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 jalview.bin.Jalview;
25 import jalview.datamodel.DBRefEntry;
26 import jalview.datamodel.DBRefSource;
27 import jalview.datamodel.PDBEntry;
28 import jalview.datamodel.SequenceI;
29 import jalview.fts.api.FTSData;
30 import jalview.fts.api.FTSDataColumnI;
31 import jalview.fts.api.FTSRestClientI;
32 import jalview.fts.core.FTSRestRequest;
33 import jalview.fts.core.FTSRestResponse;
34 import jalview.fts.service.pdb.PDBFTSRestClient;
35 import jalview.jbgui.GStructureChooser;
36 import jalview.structure.StructureSelectionManager;
37 import jalview.util.MessageManager;
38 import jalview.ws.DBRefFetcher;
39 import jalview.ws.sifts.SiftsSettings;
41 import java.awt.event.ItemEvent;
42 import java.util.ArrayList;
43 import java.util.Collection;
44 import java.util.HashSet;
45 import java.util.LinkedHashSet;
46 import java.util.List;
47 import java.util.Objects;
48 import java.util.Vector;
50 import javax.swing.JCheckBox;
51 import javax.swing.JComboBox;
52 import javax.swing.JLabel;
53 import javax.swing.JOptionPane;
54 import javax.swing.table.AbstractTableModel;
57 * Provides the behaviors for the Structure chooser Panel
62 @SuppressWarnings("serial")
63 public class StructureChooser extends GStructureChooser implements
66 private boolean structuresDiscovered = false;
68 private SequenceI selectedSequence;
70 private SequenceI[] selectedSequences;
72 private IProgressIndicator progressIndicator;
74 private Collection<FTSData> discoveredStructuresSet;
76 private FTSRestRequest lastPdbRequest;
78 private FTSRestClientI pdbRestCleint;
80 private String selectedPdbFileName;
82 private boolean isValidPBDEntry;
84 public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
88 this.selectedSequence = selectedSeq;
89 this.selectedSequences = selectedSeqs;
90 this.progressIndicator = (ap == null) ? null : ap.alignFrame;
95 * Initializes parameters used by the Structure Chooser Panel
99 if (!Jalview.isHeadlessMode())
101 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
104 Thread discoverPDBStructuresThread = new Thread(new Runnable()
109 long startTime = System.currentTimeMillis();
110 updateProgressIndicator(MessageManager
111 .getString("status.loading_cached_pdb_entries"), startTime);
112 loadLocalCachedPDBEntries();
113 updateProgressIndicator(null, startTime);
114 updateProgressIndicator(MessageManager
115 .getString("status.searching_for_pdb_structures"),
117 fetchStructuresMetaData();
118 populateFilterComboBox();
119 updateProgressIndicator(null, startTime);
120 mainFrame.setVisible(true);
124 discoverPDBStructuresThread.start();
128 * Updates the progress indicator with the specified message
131 * displayed message for the operation
133 * unique handle for this indicator
135 public void updateProgressIndicator(String message, long id)
137 if (progressIndicator != null)
139 progressIndicator.setProgressBar(message, id);
144 * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
147 public void fetchStructuresMetaData()
149 long startTime = System.currentTimeMillis();
150 pdbRestCleint = PDBFTSRestClient.getInstance();
151 Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
152 .getStructureSummaryFields();
154 discoveredStructuresSet = new LinkedHashSet<FTSData>();
155 HashSet<String> errors = new HashSet<String>();
156 for (SequenceI seq : selectedSequences)
158 FTSRestRequest pdbRequest = new FTSRestRequest();
159 pdbRequest.setAllowEmptySeq(false);
160 pdbRequest.setResponseSize(500);
161 pdbRequest.setFieldToSearchBy("(");
162 pdbRequest.setWantedFields(wantedFields);
163 pdbRequest.setSearchTerm(buildQuery(seq) + ")");
164 pdbRequest.setAssociatedSequence(seq);
165 FTSRestResponse resultList;
168 resultList = pdbRestCleint.executeRequest(pdbRequest);
169 } catch (Exception e)
172 errors.add(e.getMessage());
175 lastPdbRequest = pdbRequest;
176 if (resultList.getSearchSummary() != null
177 && !resultList.getSearchSummary().isEmpty())
179 discoveredStructuresSet.addAll(resultList.getSearchSummary());
183 int noOfStructuresFound = 0;
184 String totalTime = (System.currentTimeMillis() - startTime)
186 if (discoveredStructuresSet != null
187 && !discoveredStructuresSet.isEmpty())
189 getResultTable().setModel(
190 FTSRestResponse.getTableModel(lastPdbRequest,
191 discoveredStructuresSet));
192 structuresDiscovered = true;
193 noOfStructuresFound = discoveredStructuresSet.size();
194 mainFrame.setTitle(MessageManager.formatMessage(
195 "label.structure_chooser_no_of_structures",
196 noOfStructuresFound, totalTime));
200 mainFrame.setTitle(MessageManager
201 .getString("label.structure_chooser_manual_association"));
202 if (errors.size() > 0)
204 StringBuilder errorMsg = new StringBuilder();
205 for (String error : errors)
207 errorMsg.append(error).append("\n");
209 JOptionPane.showMessageDialog(this, errorMsg.toString(),
210 MessageManager.getString("label.pdb_web-service_error"),
211 JOptionPane.ERROR_MESSAGE);
216 public void loadLocalCachedPDBEntries()
218 ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
219 for (SequenceI seq : selectedSequences)
221 if (seq.getDatasetSequence() != null
222 && seq.getDatasetSequence().getAllPDBEntries() != null)
224 for (PDBEntry pdbEntry : seq.getDatasetSequence()
227 if (pdbEntry.getFile() != null)
229 entries.add(new CachedPDB(seq, pdbEntry));
235 PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
236 tbl_local_pdb.setModel(tableModelx);
240 * Builds a query string for a given sequences using its DBRef entries
243 * the sequences to build a query for
244 * @return the built query string
247 public static String buildQuery(SequenceI seq)
249 boolean isPDBRefsFound = false;
250 boolean isUniProtRefsFound = false;
251 StringBuilder queryBuilder = new StringBuilder();
252 HashSet<String> seqRefs = new LinkedHashSet<String>();
254 if (seq.getAllPDBEntries() != null)
256 for (PDBEntry entry : seq.getAllPDBEntries())
258 if (isValidSeqName(entry.getId()))
260 queryBuilder.append("pdb_id")
262 .append(entry.getId().toLowerCase())
264 isPDBRefsFound = true;
265 // seqRefs.add(entry.getId());
270 if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
272 for (DBRefEntry dbRef : seq.getDBRefs())
274 if (isValidSeqName(getDBRefId(dbRef)))
276 if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
279 .append("uniprot_accession").append(":")
280 .append(getDBRefId(dbRef))
283 .append("uniprot_id")
285 .append(getDBRefId(dbRef)).append(" OR ");
286 isUniProtRefsFound = true;
288 else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
291 queryBuilder.append("pdb_id")
292 .append(":").append(getDBRefId(dbRef).toLowerCase())
294 isPDBRefsFound = true;
298 seqRefs.add(getDBRefId(dbRef));
304 if (!isPDBRefsFound && !isUniProtRefsFound)
306 String seqName = seq.getName();
307 seqName = sanitizeSeqName(seqName);
308 String[] names = seqName.toLowerCase().split("\\|");
309 for (String name : names)
311 // System.out.println("Found name : " + name);
313 if (isValidSeqName(name))
319 for (String seqRef : seqRefs)
321 queryBuilder.append("text:").append(seqRef).append(" OR ");
325 int endIndex = queryBuilder.lastIndexOf(" OR ");
326 if (queryBuilder.toString().length() < 6)
330 String query = queryBuilder.toString().substring(0, endIndex);
335 * Remove the following special characters from input string +, -, &, !, (, ),
336 * {, }, [, ], ^, ", ~, *, ?, :, \
341 private static String sanitizeSeqName(String seqName)
343 Objects.requireNonNull(seqName);
344 return seqName.replaceAll("\\[\\d*\\]", "")
345 .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
350 * Ensures sequence ref names are not less than 3 characters and does not
351 * contain a database name
356 public static boolean isValidSeqName(String seqName)
358 // System.out.println("seqName : " + seqName);
359 String ignoreList = "pdb,uniprot,swiss-prot";
360 if (seqName.length() < 3)
364 if (seqName.contains(":"))
368 seqName = seqName.toLowerCase();
369 for (String ignoredEntry : ignoreList.split(","))
371 if (seqName.contains(ignoredEntry))
379 public static String getDBRefId(DBRefEntry dbRef)
381 String ref = dbRef.getAccessionId().replaceAll("GO:", "");
386 * Filters a given list of discovered structures based on supplied argument
388 * @param fieldToFilterBy
389 * the field to filter by
391 public void filterResultSet(final String fieldToFilterBy)
393 Thread filterThread = new Thread(new Runnable()
398 long startTime = System.currentTimeMillis();
399 pdbRestCleint = PDBFTSRestClient.getInstance();
400 lbl_loading.setVisible(true);
401 Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
402 .getStructureSummaryFields();
403 Collection<FTSData> filteredResponse = new HashSet<FTSData>();
404 HashSet<String> errors = new HashSet<String>();
406 for (SequenceI seq : selectedSequences)
408 FTSRestRequest pdbRequest = new FTSRestRequest();
409 if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
411 pdbRequest.setAllowEmptySeq(false);
412 pdbRequest.setResponseSize(1);
413 pdbRequest.setFieldToSearchBy("(");
414 pdbRequest.setSearchTerm(buildQuery(seq) + ")");
415 pdbRequest.setWantedFields(wantedFields);
416 pdbRequest.setAssociatedSequence(seq);
417 pdbRequest.setFacet(true);
418 pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
419 pdbRequest.setFacetPivotMinCount(1);
423 pdbRequest.setAllowEmptySeq(false);
424 pdbRequest.setResponseSize(1);
425 pdbRequest.setFieldToSearchBy("(");
426 pdbRequest.setFieldToSortBy(fieldToFilterBy,
427 !chk_invertFilter.isSelected());
428 pdbRequest.setSearchTerm(buildQuery(seq) + ")");
429 pdbRequest.setWantedFields(wantedFields);
430 pdbRequest.setAssociatedSequence(seq);
432 FTSRestResponse resultList;
435 resultList = pdbRestCleint.executeRequest(pdbRequest);
436 } catch (Exception e)
439 errors.add(e.getMessage());
442 lastPdbRequest = pdbRequest;
443 if (resultList.getSearchSummary() != null
444 && !resultList.getSearchSummary().isEmpty())
446 filteredResponse.addAll(resultList.getSearchSummary());
450 String totalTime = (System.currentTimeMillis() - startTime)
452 if (!filteredResponse.isEmpty())
454 final int filterResponseCount = filteredResponse.size();
455 Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
456 reorderedStructuresSet.addAll(filteredResponse);
457 reorderedStructuresSet.addAll(discoveredStructuresSet);
458 getResultTable().setModel(
459 FTSRestResponse.getTableModel(
460 lastPdbRequest, reorderedStructuresSet));
462 FTSRestResponse.configureTableColumn(getResultTable(),
464 getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
465 getResultTable().getColumn("Ref Sequence").setMinWidth(100);
466 getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
467 // Update table selection model here
468 getResultTable().addRowSelectionInterval(0,
469 filterResponseCount - 1);
470 mainFrame.setTitle(MessageManager.formatMessage(
471 "label.structure_chooser_filter_time", totalTime));
475 mainFrame.setTitle(MessageManager.formatMessage(
476 "label.structure_chooser_filter_time", totalTime));
477 if (errors.size() > 0)
479 StringBuilder errorMsg = new StringBuilder();
480 for (String error : errors)
482 errorMsg.append(error).append("\n");
484 JOptionPane.showMessageDialog(
487 MessageManager.getString("label.pdb_web-service_error"),
488 JOptionPane.ERROR_MESSAGE);
492 lbl_loading.setVisible(false);
494 validateSelections();
497 filterThread.start();
501 * Handles action event for btn_pdbFromFile
504 public void pdbFromFile_actionPerformed()
506 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
507 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
508 chooser.setFileView(new jalview.io.JalviewFileView());
509 chooser.setDialogTitle(MessageManager.formatMessage(
510 "label.select_pdb_file_for",
511 selectedSequence.getDisplayId(false)));
512 chooser.setToolTipText(MessageManager.formatMessage(
513 "label.load_pdb_file_associate_with_sequence",
514 selectedSequence.getDisplayId(false)));
516 int value = chooser.showOpenDialog(null);
517 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
519 selectedPdbFileName = chooser.getSelectedFile().getPath();
520 jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
521 validateSelections();
526 * Populates the filter combo-box options dynamically depending on discovered
530 protected void populateFilterComboBox()
532 if (isStructuresDiscovered())
534 cmb_filterOption.addItem(new FilterOption("Best Quality",
535 "overall_quality", VIEWS_FILTER));
536 cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage",
537 "uniprot_coverage", VIEWS_FILTER));
538 cmb_filterOption.addItem(new FilterOption("Best Resolution",
539 "resolution", VIEWS_FILTER));
540 cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
541 "number_of_protein_chains", VIEWS_FILTER));
542 cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
543 "number_of_bound_molecules", VIEWS_FILTER));
544 cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
545 "number_of_polymer_residues", VIEWS_FILTER));
547 cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
549 cmb_filterOption.addItem(new FilterOption("From File", "-",
551 cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
556 * Updates the displayed view based on the selected filter option
559 protected void updateCurrentView()
561 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
563 layout_switchableViews.show(pnl_switchableViews,
564 selectedFilterOpt.getView());
565 String filterTitle = mainFrame.getTitle();
566 mainFrame.setTitle(frameTitle);
567 chk_invertFilter.setVisible(false);
568 if (selectedFilterOpt.getView() == VIEWS_FILTER)
570 mainFrame.setTitle(filterTitle);
571 chk_invertFilter.setVisible(true);
572 filterResultSet(selectedFilterOpt.getValue());
574 else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
575 || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
577 mainFrame.setTitle(MessageManager
578 .getString("label.structure_chooser_manual_association"));
579 idInputAssSeqPanel.loadCmbAssSeq();
580 fileChooserAssSeqPanel.loadCmbAssSeq();
582 validateSelections();
586 * Validates user selection and activates the view button if all parameters
590 public void validateSelections()
592 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
594 btn_view.setEnabled(false);
595 String currentView = selectedFilterOpt.getView();
596 if (currentView == VIEWS_FILTER)
598 if (getResultTable().getSelectedRows().length > 0)
600 btn_view.setEnabled(true);
603 else if (currentView == VIEWS_LOCAL_PDB)
605 if (tbl_local_pdb.getSelectedRows().length > 0)
607 btn_view.setEnabled(true);
610 else if (currentView == VIEWS_ENTER_ID)
612 validateAssociationEnterPdb();
614 else if (currentView == VIEWS_FROM_FILE)
616 validateAssociationFromFile();
621 * Validates inputs from the Manual PDB entry panel
623 public void validateAssociationEnterPdb()
625 AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
626 .getCmb_assSeq().getSelectedItem();
627 lbl_pdbManualFetchStatus.setIcon(errorImage);
628 lbl_pdbManualFetchStatus.setToolTipText("");
629 if (txt_search.getText().length() > 0)
631 lbl_pdbManualFetchStatus
632 .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
633 .formatMessage("info.no_pdb_entry_found_for",
634 txt_search.getText())));
637 if (errorWarning.length() > 0)
639 lbl_pdbManualFetchStatus.setIcon(warningImage);
640 lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
641 true, errorWarning.toString()));
644 if (selectedSequences.length == 1
645 || !assSeqOpt.getName().equalsIgnoreCase(
646 "-Select Associated Seq-"))
648 txt_search.setEnabled(true);
651 btn_view.setEnabled(true);
652 lbl_pdbManualFetchStatus.setToolTipText("");
653 lbl_pdbManualFetchStatus.setIcon(goodImage);
658 txt_search.setEnabled(false);
659 lbl_pdbManualFetchStatus.setIcon(errorImage);
664 * Validates inputs for the manual PDB file selection options
666 public void validateAssociationFromFile()
668 AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
669 .getCmb_assSeq().getSelectedItem();
670 lbl_fromFileStatus.setIcon(errorImage);
671 if (selectedSequences.length == 1
672 || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
673 "-Select Associated Seq-")))
675 btn_pdbFromFile.setEnabled(true);
676 if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
678 btn_view.setEnabled(true);
679 lbl_fromFileStatus.setIcon(goodImage);
684 btn_pdbFromFile.setEnabled(false);
685 lbl_fromFileStatus.setIcon(errorImage);
690 public void cmbAssSeqStateChanged()
692 validateSelections();
696 * Handles the state change event for the 'filter' combo-box and 'invert'
700 protected void stateChanged(ItemEvent e)
702 if (e.getSource() instanceof JCheckBox)
708 if (e.getStateChange() == ItemEvent.SELECTED)
717 * Handles action event for btn_ok
720 public void ok_ActionPerformed()
722 final long progressSessionId = System.currentTimeMillis();
723 final StructureSelectionManager ssm = ap.getStructureSelectionManager();
724 ssm.setProgressIndicator(this);
725 ssm.setProgressSessionId(progressSessionId);
726 new Thread(new Runnable()
731 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
733 String currentView = selectedFilterOpt.getView();
734 if (currentView == VIEWS_FILTER)
736 int pdbIdColIndex = getResultTable().getColumn("PDB Id")
738 int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
740 int[] selectedRows = getResultTable().getSelectedRows();
741 PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
743 ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
744 for (int row : selectedRows)
746 String pdbIdStr = getResultTable().getValueAt(row,
749 SequenceI selectedSeq = (SequenceI) getResultTable()
752 selectedSeqsToView.add(selectedSeq);
753 PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
754 if (pdbEntry == null)
756 pdbEntry = getFindEntry(pdbIdStr,
757 selectedSeq.getAllPDBEntries());
759 if (pdbEntry == null)
761 pdbEntry = new PDBEntry();
762 pdbEntry.setId(pdbIdStr);
763 pdbEntry.setType(PDBEntry.Type.PDB);
764 selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
766 pdbEntriesToView[count++] = pdbEntry;
768 SequenceI[] selectedSeqs = selectedSeqsToView
769 .toArray(new SequenceI[selectedSeqsToView.size()]);
770 launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
772 else if (currentView == VIEWS_LOCAL_PDB)
774 int[] selectedRows = tbl_local_pdb.getSelectedRows();
775 PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
777 int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
779 int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
781 ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
782 for (int row : selectedRows)
784 PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
786 pdbEntriesToView[count++] = pdbEntry;
787 SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
789 selectedSeqsToView.add(selectedSeq);
791 SequenceI[] selectedSeqs = selectedSeqsToView
792 .toArray(new SequenceI[selectedSeqsToView.size()]);
793 launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
795 else if (currentView == VIEWS_ENTER_ID)
797 SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
798 .getCmb_assSeq().getSelectedItem()).getSequence();
799 if (userSelectedSeq != null)
801 selectedSequence = userSelectedSeq;
804 String pdbIdStr = txt_search.getText();
805 PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
806 if (pdbEntry == null)
808 pdbEntry = new PDBEntry();
809 if (pdbIdStr.split(":").length > 1)
811 pdbEntry.setChainCode(pdbIdStr.split(":")[1]);
813 pdbEntry.setId(pdbIdStr);
814 pdbEntry.setType(PDBEntry.Type.PDB);
815 selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
818 PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
819 launchStructureViewer(ssm, pdbEntriesToView, ap,
820 new SequenceI[] { selectedSequence });
822 else if (currentView == VIEWS_FROM_FILE)
824 SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
825 .getCmb_assSeq().getSelectedItem()).getSequence();
826 if (userSelectedSeq != null)
828 selectedSequence = userSelectedSeq;
830 PDBEntry fileEntry = new AssociatePdbFileWithSeq()
831 .associatePdbWithSeq(selectedPdbFileName,
832 jalview.io.AppletFormatAdapter.FILE,
833 selectedSequence, true, Desktop.instance);
835 launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
836 new SequenceI[] { selectedSequence });
843 private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
845 Objects.requireNonNull(id);
846 Objects.requireNonNull(pdbEntries);
847 PDBEntry foundEntry = null;
848 for (PDBEntry entry : pdbEntries)
850 if (entry.getId().equalsIgnoreCase(id))
858 private void launchStructureViewer(StructureSelectionManager ssm,
859 final PDBEntry[] pdbEntriesToView,
860 final AlignmentPanel alignPanel, SequenceI[] sequences)
862 ssm.setProgressBar("Launching PDB structure viewer..");
863 final StructureViewer sViewer = new StructureViewer(ssm);
865 if (SiftsSettings.isMapWithSifts())
867 ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
868 for (SequenceI seq : sequences)
870 if (seq.getSourceDBRef() == null && seq.getDBRefs() == null)
872 seqsWithoutSourceDBRef.add(seq);
876 if (!seqsWithoutSourceDBRef.isEmpty())
878 int y = seqsWithoutSourceDBRef.size();
879 ssm.setProgressBar(null);
880 ssm.setProgressBar("Fetching db refs for " + y
881 + " sequence" + (y > 1 ? "s" : "")
882 + " without valid db ref required for SIFTS mapping");
883 SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
885 for (SequenceI fSeq : seqsWithoutSourceDBRef)
887 seqWithoutSrcDBRef[x++] = fSeq;
889 new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
892 if (pdbEntriesToView.length > 1)
894 ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
895 for (SequenceI seq : sequences)
897 seqsMap.add(new SequenceI[] { seq });
899 SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
900 ssm.setProgressBar(null);
901 ssm.setProgressBar("Fetching PDB Structures for selected entries..");
902 sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
906 ssm.setProgressBar(null);
907 ssm.setProgressBar("Fetching PDB Structure for "
908 + pdbEntriesToView[0].getId());
909 sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
914 * Populates the combo-box used in associating manually fetched structures to
915 * a unique sequence when more than one sequence selection is made.
918 public void populateCmbAssociateSeqOptions(
919 JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
921 cmb_assSeq.removeAllItems();
922 cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
924 lbl_associateSeq.setVisible(false);
925 if (selectedSequences.length > 1)
927 for (SequenceI seq : selectedSequences)
929 cmb_assSeq.addItem(new AssociateSeqOptions(seq));
934 String seqName = selectedSequence.getDisplayId(false);
935 seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
936 lbl_associateSeq.setText(seqName);
937 lbl_associateSeq.setVisible(true);
938 cmb_assSeq.setVisible(false);
942 public boolean isStructuresDiscovered()
944 return structuresDiscovered;
947 public void setStructuresDiscovered(boolean structuresDiscovered)
949 this.structuresDiscovered = structuresDiscovered;
952 public Collection<FTSData> getDiscoveredStructuresSet()
954 return discoveredStructuresSet;
958 protected void txt_search_ActionPerformed()
965 errorWarning.setLength(0);
966 isValidPBDEntry = false;
967 if (txt_search.getText().length() > 0)
969 String searchTerm = txt_search.getText().toLowerCase();
970 searchTerm = searchTerm.split(":")[0];
971 // System.out.println(">>>>> search term : " + searchTerm);
972 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
973 FTSRestRequest pdbRequest = new FTSRestRequest();
974 pdbRequest.setAllowEmptySeq(false);
975 pdbRequest.setResponseSize(1);
976 pdbRequest.setFieldToSearchBy("(pdb_id:");
977 pdbRequest.setWantedFields(wantedFields);
979 .setSearchTerm(searchTerm + ")");
980 pdbRequest.setAssociatedSequence(selectedSequence);
981 pdbRestCleint = PDBFTSRestClient.getInstance();
982 wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
983 FTSRestResponse resultList;
986 resultList = pdbRestCleint.executeRequest(pdbRequest);
987 } catch (Exception e)
989 errorWarning.append(e.getMessage());
993 validateSelections();
995 if (resultList.getSearchSummary() != null
996 && resultList.getSearchSummary().size() > 0)
998 isValidPBDEntry = true;
1001 validateSelections();
1007 public void tabRefresh()
1009 if (selectedSequences != null)
1011 Thread refreshThread = new Thread(new Runnable()
1016 fetchStructuresMetaData();
1017 filterResultSet(((FilterOption) cmb_filterOption
1018 .getSelectedItem()).getValue());
1021 refreshThread.start();
1025 public class PDBEntryTableModel extends AbstractTableModel
1027 String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
1029 private List<CachedPDB> pdbEntries;
1031 public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1033 this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
1037 public String getColumnName(int columnIndex)
1039 return columns[columnIndex];
1043 public int getRowCount()
1045 return pdbEntries.size();
1049 public int getColumnCount()
1051 return columns.length;
1055 public boolean isCellEditable(int row, int column)
1061 public Object getValueAt(int rowIndex, int columnIndex)
1063 Object value = "??";
1064 CachedPDB entry = pdbEntries.get(rowIndex);
1065 switch (columnIndex)
1068 value = entry.getSequence();
1071 value = entry.getPdbEntry();
1074 value = entry.getPdbEntry().getChainCode() == null ? "_" : entry
1075 .getPdbEntry().getChainCode();
1078 value = entry.getPdbEntry().getType();
1081 value = entry.getPdbEntry().getFile();
1088 public Class<?> getColumnClass(int columnIndex)
1090 return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1093 public CachedPDB getPDBEntryAt(int row)
1095 return pdbEntries.get(row);
1100 private class CachedPDB
1102 private SequenceI sequence;
1104 private PDBEntry pdbEntry;
1106 public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1108 this.sequence = sequence;
1109 this.pdbEntry = pdbEntry;
1112 public SequenceI getSequence()
1117 public PDBEntry getPdbEntry()
1124 private IProgressIndicator progressBar;
1127 public void setProgressBar(String message, long id)
1129 progressBar.setProgressBar(message, id);
1133 public void registerHandler(long id, IProgressIndicatorHandler handler)
1135 progressBar.registerHandler(id, handler);
1139 public boolean operationInProgress()
1141 return progressBar.operationInProgress();