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 jalview.api.structures.JalviewStructureDisplayI;
47 import jalview.bin.Cache;
48 import jalview.bin.Console;
49 import jalview.bin.Jalview;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.SequenceI;
52 import jalview.fts.api.FTSData;
53 import jalview.fts.api.FTSDataColumnI;
54 import jalview.fts.api.FTSRestClientI;
55 import jalview.fts.core.FTSDataColumnPreferences;
56 import jalview.fts.core.FTSRestRequest;
57 import jalview.fts.core.FTSRestResponse;
58 import jalview.fts.service.pdb.PDBFTSRestClient;
59 import jalview.fts.service.threedbeacons.TDB_FTSData;
60 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
61 import jalview.gui.structurechooser.StructureChooserQuerySource;
62 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
63 import jalview.io.DataSourceType;
64 import jalview.io.JalviewFileChooser;
65 import jalview.io.JalviewFileView;
66 import jalview.jbgui.FilterOption;
67 import jalview.jbgui.GStructureChooser;
68 import jalview.structure.StructureImportSettings.TFType;
69 import jalview.structure.StructureMapping;
70 import jalview.structure.StructureSelectionManager;
71 import jalview.util.MessageManager;
72 import jalview.util.Platform;
73 import jalview.util.StringUtils;
74 import jalview.ws.DBRefFetcher;
75 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
76 import jalview.ws.seqfetcher.DbSourceProxy;
77 import jalview.ws.sifts.SiftsSettings;
80 * Provides the behaviors for the Structure chooser Panel
85 @SuppressWarnings("serial")
86 public class StructureChooser extends GStructureChooser
87 implements IProgressIndicator
89 private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
92 * warn user if need to fetch more than this many uniprot records at once
94 private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20;
96 private SequenceI selectedSequence;
98 private SequenceI[] selectedSequences;
100 private IProgressIndicator progressIndicator;
102 private Collection<FTSData> discoveredStructuresSet;
104 private StructureChooserQuerySource data;
107 protected FTSDataColumnPreferences getFTSDocFieldPrefs()
109 return data.getDocFieldPrefs();
112 private String selectedPdbFileName;
114 private TFType localPdbTempfacType;
116 private String localPdbPaeMatrixFileName;
118 private boolean isValidPBDEntry;
120 private boolean cachedPDBExists;
122 private Collection<FTSData> lastDiscoveredStructuresSet;
124 private boolean canQueryTDB = false;
126 private boolean notQueriedTDBYet = true;
128 List<SequenceI> seqsWithoutSourceDBRef = null;
130 private boolean showChooserGUI = true;
132 private static StructureViewer lastTargetedView = null;
134 public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
137 this(selectedSeqs, selectedSeq, ap, true);
140 public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
141 AlignmentPanel ap, boolean showGUI)
143 // which FTS engine to use
144 data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
148 this.selectedSequence = selectedSeq;
149 this.selectedSequences = selectedSeqs;
150 this.progressIndicator = (ap == null) ? null : ap.alignFrame;
151 this.showChooserGUI = showGUI;
157 * sets canQueryTDB if protein sequences without a canonical uniprot ref or at
158 * least one structure are discovered.
160 private void populateSeqsWithoutSourceDBRef()
162 seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
163 boolean needCanonical = false;
164 for (SequenceI seq : selectedSequences)
168 int dbRef = ThreeDBStructureChooserQuerySource
169 .checkUniprotRefs(seq.getDBRefs());
174 // need to retrieve canonicals
175 needCanonical = true;
176 seqsWithoutSourceDBRef.add(seq);
180 // could be a sequence with pdb ref
181 if (seq.getAllPDBEntries() == null
182 || seq.getAllPDBEntries().size() == 0)
184 seqsWithoutSourceDBRef.add(seq);
190 // retrieve database refs for protein sequences
191 if (!seqsWithoutSourceDBRef.isEmpty())
196 // triggers display of the 'Query TDB' button
197 notQueriedTDBYet = true;
203 * Initializes parameters used by the Structure Chooser Panel
205 protected void init()
207 if (!Jalview.isHeadlessMode())
209 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
212 chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
213 btn_queryTDB.addActionListener(new ActionListener()
217 public void actionPerformed(ActionEvent e)
219 promptForTDBFetch(false);
223 Executors.defaultThreadFactory().newThread(new Runnable()
228 populateSeqsWithoutSourceDBRef();
229 initialStructureDiscovery();
237 private void initialStructureDiscovery()
239 // check which FTS engine to use
240 data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences);
242 // ensure a filter option is in force for search
243 populateFilterComboBox(true, cachedPDBExists);
245 // looks for any existing structures already loaded
246 // for the sequences (the cached ones)
247 // then queries the StructureChooserQuerySource to
248 // discover more structures.
250 // Possible optimisation is to only begin querying
251 // the structure chooser if there are no cached structures.
253 long startTime = System.currentTimeMillis();
254 updateProgressIndicator(
255 MessageManager.getString("status.loading_cached_pdb_entries"),
257 loadLocalCachedPDBEntries();
258 updateProgressIndicator(null, startTime);
259 updateProgressIndicator(
260 MessageManager.getString("status.searching_for_pdb_structures"),
262 fetchStructuresMetaData();
263 // revise filter options if no results were found
264 populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
265 discoverStructureViews();
266 updateProgressIndicator(null, startTime);
267 mainFrame.setVisible(showChooserGUI);
272 * raises dialog for Uniprot fetch followed by 3D beacons search
275 * - when true, don't ask, just fetch
277 public void promptForTDBFetch(boolean ignoreGui)
279 final long progressId = System.currentTimeMillis();
281 // final action after prompting and discovering db refs
282 final Runnable strucDiscovery = new Runnable()
287 mainFrame.setEnabled(false);
288 cmb_filterOption.setEnabled(false);
289 progressBar.setProgressBar(
290 MessageManager.getString("status.searching_3d_beacons"),
292 btn_queryTDB.setEnabled(false);
293 // TODO: warn if no accessions discovered
294 populateSeqsWithoutSourceDBRef();
295 // redo initial discovery - this time with 3d beacons
297 previousWantedFields = null;
298 lastSelected = (FilterOption) cmb_filterOption.getSelectedItem();
299 cmb_filterOption.setSelectedItem(null);
300 cachedPDBExists = false; // reset to initial
301 initialStructureDiscovery();
302 if (!isStructuresDiscovered())
304 progressBar.setProgressBar(MessageManager.getString(
305 "status.no_structures_discovered_from_3d_beacons"),
307 btn_queryTDB.setToolTipText(MessageManager.getString(
308 "status.no_structures_discovered_from_3d_beacons"));
309 btn_queryTDB.setEnabled(false);
310 pnl_queryTDB.setVisible(false);
314 cmb_filterOption.setSelectedIndex(0); // select 'best'
315 btn_queryTDB.setVisible(false);
316 pnl_queryTDB.setVisible(false);
317 progressBar.setProgressBar(null, progressId);
319 mainFrame.setEnabled(true);
320 cmb_filterOption.setEnabled(true);
324 final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
328 public void finished()
330 // filter has been selected, so we set flag to remove ourselves
331 notQueriedTDBYet = false;
332 // new thread to discover structures - via 3d beacons
333 Executors.defaultThreadFactory().newThread(strucDiscovery).start();
338 // fetch db refs if OK pressed
339 final Callable discoverCanonicalDBrefs = () -> {
340 btn_queryTDB.setEnabled(false);
341 populateSeqsWithoutSourceDBRef();
343 final int y = seqsWithoutSourceDBRef.size();
346 final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
347 .toArray(new SequenceI[y]);
348 DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
349 progressBar, new DbSourceProxy[]
350 { new jalview.ws.dbsources.Uniprot() }, null, false);
351 dbRefFetcher.addListener(afterDbRefFetch);
352 // ideally this would also gracefully run with callbacks
354 dbRefFetcher.fetchDBRefs(true);
358 // call finished action directly
359 afterDbRefFetch.finished();
363 final Callable revertview = () -> {
364 if (lastSelected != null)
366 cmb_filterOption.setSelectedItem(lastSelected);
370 int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
371 THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
372 Console.debug("Using Uniprot fetch threshold of " + threshold);
373 if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
375 Executors.newSingleThreadExecutor().submit(discoverCanonicalDBrefs);
378 // need cancel and no to result in the discoverPDB action - mocked is
379 // 'cancel' TODO: mock should be OK
381 StructureChooser thisSC = this;
382 JvOptionPane.newOptionDialog(thisSC.getFrame())
383 .setResponseHandler(JvOptionPane.OK_OPTION,
384 discoverCanonicalDBrefs)
385 .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
386 .setResponseHandler(JvOptionPane.NO_OPTION, revertview)
388 MessageManager.formatMessage(
389 "label.fetch_references_for_3dbeacons",
390 seqsWithoutSourceDBRef.size()),
391 MessageManager.getString("label.3dbeacons"),
392 JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
394 { MessageManager.getString("action.ok"),
395 MessageManager.getString("action.cancel") },
396 MessageManager.getString("action.ok"), false);
400 * Builds a drop-down choice list of existing structure viewers to which new
401 * structures may be added. If this list is empty then it, and the 'Add'
402 * button, are hidden.
404 private void discoverStructureViews()
406 if (Desktop.instance != null)
408 targetView.removeAllItems();
409 if (lastTargetedView != null && !lastTargetedView.isVisible())
411 lastTargetedView = null;
413 int linkedViewsAt = 0;
414 for (StructureViewerBase view : Desktop.instance
415 .getStructureViewers(null, null))
417 StructureViewer viewHandler = (lastTargetedView != null
418 && lastTargetedView.sview == view) ? lastTargetedView
419 : StructureViewer.reconfigure(view);
421 if (view.isLinkedWith(ap))
423 targetView.insertItemAt(viewHandler, linkedViewsAt++);
427 targetView.addItem(viewHandler);
432 * show option to Add to viewer if at least 1 viewer found
434 targetView.setVisible(false);
435 if (targetView.getItemCount() > 0)
437 targetView.setVisible(true);
438 if (lastTargetedView != null)
440 targetView.setSelectedItem(lastTargetedView);
444 targetView.setSelectedIndex(0);
447 btn_add.setVisible(targetView.isVisible());
452 * Updates the progress indicator with the specified message
455 * displayed message for the operation
457 * unique handle for this indicator
459 protected void updateProgressIndicator(String message, long id)
461 if (progressIndicator != null)
463 progressIndicator.setProgressBar(message, id);
468 * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
471 void fetchStructuresMetaData()
473 long startTime = System.currentTimeMillis();
474 Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
475 .getStructureSummaryFields();
477 discoveredStructuresSet = new LinkedHashSet<>();
478 HashSet<String> errors = new HashSet<>();
480 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
483 for (SequenceI seq : selectedSequences)
486 FTSRestResponse resultList;
489 resultList = data.fetchStructuresMetaData(seq, wantedFields,
490 selectedFilterOpt, !chk_invertFilter.isSelected());
491 // null response means the FTSengine didn't yield a query for this
492 // consider designing a special exception if we really wanted to be
494 if (resultList == null)
498 } catch (Exception e)
501 errors.add(e.getMessage());
504 if (resultList.getSearchSummary() != null
505 && !resultList.getSearchSummary().isEmpty())
507 discoveredStructuresSet.addAll(resultList.getSearchSummary());
511 int noOfStructuresFound = 0;
512 String totalTime = (System.currentTimeMillis() - startTime)
514 if (discoveredStructuresSet != null
515 && !discoveredStructuresSet.isEmpty())
518 .setModel(data.getTableModel(discoveredStructuresSet));
520 noOfStructuresFound = discoveredStructuresSet.size();
521 lastDiscoveredStructuresSet = discoveredStructuresSet;
522 mainFrame.setTitle(MessageManager.formatMessage(
523 "label.structure_chooser_no_of_structures",
524 noOfStructuresFound, totalTime));
528 mainFrame.setTitle(MessageManager
529 .getString("label.structure_chooser_manual_association"));
530 if (errors.size() > 0)
532 StringBuilder errorMsg = new StringBuilder();
533 for (String error : errors)
535 errorMsg.append(error).append("\n");
537 JvOptionPane.showMessageDialog(this, errorMsg.toString(),
538 MessageManager.getString("label.pdb_web-service_error"),
539 JvOptionPane.ERROR_MESSAGE);
544 protected void loadLocalCachedPDBEntries()
546 ArrayList<CachedPDB> entries = new ArrayList<>();
547 for (SequenceI seq : selectedSequences)
549 if (seq.getDatasetSequence() != null
550 && seq.getDatasetSequence().getAllPDBEntries() != null)
552 for (PDBEntry pdbEntry : seq.getDatasetSequence()
555 if (pdbEntry.getFile() != null)
557 entries.add(new CachedPDB(seq, pdbEntry));
562 cachedPDBExists = !entries.isEmpty();
563 PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
564 tbl_local_pdb.setModel(tableModelx);
568 * Filters a given list of discovered structures based on supplied argument
570 * @param fieldToFilterBy
571 * the field to filter by
573 void filterResultSet(final String fieldToFilterBy)
575 Thread filterThread = new Thread(new Runnable()
581 long startTime = System.currentTimeMillis();
582 lbl_loading.setVisible(true);
583 Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
584 .getStructureSummaryFields();
585 Collection<FTSData> filteredResponse = new HashSet<>();
586 HashSet<String> errors = new HashSet<>();
588 for (SequenceI seq : selectedSequences)
591 FTSRestResponse resultList;
594 resultList = data.selectFirstRankedQuery(seq,
595 discoveredStructuresSet, wantedFields, fieldToFilterBy,
596 !chk_invertFilter.isSelected());
598 } catch (Exception e)
601 errors.add(e.getMessage());
604 if (resultList.getSearchSummary() != null
605 && !resultList.getSearchSummary().isEmpty())
607 filteredResponse.addAll(resultList.getSearchSummary());
611 String totalTime = (System.currentTimeMillis() - startTime)
613 if (!filteredResponse.isEmpty())
615 final int filterResponseCount = filteredResponse.size();
616 Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
617 reorderedStructuresSet.addAll(filteredResponse);
618 reorderedStructuresSet.addAll(discoveredStructuresSet);
620 .setModel(data.getTableModel(reorderedStructuresSet));
622 FTSRestResponse.configureTableColumn(getResultTable(),
623 wantedFields, tempUserPrefs);
624 getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
625 getResultTable().getColumn("Ref Sequence").setMinWidth(100);
626 getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
627 // Update table selection model here
628 getResultTable().addRowSelectionInterval(0,
629 filterResponseCount - 1);
630 mainFrame.setTitle(MessageManager.formatMessage(
631 "label.structure_chooser_filter_time", totalTime));
635 mainFrame.setTitle(MessageManager.formatMessage(
636 "label.structure_chooser_filter_time", totalTime));
637 if (errors.size() > 0)
639 StringBuilder errorMsg = new StringBuilder();
640 for (String error : errors)
642 errorMsg.append(error).append("\n");
644 JvOptionPane.showMessageDialog(null, errorMsg.toString(),
645 MessageManager.getString("label.pdb_web-service_error"),
646 JvOptionPane.ERROR_MESSAGE);
650 lbl_loading.setVisible(false);
652 validateSelections();
655 filterThread.start();
659 * Handles action event for btn_pdbFromFile
662 protected void pdbFromFile_actionPerformed()
664 // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and
667 JalviewFileChooser chooser = new JalviewFileChooser(
668 Cache.getProperty("LAST_DIRECTORY"));
669 chooser.setFileView(new JalviewFileView());
670 chooser.setDialogTitle(
671 MessageManager.formatMessage("label.select_pdb_file_for",
672 selectedSequence.getDisplayId(false)));
673 chooser.setToolTipText(MessageManager.formatMessage(
674 "label.load_pdb_file_associate_with_sequence",
675 selectedSequence.getDisplayId(false)));
677 int value = chooser.showOpenDialog(null);
678 if (value == JalviewFileChooser.APPROVE_OPTION)
680 selectedPdbFileName = chooser.getSelectedFile().getPath();
681 Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
682 localPdbPaeMatrixFileName = guessPAEFilename();
683 validateSelections();
688 * Handles action event for btn_pdbFromFile
691 protected void paeMatrixFile_actionPerformed()
693 File pdbFile = new File(selectedPdbFileName);
694 String setFile = Cache.getProperty("LAST_DIRECTORY");
695 if (localPdbPaeMatrixFileName != null)
697 File paeFile = new File(localPdbPaeMatrixFileName);
698 if (paeFile.exists())
699 setFile = paeFile.getAbsolutePath();
700 else if (paeFile.getParentFile().exists())
701 setFile = paeFile.getParentFile().getAbsolutePath();
705 String guess = guessPAEFilename();
709 JalviewFileChooser chooser = new JalviewFileChooser(setFile);
710 chooser.setFileView(new JalviewFileView());
711 chooser.setDialogTitle(MessageManager.formatMessage(
712 "label.select_pae_matrix_file_for", pdbFile.getName()));
713 chooser.setToolTipText(MessageManager.formatMessage(
714 "label.load_pae_matrix_file_associate_with_structure",
717 int value = chooser.showOpenDialog(null);
718 if (value == JalviewFileChooser.APPROVE_OPTION)
720 localPdbPaeMatrixFileName = chooser.getSelectedFile().getPath();
721 Cache.setProperty("LAST_DIRECTORY", localPdbPaeMatrixFileName);
723 validateAssociationFromFile();
726 private String guessPAEFilename()
728 if (selectedPdbFileName.toLowerCase(Locale.ROOT).endsWith(".pdb")
729 || selectedPdbFileName.toLowerCase(Locale.ROOT)
732 String jsonExt = selectedPdbFileName.substring(0,
733 selectedPdbFileName.length() - 4) + ".json";
734 // AlphaFold naming scheme
735 String guessFile1 = StringUtils.replaceLast(jsonExt, "model",
736 "predicted_aligned_error");
737 // nf-core mode naming scheme
738 String guessFile2 = StringUtils.replaceLast(jsonExt, ".json",
740 if (new File(guessFile1).exists())
744 else if (new File(jsonExt).exists())
748 else if (new File(guessFile2).exists())
757 * Populates the filter combo-box options dynamically depending on discovered
760 protected void populateFilterComboBox(boolean haveData,
761 boolean cachedPDBExist)
763 populateFilterComboBox(haveData, cachedPDBExist, null);
767 * Populates the filter combo-box options dynamically depending on discovered
770 protected void populateFilterComboBox(boolean haveData,
771 boolean cachedPDBExist, FilterOption lastSel)
775 * temporarily suspend the change listener behaviour
777 cmb_filterOption.removeItemListener(this);
779 cmb_filterOption.removeAllItems();
782 List<FilterOption> filters = data
783 .getAvailableFilterOptions(VIEWS_FILTER);
784 data.updateAvailableFilterOptions(VIEWS_FILTER, filters,
785 lastDiscoveredStructuresSet);
787 for (FilterOption filter : filters)
789 if (lastSel != null && filter.equals(lastSel))
794 cmb_filterOption.addItem(filter);
798 cmb_filterOption.addItem(
799 new FilterOption(MessageManager.getString("label.enter_pdb_id"),
800 "-", VIEWS_ENTER_ID, false, null));
801 cmb_filterOption.addItem(
802 new FilterOption(MessageManager.getString("label.from_file"),
803 "-", VIEWS_FROM_FILE, false, null));
804 if (canQueryTDB && notQueriedTDBYet)
806 btn_queryTDB.setVisible(true);
807 pnl_queryTDB.setVisible(true);
812 FilterOption cachedOption = new FilterOption(
813 MessageManager.getString("label.cached_structures"), "-",
814 VIEWS_LOCAL_PDB, false, null);
815 cmb_filterOption.addItem(cachedOption);
818 cmb_filterOption.setSelectedItem(cachedOption);
823 cmb_filterOption.setSelectedIndex(selSet);
825 cmb_filterOption.addItemListener(this);
829 * Updates the displayed view based on the selected filter option
831 protected void updateCurrentView()
833 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
836 if (lastSelected == selectedFilterOpt)
838 // don't need to do anything, probably
841 // otherwise, record selection
842 // and update the layout and dialog accordingly
843 lastSelected = selectedFilterOpt;
845 layout_switchableViews.show(pnl_switchableViews,
846 selectedFilterOpt.getView());
847 String filterTitle = mainFrame.getTitle();
848 mainFrame.setTitle(frameTitle);
849 chk_invertFilter.setVisible(false);
851 if (selectedFilterOpt.getView() == VIEWS_FILTER)
853 mainFrame.setTitle(filterTitle);
854 // TDB Query has no invert as yet
855 chk_invertFilter.setVisible(selectedFilterOpt
856 .getQuerySource() instanceof PDBStructureChooserQuerySource);
858 if (data != selectedFilterOpt.getQuerySource()
859 || data.needsRefetch(selectedFilterOpt))
861 data = selectedFilterOpt.getQuerySource();
862 // rebuild the views completely, since prefs will also change
868 filterResultSet(selectedFilterOpt.getValue());
871 else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
872 || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
874 mainFrame.setTitle(MessageManager
875 .getString("label.structure_chooser_manual_association"));
876 idInputAssSeqPanel.loadCmbAssSeq();
877 fileChooserAssSeqPanel.loadCmbAssSeq();
879 validateSelections();
883 * Validates user selection and enables the 'Add' and 'New View' buttons if
884 * all parameters are correct (the Add button will only be visible if there is
885 * at least one existing structure viewer open). This basically means at least
886 * one structure selected and no error messages.
888 * The 'Superpose Structures' option is enabled if either more than one
889 * structure is selected, or the 'Add' to existing view option is enabled, and
890 * disabled if the only option is to open a new view of a single structure.
893 protected void validateSelections()
895 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
897 btn_add.setEnabled(false);
898 String currentView = selectedFilterOpt.getView();
899 int selectedCount = 0;
900 if (currentView == VIEWS_FILTER)
902 selectedCount = getResultTable().getSelectedRows().length;
903 if (selectedCount > 0)
905 btn_add.setEnabled(true);
908 else if (currentView == VIEWS_LOCAL_PDB)
910 selectedCount = tbl_local_pdb.getSelectedRows().length;
911 if (selectedCount > 0)
913 btn_add.setEnabled(true);
916 else if (currentView == VIEWS_ENTER_ID)
918 validateAssociationEnterPdb();
920 else if (currentView == VIEWS_FROM_FILE)
922 validateAssociationFromFile();
925 btn_newView.setEnabled(btn_add.isEnabled());
928 * enable 'Superpose' option if more than one structure is selected,
929 * or there are view(s) available to add structure(s) to
932 .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
936 protected boolean showPopupFor(int selectedRow, int x, int y)
938 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
940 String currentView = selectedFilterOpt.getView();
942 if (currentView == VIEWS_FILTER
943 && data instanceof ThreeDBStructureChooserQuerySource)
946 TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data)
947 .getFTSDataFor(getResultTable(), selectedRow,
948 discoveredStructuresSet);
949 String pageUrl = row.getModelViewUrl();
950 JPopupMenu popup = new JPopupMenu("3D Beacons");
951 JMenuItem viewUrl = new JMenuItem("View model web page");
952 viewUrl.addActionListener(new ActionListener()
955 public void actionPerformed(ActionEvent e)
957 Desktop.showUrl(pageUrl);
961 SwingUtilities.invokeLater(new Runnable()
966 popup.show(getResultTable(), x, y);
971 // event not handled by us
976 * Validates inputs from the Manual PDB entry panel
978 protected void validateAssociationEnterPdb()
980 AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
981 .getCmb_assSeq().getSelectedItem();
982 lbl_pdbManualFetchStatus.setIcon(errorImage);
983 lbl_pdbManualFetchStatus.setToolTipText("");
984 if (txt_search.getText().length() > 0)
986 lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
987 MessageManager.formatMessage("info.no_pdb_entry_found_for",
988 txt_search.getText())));
991 if (errorWarning.length() > 0)
993 lbl_pdbManualFetchStatus.setIcon(warningImage);
994 lbl_pdbManualFetchStatus.setToolTipText(
995 JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
998 if (selectedSequences.length == 1 || !assSeqOpt.getName()
999 .equalsIgnoreCase("-Select Associated Seq-"))
1001 txt_search.setEnabled(true);
1002 if (isValidPBDEntry)
1004 btn_add.setEnabled(true);
1005 lbl_pdbManualFetchStatus.setToolTipText("");
1006 lbl_pdbManualFetchStatus.setIcon(goodImage);
1011 txt_search.setEnabled(false);
1012 lbl_pdbManualFetchStatus.setIcon(errorImage);
1017 * Validates inputs for the manual PDB file selection options
1019 protected void validateAssociationFromFile()
1021 AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
1022 .getCmb_assSeq().getSelectedItem();
1023 // lbl_fromFileStatus.setIcon(errorImage);
1024 String pdbFileString = "";
1025 String pdbFileTooltip = "";
1026 if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
1027 .getName().equalsIgnoreCase("-Select Associated Seq-")))
1029 btn_pdbFromFile.setEnabled(true);
1030 if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
1032 btn_add.setEnabled(true);
1033 // lbl_fromFileStatus.setIcon(goodImage);
1034 pdbFileString = new File(selectedPdbFileName).getName();
1035 pdbFileTooltip = new File(selectedPdbFileName).getAbsolutePath();
1036 setPdbOptionsEnabled(true);
1040 pdbFileString = MessageManager.getString("label.none");
1041 pdbFileTooltip = MessageManager.getString("label.nothing_selected");
1046 btn_pdbFromFile.setEnabled(false);
1047 // lbl_fromFileStatus.setIcon(errorImage);
1048 pdbFileString = MessageManager.getString("label.none");
1049 pdbFileTooltip = MessageManager.getString("label.nothing_selected");
1051 lbl_pdbFile.setText(pdbFileString);
1052 lbl_pdbFile.setToolTipText(pdbFileTooltip);
1055 String paeFileString = "";
1056 String paeFileTooltip = "";
1057 if (localPdbPaeMatrixFileName != null
1058 && localPdbPaeMatrixFileName.length() > 0)
1060 paeFileString = new File(localPdbPaeMatrixFileName).getName();
1061 paeFileTooltip = new File(localPdbPaeMatrixFileName)
1066 paeFileString = MessageManager.getString("label.none");
1067 paeFileTooltip = MessageManager.getString("label.nothing_selected");
1069 lbl_paeFile.setText(paeFileString);
1070 lbl_paeFile.setToolTipText(paeFileTooltip);
1074 protected void cmbAssSeqStateChanged()
1076 validateSelections();
1079 private FilterOption lastSelected = null;
1082 * Handles the state change event for the 'filter' combo-box and 'invert'
1086 protected void stateChanged(ItemEvent e)
1088 if (e.getSource() instanceof JCheckBox)
1090 updateCurrentView();
1094 if (e.getStateChange() == ItemEvent.SELECTED)
1096 updateCurrentView();
1103 * select structures for viewing by their PDB IDs
1106 * @return true if structures were found and marked as selected
1108 public boolean selectStructure(String... pdbids)
1110 boolean found = false;
1112 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
1113 .getSelectedItem());
1114 String currentView = selectedFilterOpt.getView();
1115 JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
1116 : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
1118 if (restable == null)
1120 // can't select (enter PDB ID, or load file - need to also select which
1121 // sequence to associate with)
1125 int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
1126 for (int r = 0; r < restable.getRowCount(); r++)
1128 for (int p = 0; p < pdbids.length; p++)
1130 if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
1131 .equalsIgnoreCase(pdbids[p]))
1133 restable.setRowSelectionInterval(r, r);
1142 * Handles the 'New View' action
1145 protected void newView_ActionPerformed()
1147 targetView.setSelectedItem(null);
1148 showStructures(false);
1152 * Handles the 'Add to existing viewer' action
1155 protected void add_ActionPerformed()
1157 showStructures(false);
1161 * structure viewer opened by this dialog, or null
1163 private StructureViewer sViewer = null;
1165 public void showStructures(boolean waitUntilFinished)
1168 final StructureSelectionManager ssm = ap.getStructureSelectionManager();
1170 final int preferredHeight = pnl_filter.getHeight();
1172 Runnable viewStruc = new Runnable()
1177 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
1178 .getSelectedItem());
1179 String currentView = selectedFilterOpt.getView();
1180 JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
1183 if (currentView == VIEWS_FILTER)
1185 int[] selectedRows = restable.getSelectedRows();
1186 PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
1187 List<SequenceI> selectedSeqsToView = new ArrayList<>();
1188 pdbEntriesToView = data.collectSelectedRows(restable,
1189 selectedRows, selectedSeqsToView);
1191 SequenceI[] selectedSeqs = selectedSeqsToView
1192 .toArray(new SequenceI[selectedSeqsToView.size()]);
1193 sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1196 else if (currentView == VIEWS_LOCAL_PDB)
1198 int[] selectedRows = tbl_local_pdb.getSelectedRows();
1199 PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
1201 int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
1203 int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
1205 List<SequenceI> selectedSeqsToView = new ArrayList<>();
1206 for (int row : selectedRows)
1208 PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
1209 .getModel()).getPDBEntryAt(row).getPdbEntry();
1211 pdbEntriesToView[count++] = pdbEntry;
1212 SequenceI selectedSeq = (SequenceI) tbl_local_pdb
1213 .getValueAt(row, refSeqColIndex);
1214 selectedSeqsToView.add(selectedSeq);
1216 SequenceI[] selectedSeqs = selectedSeqsToView
1217 .toArray(new SequenceI[selectedSeqsToView.size()]);
1218 sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1221 else if (currentView == VIEWS_ENTER_ID)
1223 SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
1224 .getCmb_assSeq().getSelectedItem()).getSequence();
1225 if (userSelectedSeq != null)
1227 selectedSequence = userSelectedSeq;
1229 String pdbIdStr = txt_search.getText();
1230 PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
1231 if (pdbEntry == null)
1233 pdbEntry = new PDBEntry();
1234 if (pdbIdStr.split(":").length > 1)
1236 pdbEntry.setId(pdbIdStr.split(":")[0]);
1237 pdbEntry.setChainCode(
1238 pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
1242 pdbEntry.setId(pdbIdStr);
1244 pdbEntry.setType(PDBEntry.Type.PDB);
1245 selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
1248 PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
1249 sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1251 { selectedSequence });
1253 else if (currentView == VIEWS_FROM_FILE)
1255 SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
1256 .getCmb_assSeq().getSelectedItem()).getSequence();
1257 if (userSelectedSeq != null)
1259 selectedSequence = userSelectedSeq;
1261 PDBEntry fileEntry = new AssociatePdbFileWithSeq()
1262 .associatePdbWithSeq(selectedPdbFileName,
1263 DataSourceType.FILE, selectedSequence, true,
1266 public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
1267 SequenceI sequence, boolean prompt,
1268 StructureSelectionManagerProvider ssmp)
1269 IN AssociatePdbFileWithSeq */
1271 // DO SOMETHING WITH
1272 if (StructureChooser.this.localPdbPaeMatrixFileName != null)
1276 if (StructureChooser.this.combo_tempFacAs
1277 .getSelectedItem() != null)
1282 sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
1284 { selectedSequence });
1286 SwingUtilities.invokeLater(new Runnable()
1291 closeAction(preferredHeight);
1292 mainFrame.dispose();
1297 Thread runner = new Thread(viewStruc);
1299 if (waitUntilFinished)
1301 while (sViewer == null ? runner.isAlive()
1302 : (sViewer.sview == null ? true
1303 : !sViewer.sview.hasMapping()))
1308 } catch (InterruptedException ie)
1317 * Answers a structure viewer (new or existing) configured to superimpose
1318 * added structures or not according to the user's choice
1323 StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)
1325 Object sv = targetView.getSelectedItem();
1327 return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
1331 * Adds PDB structures to a new or existing structure viewer
1334 * @param pdbEntriesToView
1339 private StructureViewer launchStructureViewer(
1340 StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
1341 final AlignmentPanel alignPanel, SequenceI[] sequences)
1343 long progressId = sequences.hashCode();
1344 setProgressBar(MessageManager
1345 .getString("status.launching_3d_structure_viewer"), progressId);
1346 final StructureViewer theViewer = getTargetedStructureViewer(ssm);
1347 boolean superimpose = chk_superpose.isSelected();
1348 theViewer.setSuperpose(superimpose);
1351 * remember user's choice of superimpose or not
1353 Cache.setProperty(AUTOSUPERIMPOSE,
1354 Boolean.valueOf(superimpose).toString());
1356 setProgressBar(null, progressId);
1357 if (SiftsSettings.isMapWithSifts())
1359 List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
1361 // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
1362 // real PDB ID. For moment, we can also safely do this if there is already
1363 // a known mapping between the PDBEntry and the sequence.
1364 for (SequenceI seq : sequences)
1366 PDBEntry pdbe = pdbEntriesToView[p++];
1367 if (pdbe != null && pdbe.getFile() != null)
1369 StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
1370 if (smm != null && smm.length > 0)
1372 for (StructureMapping sm : smm)
1374 if (sm.getSequence() == seq)
1381 if (seq.getPrimaryDBRefs().isEmpty())
1383 seqsWithoutSourceDBRef.add(seq);
1387 if (!seqsWithoutSourceDBRef.isEmpty())
1389 int y = seqsWithoutSourceDBRef.size();
1390 setProgressBar(MessageManager.formatMessage(
1391 "status.fetching_dbrefs_for_sequences_without_valid_refs",
1393 SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
1394 .toArray(new SequenceI[y]);
1395 DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
1396 dbRefFetcher.fetchDBRefs(true);
1398 setProgressBar("Fetch complete.", progressId); // todo i18n
1401 if (pdbEntriesToView.length > 1)
1404 MessageManager.getString(
1405 "status.fetching_3d_structures_for_selected_entries"),
1407 theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
1411 setProgressBar(MessageManager.formatMessage(
1412 "status.fetching_3d_structures_for",
1413 pdbEntriesToView[0].getId()), progressId);
1414 theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
1416 setProgressBar(null, progressId);
1417 // remember the last viewer we used...
1418 lastTargetedView = theViewer;
1423 * Populates the combo-box used in associating manually fetched structures to
1424 * a unique sequence when more than one sequence selection is made.
1427 protected void populateCmbAssociateSeqOptions(
1428 JComboBox<AssociateSeqOptions> cmb_assSeq,
1429 JLabel lbl_associateSeq)
1431 cmb_assSeq.removeAllItems();
1433 new AssociateSeqOptions("-Select Associated Seq-", null));
1434 lbl_associateSeq.setVisible(false);
1435 if (selectedSequences.length > 1)
1437 for (SequenceI seq : selectedSequences)
1439 cmb_assSeq.addItem(new AssociateSeqOptions(seq));
1444 String seqName = selectedSequence.getDisplayId(false);
1445 seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
1446 lbl_associateSeq.setText(seqName);
1447 lbl_associateSeq.setVisible(true);
1448 cmb_assSeq.setVisible(false);
1452 protected boolean isStructuresDiscovered()
1454 return discoveredStructuresSet != null
1455 && !discoveredStructuresSet.isEmpty();
1458 protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes
1460 // Doing a search for "1" or "1c" is valuable?
1461 // Those work but are enormously slow.
1464 protected void txt_search_ActionPerformed()
1466 String text = txt_search.getText().trim();
1467 if (text.length() >= PDB_ID_MIN)
1474 errorWarning.setLength(0);
1475 isValidPBDEntry = false;
1476 if (text.length() > 0)
1478 // TODO move this pdb id search into the PDB specific
1480 // for moment, it will work fine as is because it is self-contained
1481 String searchTerm = text.toLowerCase(Locale.ROOT);
1482 searchTerm = searchTerm.split(":")[0];
1483 // System.out.println(">>>>> search term : " + searchTerm);
1484 List<FTSDataColumnI> wantedFields = new ArrayList<>();
1485 FTSRestRequest pdbRequest = new FTSRestRequest();
1486 pdbRequest.setAllowEmptySeq(false);
1487 pdbRequest.setResponseSize(1);
1488 pdbRequest.setFieldToSearchBy("(pdb_id:");
1489 pdbRequest.setWantedFields(wantedFields);
1490 pdbRequest.setSearchTerm(searchTerm + ")");
1491 pdbRequest.setAssociatedSequence(selectedSequence);
1492 FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
1493 wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
1494 FTSRestResponse resultList;
1497 resultList = pdbRestClient.executeRequest(pdbRequest);
1498 } catch (Exception e)
1500 errorWarning.append(e.getMessage());
1504 validateSelections();
1506 if (resultList.getSearchSummary() != null
1507 && resultList.getSearchSummary().size() > 0)
1509 isValidPBDEntry = true;
1512 validateSelections();
1518 protected void tabRefresh()
1520 if (selectedSequences != null)
1522 lbl_loading.setVisible(true);
1523 Thread refreshThread = new Thread(new Runnable()
1528 fetchStructuresMetaData();
1529 // populateFilterComboBox(true, cachedPDBExists);
1532 ((FilterOption) cmb_filterOption.getSelectedItem())
1534 lbl_loading.setVisible(false);
1537 refreshThread.start();
1541 public class PDBEntryTableModel extends AbstractTableModel
1543 String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1546 private List<CachedPDB> pdbEntries;
1548 public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1550 this.pdbEntries = new ArrayList<>(pdbEntries);
1554 public String getColumnName(int columnIndex)
1556 return columns[columnIndex];
1560 public int getRowCount()
1562 return pdbEntries.size();
1566 public int getColumnCount()
1568 return columns.length;
1572 public boolean isCellEditable(int row, int column)
1578 public Object getValueAt(int rowIndex, int columnIndex)
1580 Object value = "??";
1581 CachedPDB entry = pdbEntries.get(rowIndex);
1582 switch (columnIndex)
1585 value = entry.getSequence();
1588 value = entry.getQualifiedId();
1591 value = entry.getPdbEntry().getChainCode() == null ? "_"
1592 : entry.getPdbEntry().getChainCode();
1595 value = entry.getPdbEntry().getType();
1598 value = entry.getPdbEntry().getFile();
1605 public Class<?> getColumnClass(int columnIndex)
1607 return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1610 public CachedPDB getPDBEntryAt(int row)
1612 return pdbEntries.get(row);
1617 private class CachedPDB
1619 private SequenceI sequence;
1621 private PDBEntry pdbEntry;
1623 public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1625 this.sequence = sequence;
1626 this.pdbEntry = pdbEntry;
1629 public String getQualifiedId()
1631 if (pdbEntry.hasProvider())
1633 return pdbEntry.getProvider() + ":" + pdbEntry.getId();
1635 return pdbEntry.toString();
1638 public SequenceI getSequence()
1643 public PDBEntry getPdbEntry()
1650 private IProgressIndicator progressBar;
1653 public void setProgressBar(String message, long id)
1655 if (!Platform.isHeadless())
1656 progressBar.setProgressBar(message, id);
1660 public void registerHandler(long id, IProgressIndicatorHandler handler)
1662 progressBar.registerHandler(id, handler);
1666 public boolean operationInProgress()
1668 return progressBar.operationInProgress();
1671 public JalviewStructureDisplayI getOpenedStructureViewer()
1673 return sViewer == null ? null : sViewer.sview;
1677 protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs)
1679 data.setDocFieldPrefs(newPrefs);
1685 * @return true when all initialisation threads have finished and dialog is
1688 public boolean isDialogVisible()
1690 return mainFrame != null && data != null && cmb_filterOption != null
1691 && mainFrame.isVisible()
1692 && cmb_filterOption.getSelectedItem() != null;
1697 * @return true if the 3D-Beacons query button will/has been displayed
1699 public boolean isCanQueryTDB()
1704 public boolean isNotQueriedTDBYet()
1706 return notQueriedTDBYet;
1710 * Open a single structure file for a given sequence
1712 public static void openStructureFileForSequence(AlignmentPanel ap,
1713 SequenceI seq, File sFile)
1715 // Open the chooser headlessly. Not sure this is actually needed ?
1716 StructureChooser sc = new StructureChooser(new SequenceI[] { seq }, seq,
1718 StructureSelectionManager ssm = ap.getStructureSelectionManager();
1719 PDBEntry fileEntry = null;
1722 fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
1723 sFile.getAbsolutePath(), DataSourceType.FILE, seq, true,
1725 } catch (Exception e)
1727 Console.error("Could not open structure file '"
1728 + sFile.getAbsolutePath() + "'");
1732 StructureViewer sViewer = sc.launchStructureViewer(ssm,
1734 { fileEntry }, ap, new SequenceI[] { seq });
1736 sc.mainFrame.dispose();