130 viewerActionMenu.add(fetchAttributes);
134 * Query Chimera for its residue attribute names and add them as items off the
137 * @param attributesMenu
139 protected void buildAttributesMenu(JMenu attributesMenu)
141 List<String> atts = jmb.sendChimeraCommand("list resattr", true);
146 attributesMenu.removeAll();
147 Collections.sort(atts);
148 for (String att : atts)
150 final String attName = att.split(" ")[1];
153 * ignore 'jv_*' attributes, as these are Jalview features that have
154 * been transferred to residue attributes in Chimera!
156 if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
158 JMenuItem menuItem = new JMenuItem(attName);
159 menuItem.addActionListener(new ActionListener()
162 public void actionPerformed(ActionEvent e)
164 getChimeraAttributes(attName);
167 attributesMenu.add(menuItem);
173 * Read residues in Chimera with the given attribute name, and set as features
174 * on the corresponding sequence positions (if any)
178 protected void getChimeraAttributes(String attName)
180 jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel());
184 * Send a command to Chimera to create residue attributes for Jalview features
186 * The syntax is: setattr r <attName> <attValue> <atomSpec>
188 * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A
190 protected void sendFeaturesToChimera()
192 int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
194 MessageManager.formatMessage("label.attributes_set", count));
198 * open a single PDB structure in a new Chimera view
205 public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
206 String[] chains, final AlignmentPanel ap)
210 openNewChimera(ap, new PDBEntry[] { pdbentry },
216 * Create a helper to manage progress bar display
218 protected void createProgressBar()
220 if (progressBar == null)
222 progressBar = new ProgressBar(statusPanel, statusBar);
226 private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys,
230 jmb = new JalviewChimeraBindingModel(this,
231 ap.getStructureSelectionManager(), pdbentrys, seqs, null);
232 addAlignmentPanel(ap);
233 useAlignmentPanelForColourbyseq(ap);
235 if (pdbentrys.length > 1)
237 useAlignmentPanelForSuperposition(ap);
239 jmb.setColourBySequence(true);
240 setSize(myWidth, myHeight);
243 addingStructures = false;
244 worker = new Thread(this);
247 this.addInternalFrameListener(new InternalFrameAdapter()
250 public void internalFrameClosing(
251 InternalFrameEvent internalFrameEvent)
260 * Create a new viewer from saved session state data including Chimera session
263 * @param chimeraSessionFile
267 * @param colourByChimera
268 * @param colourBySequence
271 public ChimeraViewFrame(String chimeraSessionFile,
272 AlignmentPanel alignPanel, PDBEntry[] pdbArray,
273 SequenceI[][] seqsArray, boolean colourByChimera,
274 boolean colourBySequence, String newViewId)
277 setViewId(newViewId);
278 this.chimeraSessionFile = chimeraSessionFile;
279 openNewChimera(alignPanel, pdbArray, seqsArray);
282 jmb.setColourBySequence(false);
283 seqColour.setSelected(false);
284 viewerColour.setSelected(true);
286 else if (colourBySequence)
288 jmb.setColourBySequence(true);
289 seqColour.setSelected(true);
290 viewerColour.setSelected(false);
295 * create a new viewer containing several structures, optionally superimposed
296 * using the given alignPanel.
302 public ChimeraViewFrame(PDBEntry[] pe, boolean alignAdded,
307 setAlignAddedStructures(alignAdded);
308 openNewChimera(ap, pe, seqs);
312 * Default constructor
314 public ChimeraViewFrame()
319 * closeViewer will decide whether or not to close this frame
320 * depending on whether user chooses to Cancel or not
322 setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
326 * Launch Chimera. If we have a chimera session file name, send Chimera the
327 * command to open its saved session file.
331 jmb.setFinishedInit(false);
332 Desktop.addInternalFrame(this,
333 jmb.getViewerTitle(getViewerName(), true), getBounds().width,
336 if (!jmb.launchChimera())
338 JvOptionPane.showMessageDialog(Desktop.desktop,
339 MessageManager.getString("label.chimera_failed"),
340 MessageManager.getString("label.error_loading_file"),
341 JvOptionPane.ERROR_MESSAGE);
346 if (this.chimeraSessionFile != null)
348 boolean opened = jmb.openSession(chimeraSessionFile);
351 System.err.println("An error occurred opening Chimera session file "
352 + chimeraSessionFile);
356 jmb.startChimeraListener();
360 * Close down this instance of Jalview's Chimera viewer, giving the user the
361 * option to close the associated Chimera window (process). They may wish to
362 * keep it open until they have had an opportunity to save any work.
364 * @param closeChimera
365 * if true, close any linked Chimera process; if false, prompt first
368 public void closeViewer(boolean closeChimera)
370 if (jmb != null && jmb.isChimeraRunning())
374 String prompt = MessageManager
375 .formatMessage("label.confirm_close_chimera", new Object[]
376 { jmb.getViewerTitle(getViewerName(), false) });
377 prompt = JvSwingUtils.wrapTooltip(true, prompt);
378 int confirm = JvOptionPane.showConfirmDialog(this, prompt,
379 MessageManager.getString("label.close_viewer"),
380 JvOptionPane.YES_NO_CANCEL_OPTION);
382 * abort closure if user hits escape or Cancel
384 if (confirm == JvOptionPane.CANCEL_OPTION
385 || confirm == JvOptionPane.CLOSED_OPTION)
389 closeChimera = confirm == JvOptionPane.YES_OPTION;
391 jmb.closeViewer(closeChimera);
393 setAlignmentPanel(null);
397 // TODO: check for memory leaks where instance isn't finalised because jmb
398 // holds a reference to the window
404 * Open any newly added PDB structures in Chimera, having first fetched data
405 * from PDB (if not already saved).
411 // todo - record which pdbids were successfully imported.
412 StringBuilder errormsgs = new StringBuilder(128);
413 StringBuilder files = new StringBuilder(128);
414 List<PDBEntry> filePDB = new ArrayList<>();
415 List<Integer> filePDBpos = new ArrayList<>();
416 PDBEntry thePdbEntry = null;
417 StructureFile pdb = null;
420 String[] curfiles = jmb.getStructureFiles(); // files currently in viewer
421 // TODO: replace with reference fetching/transfer code (validate PDBentry
423 for (int pi = 0; pi < jmb.getPdbCount(); pi++)
426 thePdbEntry = jmb.getPdbEntry(pi);
427 if (thePdbEntry.getFile() == null)
430 * Retrieve PDB data, save to file, attach to PDBEntry
432 file = fetchPdbFile(thePdbEntry);
435 errormsgs.append("'" + thePdbEntry.getId() + "' ");
441 * Got file already - ignore if already loaded in Chimera.
443 file = new File(thePdbEntry.getFile()).getAbsoluteFile()
445 if (curfiles != null && curfiles.length > 0)
447 addingStructures = true; // already files loaded.
448 for (int c = 0; c < curfiles.length; c++)
450 if (curfiles[c].equals(file))
460 filePDB.add(thePdbEntry);
461 filePDBpos.add(Integer.valueOf(pi));
462 files.append(" \"" + Platform.escapeBackslashes(file) + "\"");
465 } catch (OutOfMemoryError oomerror)
467 new OOMWarning("Retrieving PDB files: " + thePdbEntry.getId(),
469 } catch (Exception ex)
471 ex.printStackTrace();
473 "When retrieving pdbfiles for '" + thePdbEntry.getId() + "'");
475 if (errormsgs.length() > 0)
478 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
479 MessageManager.formatMessage(
480 "label.pdb_entries_couldnt_be_retrieved", new Object[]
481 { errormsgs.toString() }),
482 MessageManager.getString("label.couldnt_load_file"),
483 JvOptionPane.ERROR_MESSAGE);
486 if (files.length() > 0)
488 jmb.setFinishedInit(false);
489 if (!addingStructures)
494 } catch (Exception ex)
496 Cache.log.error("Couldn't open Chimera viewer!", ex);
500 for (PDBEntry pe : filePDB)
503 if (pe.getFile() != null)
507 int pos = filePDBpos.get(num).intValue();
508 long startTime = startProgressBar(getViewerName() + " "
509 + MessageManager.getString("status.opening_file_for")
512 jmb.addSequence(pos, jmb.getSequence()[pos]);
513 File fl = new File(pe.getFile());
514 DataSourceType protocol = DataSourceType.URL;
519 protocol = DataSourceType.FILE;
521 } catch (Throwable e)
525 stopProgressBar("", startTime);
527 // Explicitly map to the filename used by Chimera ;
529 pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
530 jmb.getChains()[pos], pe.getFile(), protocol,
532 stashFoundChains(pdb, pe.getFile());
534 } catch (OutOfMemoryError oomerror)
537 "When trying to open and map structures from Chimera!",
539 } catch (Exception ex)
542 "Couldn't open " + pe.getFile() + " in Chimera viewer!",
546 Cache.log.debug("File locations are " + files);
552 jmb.setFinishedInit(true);
553 jmb.setLoadingFromArchive(false);
556 * ensure that any newly discovered features (e.g. RESNUM)
557 * are added to any open feature settings dialog
559 FeatureRenderer fr = getBinding().getFeatureRenderer(null);
565 // refresh the sequence colours for the new structure(s)
566 for (AlignmentViewPanel avp : _colourwith)
568 jmb.updateColours(avp);
570 // do superposition if asked to
571 if (alignAddedStructures)
573 new Thread(new Runnable()
578 alignStructs_withAllAlignPanels();
582 addingStructures = false;
589 * Fetch PDB data and save to a local file. Returns the full path to the file,
590 * or null if fetch fails. TODO: refactor to common with Jmol ? duplication
592 * @param processingEntry
597 private void stashFoundChains(StructureFile pdb, String file)
599 for (int i = 0; i < pdb.getChains().size(); i++)
601 String chid = new String(
602 pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
603 jmb.getChainNames().add(chid);
604 jmb.getChainFile().put(chid, file);
608 private String fetchPdbFile(PDBEntry processingEntry) throws Exception
610 String filePath = null;
611 Pdb pdbclient = new Pdb();
612 AlignmentI pdbseq = null;
613 String pdbid = processingEntry.getId();
614 long handle = System.currentTimeMillis()
615 + Thread.currentThread().hashCode();
618 * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
620 String msg = MessageManager.formatMessage("status.fetching_pdb",
623 getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
624 // long hdl = startProgressBar(MessageManager.formatMessage(
625 // "status.fetching_pdb", new Object[]
629 pdbseq = pdbclient.getSequenceRecords(pdbid);
630 } catch (OutOfMemoryError oomerror)
632 new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
635 msg = pdbid + " " + MessageManager.getString("label.state_completed");
636 getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
637 // stopProgressBar(msg, hdl);
640 * If PDB data were saved and are not invalid (empty alignment), return the
643 if (pdbseq != null && pdbseq.getHeight() > 0)
645 // just use the file name from the first sequence's first PDBEntry
646 filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
647 .elementAt(0).getFile()).getAbsolutePath();
648 processingEntry.setFile(filePath);
654 * Convenience method to update the progress bar if there is one. Be sure to
655 * call stopProgressBar with the returned handle to remove the message.
660 public long startProgressBar(String msg)
662 // TODO would rather have startProgress/stopProgress as the
663 // IProgressIndicator interface
664 long tm = random.nextLong();
665 if (progressBar != null)
667 progressBar.setProgressBar(msg, tm);
673 * End the progress bar with the specified handle, leaving a message (if not
674 * null) on the status bar
679 public void stopProgressBar(String msg, long handle)
681 if (progressBar != null)
683 progressBar.setProgressBar(msg, handle);
688 public void eps_actionPerformed(ActionEvent e)
690 throw new Error(MessageManager
691 .getString("error.eps_generation_not_implemented"));
695 public void png_actionPerformed(ActionEvent e)
697 throw new Error(MessageManager
698 .getString("error.png_generation_not_implemented"));
702 public void showHelp_actionPerformed(ActionEvent actionEvent)
707 .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
708 } catch (IOException ex)
714 public AAStructureBindingModel getBinding()
720 * Ask Chimera to save its session to the designated file path, or to a
721 * temporary file if the path is null. Returns the file path if successful,
727 protected String saveSession(String filepath)
729 String pathUsed = filepath;
732 if (pathUsed == null)
734 File tempFile = File.createTempFile("chimera", ".py");
735 tempFile.deleteOnExit();
736 pathUsed = tempFile.getPath();
738 boolean result = jmb.saveSession(pathUsed);
741 this.chimeraSessionFile = pathUsed;
744 } catch (IOException e)
751 * Returns a string representing the state of the Chimera session. This is
752 * done by requesting Chimera to save its session to a temporary file, then
753 * reading the file contents. Returns an empty string on any error.
756 public String getStateInfo()
758 String sessionFile = saveSession(null);
759 if (sessionFile == null)
763 InputStream is = null;
766 File f = new File(sessionFile);
767 byte[] bytes = new byte[(int) f.length()];
768 is = new FileInputStream(sessionFile);
770 return new String(bytes);
771 } catch (IOException e)
781 } catch (IOException e)
790 protected void fitToWindow_actionPerformed()
796 public ViewerType getViewerType()
798 return ViewerType.CHIMERA;
802 protected String getViewerName()
808 * Sends commands to align structures according to associated alignment(s).
813 protected String alignStructs_withAllAlignPanels()
815 String reply = super.alignStructs_withAllAlignPanels();
817 reply == null ? " " : "Superposition failed: " + reply);
822 protected IProgressIndicator getIProgressIndicator()