try
{
reply = dbFetch.fetchDataAsFile(
- emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null);
+ emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
+ "xml");
} catch (Exception e)
{
stopQuery();
throw new Exception(MessageManager.formatMessage(
- "exception.ebiembl_retrieval_failed_on", new String[] {
- emprefx.toLowerCase(), query.trim() }), e);
+ "exception.ebiembl_retrieval_failed_on", new String[]
+ { emprefx.toLowerCase(), query.trim() }), e);
}
return getEmblSequenceRecords(emprefx, query, reply);
}
}
}
+ /*
+ * invalid accession gets a reply with no <entry> elements, text content of
+ * EmbFile reads something like (e.g.) this ungrammatical phrase
+ * Entry: <acc> display type is either not supported or entry is not found.
+ */
List<SequenceI> peptides = new ArrayList<SequenceI>();
- if (efile != null)
+ if (efile != null && efile.getEntries() != null)
{
for (EmblEntry entry : efile.getEntries())
{