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.Objects;
import java.util.Set;
import javax.swing.JTable;
-import javax.swing.table.TableModel;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
-import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
-import jalview.jbgui.GStructureChooser.FilterOption;
+import jalview.jbgui.FilterOption;
+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
*/
private static int MAX_QLENGTH = 7820;
+ protected FTSRestRequest lastTdbRequest;
+
+ protected FTSRestClientI tdbRestClient;
+
+ private FTSRestRequest lastPdbRequest;
+
public ThreeDBStructureChooserQuerySource()
{
- pdbRestClient = TDBeaconsFTSRestClient.getInstance();
+ 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);
+ FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
+ resultList = tdbRestClient.executeRequest(tdbRequest);
- lastPdbRequest = pdbRequest;
+ 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
+ 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));
+
+ return filters;
+ }
+
+ /**
+ * model categories - update as needed. warnings output if unknown types
+ * encountered.
+ *
+ * Order denotes 'trust'
+ */
+ private static List<String> EXP_CATEGORIES = Arrays
+ .asList(new String[]
+ { "EXPERIMENTALLY DETERMINED", "DEEP LEARNING", "TEMPLATE-BASED" });
/**
* FTSRestClient specific query builder to pick top ranked entry from a
* @throws Exception
*/
public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+ Collection<FTSData> collectedResults,
Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
boolean b) throws Exception
{
- FTSRestResponse resultList;
- FTSRestRequest pdbRequest = getTDBeaconsRequest(seq, wantedFields);
- if (pdbRequest == null) {
- return null;
+ List<FTSData> filteredResponse = new ArrayList<FTSData>();
+ final int idx_ups = lastTdbRequest.getFieldIndex("Uniprot Start");
+ final int idx_upe = lastTdbRequest.getFieldIndex("Uniprot End");
+ final int idx_mcat = lastTdbRequest.getFieldIndex("Model Category");
+ final int idx_mqual = lastTdbRequest.getFieldIndex("Qmean");
+ final int idx_resol = lastTdbRequest.getFieldIndex("Resolution");
+
+ // ignore anything outside the sequence region
+ for (FTSData row : collectedResults)
+ {
+ int up_s = (Integer) row.getSummaryData()[idx_ups];
+ int up_e = (Integer) row.getSummaryData()[idx_upe];
+
+ if (seq == row.getSummaryData()[0] && up_e > seq.getStart()
+ && up_s < seq.getEnd())
+ {
+ filteredResponse.add(row);
+ }
}
- pdbRequest.setResponseSize(1);
- resultList = pdbRestClient.executeRequest(pdbRequest);
-
- // TODO: client side filtering - sort results and pick top one (or N)
+ // sort according to decreasing length,
+ // increasing start
+ Collections.sort(filteredResponse, new Comparator<FTSData>()
+ {
- lastPdbRequest = pdbRequest;
+ private final int scoreCategory(String cat)
+ {
+ // TODO: make quicker
+ int idx = EXP_CATEGORIES.indexOf(cat.toUpperCase());
+ if (idx == -1)
+ {
+ System.out.println("Unknown category: '" + cat + "'");
+ }
+ return -EXP_CATEGORIES.size() - idx;
+ }
+
+ @Override
+ public int compare(FTSData o1, FTSData o2)
+ {
+ int o1_s = (Integer) o1.getSummaryData()[idx_ups];
+ int o1_e = (Integer) o1.getSummaryData()[idx_upe];
+ int o1_cat = scoreCategory((String) o1.getSummaryData()[idx_mcat]);
+ int o2_s = (Integer) o2.getSummaryData()[idx_ups];
+ int o2_e = (Integer) o2.getSummaryData()[idx_upe];
+ int o2_cat = scoreCategory((String) o2.getSummaryData()[idx_mcat]);
+
+ if (o1_cat == o2_cat)
+ {
+ if (o1_s == o2_s)
+ {
+ int o1_xtent = o1_e - o1_s;
+ int o2_xtent = o2_e - o2_s;
+ if (o1_xtent == o2_xtent)
+ {
+ if (o1_cat == scoreCategory(EXP_CATEGORIES.get(0)))
+ {
+ // experimental structures, so rank on quality
+ double o1_res = (Double) o1.getSummaryData()[idx_resol];
+ double o2_res = (Double) o2.getSummaryData()[idx_resol];
+ return (o2_res < o1_res) ? 1 : (o2_res == o1_res) ? 0 : -1;
+ }
+ else
+ {
+ // models, so rank on qmean
+ float o1_mq = (Float) o1.getSummaryData()[idx_mqual];
+ float o2_mq = (Float) o2.getSummaryData()[idx_mqual];
+ return (o2_mq < o1_mq) ? 1 : (o2_mq == o1_mq) ? 0 : -1;
+ }
+ }
+ else
+ {
+ return o1_xtent - o2_xtent;
+ }
+ }
+ else
+ {
+ return o1_s - o2_s;
+ }
+ }
+ else
+ {
+ return o2_cat - o1_cat;
+ }
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ return super.equals(obj);
+ }
+ });
+ FTSRestResponse resultList = new FTSRestResponse();
+ resultList.setNumberOfItemsFound(filteredResponse.size());
+ resultList.setSearchSummary(filteredResponse);
return resultList;
}
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