Stack<String> queriesLeft = new Stack<String>();
queriesLeft.addAll(query);
- for (DbSourceProxy fetcher : getSourceProxy(db))
+ List<DbSourceProxy> proxies = getSourceProxy(db);
+ for (DbSourceProxy fetcher : proxies)
{
List<String> queriesMade = new ArrayList<String>();
HashSet<String> queriesFound = new HashSet<String>();
{
continue; // wrong sort of data
}
- boolean doMultiple = fetcher.getAccessionSeparator() != null;
- // No separator - no Multiple Queries
+ boolean doMultiple = fetcher.getMaximumQueryCount() > 1;
while (!queriesLeft.isEmpty())
{
StringBuffer qsb = new StringBuffer();
try
{
// create a fetcher and go to it
- seqset = fetcher.getSequenceRecords(qsb.toString()); // ,
- // queriesFailed);
+ seqset = fetcher.getSequenceRecords(qsb.toString());
} catch (Exception ex)
{
System.err.println("Failed to retrieve the following from "
{
rseqs.addElement(seqs[is]);
DBRefEntry[] frefs = DBRefUtils.searchRefs(seqs[is]
- .getDBRef(), new DBRefEntry(db, null, null));
+ .getDBRefs(), new DBRefEntry(db, null, null));
if (frefs != null)
{
for (DBRefEntry dbr : frefs)
{
System.out.println("# Adding " + queriesMade.size()
+ " ids back to queries list for searching again (" + db
- + ".");
+ + ")");
queriesLeft.addAll(queriesMade);
}
}