import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
import jalview.fts.core.FTSDataColumnPreferences;
protected FTSRestClientI tdbRestClient;
+ private FTSRestRequest lastPdbRequest;
+
public ThreeDBStructureChooserQuerySource()
{
tdbRestClient = TDBeaconsFTSRestClient.getInstance();
}
-
/**
- * Builds a query string for a given sequences using its DBRef entries
- * 3d Beacons is only useful for uniprot IDs
+ * Builds a query string for a given sequences using its DBRef entries 3d
+ * Beacons is only useful for uniprot IDs
+ *
* @param seq
* the sequences to build a query for
* @return the built query string
if (isValidSeqName(getDBRefId(dbRef))
&& queryBuilder.length() < MAX_QLENGTH)
{
- if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) && dbRef.isCanonical())
+ if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)
+ && dbRef.isCanonical())
{
- // TODO: pick best Uniprot accession
- isUniProtRefsFound=true;
+ // TODO: pick best Uniprot accession
+ isUniProtRefsFound = true;
return getDBRefId(dbRef);
-
+
}
}
}
return null;
}
-
-
/**
* Ensures sequence ref names are not less than 3 characters and does not
* contain a database name
lastTdbRequest = tdbRequest;
return resultList;
}
-
- private FTSRestRequest getTDBeaconsRequest(SequenceI seq, Collection<FTSDataColumnI> wantedFields)
+ private FTSRestRequest getTDBeaconsRequest(SequenceI seq,
+ Collection<FTSDataColumnI> wantedFields)
{
FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(500);
pdbRequest.setWantedFields(wantedFields);
String query = buildQuery(seq);
- if (query==null) {
+ if (query == null)
+ {
return null;
}
pdbRequest.setSearchTerm(query + ".json");
return pdbRequest;
}
-@Override
+ @Override
public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
{
List<FilterOption> filters = new ArrayList<FilterOption>();
+ filters.add(
+ new FilterOption(MessageManager.getString("label.best_quality"),
+ "overall_quality", VIEWS_FILTER, false));
filters.add(new FilterOption(
- MessageManager.getString("label.best_quality"),
- "overall_quality", VIEWS_FILTER, false));
- filters.add(new FilterOption(
- MessageManager.getString("label.best_resolution"),
- "resolution", VIEWS_FILTER, false));
+ MessageManager.getString("label.best_resolution"), "resolution",
+ VIEWS_FILTER, false));
filters.add(new FilterOption(
MessageManager.getString("label.most_protein_chain"),
"number_of_protein_chains", VIEWS_FILTER, false));
filters.add(new FilterOption(
MessageManager.getString("label.most_polymer_residues"),
"number_of_polymer_residues", VIEWS_FILTER, true));
-
+
return filters;
}
+
/**
* FTSRestClient specific query builder to pick top ranked entry from a
* fetchStructuresMetaData query
FTSRestResponse resultList;
FTSRestRequest pdbRequest = getTDBeaconsRequest(seq, wantedFields);
- if (pdbRequest == null) {
+ if (pdbRequest == null)
+ {
return null;
}
pdbRequest.setResponseSize(1);
resultList = tdbRestClient.executeRequest(pdbRequest);
-
+
// TODO: client side filtering - sort results and pick top one (or N)
lastTdbRequest = pdbRequest;
public PDBEntry[] collectSelectedRows(JTable restable, int[] selectedRows,
List<SequenceI> selectedSeqsToView)
{
- int refSeqColIndex = restable.getColumn("Ref Sequence")
- .getModelIndex();
+ int refSeqColIndex = restable.getColumn("Ref Sequence").getModelIndex();
- PDBEntry[] pdbEntriesToView=new PDBEntry[selectedRows.length];
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
int idColumnIndex = restable.getColumn("Model id").getModelIndex();
int urlColumnIndex = restable.getColumn("Url").getModelIndex();
int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
- int categoryColumnIndex = restable.getColumn("Model Category").getModelIndex();
-
+ int categoryColumnIndex = restable.getColumn("Model Category")
+ .getModelIndex();
+
for (int row : selectedRows)
{
// unique id - could be a horrible hash
-
- String pdbIdStr = restable.getValueAt(row,idColumnIndex)
- .toString();
- String urlStr = restable.getValueAt(row,urlColumnIndex)
- .toString();
- String typeColumn = restable.getValueAt(row,typeColumnIndex)
+
+ String pdbIdStr = restable.getValueAt(row, idColumnIndex).toString();
+ String urlStr = restable.getValueAt(row, urlColumnIndex).toString();
+ String typeColumn = restable.getValueAt(row, typeColumnIndex)
.toString();
SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
refSeqColIndex);
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
{
- pdbEntry = getFindEntry(pdbIdStr,
- selectedSeq.getAllPDBEntries());
+ pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries());
}
if (pdbEntry == null)
return pdbEntriesToView;
}
-
@Override
protected FTSRestRequest getLastFTSRequest()
{
return lastTdbRequest;
}
+
+ /**
+ * generate a query for PDBFTS to retrieve structure metadata
+ *
+ * @param ftsRestRequest
+ * @param upResponse
+ * @return
+ */
+
+ public String buildPDBFTSQueryFor(FTSRestResponse upResponse)
+ {
+ List<String> pdbIds = new ArrayList<String>();
+ int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
+ int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
+ for (FTSData row : upResponse.getSearchSummary())
+ {
+ String id = (String) row.getSummaryData()[idx_modelId];
+ String provider = (String) row.getSummaryData()[idx_provider];
+ if ("PDBe".equalsIgnoreCase(provider))
+ {
+ pdbIds.add(id);
+ }
+ }
+ return String.join(" OR ", pdbIds).toString();
+ }
+
+ /**
+ * query PDBe for structure metadata
+ *
+ * @param pdbquery
+ * @param upResponse
+ * @return FTSRestResponse via PDBStructureChooserQuerySource
+ */
+ public FTSRestResponse fetchStructuresMetaDataFor(
+ PDBStructureChooserQuerySource pdbquery,
+ FTSRestResponse upResponse) throws Exception
+ {
+
+ String pdb_Query = buildPDBFTSQueryFor(upResponse);
+
+ FTSRestResponse resultList;
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setFieldToSearchBy("(");
+ // pdbRequest.setFieldToSortBy("pdb_id");
+ pdbRequest.setWantedFields(
+ pdbquery.getDocFieldPrefs().getStructureSummaryFields());
+ pdbRequest.setSearchTerm(pdb_Query + ")");
+ resultList = pdbquery.executePDBFTSRestRequest(pdbRequest);
+
+ lastPdbRequest = pdbRequest;
+ return resultList;
+ }
+
+ public FTSRestResponse joinResponses(FTSRestResponse upResponse,
+ FTSRestResponse pdbResponse)
+ {
+ int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
+ // join on
+ int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
+ int pdbIdx = lastPdbRequest.getFieldIndex("pdb_id");
+ for (FTSData row : upResponse.getSearchSummary())
+ {
+ String id = (String) row.getSummaryData()[idx_modelId];
+ String provider = (String) row.getSummaryData()[idx_provider];
+ if ("PDBe".equalsIgnoreCase(provider))
+ {
+ for (FTSData pdbrow : pdbResponse.getSearchSummary())
+ {
+ String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
+ if (id.equalsIgnoreCase(pdbid))
+ {
+ // often multiple entries per PDB ID so we bail after first
+ // get wanted fields
+ // append to FTSRestResponse array
+ }
+ }
+ }
+ }
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff