// complementary
foreach(U2Region complementaryRegion, regionsComplementary){
translatedSeq.clear();
U2SequenceImporter importer;
importer.startSequence(stateInfo, dbiRef, U2ObjectDbi::ROOT_FOLDER, seqObj->getSequenceName()+ " " + resultName + QString(" %1").arg(currentSeq) + " complementary", false);
QByteArray complementarySeq;
char* complSeq = NULL;
int blockCounter = 0;
qint64 end = complementaryRegion.endPos() - 1 - complementaryRegion.length / 3 * 3;
for(qint64 i = complementaryRegion.endPos() - 1 ; i > end ;i-=3, blockCounter += 3){
if( (blockCounter % NUM_DB_READ) == 0 ){
importer.addBlock(translatedSeq.constData(), translatedSeq.size(), stateInfo);
complementarySeq.clear();
seq.clear();
translatedSeq.clear();
seq = seqObj->getSequenceData(U2Region(qMax(end + 1, static_cast<qint64>(i - NUM_DB_READ + 1)), qMin(static_cast<qint64>(NUM_DB_READ), i - end)), stateInfo);
CHECK_OP(stateInfo, );
complementarySeq.reserve(seq.size());
complSeq = complementarySeq.data();
TextUtils::translate(complTT->getOne2OneMapper(), seq, seq.size(), complSeq);
TextUtils::reverse(complSeq, seq.size());
blockCounter = 0;
}
SAFE_POINT(complSeq != NULL, "complSeq is NULL", );
translatedSeq.append(aminoTT->translate3to1(complSeq[blockCounter], complSeq[blockCounter + 1], complSeq[blockCounter + 2]));
}
U2SequenceObject * DocumentFormatUtils::addSequenceObject(const U2DbiRef& dbiRef,
const QString& name,
const QByteArray& seq,
bool circular,
const QVariantMap& hints,
U2OpStatus& os)
{
U2SequenceImporter importer;
const QString folder = hints.value(DocumentFormat::DBI_FOLDER_HINT, U2ObjectDbi::ROOT_FOLDER).toString();
importer.startSequence(dbiRef, folder, name, circular, os);
CHECK_OP(os, NULL);
importer.addBlock(seq.constData(), seq.length(), os);
CHECK_OP(os, NULL);
U2Sequence sequence = importer.finalizeSequenceAndValidate(os);
TmpDbiObjects dbiObjects(dbiRef, os);
dbiObjects.objects << sequence.id;
CHECK_OP(os, NULL);
U2SequenceObject* so = new U2SequenceObject(name, U2EntityRef(dbiRef, sequence.id));
return so;
}
