package jalview.gui.structurechooser;
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 java.util.List;
+import java.util.Locale;
import java.util.Set;
import javax.swing.JTable;
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;
import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.core.FTSRestRequest;
import jalview.util.MessageManager;
/**
- * logic for querying the PDBe API for structures of sequences
+ * logic for querying the 3DBeacons API for structures of sequences
*
* @author jprocter
*/
extends StructureChooserQuerySource
{
+ private Set<String> tdBeaconsFilters = null, defaultFilters = null;
+
+ public static final String FILTER_TDBEACONS_COVERAGE = "3d_beacons_coverage";
+
+ public static final String FILTER_FIRST_BEST_COVERAGE = "3d_beacons_first_best_coverage";
+
+ private static final String FILTER_SOURCE_PREFIX = "only_";
+
private static int MAX_QLENGTH = 7820;
+ protected FTSRestRequest lastTdbRequest;
+
+ protected FTSRestClientI tdbRestClient;
+
+ private FTSRestRequest lastPdbRequest;
+
public ThreeDBStructureChooserQuerySource()
{
- pdbRestClient = TDBeaconsFTSRestClient.getInstance();
+ defaultFilters = new LinkedHashSet<String>();
+ defaultFilters.add(FILTER_TDBEACONS_COVERAGE);
+ defaultFilters.add(FILTER_FIRST_BEST_COVERAGE);
+
+ tdbRestClient = TDBeaconsFTSRestClient.getInstance();
docFieldPrefs = new FTSDataColumnPreferences(
PreferenceSource.STRUCTURE_CHOOSER,
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
FilterOption selectedFilterOpt, boolean b) throws Exception
{
FTSRestResponse resultList;
- FTSRestRequest pdbRequest = getTDBeaconsRequest(seq, wantedFields);
- resultList = pdbRestClient.executeRequest(pdbRequest);
+ if (selectedFilterOpt!=null && tdBeaconsFilter(selectedFilterOpt.getValue()))
+ {
+ FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
+ resultList = tdbRestClient.executeRequest(tdbRequest);
- lastPdbRequest = pdbRequest;
+ lastTdbRequest = tdbRequest;
+
+ // Query the PDB and add additional metadata
+ FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
+ getPDBQuerySource(), resultList);
+ FTSRestResponse joinedResp = joinResponses(resultList, pdbResponse);
+ return resultList;
+ }
+ // use the PDBFTS directly
+ resultList = getPDBQuerySource().fetchStructuresMetaData(seq,
+ wantedFields, selectedFilterOpt, b);
+ lastTdbRequest = getPDBQuerySource().lastPdbRequest;
+ lastPdbRequest = lastTdbRequest; // both queries the same - indicates we
+ // rank using PDBe
return resultList;
+
}
-
- private FTSRestRequest getTDBeaconsRequest(SequenceI seq, Collection<FTSDataColumnI> wantedFields)
+ PDBStructureChooserQuerySource pdbQuerySource = null;
+
+ private PDBStructureChooserQuerySource getPDBQuerySource()
+ {
+ if (pdbQuerySource == null)
+ {
+ pdbQuerySource = new PDBStructureChooserQuerySource();
+ }
+ return pdbQuerySource;
+ }
+
+ 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_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_bound_molecules"),
- "number_of_bound_molecules", VIEWS_FILTER, false));
- filters.add(new FilterOption(
- MessageManager.getString("label.most_polymer_residues"),
- "number_of_polymer_residues", VIEWS_FILTER, true));
-
+ List<FilterOption> filters = getPDBQuerySource()
+ .getAvailableFilterOptions(VIEWS_FILTER);
+ tdBeaconsFilters = new LinkedHashSet<String>();
+ tdBeaconsFilters.addAll(defaultFilters);
+ filters.add(0, new FilterOption("Best 3D-Beacons Coverage",
+ FILTER_FIRST_BEST_COVERAGE, VIEWS_FILTER, false, this));
+ filters.add(1, new FilterOption("Multiple 3D-Beacons Coverage",
+ FILTER_TDBEACONS_COVERAGE, VIEWS_FILTER, true, this));
+
return filters;
}
+
+ @Override
+ public void updateAvailableFilterOptions(String VIEWS_FILTER,
+ List<FilterOption> xtantOptions, Collection<FTSData> tdbEntries)
+ {
+ if (tdbEntries !=null && lastTdbRequest != null)
+ {
+ int prov_idx = lastTdbRequest.getFieldIndex("Provider");
+
+ 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);
+ if (!xtantOptions.contains(providerOpt))
+ {
+ xtantOptions.add(1,
+ providerOpt);
+ tdBeaconsFilters.add(FILTER_SOURCE_PREFIX+provider);
+
+ }
+ }
+ }
+
+ }
+
+ private boolean tdBeaconsFilter(String fieldToFilterBy)
+ {
+ return tdBeaconsFilters != null
+ && tdBeaconsFilters.contains(fieldToFilterBy);
+ }
+
+ private String remove_prefix(String fieldToFilterBy)
+ {
+ if (tdBeaconsFilters != null
+ && tdBeaconsFilters.contains(fieldToFilterBy)
+ && !defaultFilters.contains(fieldToFilterBy))
+ {
+ return fieldToFilterBy.substring(FILTER_SOURCE_PREFIX.length());
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ @Override
+ public boolean needsRefetch(FilterOption selectedFilterOpt)
+ {
+ return selectedFilterOpt==null || !tdBeaconsFilter(selectedFilterOpt.getValue())
+ && lastPdbRequest != lastTdbRequest;
+ }
+
/**
* FTSRestClient specific query builder to pick top ranked entry from a
* fetchStructuresMetaData query
* @throws Exception
*/
public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+ Collection<FTSData> collectedResults,
Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
boolean b) throws Exception
{
+ if (fieldToFilterBy!=null && tdBeaconsFilter(fieldToFilterBy))
+ {
+ TDBResultAnalyser analyser = new TDBResultAnalyser(seq,
+ collectedResults, lastTdbRequest, fieldToFilterBy,
+ remove_prefix(fieldToFilterBy));
- FTSRestResponse resultList;
- FTSRestRequest pdbRequest = getTDBeaconsRequest(seq, wantedFields);
- if (pdbRequest == null) {
- return null;
- }
- pdbRequest.setResponseSize(1);
- resultList = pdbRestClient.executeRequest(pdbRequest);
-
- // TODO: client side filtering - sort results and pick top one (or N)
+ FTSRestResponse resultList = new FTSRestResponse();
- lastPdbRequest = pdbRequest;
- return resultList;
+ List<FTSData> filteredResponse = analyser.getFilteredResponse();
+
+ List<FTSData> selectedStructures = analyser
+ .selectStructures(filteredResponse);
+ resultList.setNumberOfItemsFound(selectedStructures.size());
+ resultList.setSearchSummary(selectedStructures);
+ return resultList;
+ }
+ // Fall back to PDBe rankings
+ return getPDBQuerySource().selectFirstRankedQuery(seq, collectedResults,
+ wantedFields, fieldToFilterBy, b);
}
@Override
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();
-
- for (int row : selectedRows)
+ int categoryColumnIndex = restable.getColumn("Model Category")
+ .getModelIndex();
+ final int up_start_idx = restable.getColumn("Uniprot Start")
+ .getModelIndex();
+ final int up_end_idx = restable.getColumn("Uniprot End")
+ .getModelIndex();
+ int i = 0;
+
+ // bleugh!
+ Integer[] sellist = new Integer[selectedRows.length];
+ for (Integer row : selectedRows)
+ {
+ sellist[i++] = row;
+ }
+ // Sort rows by coverage
+ Arrays.sort(sellist, new Comparator<Integer>()
+ {
+ @Override
+ public int compare(Integer o1, Integer o2)
+ {
+ int o1_xt = ((Integer) restable.getValueAt(o1, up_end_idx))
+ - (Integer) restable.getValueAt(o1, up_start_idx);
+ int o2_xt = ((Integer) restable.getValueAt(o2, up_end_idx))
+ - (Integer) restable.getValueAt(o2, up_start_idx);
+ return o2_xt - o1_xt;
+ }
+ });
+
+ for (int row : sellist)
{
// 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)
{
pdbEntry = new PDBEntry();
pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.MMCIF);
+ 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);
if (!"PDBe".equalsIgnoreCase(typeColumn))
{
pdbEntry.setRetrievalUrl(urlStr);
}
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);
+ if (pdb_Query.length()==0)
+ {
+ return null;
+ }
+ 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)
+ {
+ boolean hasPdbResp = lastPdbRequest != null;
+
+ int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
+ // join on
+ int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
+ 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>();
+ for (final FTSData row : upResponse.getSearchSummary())
+ {
+ String id = (String) row.getSummaryData()[idx_modelId];
+ String provider = (String) row.getSummaryData()[idx_provider];
+ if ("PDBe".equalsIgnoreCase(provider))
+ {
+ if (!hasPdbResp)
+ {
+ System.out.println(
+ "Warning: seems like we couldn't get to the PDBe search interface.");
+ }
+ else
+ {
+ for (final FTSData pdbrow : pdbResponse.getSearchSummary())
+ {
+ String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
+ if (id.equalsIgnoreCase(pdbid))
+ {
+ row.getSummaryData()[tdbTitle_idx] = pdbrow
+ .getSummaryData()[pdbTitle_idx];
+ }
+ }
+ }
+
+ }
+ else
+ {
+ row.getSummaryData()[tdbTitle_idx] = "Model from TDB";
+ }
+ }
+ return upResponse;
+ }
+
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff