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.
21 package jalview.gui.structurechooser;
23 import java.util.ArrayList;
24 import java.util.Arrays;
25 import java.util.Collection;
26 import java.util.Comparator;
27 import java.util.HashSet;
28 import java.util.LinkedHashSet;
29 import java.util.List;
30 import java.util.Locale;
33 import javax.swing.JTable;
35 import jalview.bin.Console;
36 import jalview.datamodel.DBRefEntry;
37 import jalview.datamodel.DBRefSource;
38 import jalview.datamodel.PDBEntry;
39 import jalview.datamodel.SequenceI;
40 import jalview.fts.api.FTSData;
41 import jalview.fts.api.FTSDataColumnI;
42 import jalview.fts.api.FTSRestClientI;
43 import jalview.fts.core.FTSDataColumnPreferences;
44 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
45 import jalview.fts.core.FTSRestRequest;
46 import jalview.fts.core.FTSRestResponse;
47 import jalview.fts.service.threedbeacons.TDB_FTSData;
48 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
49 import jalview.jbgui.FilterOption;
52 * logic for querying the 3DBeacons API for structures of sequences
56 public class ThreeDBStructureChooserQuerySource
57 extends StructureChooserQuerySource
60 private Set<String> tdBeaconsFilters = null, defaultFilters = null;
62 public static final String FILTER_TDBEACONS_COVERAGE = "3d_beacons_coverage";
64 public static final String FILTER_FIRST_BEST_COVERAGE = "3d_beacons_first_best_coverage";
66 private static final String FILTER_SOURCE_PREFIX = "only_";
68 protected FTSRestRequest lastTdbRequest;
70 protected FTSRestClientI tdbRestClient;
72 private FTSRestRequest lastPdbRequest;
74 public ThreeDBStructureChooserQuerySource()
76 defaultFilters = new LinkedHashSet<String>();
77 defaultFilters.add(FILTER_TDBEACONS_COVERAGE);
78 defaultFilters.add(FILTER_FIRST_BEST_COVERAGE);
80 tdbRestClient = TDBeaconsFTSRestClient.getInstance();
81 docFieldPrefs = new FTSDataColumnPreferences(
82 PreferenceSource.STRUCTURE_CHOOSER,
83 TDBeaconsFTSRestClient.getInstance());
87 * Builds a query string for a given sequences using its DBRef entries 3d
88 * Beacons is only useful for uniprot IDs
91 * the sequences to build a query for
92 * @return the built query string
95 public String buildQuery(SequenceI seq)
97 List<DBRefEntry> refs = seq.getDBRefs();
98 int ib = checkUniprotRefs(refs);
101 return getDBRefId(refs.get(ib));
107 * Searches DBRefEntry for uniprot refs
110 * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of
111 * Uniprot canonical DBRefEntry
113 public static int checkUniprotRefs(List<DBRefEntry> refs)
115 boolean hasUniprot = false;
116 if (refs != null && refs.size() != 0)
118 for (int ib = 0, nb = refs.size(); ib < nb; ib++)
120 DBRefEntry dbRef = refs.get(ib);
121 if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
124 if (dbRef.isCanonical())
131 return hasUniprot ? -1 : -2;
135 * Ensures sequence ref names are not less than 3 characters and does not
136 * contain a database name
141 static boolean isValidSeqName(String seqName)
143 String ignoreList = "pdb,uniprot,swiss-prot";
144 if (seqName.length() < 3)
148 if (seqName.contains(":"))
152 seqName = seqName.toLowerCase(Locale.ROOT);
153 for (String ignoredEntry : ignoreList.split(","))
155 if (seqName.contains(ignoredEntry))
163 static String getDBRefId(DBRefEntry dbRef)
165 String ref = dbRef.getAccessionId().replaceAll("GO:", "");
170 * FTSRestClient specific query builder to recover associated structure data
171 * records for a sequence
174 * - seq to generate a query for
175 * @param wantedFields
176 * - fields to retrieve
177 * @param selectedFilterOpt
178 * - criterion for ranking results (e.g. resolution)
180 * - sort ascending or descending
184 public FTSRestResponse fetchStructuresMetaData(SequenceI seq,
185 Collection<FTSDataColumnI> wantedFields,
186 FilterOption selectedFilterOpt, boolean b) throws Exception
188 FTSRestResponse resultList;
189 if (selectedFilterOpt != null
190 && tdBeaconsFilter(selectedFilterOpt.getValue()))
192 FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
193 resultList = tdbRestClient.executeRequest(tdbRequest);
195 lastTdbRequest = tdbRequest;
196 if (resultList != null)
197 { // Query the PDB and add additional metadata
198 FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
199 getPDBQuerySource(), resultList);
201 resultList = joinResponses(resultList, pdbResponse);
205 // use the PDBFTS directly
206 resultList = getPDBQuerySource().fetchStructuresMetaData(seq,
207 wantedFields, selectedFilterOpt, b);
208 lastTdbRequest = getPDBQuerySource().lastPdbRequest;
209 lastPdbRequest = lastTdbRequest; // both queries the same - indicates we
215 PDBStructureChooserQuerySource pdbQuerySource = null;
217 private PDBStructureChooserQuerySource getPDBQuerySource()
219 if (pdbQuerySource == null)
221 pdbQuerySource = new PDBStructureChooserQuerySource();
223 return pdbQuerySource;
226 private FTSRestRequest getTDBeaconsRequest(SequenceI seq,
227 Collection<FTSDataColumnI> wantedFields)
229 FTSRestRequest pdbRequest = new FTSRestRequest();
230 pdbRequest.setAllowEmptySeq(false);
231 pdbRequest.setResponseSize(500);
232 pdbRequest.setWantedFields(wantedFields);
233 String query = buildQuery(seq);
238 pdbRequest.setSearchTerm(query + ".json");
239 pdbRequest.setAssociatedSequence(seq);
244 public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
246 List<FilterOption> filters = getPDBQuerySource()
247 .getAvailableFilterOptions(VIEWS_FILTER);
248 tdBeaconsFilters = new LinkedHashSet<String>();
249 tdBeaconsFilters.addAll(defaultFilters);
250 filters.add(0, new FilterOption("Best 3D-Beacons Coverage",
251 FILTER_FIRST_BEST_COVERAGE, VIEWS_FILTER, false, this));
252 filters.add(1, new FilterOption("Multiple 3D-Beacons Coverage",
253 FILTER_TDBEACONS_COVERAGE, VIEWS_FILTER, true, this));
259 public void updateAvailableFilterOptions(String VIEWS_FILTER,
260 List<FilterOption> xtantOptions, Collection<FTSData> tdbEntries)
262 if (tdbEntries != null && lastTdbRequest != null)
264 boolean hasPDBe = false;
265 for (FTSData _row : tdbEntries)
267 // tdb returns custom object
268 TDB_FTSData row = (TDB_FTSData) _row;
269 String provider = (String) row.getProvider();
270 FilterOption providerOpt = new FilterOption(
271 "3DB Provider - " + provider,
272 FILTER_SOURCE_PREFIX + provider, VIEWS_FILTER, false, this);
273 if (!xtantOptions.contains(providerOpt))
275 xtantOptions.add(1, providerOpt);
276 tdBeaconsFilters.add(FILTER_SOURCE_PREFIX + provider);
277 if ("PDBe".equalsIgnoreCase(provider))
285 // remove the PDBe options from the available filters
287 while (op < xtantOptions.size())
289 FilterOption filter = xtantOptions.get(op);
291 .getQuerySource() instanceof PDBStructureChooserQuerySource)
293 xtantOptions.remove(op);
305 private boolean tdBeaconsFilter(String fieldToFilterBy)
307 return tdBeaconsFilters != null
308 && tdBeaconsFilters.contains(fieldToFilterBy);
311 private String remove_prefix(String fieldToFilterBy)
313 if (tdBeaconsFilters != null
314 && tdBeaconsFilters.contains(fieldToFilterBy)
315 && !defaultFilters.contains(fieldToFilterBy))
317 return fieldToFilterBy.substring(FILTER_SOURCE_PREFIX.length());
326 public boolean needsRefetch(FilterOption selectedFilterOpt)
328 return selectedFilterOpt == null
329 || !tdBeaconsFilter(selectedFilterOpt.getValue())
330 && lastPdbRequest != lastTdbRequest;
334 * FTSRestClient specific query builder to pick top ranked entry from a
335 * fetchStructuresMetaData query
338 * - seq to generate a query for
339 * @param wantedFields
340 * - fields to retrieve
341 * @param selectedFilterOpt
342 * - criterion for ranking results (e.g. resolution)
344 * - sort ascending or descending
348 public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
349 Collection<FTSData> collectedResults,
350 Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
351 boolean b) throws Exception
353 if (fieldToFilterBy != null && tdBeaconsFilter(fieldToFilterBy))
355 TDBResultAnalyser analyser = new TDBResultAnalyser(seq,
356 collectedResults, lastTdbRequest, fieldToFilterBy,
357 remove_prefix(fieldToFilterBy));
359 FTSRestResponse resultList = new FTSRestResponse();
361 List<FTSData> filteredResponse = analyser.getFilteredResponse();
363 List<FTSData> selectedStructures = analyser
364 .selectStructures(filteredResponse);
365 resultList.setNumberOfItemsFound(selectedStructures.size());
366 resultList.setSearchSummary(selectedStructures);
369 // Fall back to PDBe rankings
370 return getPDBQuerySource().selectFirstRankedQuery(seq, collectedResults,
371 wantedFields, fieldToFilterBy, b);
375 public PDBEntry[] collectSelectedRows(JTable restable, int[] selectedRows,
376 List<SequenceI> selectedSeqsToView)
378 int refSeqColIndex = restable.getColumn("Ref Sequence").getModelIndex();
380 PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
382 int idColumnIndex = restable.getColumn("Model id").getModelIndex();
383 int urlColumnIndex = restable.getColumn("Url").getModelIndex();
384 int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
385 int humanUrl = restable.getColumn("Page URL").getModelIndex();
386 int modelformat = restable.getColumn("Model Format").getModelIndex();
387 final int up_start_idx = restable.getColumn("Uniprot Start")
389 final int up_end_idx = restable.getColumn("Uniprot End")
394 Integer[] sellist = new Integer[selectedRows.length];
395 for (Integer row : selectedRows)
399 // Sort rows by coverage
400 Arrays.sort(sellist, new Comparator<Integer>()
403 public int compare(Integer o1, Integer o2)
405 int o1_xt = ((Integer) restable.getValueAt(o1, up_end_idx))
406 - (Integer) restable.getValueAt(o1, up_start_idx);
407 int o2_xt = ((Integer) restable.getValueAt(o2, up_end_idx))
408 - (Integer) restable.getValueAt(o2, up_start_idx);
409 return o2_xt - o1_xt;
413 for (int row : sellist)
415 // unique id - could be a horrible hash
417 String pdbIdStr = restable.getValueAt(row, idColumnIndex).toString();
418 String urlStr = restable.getValueAt(row, urlColumnIndex).toString();
419 String typeColumn = restable.getValueAt(row, typeColumnIndex)
421 String modelPage = humanUrl < 1 ? null
422 : (String) restable.getValueAt(row, humanUrl);
423 String strucFormat = restable.getValueAt(row, modelformat).toString();
425 SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
427 selectedSeqsToView.add(selectedSeq);
428 PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
429 if (pdbEntry == null)
431 pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries());
434 if (pdbEntry == null)
436 pdbEntry = new PDBEntry();
437 pdbEntry.setId(pdbIdStr);
438 pdbEntry.setAuthoritative(true);
441 pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
442 } catch (Exception q)
444 Console.warn("Unknown filetype for 3D Beacons Model from: "
445 + strucFormat + " - " + pdbIdStr + " - " + modelPage);
448 if (!"PDBe".equalsIgnoreCase(typeColumn))
450 pdbEntry.setRetrievalUrl(urlStr);
452 pdbEntry.setProvider(typeColumn);
453 pdbEntry.setProviderPage(modelPage);
454 selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
456 pdbEntriesToView[count++] = pdbEntry;
458 return pdbEntriesToView;
462 protected FTSRestRequest getLastFTSRequest()
464 return lastTdbRequest;
468 * generate a query for PDBFTS to retrieve structure metadata
470 * @param ftsRestRequest
475 public String buildPDBFTSQueryFor(FTSRestResponse upResponse)
477 Set<String> pdbIds = new HashSet<String>();
478 int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
479 int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
480 for (FTSData row : upResponse.getSearchSummary())
482 String id = (String) row.getSummaryData()[idx_modelId];
483 String provider = (String) row.getSummaryData()[idx_provider];
484 if ("PDBe".equalsIgnoreCase(provider))
489 return String.join(" OR ", pdbIds).toString();
493 * query PDBe for structure metadata
497 * @return FTSRestResponse via PDBStructureChooserQuerySource
499 public FTSRestResponse fetchStructuresMetaDataFor(
500 PDBStructureChooserQuerySource pdbquery,
501 FTSRestResponse upResponse) throws Exception
504 String pdb_Query = buildPDBFTSQueryFor(upResponse);
505 if (pdb_Query.length() == 0)
509 FTSRestResponse resultList;
510 FTSRestRequest pdbRequest = new FTSRestRequest();
511 pdbRequest.setAllowEmptySeq(false);
512 pdbRequest.setResponseSize(500);
513 pdbRequest.setFieldToSearchBy("(");
514 // pdbRequest.setFieldToSortBy("pdb_id");
515 pdbRequest.setWantedFields(
516 pdbquery.getDocFieldPrefs().getStructureSummaryFields());
517 pdbRequest.setSearchTerm(pdb_Query + ")");
519 resultList = pdbquery.executePDBFTSRestRequest(pdbRequest);
521 lastPdbRequest = pdbRequest;
525 public FTSRestResponse joinResponses(FTSRestResponse upResponse,
526 FTSRestResponse pdbResponse)
528 boolean hasPdbResp = lastPdbRequest != null;
530 int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
532 int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
533 int pdbIdx = hasPdbResp ? lastPdbRequest.getFieldIndex("PDB Id") : -1;
534 int pdbTitle_idx = hasPdbResp ? lastPdbRequest.getFieldIndex("Title")
536 int tdbTitle_idx = getLastFTSRequest().getFieldIndex("Title");
538 for (final FTSData row : upResponse.getSearchSummary())
540 String id = (String) row.getSummaryData()[idx_modelId];
541 String provider = (String) row.getSummaryData()[idx_provider];
542 if ("PDBe".equalsIgnoreCase(provider))
547 "Warning: seems like we couldn't get to the PDBe search interface.");
551 for (final FTSData pdbrow : pdbResponse.getSearchSummary())
553 String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
554 if (id.equalsIgnoreCase(pdbid))
556 row.getSummaryData()[tdbTitle_idx] = pdbrow
557 .getSummaryData()[pdbTitle_idx];
565 row.getSummaryData()[tdbTitle_idx] = "Model from TDB";
571 public TDB_FTSData getFTSDataFor(JTable restable, int selectedRow,
572 Collection<FTSData> discoveredStructuresSet)
574 int idColumnIndex = restable.getColumn("Model id").getModelIndex();
576 String modelId = (String) restable.getValueAt(selectedRow,
578 for (FTSData row : discoveredStructuresSet)
580 if (row instanceof TDB_FTSData
581 && ((TDB_FTSData) row).getModelId().equals(modelId))
583 return ((TDB_FTSData) row);