private void loadGroup(DomainFile domainFile, String gene, DomainAcc acc, Polypeptide polypeptide)
throws IOException {
logger.debug("In loadGroup()");
DbXRef interProDbxref = null;
if (acc != DomainAcc.NULL && analysis.getProgram().equals("iprscan")) {
logger.debug(
String.format(
"Creating InterPro dbxref for '%s' with description '%s'",
acc.getId(), acc.getDescription()));
interProDbxref = objectManager.getDbXRef("InterPro", acc.getId(), acc.getDescription());
}
int n = -1;
for (DomainRow row : domainFile.rows(gene, acc)) {
n++;
logger.debug(row);
// Insert polypeptide_domain
DbXRef dbxref = objectManager.getDbXRef(row.db(), row.nativeAcc(), row.nativeDesc());
if (dbxref == null) {
throw new RuntimeException(
String.format("Could not find database '%s' on line %d", row.db(), row.lineNumber()));
}
String domainUniqueName;
String accessionNumber = acc.getId();
if (accessionNumber == null) {
accessionNumber = row.nativeAcc();
}
if (n == 0) {
domainUniqueName =
String.format("%s:%s:%s", polypeptide.getUniqueName(), row.db(), accessionNumber);
} else {
domainUniqueName =
String.format("%s:%s:%s:%d", polypeptide.getUniqueName(), row.db(), accessionNumber, n);
}
PolypeptideDomain polypeptideDomain =
sequenceDao.createPolypeptideDomain(
domainUniqueName,
polypeptide,
row.score(),
row.acc().getDescription(),
row.fmin(),
row.fmax(),
dbxref,
row.evalue(),
analysis);
// add GO terms
addGoTerms(row.getGoTerms(), polypeptide, polypeptideDomain, row.getGoTermComment());
// link to InterPro dbxref if applicable
if (interProDbxref != null && analysis.getProgram().equals("iprscan")) {
FeatureDbXRef featureDbXRef = new FeatureDbXRef(interProDbxref, polypeptideDomain, true);
sequenceDao.persist(featureDbXRef);
polypeptideDomain.addFeatureDbXRef(featureDbXRef);
}
}
}
private void addGoTerms(
Set<GoInstance> goTerms,
Polypeptide polypeptide,
PolypeptideDomain polypeptideDomain,
String comment) {
for (GoInstance goInstance : goTerms) {
try {
if (polypeptide.getGo().contains(goInstance.getId())) {
logger.info(
String.format(
"The GO term '%s' has already been added to polypeptide '%s'",
goInstance.getId(), polypeptide));
continue;
}
logger.info(
String.format(
"Creating %s GO term '%s' for domain '%s'",
comment, goInstance.getId(), polypeptideDomain.getUniqueName()));
DbXRef withFrom = null;
if (goInstance.getWithFrom() != null)
withFrom = featureUtils.findOrCreateDbXRefForWithFrom(goInstance.getWithFrom());
featureUtils.createGoEntries(polypeptide, goInstance, comment, withFrom);
} catch (ParsingException e) {
logger.error(e);
}
}
}