--- /dev/null
+package jalview.gui.structurechooser;
+
+import java.util.Locale;
+
+import java.util.ArrayList;
+import java.util.Collection;
+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.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.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.jbgui.FilterOption;
+import jalview.util.MessageManager;
+
+/**
+ * logic for querying the PDBe API for structures of sequences
+ *
+ * @author jprocter
+ */
+public class PDBStructureChooserQuerySource
+ extends StructureChooserQuerySource
+{
+
+ private static int MAX_QLENGTH = 7820;
+
+ protected FTSRestRequest lastPdbRequest;
+
+ protected FTSRestClientI pdbRestClient;
+
+ public PDBStructureChooserQuerySource()
+ {
+ pdbRestClient = PDBFTSRestClient.getInstance();
+ docFieldPrefs = new FTSDataColumnPreferences(
+ PreferenceSource.STRUCTURE_CHOOSER,
+ PDBFTSRestClient.getInstance());
+
+ }
+
+
+ /**
+ * Builds a query string for a given sequences using its DBRef entries
+ *
+ * @param seq
+ * the sequences to build a query for
+ * @return the built query string
+ */
+
+ 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<>();
+
+ if (seq.getAllPDBEntries() != null
+ && queryBuilder.length() < MAX_QLENGTH)
+ {
+ for (PDBEntry entry : seq.getAllPDBEntries())
+ {
+ if (isValidSeqName(entry.getId()))
+ {
+ String id = entry.getId().toLowerCase(Locale.ROOT);
+ queryBuilder.append("pdb_id:").append(id).append(" OR ");
+ isPDBRefsFound = true;
+ pdbids.add(id);
+ }
+ }
+ }
+
+ List<DBRefEntry> refs = seq.getDBRefs();
+ 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))
+ {
+ queryBuilder.append("uniprot_accession:")
+ .append(getDBRefId(dbRef)).append(" OR ");
+ queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
+ .append(" OR ");
+ isUniProtRefsFound = true;
+ }
+ else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
+ {
+
+ String id = getDBRefId(dbRef).toLowerCase(Locale.ROOT);
+ if (!pdbids.contains(id))
+ {
+ queryBuilder.append("pdb_id:").append(id).append(" OR ");
+ isPDBRefsFound = true;
+ pdbids.add(id);
+ }
+ }
+ else
+ {
+ seqRefs.add(getDBRefId(dbRef));
+ }
+ }
+ }
+ }
+
+ if (!isPDBRefsFound && !isUniProtRefsFound)
+ {
+ String seqName = seq.getName();
+ seqName = sanitizeSeqName(seqName);
+ String[] names = seqName.toLowerCase(Locale.ROOT).split("\\|");
+ for (String name : names)
+ {
+ // System.out.println("Found name : " + name);
+ name.trim();
+ if (isValidSeqName(name))
+ {
+ seqRefs.add(name);
+ }
+ }
+
+ for (String seqRef : seqRefs)
+ {
+ queryBuilder.append("text:").append(seqRef).append(" OR ");
+ }
+ }
+
+ int endIndex = queryBuilder.lastIndexOf(" OR ");
+ if (queryBuilder.toString().length() < 6)
+ {
+ return null;
+ }
+ String query = queryBuilder.toString().substring(0, endIndex);
+ return query;
+ }
+
+ /**
+ * Remove the following special characters from input string +, -, &, !, (, ),
+ * {, }, [, ], ^, ", ~, *, ?, :, \
+ *
+ * @param seqName
+ * @return
+ */
+ public static String sanitizeSeqName(String seqName)
+ {
+ Objects.requireNonNull(seqName);
+ return seqName.replaceAll("\\[\\d*\\]", "")
+ .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
+ }
+
+ /**
+ * Ensures sequence ref names are not less than 3 characters and does not
+ * contain a database name
+ *
+ * @param seqName
+ * @return
+ */
+ static boolean isValidSeqName(String seqName)
+ {
+ // System.out.println("seqName : " + seqName);
+ String ignoreList = "pdb,uniprot,swiss-prot";
+ if (seqName.length() < 3)
+ {
+ return false;
+ }
+ if (seqName.contains(":"))
+ {
+ return false;
+ }
+ seqName = seqName.toLowerCase(Locale.ROOT);
+ for (String ignoredEntry : ignoreList.split(","))
+ {
+ if (seqName.contains(ignoredEntry))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ static String getDBRefId(DBRefEntry dbRef)
+ {
+ String ref = dbRef.getAccessionId().replaceAll("GO:", "");
+ return ref;
+ }
+
+ /**
+ * FTSRestClient specific query builder to recover associated structure data
+ * records for a sequence
+ *
+ * @param seq
+ * - seq to generate a query for
+ * @param wantedFields
+ * - fields to retrieve
+ * @param selectedFilterOpt
+ * - criterion for ranking results (e.g. resolution)
+ * @param b
+ * - sort ascending or descending
+ * @return
+ * @throws Exception
+ */
+ public FTSRestResponse fetchStructuresMetaData(SequenceI seq,
+ Collection<FTSDataColumnI> wantedFields,
+ FilterOption selectedFilterOpt, boolean b) throws Exception
+ {
+ FTSRestResponse resultList;
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setFieldToSearchBy("(");
+ pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(), b);
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setAssociatedSequence(seq);
+ resultList = pdbRestClient.executeRequest(pdbRequest);
+
+ lastPdbRequest = pdbRequest;
+ return resultList;
+ }
+ public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
+ {
+ List<FilterOption> filters = new ArrayList<FilterOption>();
+ filters.add(new FilterOption("PDBe "+
+ MessageManager.getString("label.best_quality"),
+ "overall_quality", VIEWS_FILTER, false,this));
+ filters.add(new FilterOption("PDBe "+
+ MessageManager.getString("label.best_resolution"),
+ "resolution", VIEWS_FILTER, false,this));
+ filters.add(new FilterOption("PDBe "+
+ MessageManager.getString("label.most_protein_chain"),
+ "number_of_protein_chains", VIEWS_FILTER, false,this));
+ filters.add(new FilterOption("PDBe "+
+ MessageManager.getString("label.most_bound_molecules"),
+ "number_of_bound_molecules", VIEWS_FILTER, false,this));
+ filters.add(new FilterOption("PDBe "+
+ MessageManager.getString("label.most_polymer_residues"),
+ "number_of_polymer_residues", VIEWS_FILTER, true,this));
+
+ return filters;
+ }
+
+ @Override
+ public boolean needsRefetch(FilterOption selectedFilterOpt)
+ {
+ // PDBe queries never need a refetch first
+ return false;
+ }
+
+ /**
+ * FTSRestClient specific query builder to pick top ranked entry from a
+ * fetchStructuresMetaData query
+ *
+ * @param seq
+ * - seq to generate a query for
+ * @param wantedFields
+ * - fields to retrieve
+ * @param selectedFilterOpt
+ * - criterion for ranking results (e.g. resolution)
+ * @param b
+ * - sort ascending or descending
+ * @return
+ * @throws Exception
+ */
+ public FTSRestResponse selectFirstRankedQuery(SequenceI seq, Collection<FTSData> collectedResults,
+ Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
+ boolean b) throws Exception
+ {
+
+ FTSRestResponse resultList;
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
+ {
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(");
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq);
+ pdbRequest.setFacet(true);
+ pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
+ pdbRequest.setFacetPivotMinCount(1);
+ }
+ else
+ {
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(");
+ pdbRequest.setFieldToSortBy(fieldToFilterBy, b);
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq);
+ }
+ resultList = pdbRestClient.executeRequest(pdbRequest);
+
+ lastPdbRequest = pdbRequest;
+ return resultList;
+ }
+
+
+ @Override
+ public PDBEntry[] collectSelectedRows(JTable restable, int[] selectedRows,
+ List<SequenceI> selectedSeqsToView)
+ {
+ int refSeqColIndex = restable.getColumn("Ref Sequence")
+ .getModelIndex();
+
+ PDBEntry[] pdbEntriesToView=new PDBEntry[selectedRows.length];
+ int count = 0;
+ int idColumnIndex=-1;
+ boolean fromTDB=true;
+ idColumnIndex = restable.getColumn("PDB Id").getModelIndex();
+
+ for (int row : selectedRows)
+ {
+
+ String pdbIdStr = restable.getValueAt(row,idColumnIndex)
+ .toString();
+ SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
+ refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = getFindEntry(pdbIdStr,
+ selectedSeq.getAllPDBEntries());
+ }
+
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.MMCIF);
+ selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+ }
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ return pdbEntriesToView;
+ }
+
+
+ @Override
+ protected FTSRestRequest getLastFTSRequest()
+ {
+ return lastPdbRequest;
+ }
+
+
+ public FTSRestResponse executePDBFTSRestRequest(FTSRestRequest pdbRequest) throws Exception
+ {
+ return pdbRestClient.executeRequest(pdbRequest);
+ }
+
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff