+/*
+ * 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.ws.dbsources;
+import java.util.Locale;
+
import java.io.File;
import java.io.IOException;
import com.stevesoft.pat.Regex;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
try
{
reply = dbFetch.fetchDataAsFile(
- dbName.toLowerCase() + ":" + query.trim(), null, "txt");
+ dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null,
+ "gz");
} catch (Exception e)
{
stopQuery();
throw new Exception(
- String.format("EBI EMBL XML retrieval failed for %s:%s",
- dbName.toLowerCase(), query.trim()),
+ String.format("EBI EMBL retrieval failed for %s:%s",
+ dbName.toLowerCase(Locale.ROOT), query.trim()),
e);
}
return getEmblSequenceRecords(dbName, query, reply);
file = reply.getAbsolutePath();
FileParse fp = new FileParse(file, DataSourceType.FILE);
EmblFlatFile emblParser = new EmblFlatFile(fp, getDbSource());
- emblParser.parse();
SequenceI[] seqs = emblParser.getSeqsAsArray();
if (seqs.length > 0)
{
if (al == null)
{
- Cache.log.error(
- "No record found for '" + dbName + ":" + query + "'");
+ Console.error("No record found for '" + dbName + ":" + query + "'");
}
}
stopQuery();
return al;
}
+
+ @Override
+ public boolean isDnaCoding()
+ {
+ return true;
+ }
}