1 package jalview.gui.structurechooser;
3 import java.util.ArrayList;
4 import java.util.Arrays;
5 import java.util.Collection;
6 import java.util.Comparator;
7 import java.util.HashSet;
8 import java.util.LinkedHashSet;
10 import java.util.Locale;
13 import javax.swing.JTable;
15 import jalview.datamodel.DBRefEntry;
16 import jalview.datamodel.DBRefSource;
17 import jalview.datamodel.PDBEntry;
18 import jalview.datamodel.SequenceI;
19 import jalview.fts.api.FTSData;
20 import jalview.fts.api.FTSDataColumnI;
21 import jalview.fts.api.FTSRestClientI;
22 import jalview.fts.core.FTSDataColumnPreferences;
23 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
24 import jalview.fts.core.FTSRestRequest;
25 import jalview.fts.core.FTSRestResponse;
26 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
27 import jalview.jbgui.FilterOption;
30 * logic for querying the 3DBeacons API for structures of sequences
34 public class ThreeDBStructureChooserQuerySource
35 extends StructureChooserQuerySource
38 private Set<String> tdBeaconsFilters = null, defaultFilters = null;
40 public static final String FILTER_TDBEACONS_COVERAGE = "3d_beacons_coverage";
42 public static final String FILTER_FIRST_BEST_COVERAGE = "3d_beacons_first_best_coverage";
44 private static final String FILTER_SOURCE_PREFIX = "only_";
46 private static int MAX_QLENGTH = 7820;
48 protected FTSRestRequest lastTdbRequest;
50 protected FTSRestClientI tdbRestClient;
52 private FTSRestRequest lastPdbRequest;
54 public ThreeDBStructureChooserQuerySource()
56 defaultFilters = new LinkedHashSet<String>();
57 defaultFilters.add(FILTER_TDBEACONS_COVERAGE);
58 defaultFilters.add(FILTER_FIRST_BEST_COVERAGE);
60 tdbRestClient = TDBeaconsFTSRestClient.getInstance();
61 docFieldPrefs = new FTSDataColumnPreferences(
62 PreferenceSource.STRUCTURE_CHOOSER,
63 TDBeaconsFTSRestClient.getInstance());
67 * Builds a query string for a given sequences using its DBRef entries 3d
68 * Beacons is only useful for uniprot IDs
71 * the sequences to build a query for
72 * @return the built query string
75 public String buildQuery(SequenceI seq)
77 boolean isPDBRefsFound = false;
78 boolean isUniProtRefsFound = false;
79 StringBuilder queryBuilder = new StringBuilder();
80 Set<String> seqRefs = new LinkedHashSet<>();
83 * note PDBs as DBRefEntry so they are not duplicated in query
85 Set<String> pdbids = new HashSet<>();
87 List<DBRefEntry> refs = seq.getDBRefs();
88 int ib = checkUniprotRefs(refs);
91 return getDBRefId(refs.get(ib));
97 * Searches DBRefEntry for uniprot refs
99 * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of Uniprot canonical DBRefEntry
101 public static int checkUniprotRefs(List<DBRefEntry> refs)
103 boolean hasUniprot = false;
104 if (refs != null && refs.size() != 0)
106 for (int ib = 0, nb = refs.size(); ib < nb; ib++)
108 DBRefEntry dbRef = refs.get(ib);
109 if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
112 if (dbRef.isCanonical())
119 return hasUniprot ? -1 : -2;
123 * Ensures sequence ref names are not less than 3 characters and does not
124 * contain a database name
129 static boolean isValidSeqName(String seqName)
131 // System.out.println("seqName : " + seqName);
132 String ignoreList = "pdb,uniprot,swiss-prot";
133 if (seqName.length() < 3)
137 if (seqName.contains(":"))
141 seqName = seqName.toLowerCase(Locale.ROOT);
142 for (String ignoredEntry : ignoreList.split(","))
144 if (seqName.contains(ignoredEntry))
152 static String getDBRefId(DBRefEntry dbRef)
154 String ref = dbRef.getAccessionId().replaceAll("GO:", "");
159 * FTSRestClient specific query builder to recover associated structure data
160 * records for a sequence
163 * - seq to generate a query for
164 * @param wantedFields
165 * - fields to retrieve
166 * @param selectedFilterOpt
167 * - criterion for ranking results (e.g. resolution)
169 * - sort ascending or descending
173 public FTSRestResponse fetchStructuresMetaData(SequenceI seq,
174 Collection<FTSDataColumnI> wantedFields,
175 FilterOption selectedFilterOpt, boolean b) throws Exception
177 FTSRestResponse resultList;
178 if (selectedFilterOpt != null
179 && tdBeaconsFilter(selectedFilterOpt.getValue()))
181 FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
182 resultList = tdbRestClient.executeRequest(tdbRequest);
184 lastTdbRequest = tdbRequest;
185 if (resultList!=null)
186 { // Query the PDB and add additional metadata
187 FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
188 getPDBQuerySource(), resultList);
189 FTSRestResponse joinedResp = joinResponses(resultList, pdbResponse);
193 // use the PDBFTS directly
194 resultList = getPDBQuerySource().fetchStructuresMetaData(seq,
195 wantedFields, selectedFilterOpt, b);
196 lastTdbRequest = getPDBQuerySource().lastPdbRequest;
197 lastPdbRequest = lastTdbRequest; // both queries the same - indicates we
203 PDBStructureChooserQuerySource pdbQuerySource = null;
205 private PDBStructureChooserQuerySource getPDBQuerySource()
207 if (pdbQuerySource == null)
209 pdbQuerySource = new PDBStructureChooserQuerySource();
211 return pdbQuerySource;
214 private FTSRestRequest getTDBeaconsRequest(SequenceI seq,
215 Collection<FTSDataColumnI> wantedFields)
217 FTSRestRequest pdbRequest = new FTSRestRequest();
218 pdbRequest.setAllowEmptySeq(false);
219 pdbRequest.setResponseSize(500);
220 pdbRequest.setWantedFields(wantedFields);
221 String query = buildQuery(seq);
226 pdbRequest.setSearchTerm(query + ".json");
227 pdbRequest.setAssociatedSequence(seq);
232 public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
234 List<FilterOption> filters = getPDBQuerySource()
235 .getAvailableFilterOptions(VIEWS_FILTER);
236 tdBeaconsFilters = new LinkedHashSet<String>();
237 tdBeaconsFilters.addAll(defaultFilters);
238 filters.add(0, new FilterOption("Best 3D-Beacons Coverage",
239 FILTER_FIRST_BEST_COVERAGE, VIEWS_FILTER, false, this));
240 filters.add(1, new FilterOption("Multiple 3D-Beacons Coverage",
241 FILTER_TDBEACONS_COVERAGE, VIEWS_FILTER, true, this));
247 public void updateAvailableFilterOptions(String VIEWS_FILTER,
248 List<FilterOption> xtantOptions, Collection<FTSData> tdbEntries)
250 if (tdbEntries != null && lastTdbRequest != null)
252 int prov_idx = lastTdbRequest.getFieldIndex("Provider");
253 boolean hasPDBe=false;
254 for (FTSData row : tdbEntries)
256 String provider = (String) row.getSummaryData()[prov_idx];
257 FilterOption providerOpt = new FilterOption(
258 "3DB Provider - " + provider,
259 FILTER_SOURCE_PREFIX + provider, VIEWS_FILTER, false, this);
260 if (!xtantOptions.contains(providerOpt))
262 xtantOptions.add(1, providerOpt);
263 tdBeaconsFilters.add(FILTER_SOURCE_PREFIX + provider);
264 if ("PDBe".equalsIgnoreCase(provider))
272 // remove the PDBe options from the available filters
274 while (op<xtantOptions.size())
276 FilterOption filter = xtantOptions.get(op);
277 if (filter.getQuerySource() instanceof PDBStructureChooserQuerySource)
279 xtantOptions.remove(op);
289 private boolean tdBeaconsFilter(String fieldToFilterBy)
291 return tdBeaconsFilters != null
292 && tdBeaconsFilters.contains(fieldToFilterBy);
295 private String remove_prefix(String fieldToFilterBy)
297 if (tdBeaconsFilters != null
298 && tdBeaconsFilters.contains(fieldToFilterBy)
299 && !defaultFilters.contains(fieldToFilterBy))
301 return fieldToFilterBy.substring(FILTER_SOURCE_PREFIX.length());
310 public boolean needsRefetch(FilterOption selectedFilterOpt)
312 return selectedFilterOpt == null
313 || !tdBeaconsFilter(selectedFilterOpt.getValue())
314 && lastPdbRequest != lastTdbRequest;
318 * FTSRestClient specific query builder to pick top ranked entry from a
319 * fetchStructuresMetaData query
322 * - seq to generate a query for
323 * @param wantedFields
324 * - fields to retrieve
325 * @param selectedFilterOpt
326 * - criterion for ranking results (e.g. resolution)
328 * - sort ascending or descending
332 public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
333 Collection<FTSData> collectedResults,
334 Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
335 boolean b) throws Exception
337 if (fieldToFilterBy != null && tdBeaconsFilter(fieldToFilterBy))
339 TDBResultAnalyser analyser = new TDBResultAnalyser(seq,
340 collectedResults, lastTdbRequest, fieldToFilterBy,
341 remove_prefix(fieldToFilterBy));
343 FTSRestResponse resultList = new FTSRestResponse();
345 List<FTSData> filteredResponse = analyser.getFilteredResponse();
347 List<FTSData> selectedStructures = analyser
348 .selectStructures(filteredResponse);
349 resultList.setNumberOfItemsFound(selectedStructures.size());
350 resultList.setSearchSummary(selectedStructures);
353 // Fall back to PDBe rankings
354 return getPDBQuerySource().selectFirstRankedQuery(seq, collectedResults,
355 wantedFields, fieldToFilterBy, b);
359 public PDBEntry[] collectSelectedRows(JTable restable, int[] selectedRows,
360 List<SequenceI> selectedSeqsToView)
362 int refSeqColIndex = restable.getColumn("Ref Sequence").getModelIndex();
364 PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
366 int idColumnIndex = restable.getColumn("Model id").getModelIndex();
367 int urlColumnIndex = restable.getColumn("Url").getModelIndex();
368 int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
369 int humanUrl = restable.getColumn("Page URL").getModelIndex();
370 int categoryColumnIndex = restable.getColumn("Model Category")
372 final int up_start_idx = restable.getColumn("Uniprot Start")
374 final int up_end_idx = restable.getColumn("Uniprot End")
379 Integer[] sellist = new Integer[selectedRows.length];
380 for (Integer row : selectedRows)
384 // Sort rows by coverage
385 Arrays.sort(sellist, new Comparator<Integer>()
388 public int compare(Integer o1, Integer o2)
390 int o1_xt = ((Integer) restable.getValueAt(o1, up_end_idx))
391 - (Integer) restable.getValueAt(o1, up_start_idx);
392 int o2_xt = ((Integer) restable.getValueAt(o2, up_end_idx))
393 - (Integer) restable.getValueAt(o2, up_start_idx);
394 return o2_xt - o1_xt;
398 for (int row : sellist)
400 // unique id - could be a horrible hash
402 String pdbIdStr = restable.getValueAt(row, idColumnIndex).toString();
403 String urlStr = restable.getValueAt(row, urlColumnIndex).toString();
404 String typeColumn = restable.getValueAt(row, typeColumnIndex)
406 String modelPage = humanUrl < 1 ? null
407 : (String) restable.getValueAt(row, humanUrl);
408 SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
410 selectedSeqsToView.add(selectedSeq);
411 PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
412 if (pdbEntry == null)
414 pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries());
417 if (pdbEntry == null)
419 pdbEntry = new PDBEntry();
420 pdbEntry.setId(pdbIdStr);
421 boolean hasCif = urlStr.toLowerCase(Locale.ENGLISH).endsWith("cif");
422 boolean probablyPdb = urlStr.toLowerCase(Locale.ENGLISH)
424 pdbEntry.setType(hasCif ? PDBEntry.Type.MMCIF
425 : probablyPdb ? PDBEntry.Type.PDB : PDBEntry.Type.FILE);
426 if (!"PDBe".equalsIgnoreCase(typeColumn))
428 pdbEntry.setRetrievalUrl(urlStr);
430 pdbEntry.setProvider(typeColumn);
431 pdbEntry.setProviderPage(modelPage);
432 selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
434 pdbEntriesToView[count++] = pdbEntry;
436 return pdbEntriesToView;
440 protected FTSRestRequest getLastFTSRequest()
442 return lastTdbRequest;
446 * generate a query for PDBFTS to retrieve structure metadata
448 * @param ftsRestRequest
453 public String buildPDBFTSQueryFor(FTSRestResponse upResponse)
455 List<String> pdbIds = new ArrayList<String>();
456 int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
457 int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
458 for (FTSData row : upResponse.getSearchSummary())
460 String id = (String) row.getSummaryData()[idx_modelId];
461 String provider = (String) row.getSummaryData()[idx_provider];
462 if ("PDBe".equalsIgnoreCase(provider))
467 return String.join(" OR ", pdbIds).toString();
471 * query PDBe for structure metadata
475 * @return FTSRestResponse via PDBStructureChooserQuerySource
477 public FTSRestResponse fetchStructuresMetaDataFor(
478 PDBStructureChooserQuerySource pdbquery,
479 FTSRestResponse upResponse) throws Exception
482 String pdb_Query = buildPDBFTSQueryFor(upResponse);
483 if (pdb_Query.length() == 0)
487 FTSRestResponse resultList;
488 FTSRestRequest pdbRequest = new FTSRestRequest();
489 pdbRequest.setAllowEmptySeq(false);
490 pdbRequest.setResponseSize(500);
491 pdbRequest.setFieldToSearchBy("(");
492 // pdbRequest.setFieldToSortBy("pdb_id");
493 pdbRequest.setWantedFields(
494 pdbquery.getDocFieldPrefs().getStructureSummaryFields());
495 pdbRequest.setSearchTerm(pdb_Query + ")");
497 resultList = pdbquery.executePDBFTSRestRequest(pdbRequest);
499 lastPdbRequest = pdbRequest;
503 public FTSRestResponse joinResponses(FTSRestResponse upResponse,
504 FTSRestResponse pdbResponse)
506 boolean hasPdbResp = lastPdbRequest != null;
508 int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
510 int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
511 int pdbIdx = hasPdbResp ? lastPdbRequest.getFieldIndex("PDB Id") : -1;
512 int pdbTitle_idx = hasPdbResp ? lastPdbRequest.getFieldIndex("Title")
514 int tdbTitle_idx = getLastFTSRequest().getFieldIndex("Title");
516 List<FTSData> joinedRows = new ArrayList<FTSData>();
517 for (final FTSData row : upResponse.getSearchSummary())
519 String id = (String) row.getSummaryData()[idx_modelId];
520 String provider = (String) row.getSummaryData()[idx_provider];
521 if ("PDBe".equalsIgnoreCase(provider))
526 "Warning: seems like we couldn't get to the PDBe search interface.");
530 for (final FTSData pdbrow : pdbResponse.getSearchSummary())
532 String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
533 if (id.equalsIgnoreCase(pdbid))
535 row.getSummaryData()[tdbTitle_idx] = pdbrow
536 .getSummaryData()[pdbTitle_idx];
544 row.getSummaryData()[tdbTitle_idx] = "Model from TDB";