MultipleSequenceAlignmentRowData::MultipleSequenceAlignmentRowData(const U2MsaRow &rowInDb, const QString &rowName, const QByteArray &rawData, MultipleSequenceAlignmentData *msaData)
: MultipleAlignmentRowData(),
alignment(msaData),
initialRowInDb(rowInDb)
{
QByteArray sequenceData;
U2MsaRowGapModel gapModel;
MaDbiUtils::splitBytesToCharsAndGaps(rawData, sequenceData, gapModel);
sequence = DNASequence(rowName, sequenceData);
setGapModel(gapModel);
}
void
readFasta(istream& istr, SQDict& dict, bool parseSeqOffset)
{
string name;
vector<char> buffer;
while (true) {
string s;
getline(istr, s);
if (istr.bad()) {
cerr << "error reading SAM file" << endl;
exit(1);
}
if (istr.eof() or s[0] == '>') {
if (name.length() > 0) {
// add previous sequence
long long int seqOffset = 0;
if (parseSeqOffset) {
int j = name.find(':');
if (j < (int)name.length()) {
seqOffset = atoll(&name.c_str()[j + 1]) - 1;
name = name.substr(0, j);
}
}
Contig& c = dict[name];
if (c.name.length() == 0) {
c.name = name;
c.len = buffer.size();
c.idx = dict.size() - 1;
c.seq[0] = DNASequence(buffer.begin(), buffer.end());
c.seqOffset[0] = seqOffset;
cerr << "added contig [" << c.name << "] of length [" << c.len << "]"
<< " with start offset [" << c.seqOffset[0] << "]" << endl;
}
}
if (istr.eof())
break;
int stop = s.find(" ")-1;
if (stop > 0) {
name = s.substr(1,stop);
} else {
name = s.substr(1);
}
buffer.clear();
} else {
buffer.insert(buffer.end(), s.begin(), s.end());
}
}
}
QList<Task*> DNASequenceGeneratorTask::onGenerateTaskFinished( ) {
QList<Task *> resultTasks;
SAFE_POINT( generateTask->isFinished( ) && !generateTask->getStateInfo( ).isCoR( ),
"Invalid task encountered", resultTasks );
IOAdapterFactory *iof = AppContext::getIOAdapterRegistry( )->getIOAdapterFactoryById(
IOAdapterUtils::url2io( cfg.getOutUrlString( ) ) );
if (cfg.saveDoc) {
DocumentFormat *format = AppContext::getDocumentFormatRegistry()->getFormatById(cfg.getDocumentFormatId());
Document* doc = format->createNewLoadedDocument(iof, cfg.getOutUrlString(), stateInfo);
CHECK_OP( stateInfo, resultTasks );
const QSet<QString> &supportedFormats = format->getSupportedObjectTypes( );
const bool isSequenceFormat = supportedFormats.contains( GObjectTypes::SEQUENCE );
if ( isSequenceFormat) {
addSequencesToSeqDoc( doc );
} else { // consider alignment format
SAFE_POINT( supportedFormats.contains( GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT ),
"Unexpected format encountered", resultTasks );
addSequencesToMsaDoc( doc );
}
saveTask = new SaveDocumentTask(doc, SaveDoc_Overwrite);
resultTasks << saveTask;
} else { // TODO: avoid high memory consumption here
const DNAAlphabet *alp = cfg.getAlphabet( );
SAFE_POINT( NULL != alp, "Generated sequence has invalid alphabet", resultTasks );
const U2DbiRef dbiRef = generateTask->getDbiRef( );
const QString baseSeqName = cfg.getSequenceName( );
QList<U2Sequence> seqs = generateTask->getResults( );
for ( int sequenceNum = 0, totalSeqCount = seqs.size( ); sequenceNum < totalSeqCount;
++sequenceNum )
{
const QString seqName = ( 1 < totalSeqCount )
? ( baseSeqName + " " + QString::number( sequenceNum + 1 ) ) : baseSeqName;
DbiConnection con( dbiRef, stateInfo );
CHECK_OP( stateInfo, resultTasks );
const QByteArray seqContent = con.dbi->getSequenceDbi( )->getSequenceData(
seqs[sequenceNum].id, U2_REGION_MAX, stateInfo );
results << DNASequence( seqName, seqContent, alp );
}
}
return resultTasks;
}