*/
package jalview.ws.dbsources;
-import jalview.bin.Cache;
+import java.util.Locale;
+
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.io.DataSourceType;
// TODO: trap HTTP 404 exceptions and return null
String xfamUrl = getURL(queries);
- if (Cache.log != null)
- {
- Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl);
- }
+ Console.debug("XFAM URL for retrieval is: " + xfamUrl);
AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
DataSourceType.URL, FileFormat.Stockholm);
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
// getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
+ getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
if (!getDbSource().equals(getXfamSource()))
{ // add the specific ref too
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
+ getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
}
}
stopQuery();
String getURL(String queries)
{
- return getURLPrefix() + "/family/" + queries.trim().toUpperCase()
- + getURLSuffix();
+ return getURLPrefix() + "/family/"
+ + queries.trim().toUpperCase(Locale.ROOT) + getURLSuffix();
}
/**