String msg = "Aborting ID retrieval after " + v
+ " chunks. Unexpected problem (" + r.getLocalizedMessage()
+ ")";
- System.err.println(msg);
+ jalview.bin.Console.errPrintln(msg);
r.printStackTrace();
break;
}
}
} catch (IOException e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Error transferring Ensembl features: " + e.getMessage());
}
// Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK);
String accId = querySeq.getName();
try
{
- System.out.println("Adding protein product for " + accId);
+ jalview.bin.Console.outPrintln("Adding protein product for " + accId);
AlignmentI protein = new EnsemblProtein(getDomain())
.getSequenceRecords(accId);
if (protein == null || protein.getHeight() == 0)
{
- System.out.println("No protein product found for " + accId);
+ jalview.bin.Console.outPrintln("No protein product found for " + accId);
return;
}
SequenceI proteinSeq = protein.getSequenceAt(0);
seq.addDBRef(xrefs.get(i));
}
- // System.out.println("primaries are " + seq.getPrimaryDBRefs().toString());
+ // jalview.bin.Console.outPrintln("primaries are " + seq.getPrimaryDBRefs().toString());
/*
* and add a reference to itself
*/
if (seqs.size() != ids.size())
{
- System.out.println(String.format(
+ jalview.bin.Console.outPrintln(String.format(
"Only retrieved %d sequences for %d query strings",
seqs.size(), ids.size()));
}
result.add(sequence);
} catch (ParseException | IOException e)
{
- System.err.println("Error processing JSON response: " + e.toString());
+ jalview.bin.Console.errPrintln("Error processing JSON response: " + e.toString());
// ignore
}
// Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK);
if (regions.isEmpty())
{
- System.out.println("Failed to identify target sequence for " + accId
+ jalview.bin.Console.outPrintln("Failed to identify target sequence for " + accId
+ " from genomic features");
return null;
}
boolean result = transferFeatures(sfs, targetSequence, mapping,
accessionId);
- // System.out.println("transferFeatures (" + (sfs.size()) + " --> "
+ // jalview.bin.Console.outPrintln("transferFeatures (" + (sfs.size()) + " --> "
// + targetSequence.getFeatures().getFeatureCount(true) + ") to "
// + targetSequence.getName() + " took "
// + (System.currentTimeMillis() - start) + "ms");