package jalview.gui.structurechooser;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
{
if (isValidSeqName(entry.getId()))
{
- String id = entry.getId().toLowerCase();
+ String id = entry.getId().toLowerCase(Locale.ROOT);
queryBuilder.append("pdb_id:").append(id).append(" OR ");
isPDBRefsFound = true;
pdbids.add(id);
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- String id = getDBRefId(dbRef).toLowerCase();
+ String id = getDBRefId(dbRef).toLowerCase(Locale.ROOT);
if (!pdbids.contains(id))
{
queryBuilder.append("pdb_id:").append(id).append(" OR ");
{
String seqName = seq.getName();
seqName = sanitizeSeqName(seqName);
- String[] names = seqName.toLowerCase().split("\\|");
+ String[] names = seqName.toLowerCase(Locale.ROOT).split("\\|");
for (String name : names)
{
// System.out.println("Found name : " + name);
{
return false;
}
- seqName = seqName.toLowerCase();
+ seqName = seqName.toLowerCase(Locale.ROOT);
for (String ignoredEntry : ignoreList.split(","))
{
if (seqName.contains(ignoredEntry))
public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
{
List<FilterOption> filters = new ArrayList<FilterOption>();
- filters.add(new FilterOption(
+ filters.add(new FilterOption("PDBe "+
MessageManager.getString("label.best_quality"),
- "overall_quality", VIEWS_FILTER, false));
- filters.add(new FilterOption(
+ "overall_quality", VIEWS_FILTER, false,this));
+ filters.add(new FilterOption("PDBe "+
MessageManager.getString("label.best_resolution"),
- "resolution", VIEWS_FILTER, false));
- filters.add(new FilterOption(
+ "resolution", VIEWS_FILTER, false,this));
+ filters.add(new FilterOption("PDBe "+
MessageManager.getString("label.most_protein_chain"),
- "number_of_protein_chains", VIEWS_FILTER, false));
- filters.add(new FilterOption(
+ "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));
- filters.add(new FilterOption(
+ "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));
+ "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
* @return
* @throws Exception
*/
- public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+ public FTSRestResponse selectFirstRankedQuery(SequenceI seq, Collection<FTSData> collectedResults,
Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
boolean b) throws Exception
{
return lastPdbRequest;
}
+
+ public FTSRestResponse executePDBFTSRestRequest(FTSRestRequest pdbRequest) throws Exception
+ {
+ return pdbRestClient.executeRequest(pdbRequest);
+ }
+
}
\ No newline at end of file