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.
24 import java.awt.event.ActionEvent;
25 import java.awt.event.ActionListener;
26 import java.awt.event.ItemEvent;
28 import java.util.ArrayList;
29 import java.util.Collection;
30 import java.util.HashSet;
31 import java.util.LinkedHashSet;
32 import java.util.List;
33 import java.util.Locale;
34 import java.util.concurrent.Callable;
35 import java.util.concurrent.Executors;
37 import javax.swing.JCheckBox;
38 import javax.swing.JComboBox;
39 import javax.swing.JLabel;
40 import javax.swing.JMenuItem;
41 import javax.swing.JPopupMenu;
42 import javax.swing.JTable;
43 import javax.swing.SwingUtilities;
44 import javax.swing.table.AbstractTableModel;
46 import com.stevesoft.pat.Regex;
48 import jalview.api.structures.JalviewStructureDisplayI;
49 import jalview.bin.Cache;
50 import jalview.bin.Console;
51 import jalview.bin.Jalview;
52 import jalview.datamodel.PDBEntry;
53 import jalview.datamodel.SequenceI;
54 import jalview.ext.jmol.JmolParser;
55 import jalview.fts.api.FTSData;
56 import jalview.fts.api.FTSDataColumnI;
57 import jalview.fts.api.FTSRestClientI;
58 import jalview.fts.core.FTSDataColumnPreferences;
59 import jalview.fts.core.FTSRestRequest;
60 import jalview.fts.core.FTSRestResponse;
61 import jalview.fts.service.pdb.PDBFTSRestClient;
62 import jalview.fts.service.threedbeacons.TDB_FTSData;
63 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
64 import jalview.gui.structurechooser.StructureChooserQuerySource;
65 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
66 import jalview.io.DataSourceType;
67 import jalview.io.FileFormatException;
68 import jalview.io.JalviewFileChooser;
69 import jalview.io.JalviewFileView;
70 import jalview.jbgui.FilterOption;
71 import jalview.jbgui.GStructureChooser;
72 import jalview.structure.StructureImportSettings.TFType;
73 import jalview.structure.StructureMapping;
74 import jalview.structure.StructureSelectionManager;
75 import jalview.util.MessageManager;
76 import jalview.util.Platform;
77 import jalview.util.StringUtils;
78 import jalview.ws.DBRefFetcher;
79 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
80 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
81 import jalview.ws.dbsources.EBIAlfaFold;
82 import jalview.ws.seqfetcher.DbSourceProxy;
83 import jalview.ws.sifts.SiftsSettings;
86 * Provides the behaviors for the Structure chooser Panel
91 @SuppressWarnings("serial")
92 public class StructureChooser extends GStructureChooser
93 implements IProgressIndicator
95 private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
98 * warn user if need to fetch more than this many uniprot records at once
100 private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20;
102 private SequenceI selectedSequence;
104 private SequenceI[] selectedSequences;
106 private IProgressIndicator progressIndicator;
108 private Collection<FTSData> discoveredStructuresSet;
110 private StructureChooserQuerySource data;
113 protected FTSDataColumnPreferences getFTSDocFieldPrefs()
115 return data.getDocFieldPrefs();
118 private String selectedPdbFileName;
120 private TFType localPdbTempfacType;
122 private String localPdbPaeMatrixFileName;
124 private boolean isValidPBDEntry;
126 private boolean cachedPDBExists;
128 private Collection<FTSData> lastDiscoveredStructuresSet;
130 private boolean canQueryTDB = false;
132 private boolean notQueriedTDBYet = true;
134 List<SequenceI> seqsWithoutSourceDBRef = null;
136 private boolean showChooserGUI = true;
138 private static StructureViewer lastTargetedView = null;
140 public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
143 this(selectedSeqs, selectedSeq, ap, true);
146 public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
147 AlignmentPanel ap, boolean showGUI)
149 // which FTS engine to use
150 data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
154 this.selectedSequence = selectedSeq;
155 this.selectedSequences = selectedSeqs;
156 this.progressIndicator = (ap == null) ? null : ap.alignFrame;
157 this.showChooserGUI = showGUI;
163 * sets canQueryTDB if protein sequences without a canonical uniprot ref or at
164 * least one structure are discovered.
166 private void populateSeqsWithoutSourceDBRef()
168 seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
169 boolean needCanonical = false;
170 for (SequenceI seq : selectedSequences)
174 int dbRef = ThreeDBStructureChooserQuerySource
175 .checkUniprotRefs(seq.getDBRefs());
180 // need to retrieve canonicals
181 needCanonical = true;
182 seqsWithoutSourceDBRef.add(seq);
186 // could be a sequence with pdb ref
187 if (seq.getAllPDBEntries() == null
188 || seq.getAllPDBEntries().size() == 0)
190 seqsWithoutSourceDBRef.add(seq);
196 // retrieve database refs for protein sequences
197 if (!seqsWithoutSourceDBRef.isEmpty())
202 // triggers display of the 'Query TDB' button
203 notQueriedTDBYet = true;
209 * Initializes parameters used by the Structure Chooser Panel
211 protected void init()
213 if (!Jalview.isHeadlessMode())
215 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
218 chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
219 btn_queryTDB.addActionListener(new ActionListener()
223 public void actionPerformed(ActionEvent e)
225 promptForTDBFetch(false);
229 Executors.defaultThreadFactory().newThread(new Runnable()
234 populateSeqsWithoutSourceDBRef();
235 initialStructureDiscovery();
243 private void initialStructureDiscovery()
245 // check which FTS engine to use
246 data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences);
248 // ensure a filter option is in force for search
249 populateFilterComboBox(true, cachedPDBExists);
251 // looks for any existing structures already loaded
252 // for the sequences (the cached ones)
253 // then queries the StructureChooserQuerySource to
254 // discover more structures.
256 // Possible optimisation is to only begin querying
257 // the structure chooser if there are no cached structures.
259 long startTime = System.currentTimeMillis();
260 updateProgressIndicator(
261 MessageManager.getString("status.loading_cached_pdb_entries"),
263 loadLocalCachedPDBEntries();
264 updateProgressIndicator(null, startTime);
265 updateProgressIndicator(
266 MessageManager.getString("status.searching_for_pdb_structures"),
268 fetchStructuresMetaData();
269 // revise filter options if no results were found
270 populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
271 discoverStructureViews();
272 updateProgressIndicator(null, startTime);
273 mainFrame.setVisible(showChooserGUI);
278 * raises dialog for Uniprot fetch followed by 3D beacons search
281 * - when true, don't ask, just fetch
283 public void promptForTDBFetch(boolean ignoreGui)
285 final long progressId = System.currentTimeMillis();
287 // final action after prompting and discovering db refs
288 final Runnable strucDiscovery = new Runnable()
293 mainFrame.setEnabled(false);
294 cmb_filterOption.setEnabled(false);
295 progressBar.setProgressBar(
296 MessageManager.getString("status.searching_3d_beacons"),
298 btn_queryTDB.setEnabled(false);
299 // TODO: warn if no accessions discovered
300 populateSeqsWithoutSourceDBRef();
301 // redo initial discovery - this time with 3d beacons
303 previousWantedFields = null;
304 lastSelected = (FilterOption) cmb_filterOption.getSelectedItem();
305 cmb_filterOption.setSelectedItem(null);
306 cachedPDBExists = false; // reset to initial
307 initialStructureDiscovery();
308 if (!isStructuresDiscovered())
310 progressBar.setProgressBar(MessageManager.getString(
311 "status.no_structures_discovered_from_3d_beacons"),
313 btn_queryTDB.setToolTipText(MessageManager.getString(
314 "status.no_structures_discovered_from_3d_beacons"));
315 btn_queryTDB.setEnabled(false);
316 pnl_queryTDB.setVisible(false);
320 cmb_filterOption.setSelectedIndex(0); // select 'best'
321 btn_queryTDB.setVisible(false);
322 pnl_queryTDB.setVisible(false);
323 progressBar.setProgressBar(null, progressId);
325 mainFrame.setEnabled(true);
326 cmb_filterOption.setEnabled(true);
330 final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
334 public void finished()
336 // filter has been selected, so we set flag to remove ourselves
337 notQueriedTDBYet = false;
338 // new thread to discover structures - via 3d beacons
339 Executors.defaultThreadFactory().newThread(strucDiscovery).start();
344 // fetch db refs if OK pressed
345 final Callable discoverCanonicalDBrefs = () -> {
346 btn_queryTDB.setEnabled(false);
347 populateSeqsWithoutSourceDBRef();
349 final int y = seqsWithoutSourceDBRef.size();
352 final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
353 .toArray(new SequenceI[y]);
354 DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
355 progressBar, new DbSourceProxy[]
356 { new jalview.ws.dbsources.Uniprot() }, null, false);
357 dbRefFetcher.addListener(afterDbRefFetch);
358 // ideally this would also gracefully run with callbacks
360 dbRefFetcher.fetchDBRefs(true);
364 // call finished action directly
365 afterDbRefFetch.finished();
369 final Callable revertview = () -> {
370 if (lastSelected != null)
372 cmb_filterOption.setSelectedItem(lastSelected);
376 int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
377 THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
378 Console.debug("Using Uniprot fetch threshold of " + threshold);
379 if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
381 Executors.newSingleThreadExecutor().submit(discoverCanonicalDBrefs);
384 // need cancel and no to result in the discoverPDB action - mocked is
385 // 'cancel' TODO: mock should be OK
387 StructureChooser thisSC = this;
388 JvOptionPane.newOptionDialog(thisSC.getFrame())
389 .setResponseHandler(JvOptionPane.OK_OPTION,
390 discoverCanonicalDBrefs)
391 .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
392 .setResponseHandler(JvOptionPane.NO_OPTION, revertview)
394 MessageManager.formatMessage(
395 "label.fetch_references_for_3dbeacons",
396 seqsWithoutSourceDBRef.size()),
397 MessageManager.getString("label.3dbeacons"),
398 JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
400 { MessageManager.getString("action.ok"),
401 MessageManager.getString("action.cancel") },
402 MessageManager.getString("action.ok"), false);
406 * Builds a drop-down choice list of existing structure viewers to which new
407 * structures may be added. If this list is empty then it, and the 'Add'
408 * button, are hidden.
410 private void discoverStructureViews()
412 if (Desktop.instance != null)
414 targetView.removeAllItems();
415 if (lastTargetedView != null && !lastTargetedView.isVisible())
417 lastTargetedView = null;
419 int linkedViewsAt = 0;
420 for (StructureViewerBase view : Desktop.instance
421 .getStructureViewers(null, null))
423 StructureViewer viewHandler = (lastTargetedView != null
424 && lastTargetedView.sview == view) ? lastTargetedView
425 : StructureViewer.reconfigure(view);
427 if (view.isLinkedWith(ap))
429 targetView.insertItemAt(viewHandler, linkedViewsAt++);
433 targetView.addItem(viewHandler);
438 * show option to Add to viewer if at least 1 viewer found
440 targetView.setVisible(false);
441 if (targetView.getItemCount() > 0)
443 targetView.setVisible(true);
444 if (lastTargetedView != null)
446 targetView.setSelectedItem(lastTargetedView);
450 targetView.setSelectedIndex(0);
453 btn_add.setVisible(targetView.isVisible());
458 * Updates the progress indicator with the specified message
461 * displayed message for the operation
463 * unique handle for this indicator
465 protected void updateProgressIndicator(String message, long id)
467 if (progressIndicator != null)
469 progressIndicator.setProgressBar(message, id);
474 * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
477 void fetchStructuresMetaData()
479 long startTime = System.currentTimeMillis();
480 Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
481 .getStructureSummaryFields();
483 discoveredStructuresSet = new LinkedHashSet<>();
484 HashSet<String> errors = new HashSet<>();
486 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
489 for (SequenceI seq : selectedSequences)
492 FTSRestResponse resultList;
495 resultList = data.fetchStructuresMetaData(seq, wantedFields,
496 selectedFilterOpt, !chk_invertFilter.isSelected());
497 // null response means the FTSengine didn't yield a query for this
498 // consider designing a special exception if we really wanted to be
500 if (resultList == null)
504 } catch (Exception e)
507 errors.add(e.getMessage());
510 if (resultList.getSearchSummary() != null
511 && !resultList.getSearchSummary().isEmpty())
513 discoveredStructuresSet.addAll(resultList.getSearchSummary());
517 int noOfStructuresFound = 0;
518 String totalTime = (System.currentTimeMillis() - startTime)
520 if (discoveredStructuresSet != null
521 && !discoveredStructuresSet.isEmpty())
524 .setModel(data.getTableModel(discoveredStructuresSet));
526 noOfStructuresFound = discoveredStructuresSet.size();
527 lastDiscoveredStructuresSet = discoveredStructuresSet;
528 mainFrame.setTitle(MessageManager.formatMessage(
529 "label.structure_chooser_no_of_structures",
530 noOfStructuresFound, totalTime));
534 mainFrame.setTitle(MessageManager
535 .getString("label.structure_chooser_manual_association"));
536 if (errors.size() > 0)
538 StringBuilder errorMsg = new StringBuilder();
539 for (String error : errors)
541 errorMsg.append(error).append("\n");
543 JvOptionPane.showMessageDialog(this, errorMsg.toString(),
544 MessageManager.getString("label.pdb_web-service_error"),
545 JvOptionPane.ERROR_MESSAGE);
550 protected void loadLocalCachedPDBEntries()
552 ArrayList<CachedPDB> entries = new ArrayList<>();
553 for (SequenceI seq : selectedSequences)
555 if (seq.getDatasetSequence() != null
556 && seq.getDatasetSequence().getAllPDBEntries() != null)
558 for (PDBEntry pdbEntry : seq.getDatasetSequence()
561 if (pdbEntry.getFile() != null)
563 entries.add(new CachedPDB(seq, pdbEntry));
568 cachedPDBExists = !entries.isEmpty();
569 PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
570 tbl_local_pdb.setModel(tableModelx);
574 * Filters a given list of discovered structures based on supplied argument
576 * @param fieldToFilterBy
577 * the field to filter by
579 void filterResultSet(final String fieldToFilterBy)
581 Thread filterThread = new Thread(new Runnable()
587 long startTime = System.currentTimeMillis();
588 lbl_loading.setVisible(true);
589 Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
590 .getStructureSummaryFields();
591 Collection<FTSData> filteredResponse = new HashSet<>();
592 HashSet<String> errors = new HashSet<>();
594 for (SequenceI seq : selectedSequences)
597 FTSRestResponse resultList;
600 resultList = data.selectFirstRankedQuery(seq,
601 discoveredStructuresSet, wantedFields, fieldToFilterBy,
602 !chk_invertFilter.isSelected());
604 } catch (Exception e)
607 errors.add(e.getMessage());
610 if (resultList.getSearchSummary() != null
611 && !resultList.getSearchSummary().isEmpty())
613 filteredResponse.addAll(resultList.getSearchSummary());
617 String totalTime = (System.currentTimeMillis() - startTime)
619 if (!filteredResponse.isEmpty())
621 final int filterResponseCount = filteredResponse.size();
622 Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
623 reorderedStructuresSet.addAll(filteredResponse);
624 reorderedStructuresSet.addAll(discoveredStructuresSet);
626 .setModel(data.getTableModel(reorderedStructuresSet));
628 FTSRestResponse.configureTableColumn(getResultTable(),
629 wantedFields, tempUserPrefs);
630 getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
631 getResultTable().getColumn("Ref Sequence").setMinWidth(100);
632 getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
633 // Update table selection model here
634 getResultTable().addRowSelectionInterval(0,
635 filterResponseCount - 1);
636 mainFrame.setTitle(MessageManager.formatMessage(
637 "label.structure_chooser_filter_time", totalTime));
641 mainFrame.setTitle(MessageManager.formatMessage(
642 "label.structure_chooser_filter_time", totalTime));
643 if (errors.size() > 0)
645 StringBuilder errorMsg = new StringBuilder();
646 for (String error : errors)
648 errorMsg.append(error).append("\n");
650 JvOptionPane.showMessageDialog(null, errorMsg.toString(),
651 MessageManager.getString("label.pdb_web-service_error"),
652 JvOptionPane.ERROR_MESSAGE);
656 lbl_loading.setVisible(false);
658 validateSelections();
661 filterThread.start();
665 * Handles action event for btn_pdbFromFile
668 protected void pdbFromFile_actionPerformed()
670 // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and
673 JalviewFileChooser chooser = new JalviewFileChooser(
674 Cache.getProperty("LAST_DIRECTORY"));
675 chooser.setFileView(new JalviewFileView());
676 chooser.setDialogTitle(
677 MessageManager.formatMessage("label.select_pdb_file_for",
678 selectedSequence.getDisplayId(false)));
679 chooser.setToolTipText(MessageManager.formatMessage(
680 "label.load_pdb_file_associate_with_sequence",
681 selectedSequence.getDisplayId(false)));
683 int value = chooser.showOpenDialog(null);
684 if (value == JalviewFileChooser.APPROVE_OPTION)
686 selectedPdbFileName = chooser.getSelectedFile().getPath();
687 Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
688 boolean guessTFType = localPdbPaeMatrixFileName == null;
689 localPdbPaeMatrixFileName = guessPAEFilename();
690 guessTFType |= localPdbPaeMatrixFileName != null;
691 Regex alphaFold = JmolParser.getNewAlphafoldValidator();
693 && alphaFold.search(new File(selectedPdbFileName).getName())
694 && !tempFacAsChanged)
696 // localPdbPaeMatrixFileName was null and now isn't and filename could
697 // well be AlphaFold and user hasn't adjusted the tempFacType
698 combo_tempFacAs.setSelectedItem(TFType.PLDDT);
700 validateSelections();
705 * Handles action event for btn_paeMatrixFile
708 protected void paeMatrixFile_actionPerformed()
710 File pdbFile = new File(selectedPdbFileName);
711 String setFile = Cache.getProperty("LAST_DIRECTORY");
712 if (localPdbPaeMatrixFileName != null)
714 File paeFile = new File(localPdbPaeMatrixFileName);
715 if (paeFile.exists())
716 setFile = paeFile.getAbsolutePath();
717 else if (paeFile.getParentFile().exists())
718 setFile = paeFile.getParentFile().getAbsolutePath();
722 String guess = guessPAEFilename();
726 JalviewFileChooser chooser = new JalviewFileChooser(setFile);
727 chooser.setFileView(new JalviewFileView());
728 chooser.setDialogTitle(MessageManager.formatMessage(
729 "label.select_pae_matrix_file_for", pdbFile.getName()));
730 chooser.setToolTipText(MessageManager.formatMessage(
731 "label.load_pae_matrix_file_associate_with_structure",
734 // TODO convert to Callable/Promise
735 int value = chooser.showOpenDialog(null);
736 if (value == JalviewFileChooser.APPROVE_OPTION)
738 String fileName = chooser.getSelectedFile().getPath();
741 PAEContactMatrix.validateContactMatrixFile(fileName);
742 } catch (Exception thr)
744 JvOptionPane.showInternalMessageDialog(this, MessageManager
745 .formatMessage("label.couldnt_load_file", new Object[]
746 { fileName }) + "<br>" + thr.getLocalizedMessage(),
747 MessageManager.getString("label.error_loading_file"),
748 JvOptionPane.WARNING_MESSAGE);
749 Console.error("Couldn't import " + fileName + " as a PAE matrix",
753 localPdbPaeMatrixFileName = fileName;
754 Cache.setProperty("LAST_DIRECTORY", localPdbPaeMatrixFileName);
756 validateAssociationFromFile();
759 private String guessPAEFilename()
761 if (selectedPdbFileName.toLowerCase(Locale.ROOT).endsWith(".pdb")
762 || selectedPdbFileName.toLowerCase(Locale.ROOT)
765 String jsonExt = selectedPdbFileName.substring(0,
766 selectedPdbFileName.length() - 4) + ".json";
767 // AlphaFold naming scheme
768 String guessFile1 = StringUtils.replaceLast(jsonExt, "model",
769 "predicted_aligned_error");
770 // nf-core mode naming scheme
771 String guessFile2 = StringUtils.replaceLast(jsonExt, ".json",
773 if (new File(guessFile1).exists())
777 else if (new File(jsonExt).exists())
781 else if (new File(guessFile2).exists())
790 * Populates the filter combo-box options dynamically depending on discovered
793 protected void populateFilterComboBox(boolean haveData,
794 boolean cachedPDBExist)
796 populateFilterComboBox(haveData, cachedPDBExist, null);
800 * Populates the filter combo-box options dynamically depending on discovered
803 protected void populateFilterComboBox(boolean haveData,
804 boolean cachedPDBExist, FilterOption lastSel)
808 * temporarily suspend the change listener behaviour
810 cmb_filterOption.removeItemListener(this);
812 cmb_filterOption.removeAllItems();
815 List<FilterOption> filters = data
816 .getAvailableFilterOptions(VIEWS_FILTER);
817 data.updateAvailableFilterOptions(VIEWS_FILTER, filters,
818 lastDiscoveredStructuresSet);
820 for (FilterOption filter : filters)
822 if (lastSel != null && filter.equals(lastSel))
827 cmb_filterOption.addItem(filter);
831 cmb_filterOption.addItem(
832 new FilterOption(MessageManager.getString("label.enter_pdb_id"),
833 "-", VIEWS_ENTER_ID, false, null));
834 cmb_filterOption.addItem(
835 new FilterOption(MessageManager.getString("label.from_file"),
836 "-", VIEWS_FROM_FILE, false, null));
837 if (canQueryTDB && notQueriedTDBYet)
839 btn_queryTDB.setVisible(true);
840 pnl_queryTDB.setVisible(true);
845 FilterOption cachedOption = new FilterOption(
846 MessageManager.getString("label.cached_structures"), "-",
847 VIEWS_LOCAL_PDB, false, null);
848 cmb_filterOption.addItem(cachedOption);
851 cmb_filterOption.setSelectedItem(cachedOption);
856 cmb_filterOption.setSelectedIndex(selSet);
858 cmb_filterOption.addItemListener(this);
862 * Updates the displayed view based on the selected filter option
864 protected void updateCurrentView()
866 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
869 if (lastSelected == selectedFilterOpt)
871 // don't need to do anything, probably
874 // otherwise, record selection
875 // and update the layout and dialog accordingly
876 lastSelected = selectedFilterOpt;
878 layout_switchableViews.show(pnl_switchableViews,
879 selectedFilterOpt.getView());
880 String filterTitle = mainFrame.getTitle();
881 mainFrame.setTitle(frameTitle);
882 chk_invertFilter.setVisible(false);
884 if (selectedFilterOpt.getView() == VIEWS_FILTER)
886 mainFrame.setTitle(filterTitle);
887 // TDB Query has no invert as yet
888 chk_invertFilter.setVisible(selectedFilterOpt
889 .getQuerySource() instanceof PDBStructureChooserQuerySource);
891 if (data != selectedFilterOpt.getQuerySource()
892 || data.needsRefetch(selectedFilterOpt))
894 data = selectedFilterOpt.getQuerySource();
895 // rebuild the views completely, since prefs will also change
901 filterResultSet(selectedFilterOpt.getValue());
904 else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
905 || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
907 mainFrame.setTitle(MessageManager
908 .getString("label.structure_chooser_manual_association"));
909 idInputAssSeqPanel.loadCmbAssSeq();
910 fileChooserAssSeqPanel.loadCmbAssSeq();
912 validateSelections();
916 * Validates user selection and enables the 'Add' and 'New View' buttons if
917 * all parameters are correct (the Add button will only be visible if there is
918 * at least one existing structure viewer open). This basically means at least
919 * one structure selected and no error messages.
921 * The 'Superpose Structures' option is enabled if either more than one
922 * structure is selected, or the 'Add' to existing view option is enabled, and
923 * disabled if the only option is to open a new view of a single structure.
926 protected void validateSelections()
928 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
930 btn_add.setEnabled(false);
931 String currentView = selectedFilterOpt.getView();
932 int selectedCount = 0;
933 if (currentView == VIEWS_FILTER)
935 selectedCount = getResultTable().getSelectedRows().length;
936 if (selectedCount > 0)
938 btn_add.setEnabled(true);
941 else if (currentView == VIEWS_LOCAL_PDB)
943 selectedCount = tbl_local_pdb.getSelectedRows().length;
944 if (selectedCount > 0)
946 btn_add.setEnabled(true);
949 else if (currentView == VIEWS_ENTER_ID)
951 validateAssociationEnterPdb();
953 else if (currentView == VIEWS_FROM_FILE)
955 validateAssociationFromFile();
958 btn_newView.setEnabled(btn_add.isEnabled());
961 * enable 'Superpose' option if more than one structure is selected,
962 * or there are view(s) available to add structure(s) to
965 .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
969 protected boolean showPopupFor(int selectedRow, int x, int y)
971 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
973 String currentView = selectedFilterOpt.getView();
975 if (currentView == VIEWS_FILTER
976 && data instanceof ThreeDBStructureChooserQuerySource)
979 TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data)
980 .getFTSDataFor(getResultTable(), selectedRow,
981 discoveredStructuresSet);
982 String pageUrl = row.getModelViewUrl();
983 JPopupMenu popup = new JPopupMenu("3D Beacons");
984 JMenuItem viewUrl = new JMenuItem("View model web page");
985 viewUrl.addActionListener(new ActionListener()
988 public void actionPerformed(ActionEvent e)
990 Desktop.showUrl(pageUrl);
994 SwingUtilities.invokeLater(new Runnable()
999 popup.show(getResultTable(), x, y);
1004 // event not handled by us
1009 * Validates inputs from the Manual PDB entry panel
1011 protected void validateAssociationEnterPdb()
1013 AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
1014 .getCmb_assSeq().getSelectedItem();
1015 lbl_pdbManualFetchStatus.setIcon(errorImage);
1016 lbl_pdbManualFetchStatus.setToolTipText("");
1017 if (txt_search.getText().length() > 0)
1019 lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
1020 MessageManager.formatMessage("info.no_pdb_entry_found_for",
1021 txt_search.getText())));
1024 if (errorWarning.length() > 0)
1026 lbl_pdbManualFetchStatus.setIcon(warningImage);
1027 lbl_pdbManualFetchStatus.setToolTipText(
1028 JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
1031 if (selectedSequences.length == 1 || !assSeqOpt.getName()
1032 .equalsIgnoreCase("-Select Associated Seq-"))
1034 txt_search.setEnabled(true);
1035 if (isValidPBDEntry)
1037 btn_add.setEnabled(true);
1038 lbl_pdbManualFetchStatus.setToolTipText("");
1039 lbl_pdbManualFetchStatus.setIcon(goodImage);
1044 txt_search.setEnabled(false);
1045 lbl_pdbManualFetchStatus.setIcon(errorImage);
1050 * Validates inputs for the manual PDB file selection options
1052 protected void validateAssociationFromFile()
1054 AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
1055 .getCmb_assSeq().getSelectedItem();
1056 // lbl_fromFileStatus.setIcon(errorImage);
1057 String pdbFileString = "";
1058 String pdbFileTooltip = "";
1059 if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
1060 .getName().equalsIgnoreCase("-Select Associated Seq-")))
1062 btn_pdbFromFile.setEnabled(true);
1063 if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
1065 btn_add.setEnabled(true);
1066 // lbl_fromFileStatus.setIcon(goodImage);
1067 pdbFileString = new File(selectedPdbFileName).getName();
1068 pdbFileTooltip = new File(selectedPdbFileName).getAbsolutePath();
1069 setPdbOptionsEnabled(true);
1073 pdbFileString = MessageManager.getString("label.none");
1074 pdbFileTooltip = MessageManager.getString("label.nothing_selected");
1075 setPdbOptionsEnabled(false);
1080 btn_pdbFromFile.setEnabled(false);
1081 setPdbOptionsEnabled(false);
1082 // lbl_fromFileStatus.setIcon(errorImage);
1083 pdbFileString = MessageManager.getString("label.none");
1084 pdbFileTooltip = MessageManager.getString("label.nothing_selected");
1086 lbl_pdbFile.setText(pdbFileString);
1087 lbl_pdbFile.setToolTipText(pdbFileTooltip);
1090 String paeFileString = "";
1091 String paeFileTooltip = "";
1092 if (localPdbPaeMatrixFileName != null
1093 && localPdbPaeMatrixFileName.length() > 0)
1095 paeFileString = new File(localPdbPaeMatrixFileName).getName();
1096 paeFileTooltip = new File(localPdbPaeMatrixFileName)
1101 paeFileString = MessageManager.getString("label.none");
1102 paeFileTooltip = MessageManager.getString("label.nothing_selected");
1104 lbl_paeFile.setText(paeFileString);
1105 lbl_paeFile.setToolTipText(paeFileTooltip);
1109 protected void cmbAssSeqStateChanged()
1111 validateSelections();
1114 private FilterOption lastSelected = null;
1117 * Handles the state change event for the 'filter' combo-box and 'invert'
1121 protected void stateChanged(ItemEvent e)
1123 if (e.getSource() instanceof JCheckBox)
1125 updateCurrentView();
1129 if (e.getStateChange() == ItemEvent.SELECTED)
1131 updateCurrentView();
1138 * select structures for viewing by their PDB IDs
1141 * @return true if structures were found and marked as selected
1143 public boolean selectStructure(String... pdbids)
1145 boolean found = false;
1147 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
1148 .getSelectedItem());
1149 String currentView = selectedFilterOpt.getView();
1150 JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
1151 : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
1153 if (restable == null)
1155 // can't select (enter PDB ID, or load file - need to also select which
1156 // sequence to associate with)
1160 int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
1161 for (int r = 0; r < restable.getRowCount(); r++)
1163 for (int p = 0; p < pdbids.length; p++)
1165 if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
1166 .equalsIgnoreCase(pdbids[p]))
1168 restable.setRowSelectionInterval(r, r);
1177 * Handles the 'New View' action
1180 protected void newView_ActionPerformed()
1182 targetView.setSelectedItem(null);
1183 showStructures(false);
1187 * Handles the 'Add to existing viewer' action
1190 protected void add_ActionPerformed()
1192 showStructures(false);
1196 * structure viewer opened by this dialog, or null
1198 private StructureViewer sViewer = null;
1200 public void showStructures(boolean waitUntilFinished)
1203 final StructureSelectionManager ssm = ap.getStructureSelectionManager();
1205 final int preferredHeight = pnl_filter.getHeight();
1206 btn_add.setEnabled(false);
1207 btn_newView.setEnabled(false);
1208 btn_cancel.setEnabled(false);
1209 actionsPanel.setEnabled(false);
1211 final String progress = MessageManager
1212 .getString("label.working_ellipsis");
1213 setProgressBar(progress, progress.hashCode());
1214 Runnable viewStruc = new Runnable()
1219 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
1220 .getSelectedItem());
1221 String currentView = selectedFilterOpt.getView();
1222 JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
1225 if (currentView == VIEWS_FILTER)
1227 int[] selectedRows = restable.getSelectedRows();
1228 PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
1229 List<SequenceI> selectedSeqsToView = new ArrayList<>();
1230 pdbEntriesToView = data.collectSelectedRows(restable,
1231 selectedRows, selectedSeqsToView);
1233 SequenceI[] selectedSeqs = selectedSeqsToView
1234 .toArray(new SequenceI[selectedSeqsToView.size()]);
1235 sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1238 else if (currentView == VIEWS_LOCAL_PDB)
1240 int[] selectedRows = tbl_local_pdb.getSelectedRows();
1241 PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
1243 int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
1245 int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
1247 List<SequenceI> selectedSeqsToView = new ArrayList<>();
1248 for (int row : selectedRows)
1250 PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
1251 .getModel()).getPDBEntryAt(row).getPdbEntry();
1253 pdbEntriesToView[count++] = pdbEntry;
1254 SequenceI selectedSeq = (SequenceI) tbl_local_pdb
1255 .getValueAt(row, refSeqColIndex);
1256 selectedSeqsToView.add(selectedSeq);
1258 SequenceI[] selectedSeqs = selectedSeqsToView
1259 .toArray(new SequenceI[selectedSeqsToView.size()]);
1260 sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1263 else if (currentView == VIEWS_ENTER_ID)
1265 SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
1266 .getCmb_assSeq().getSelectedItem()).getSequence();
1267 if (userSelectedSeq != null)
1269 selectedSequence = userSelectedSeq;
1271 String pdbIdStr = txt_search.getText();
1272 PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
1273 if (pdbEntry == null)
1275 pdbEntry = new PDBEntry();
1276 if (pdbIdStr.split(":").length > 1)
1278 pdbEntry.setId(pdbIdStr.split(":")[0]);
1279 pdbEntry.setChainCode(
1280 pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
1284 pdbEntry.setId(pdbIdStr);
1286 pdbEntry.setType(PDBEntry.Type.PDB);
1287 selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
1290 PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
1291 sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1293 { selectedSequence });
1295 else if (currentView == VIEWS_FROM_FILE)
1297 StructureChooser sc = StructureChooser.this;
1298 TFType tft = (TFType) sc.combo_tempFacAs.getSelectedItem();
1299 String paeFilename = sc.localPdbPaeMatrixFileName;
1300 AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
1301 .getCmb_assSeq().getSelectedItem();
1302 SequenceI userSelectedSeq = assSeqOpt.getSequence();
1303 if (userSelectedSeq != null)
1305 selectedSequence = userSelectedSeq;
1307 String pdbFilename = selectedPdbFileName;
1309 StructureChooser.openStructureFileForSequence(ssm, sc, ap,
1310 selectedSequence, true, pdbFilename, tft, paeFilename);
1312 SwingUtilities.invokeLater(new Runnable()
1317 setProgressBar("Complete.", progress.hashCode());
1318 closeAction(preferredHeight);
1319 mainFrame.dispose();
1324 Thread runner = new Thread(viewStruc);
1326 if (waitUntilFinished)
1328 while (sViewer == null ? runner.isAlive()
1329 : (sViewer.sview == null ? true
1330 : !sViewer.sview.hasMapping()))
1335 } catch (InterruptedException ie)
1344 * Answers a structure viewer (new or existing) configured to superimpose
1345 * added structures or not according to the user's choice
1350 StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)
1352 Object sv = targetView.getSelectedItem();
1354 return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
1358 * Adds PDB structures to a new or existing structure viewer
1361 * @param pdbEntriesToView
1366 private StructureViewer launchStructureViewer(
1367 StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
1368 final AlignmentPanel alignPanel, SequenceI[] sequences)
1370 long progressId = sequences.hashCode();
1371 setProgressBar(MessageManager
1372 .getString("status.launching_3d_structure_viewer"), progressId);
1373 final StructureViewer theViewer = getTargetedStructureViewer(ssm);
1374 boolean superimpose = chk_superpose.isSelected();
1375 theViewer.setSuperpose(superimpose);
1378 * remember user's choice of superimpose or not
1380 Cache.setProperty(AUTOSUPERIMPOSE,
1381 Boolean.valueOf(superimpose).toString());
1383 setProgressBar(null, progressId);
1384 if (SiftsSettings.isMapWithSifts())
1386 List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
1388 // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
1389 // real PDB ID. For moment, we can also safely do this if there is already
1390 // a known mapping between the PDBEntry and the sequence.
1391 for (SequenceI seq : sequences)
1393 PDBEntry pdbe = pdbEntriesToView[p++];
1394 if (pdbe != null && pdbe.getFile() != null)
1396 StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
1397 if (smm != null && smm.length > 0)
1399 for (StructureMapping sm : smm)
1401 if (sm.getSequence() == seq)
1408 if (seq.getPrimaryDBRefs().isEmpty())
1410 seqsWithoutSourceDBRef.add(seq);
1414 if (!seqsWithoutSourceDBRef.isEmpty())
1416 int y = seqsWithoutSourceDBRef.size();
1417 setProgressBar(MessageManager.formatMessage(
1418 "status.fetching_dbrefs_for_sequences_without_valid_refs",
1420 SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
1421 .toArray(new SequenceI[y]);
1422 DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
1423 dbRefFetcher.fetchDBRefs(true);
1425 setProgressBar("Fetch complete.", progressId); // todo i18n
1428 if (pdbEntriesToView.length > 1)
1431 MessageManager.getString(
1432 "status.fetching_3d_structures_for_selected_entries"),
1434 theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
1438 setProgressBar(MessageManager.formatMessage(
1439 "status.fetching_3d_structures_for",
1440 pdbEntriesToView[0].getId()), progressId);
1441 // Can we pass a pre-computeMappinged pdbFile?
1442 theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
1444 setProgressBar(null, progressId);
1445 // remember the last viewer we used...
1446 lastTargetedView = theViewer;
1451 * Populates the combo-box used in associating manually fetched structures to
1452 * a unique sequence when more than one sequence selection is made.
1455 protected void populateCmbAssociateSeqOptions(
1456 JComboBox<AssociateSeqOptions> cmb_assSeq,
1457 JLabel lbl_associateSeq)
1459 cmb_assSeq.removeAllItems();
1461 new AssociateSeqOptions("-Select Associated Seq-", null));
1462 lbl_associateSeq.setVisible(false);
1463 if (selectedSequences.length > 1)
1465 for (SequenceI seq : selectedSequences)
1467 cmb_assSeq.addItem(new AssociateSeqOptions(seq));
1472 String seqName = selectedSequence.getDisplayId(false);
1473 seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
1474 lbl_associateSeq.setText(seqName);
1475 lbl_associateSeq.setVisible(true);
1476 cmb_assSeq.setVisible(false);
1480 protected boolean isStructuresDiscovered()
1482 return discoveredStructuresSet != null
1483 && !discoveredStructuresSet.isEmpty();
1486 protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes
1488 // Doing a search for "1" or "1c" is valuable?
1489 // Those work but are enormously slow.
1492 protected void txt_search_ActionPerformed()
1494 String text = txt_search.getText().trim();
1495 if (text.length() >= PDB_ID_MIN)
1502 errorWarning.setLength(0);
1503 isValidPBDEntry = false;
1504 if (text.length() > 0)
1506 // TODO move this pdb id search into the PDB specific
1508 // for moment, it will work fine as is because it is self-contained
1509 String searchTerm = text.toLowerCase(Locale.ROOT);
1510 searchTerm = searchTerm.split(":")[0];
1511 // System.out.println(">>>>> search term : " + searchTerm);
1512 List<FTSDataColumnI> wantedFields = new ArrayList<>();
1513 FTSRestRequest pdbRequest = new FTSRestRequest();
1514 pdbRequest.setAllowEmptySeq(false);
1515 pdbRequest.setResponseSize(1);
1516 pdbRequest.setFieldToSearchBy("(pdb_id:");
1517 pdbRequest.setWantedFields(wantedFields);
1518 pdbRequest.setSearchTerm(searchTerm + ")");
1519 pdbRequest.setAssociatedSequence(selectedSequence);
1520 FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
1521 wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
1522 FTSRestResponse resultList;
1525 resultList = pdbRestClient.executeRequest(pdbRequest);
1526 } catch (Exception e)
1528 errorWarning.append(e.getMessage());
1532 validateSelections();
1534 if (resultList.getSearchSummary() != null
1535 && resultList.getSearchSummary().size() > 0)
1537 isValidPBDEntry = true;
1540 validateSelections();
1546 protected void tabRefresh()
1548 if (selectedSequences != null)
1550 lbl_loading.setVisible(true);
1551 Thread refreshThread = new Thread(new Runnable()
1556 fetchStructuresMetaData();
1557 // populateFilterComboBox(true, cachedPDBExists);
1560 ((FilterOption) cmb_filterOption.getSelectedItem())
1562 lbl_loading.setVisible(false);
1565 refreshThread.start();
1569 public class PDBEntryTableModel extends AbstractTableModel
1571 String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1574 private List<CachedPDB> pdbEntries;
1576 public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1578 this.pdbEntries = new ArrayList<>(pdbEntries);
1582 public String getColumnName(int columnIndex)
1584 return columns[columnIndex];
1588 public int getRowCount()
1590 return pdbEntries.size();
1594 public int getColumnCount()
1596 return columns.length;
1600 public boolean isCellEditable(int row, int column)
1606 public Object getValueAt(int rowIndex, int columnIndex)
1608 Object value = "??";
1609 CachedPDB entry = pdbEntries.get(rowIndex);
1610 switch (columnIndex)
1613 value = entry.getSequence();
1616 value = entry.getQualifiedId();
1619 value = entry.getPdbEntry().getChainCode() == null ? "_"
1620 : entry.getPdbEntry().getChainCode();
1623 value = entry.getPdbEntry().getType();
1626 value = entry.getPdbEntry().getFile();
1633 public Class<?> getColumnClass(int columnIndex)
1635 return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1638 public CachedPDB getPDBEntryAt(int row)
1640 return pdbEntries.get(row);
1645 private class CachedPDB
1647 private SequenceI sequence;
1649 private PDBEntry pdbEntry;
1651 public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1653 this.sequence = sequence;
1654 this.pdbEntry = pdbEntry;
1657 public String getQualifiedId()
1659 if (pdbEntry.hasProvider())
1661 return pdbEntry.getProvider() + ":" + pdbEntry.getId();
1663 return pdbEntry.toString();
1666 public SequenceI getSequence()
1671 public PDBEntry getPdbEntry()
1678 private IProgressIndicator progressBar;
1681 public void setProgressBar(String message, long id)
1683 if (!Platform.isHeadless())
1684 progressBar.setProgressBar(message, id);
1688 public void registerHandler(long id, IProgressIndicatorHandler handler)
1690 progressBar.registerHandler(id, handler);
1694 public boolean operationInProgress()
1696 return progressBar.operationInProgress();
1699 public JalviewStructureDisplayI getOpenedStructureViewer()
1701 return sViewer == null ? null : sViewer.sview;
1705 protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs)
1707 data.setDocFieldPrefs(newPrefs);
1713 * @return true when all initialisation threads have finished and dialog is
1716 public boolean isDialogVisible()
1718 return mainFrame != null && data != null && cmb_filterOption != null
1719 && mainFrame.isVisible()
1720 && cmb_filterOption.getSelectedItem() != null;
1725 * @return true if the 3D-Beacons query button will/has been displayed
1727 public boolean isCanQueryTDB()
1732 public boolean isNotQueriedTDBYet()
1734 return notQueriedTDBYet;
1738 * Open a single structure file for a given sequence
1740 public static void openStructureFileForSequence(
1741 StructureSelectionManager ssm, StructureChooser sc,
1742 AlignmentPanel ap, SequenceI seq, boolean prompt,
1743 String sFilename, TFType tft, String paeFilename)
1745 boolean headless = false;
1749 sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
1752 ssm = ap.getStructureSelectionManager();
1754 PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
1755 sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance,
1758 StructureViewer sViewer = sc.launchStructureViewer(ssm,
1760 { fileEntry }, ap, new SequenceI[] { seq });
1763 sc.mainFrame.dispose();