+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui.structurechooser;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
}
-
/**
* Builds a query string for a given sequences using its DBRef entries
*
{
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))
lastPdbRequest = pdbRequest;
return resultList;
}
+
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));
+ "PDBe " + MessageManager.getString("label.best_quality"),
+ "overall_quality", VIEWS_FILTER, false, this));
filters.add(new FilterOption(
- MessageManager.getString("label.best_resolution"),
- "resolution", VIEWS_FILTER, false));
+ "PDBe " + MessageManager.getString("label.best_resolution"),
+ "resolution", VIEWS_FILTER, false, this));
filters.add(new FilterOption(
- MessageManager.getString("label.most_protein_chain"),
- "number_of_protein_chains", VIEWS_FILTER, false));
+ "PDBe " + MessageManager.getString("label.most_protein_chain"),
+ "number_of_protein_chains", VIEWS_FILTER, false, this));
filters.add(new FilterOption(
- MessageManager.getString("label.most_bound_molecules"),
- "number_of_bound_molecules", VIEWS_FILTER, false));
+ "PDBe " + MessageManager
+ .getString("label.most_bound_molecules"),
+ "number_of_bound_molecules", VIEWS_FILTER, false, this));
filters.add(new FilterOption(
- MessageManager.getString("label.most_polymer_residues"),
- "number_of_polymer_residues", VIEWS_FILTER, true));
-
+ "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
* @throws Exception
*/
public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+ Collection<FTSData> collectedResults,
Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
boolean b) throws Exception
{
return resultList;
}
-
@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=-1;
- boolean fromTDB=true;
+ int idColumnIndex = -1;
+ boolean fromTDB = true;
idColumnIndex = restable.getColumn("PDB Id").getModelIndex();
-
+
for (int row : selectedRows)
{
-
- String pdbIdStr = restable.getValueAt(row,idColumnIndex)
- .toString();
+
+ 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());
+ pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries());
}
if (pdbEntry == null)
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