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.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.threedbeacons.TDB_FTSData;
import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
import jalview.jbgui.FilterOption;
-import jalview.util.MessageManager;
/**
* logic for querying the 3DBeacons API for structures of sequences
extends StructureChooserQuerySource
{
- private static final String FILTER_TDBEACONS_COVERAGE = "3d_beacons_coverage";
+ private Set<String> tdBeaconsFilters = null, defaultFilters = null;
- private static int MAX_QLENGTH = 7820;
+ 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_";
protected FTSRestRequest lastTdbRequest;
public ThreeDBStructureChooserQuerySource()
{
+ 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
public String buildQuery(SequenceI seq)
{
- boolean isPDBRefsFound = false;
- boolean isUniProtRefsFound = false;
- StringBuilder queryBuilder = new StringBuilder();
- Set<String> seqRefs = new LinkedHashSet<>();
-
- /*
- * note PDBs as DBRefEntry so they are not duplicated in query
- */
- 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;
}
/**
*/
static boolean isValidSeqName(String seqName)
{
- // System.out.println("seqName : " + seqName);
String ignoreList = "pdb,uniprot,swiss-prot";
if (seqName.length() < 3)
{
{
return false;
}
- seqName = seqName.toLowerCase();
+ seqName = seqName.toLowerCase(Locale.ROOT);
for (String ignoredEntry : ignoreList.split(","))
{
if (seqName.contains(ignoredEntry))
FilterOption selectedFilterOpt, boolean b) throws Exception
{
FTSRestResponse resultList;
- if (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);
- return resultList;
- }
+ if (selectedFilterOpt != null
+ && tdBeaconsFilter(selectedFilterOpt.getValue()))
+ {
+ FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
+ resultList = tdbRestClient.executeRequest(tdbRequest);
+
+ lastTdbRequest = tdbRequest;
+ if (resultList != null)
+ { // Query the PDB and add additional metadata
+ FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
+ getPDBQuerySource(), resultList);
+
+ resultList = joinResponses(resultList, pdbResponse);
+ }
+ return resultList;
+ }
// use the PDBFTS directly
- resultList = getPDBQuerySource().fetchStructuresMetaData(seq, wantedFields, selectedFilterOpt, b);
+ resultList = getPDBQuerySource().fetchStructuresMetaData(seq,
+ wantedFields, selectedFilterOpt, b);
lastTdbRequest = getPDBQuerySource().lastPdbRequest;
- lastPdbRequest = lastTdbRequest; // both queries the same - indicates we rank using PDBe
+ lastPdbRequest = lastTdbRequest; // both queries the same - indicates we
+ // rank using PDBe
return resultList;
-
+
}
- PDBStructureChooserQuerySource pdbQuerySource=null;
+ PDBStructureChooserQuerySource pdbQuerySource = null;
+
private PDBStructureChooserQuerySource getPDBQuerySource()
{
- if (pdbQuerySource==null)
+ if (pdbQuerySource == null)
{
pdbQuerySource = new PDBStructureChooserQuerySource();
}
@Override
public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
{
- List<FilterOption> filters = getPDBQuerySource().getAvailableFilterOptions(VIEWS_FILTER);
-
- filters.add(0,
- new FilterOption("3D-Beacons Coverage",
- FILTER_TDBEACONS_COVERAGE, VIEWS_FILTER, true, this));
+ 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)
+ {
+ boolean hasPDBe = false;
+ for (FTSData _row : tdbEntries)
+ {
+ // tdb returns custom object
+ TDB_FTSData row = (TDB_FTSData) _row;
+ String provider = (String) row.getProvider();
+ 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);
+ 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++;
+ }
+ }
+ }
+ }
+
+ }
+
private boolean tdBeaconsFilter(String fieldToFilterBy)
{
- return FILTER_TDBEACONS_COVERAGE.equals(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 tdBeaconsFilter(selectedFilterOpt.getValue()) && lastPdbRequest!=lastTdbRequest;
+ return selectedFilterOpt == null
+ || !tdBeaconsFilter(selectedFilterOpt.getValue())
+ && lastPdbRequest != lastTdbRequest;
}
+
/**
* FTSRestClient specific query builder to pick top ranked entry from a
* fetchStructuresMetaData query
Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
boolean b) throws Exception
{
- if (tdBeaconsFilter(fieldToFilterBy))
+ if (fieldToFilterBy != null && tdBeaconsFilter(fieldToFilterBy))
{
TDBResultAnalyser analyser = new TDBResultAnalyser(seq,
- collectedResults, lastTdbRequest);
+ collectedResults, lastTdbRequest, fieldToFilterBy,
+ remove_prefix(fieldToFilterBy));
FTSRestResponse resultList = new FTSRestResponse();
return resultList;
}
// Fall back to PDBe rankings
- return getPDBQuerySource().selectFirstRankedQuery(seq, collectedResults, wantedFields, fieldToFilterBy, b);
+ return getPDBQuerySource().selectFirstRankedQuery(seq, collectedResults,
+ wantedFields, fieldToFilterBy, b);
}
-
@Override
public PDBEntry[] collectSelectedRows(JTable restable, int[] selectedRows,
List<SequenceI> selectedSeqsToView)
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")
+ int humanUrl = restable.getColumn("Page URL").getModelIndex();
+ int modelformat = restable.getColumn("Model Format").getModelIndex();
+ final int up_start_idx = restable.getColumn("Uniprot Start")
+ .getModelIndex();
+ final int up_end_idx = restable.getColumn("Uniprot End")
.getModelIndex();
- final int up_start_idx = restable.getColumn("Uniprot Start").getModelIndex();
- final int up_end_idx = restable.getColumn("Uniprot End").getModelIndex();
- int i=0;
-
+ int i = 0;
+
// bleugh!
Integer[] sellist = new Integer[selectedRows.length];
- for (Integer row: selectedRows)
+ for (Integer row : selectedRows)
{
sellist[i++] = row;
}
// Sort rows by coverage
- Arrays.sort(sellist,new Comparator<Integer>()
+ 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;
+ 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 urlStr = restable.getValueAt(row, urlColumnIndex).toString();
String typeColumn = restable.getValueAt(row, typeColumnIndex)
.toString();
+ String modelPage = humanUrl < 1 ? null
+ : (String) restable.getValueAt(row, humanUrl);
+ String strucFormat = restable.getValueAt(row, modelformat).toString();
+
SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
{
pdbEntry = new PDBEntry();
pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.MMCIF);
+ pdbEntry.setAuthoritative(true);
+ try
+ {
+ pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
+ } catch (Exception q)
+ {
+ Console.warn("Unknown filetype for 3D Beacons Model from: "
+ + strucFormat + " - " + pdbIdStr + " - " + modelPage);
+ }
+
if (!"PDBe".equalsIgnoreCase(typeColumn))
{
pdbEntry.setRetrievalUrl(urlStr);
}
+ pdbEntry.setProvider(typeColumn);
+ pdbEntry.setProviderPage(modelPage);
selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
}
pdbEntriesToView[count++] = pdbEntry;
public String buildPDBFTSQueryFor(FTSRestResponse upResponse)
{
- List<String> pdbIds = new ArrayList<String>();
+ Set<String> pdbIds = new HashSet<String>();
int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
for (FTSData row : upResponse.getSearchSummary())
{
String pdb_Query = buildPDBFTSQueryFor(upResponse);
-
+ if (pdb_Query.length() == 0)
+ {
+ return null;
+ }
FTSRestResponse resultList;
FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
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>();
+
for (final FTSData row : upResponse.getSearchSummary())
{
String id = (String) row.getSummaryData()[idx_modelId];
String provider = (String) row.getSummaryData()[idx_provider];
if ("PDBe".equalsIgnoreCase(provider))
{
- for (final FTSData pdbrow : pdbResponse.getSearchSummary())
+ if (!hasPdbResp)
+ {
+ System.out.println(
+ "Warning: seems like we couldn't get to the PDBe search interface.");
+ }
+ else
{
- String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
- if (id.equalsIgnoreCase(pdbid))
+ 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 {
+
+ }
+ else
+ {
row.getSummaryData()[tdbTitle_idx] = "Model from TDB";
}
}
return upResponse;
}
+ public TDB_FTSData getFTSDataFor(JTable restable, int selectedRow,
+ Collection<FTSData> discoveredStructuresSet)
+ {
+ int idColumnIndex = restable.getColumn("Model id").getModelIndex();
+
+ String modelId = (String) restable.getValueAt(selectedRow,
+ idColumnIndex);
+ for (FTSData row : discoveredStructuresSet)
+ {
+ if (row instanceof TDB_FTSData
+ && ((TDB_FTSData) row).getModelId().equals(modelId))
+ {
+ return ((TDB_FTSData) row);
+ }
+ }
+ return null;
+ }
+
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff