// 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]));
}
void finishSequence(QList<GObject*>& objects, IOAdapter* io, U2OpStatus& os, const U2DbiRef& dbiRef, const QVariantMap& fs, TmpDbiObjects& dbiObjects, U2SequenceImporter& seqImporter){
U2Sequence u2seq = seqImporter.finalizeSequence(os);
dbiObjects.objects << u2seq.id;
CHECK_OP(os, );
GObjectReference sequenceRef(io->getURL().getURLString(), u2seq.visualName, GObjectTypes::SEQUENCE, U2EntityRef(dbiRef, u2seq.id));
U1AnnotationUtils::addAnnotations(objects, seqImporter.getCaseAnnotations(), sequenceRef, NULL, fs);
objects << new U2SequenceObject(u2seq.visualName,U2EntityRef(dbiRef, u2seq.id));
}
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;
}
bool SwissProtPlainTextFormat::readSequence(ParserState *st, U2SequenceImporter& seqImporter, int& sequenceLen, int& fullSequenceLen, U2OpStatus& os){
QByteArray res;
IOAdapter* io = st->io;
U2OpStatus& si = st->si;
si.setDescription(tr("Reading sequence %1").arg(st->entry->name));
int headerSeqLen = st->entry->seqLen;
res.reserve(res.size() + headerSeqLen);
QByteArray readBuffer(READ_BUFF_SIZE, '\0');
char* buff = readBuffer.data();
//reading sequence
QBuffer writer(&res);
writer.open( QIODevice::WriteOnly);
bool ok = true;
int len;
while (ok && (len = io->readLine(buff, READ_BUFF_SIZE)) > 0) {
if (si.isCoR()) {
res.clear();
break;
}
if (len <= 0) {
si.setError(tr("Error parsing sequence: unexpected empty line"));
break;
}
if (buff[0] == '/') { //end of the sequence
break;
}
bool isSeek = writer.seek(0);
assert(isSeek); Q_UNUSED(isSeek);
//add buffer to result
for (int i= 0; i < len; i++) {
char c = buff[i];
if (c != ' ' && c != '\t') {
ok = writer.putChar(c);
if (!ok) {
break;
}
}
}
if (!ok) {
si.setError(tr("Error reading sequence: memory allocation failed"));
break;
}
seqImporter.addBlock(res,res.size(),os);
if(os.isCoR()){
break;
}
sequenceLen += res.size();
fullSequenceLen += res.size();
res.clear();
si.setProgress(io->getProgress());
}
if (!si.isCoR() && buff[0] != '/') {
si.setError(tr("Sequence is truncated"));
}
writer.close();
return true;
}
