String accId = querySeq.getName();
try
{
- System.out.println("Adding protein product for " + accId);
+ Cache.log.info("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);
+ Cache.log.info("No protein product found for " + accId);
return;
}
SequenceI proteinSeq = protein.getSequenceAt(0);
if (seqs.size() != ids.size())
{
- System.out.println(String.format(
+ Cache.log.warn(String.format(
"Only retrieved %d sequences for %d query strings",
seqs.size(), ids.size()));
}
if (regions.isEmpty())
{
- System.out.println("Failed to identify target sequence for " + accId
+ Cache.log.warn("Failed to identify target sequence for " + accId
+ " from genomic features");
return null;
}