import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
-import java.util.Collections;
import java.util.Comparator;
import java.util.HashSet;
import java.util.LinkedHashSet;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
import jalview.jbgui.FilterOption;
-import jalview.util.MessageManager;
/**
* logic for querying the 3DBeacons API for structures of sequences
Set<String> pdbids = new HashSet<>();
List<DBRefEntry> refs = seq.getDBRefs();
+ int ib = checkUniprotRefs(refs);
+ if (ib>-1)
+ {
+ return getDBRefId(refs.get(ib));
+ }
+ return null;
+ }
+
+ /**
+ * Searches DBRefEntry for uniprot refs
+ * @param seq
+ * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of Uniprot canonical DBRefEntry
+ */
+ public static int checkUniprotRefs(List<DBRefEntry> refs)
+ {
+ boolean hasUniprot = false;
if (refs != null && refs.size() != 0)
{
for (int ib = 0, nb = refs.size(); ib < nb; ib++)
{
DBRefEntry dbRef = refs.get(ib);
- if (isValidSeqName(getDBRefId(dbRef))
- && queryBuilder.length() < MAX_QLENGTH)
+ if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
- if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)
- && dbRef.isCanonical())
+ hasUniprot = true;
+ if (dbRef.isCanonical())
{
- // TODO: pick best Uniprot accession
- isUniProtRefsFound = true;
- return getDBRefId(dbRef);
-
+ return ib;
}
}
}
}
- return null;
+ return hasUniprot ? -1 : -2;
}
/**
FilterOption selectedFilterOpt, boolean b) throws Exception
{
FTSRestResponse resultList;
- if (selectedFilterOpt!=null && tdBeaconsFilter(selectedFilterOpt.getValue()))
+ if (selectedFilterOpt != null
+ && tdBeaconsFilter(selectedFilterOpt.getValue()))
{
FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
resultList = tdbRestClient.executeRequest(tdbRequest);
-
+
lastTdbRequest = tdbRequest;
-
- // Query the PDB and add additional metadata
- FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
- getPDBQuerySource(), resultList);
- FTSRestResponse joinedResp = joinResponses(resultList, pdbResponse);
+ if (resultList!=null)
+ { // Query the PDB and add additional metadata
+ FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
+ getPDBQuerySource(), resultList);
+ FTSRestResponse joinedResp = joinResponses(resultList, pdbResponse);
+ }
return resultList;
}
// use the PDBFTS directly
wantedFields, selectedFilterOpt, b);
lastTdbRequest = getPDBQuerySource().lastPdbRequest;
lastPdbRequest = lastTdbRequest; // both queries the same - indicates we
- // rank using PDBe
+ // rank using PDBe
return resultList;
}
public void updateAvailableFilterOptions(String VIEWS_FILTER,
List<FilterOption> xtantOptions, Collection<FTSData> tdbEntries)
{
- if (tdbEntries !=null && lastTdbRequest != null)
+ if (tdbEntries != null && lastTdbRequest != null)
{
int prov_idx = lastTdbRequest.getFieldIndex("Provider");
-
+ boolean hasPDBe=false;
for (FTSData row : tdbEntries)
{
String provider = (String) row.getSummaryData()[prov_idx];
- FilterOption providerOpt = new FilterOption("3DB Provider - " + provider,
- FILTER_SOURCE_PREFIX + provider, VIEWS_FILTER,
- false, this);
+ FilterOption providerOpt = new FilterOption(
+ "3DB Provider - " + provider,
+ FILTER_SOURCE_PREFIX + provider, VIEWS_FILTER, false, this);
if (!xtantOptions.contains(providerOpt))
{
- xtantOptions.add(1,
- providerOpt);
- tdBeaconsFilters.add(FILTER_SOURCE_PREFIX+provider);
-
+ xtantOptions.add(1, providerOpt);
+ tdBeaconsFilters.add(FILTER_SOURCE_PREFIX + provider);
+ if ("PDBe".equalsIgnoreCase(provider))
+ {
+ hasPDBe=true;
+ }
+ }
+ }
+ if (!hasPDBe)
+ {
+ // remove the PDBe options from the available filters
+ int op=0;
+ while (op<xtantOptions.size())
+ {
+ FilterOption filter = xtantOptions.get(op);
+ if (filter.getQuerySource() instanceof PDBStructureChooserQuerySource)
+ {
+ xtantOptions.remove(op);
+ } else {
+ op++;
+ }
}
}
}
@Override
public boolean needsRefetch(FilterOption selectedFilterOpt)
{
- return selectedFilterOpt==null || !tdBeaconsFilter(selectedFilterOpt.getValue())
- && lastPdbRequest != lastTdbRequest;
+ return selectedFilterOpt == null
+ || !tdBeaconsFilter(selectedFilterOpt.getValue())
+ && lastPdbRequest != lastTdbRequest;
}
/**
Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
boolean b) throws Exception
{
- if (fieldToFilterBy!=null && tdBeaconsFilter(fieldToFilterBy))
+ if (fieldToFilterBy != null && tdBeaconsFilter(fieldToFilterBy))
{
TDBResultAnalyser analyser = new TDBResultAnalyser(seq,
collectedResults, lastTdbRequest, fieldToFilterBy,
int idColumnIndex = restable.getColumn("Model id").getModelIndex();
int urlColumnIndex = restable.getColumn("Url").getModelIndex();
int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
+ int humanUrl = restable.getColumn("Page URL").getModelIndex();
int categoryColumnIndex = restable.getColumn("Model Category")
.getModelIndex();
final int up_start_idx = restable.getColumn("Uniprot Start")
String urlStr = restable.getValueAt(row, urlColumnIndex).toString();
String typeColumn = restable.getValueAt(row, typeColumnIndex)
.toString();
+ String modelPage = humanUrl < 1 ? null
+ : (String) restable.getValueAt(row, humanUrl);
SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
pdbEntry = new PDBEntry();
pdbEntry.setId(pdbIdStr);
boolean hasCif = urlStr.toLowerCase(Locale.ENGLISH).endsWith("cif");
- boolean probablyPdb = urlStr.toLowerCase(Locale.ENGLISH).contains("pdb");
- pdbEntry.setType(hasCif ? PDBEntry.Type.MMCIF : probablyPdb ? PDBEntry.Type.PDB : PDBEntry.Type.FILE);
+ boolean probablyPdb = urlStr.toLowerCase(Locale.ENGLISH)
+ .contains("pdb");
+ pdbEntry.setType(hasCif ? PDBEntry.Type.MMCIF
+ : probablyPdb ? PDBEntry.Type.PDB : PDBEntry.Type.FILE);
if (!"PDBe".equalsIgnoreCase(typeColumn))
{
pdbEntry.setRetrievalUrl(urlStr);
}
+ pdbEntry.setProvider(typeColumn);
+ pdbEntry.setProviderPage(modelPage);
selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
}
pdbEntriesToView[count++] = pdbEntry;
{
String pdb_Query = buildPDBFTSQueryFor(upResponse);
- if (pdb_Query.length()==0)
+ if (pdb_Query.length() == 0)
{
return null;
}
pdbRequest.setWantedFields(
pdbquery.getDocFieldPrefs().getStructureSummaryFields());
pdbRequest.setSearchTerm(pdb_Query + ")");
-
+
resultList = pdbquery.executePDBFTSRestRequest(pdbRequest);
lastPdbRequest = pdbRequest;
public FTSRestResponse joinResponses(FTSRestResponse upResponse,
FTSRestResponse pdbResponse)
{
+ boolean hasPdbResp = lastPdbRequest != null;
+
int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
// join on
int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
- int pdbIdx = lastPdbRequest.getFieldIndex("PDB Id");
- int pdbTitle_idx = lastPdbRequest.getFieldIndex("Title");
+ int pdbIdx = hasPdbResp ? lastPdbRequest.getFieldIndex("PDB Id") : -1;
+ int pdbTitle_idx = hasPdbResp ? lastPdbRequest.getFieldIndex("Title")
+ : -1;
int tdbTitle_idx = getLastFTSRequest().getFieldIndex("Title");
List<FTSData> joinedRows = new ArrayList<FTSData>();
String provider = (String) row.getSummaryData()[idx_provider];
if ("PDBe".equalsIgnoreCase(provider))
{
- for (final FTSData pdbrow : pdbResponse.getSearchSummary())
+ if (!hasPdbResp)
{
- String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
- if (id.equalsIgnoreCase(pdbid))
+ System.out.println(
+ "Warning: seems like we couldn't get to the PDBe search interface.");
+ }
+ else
+ {
+ for (final FTSData pdbrow : pdbResponse.getSearchSummary())
{
- row.getSummaryData()[tdbTitle_idx] = pdbrow
- .getSummaryData()[pdbTitle_idx];
+ String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
+ if (id.equalsIgnoreCase(pdbid))
+ {
+ row.getSummaryData()[tdbTitle_idx] = pdbrow
+ .getSummaryData()[pdbTitle_idx];
+ }
}
}
+
}
else
{
git://source.jalview.org / jalview.git / blobdiff