seqset = fetcher.getSequenceRecords(qsb.toString());
} catch (Exception ex)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to retrieve the following from " + db);
- System.err.println(qsb);
+ jalview.bin.Console.errPrintln(qsb);
ex.printStackTrace(System.err);
}
// TODO: Merge alignment together - perhaps
// BH 2015.01.25 check about version/accessid being null here
List<DBRefEntry> frefs = DBRefUtils.searchRefs(
seqs[is].getDBRefs(),
- new DBRefEntry(db, null, null), DBRefUtils.SEARCH_MODE_FULL);
+ new DBRefEntry(db, null, null),
+ DBRefUtils.SEARCH_MODE_FULL);
for (DBRefEntry dbr : frefs)
{
queriesFound.add(dbr.getAccessionId());
{
if (fetcher.getRawRecords() != null)
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"# Retrieved from " + db + ":" + qsb.toString());
StringBuffer rrb = fetcher.getRawRecords();
/*
/*
* } else { hdr = "# part "+rr; }
*/
- System.out.println(hdr);
+ jalview.bin.Console.outPrintln(hdr);
if (rrb != null)
{
- System.out.println(rrb);
+ jalview.bin.Console.outPrintln(rrb);
}
- System.out.println("# end of " + hdr);
+ jalview.bin.Console.outPrintln("# end of " + hdr);
}
}
}
if (queriesMade.size() > 0)
{
- System.out.println("# Adding " + queriesMade.size()
+ jalview.bin.Console.outPrintln("# Adding " + queriesMade.size()
+ " ids back to queries list for searching again (" + db
+ ")");
queriesLeft.addAll(queriesMade);
Exception ex)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to retrieve the following references from " + db);
int n = 0;
for (String qv : queriesMade)
System.err.print(" " + qv + ";");
if (n++ > 10)
{
- System.err.println();
+ jalview.bin.Console.errPrintln();
n = 0;
}
}
- System.err.println();
+ jalview.bin.Console.errPrintln();
ex.printStackTrace();
}
.get(proxy.getDbSource());
if (slist == null)
{
- fetchableDbs.put(proxy.getDbSource(),
- slist = new Hashtable<>());
+ fetchableDbs.put(proxy.getDbSource(), slist = new Hashtable<>());
}
slist.put(proxy.getDbName(), proxy);
}