+/*
+ * 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.ext.ensembl;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.util.JSONUtils;
{
fetchDivisions();
}
- return divisions.get(division.toUpperCase());
+ return divisions.get(division.toUpperCase(Locale.ROOT));
}
/**
/*
* for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
*/
- divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ensemblDomain);
+ divisions.put(DBRefSource.ENSEMBL.toUpperCase(Locale.ROOT),
+ ensemblDomain);
try
{
@SuppressWarnings("unchecked")
- Iterator<Object> rvals = (Iterator<Object>) getJSON(getDivisionsUrl(ensemblGenomesDomain), null, -1, MODE_ITERATOR, null);
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(
+ getDivisionsUrl(ensemblGenomesDomain), null, -1,
+ MODE_ITERATOR, null);
if (rvals == null)
- return;
+ return;
while (rvals.hasNext())
{
String division = rvals.next().toString();
- divisions.put(division.toUpperCase(), ensemblGenomesDomain);
+ divisions.put(division.toUpperCase(Locale.ROOT),
+ ensemblGenomesDomain);
}
} catch (IOException | ParseException | NumberFormatException e)
{
/**
* Constructs the URL for the EnsemblGenomes /info/divisions REST service
- * @param domain TODO
+ *
+ * @param domain
+ * TODO
*
* @return
* @throws MalformedURLException
*/
URL getDivisionsUrl(String domain) throws MalformedURLException
{
- return new URL(domain
- + "/info/divisions?content-type=application/json");
+ return new URL(
+ domain + "/info/divisions?content-type=application/json");
}
/**
*
* @return
*/
- public Set<String> getDivisions() {
+ public Set<String> getDivisions()
+ {
if (divisions == null)
{
fetchDivisions();