void DNASequenceGeneratorTask::addSequencesToMsaDoc( Document *source )
{
const QSet<QString> &supportedFormats = source->getDocumentFormat( )->getSupportedObjectTypes( );
SAFE_POINT( supportedFormats.contains( GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT ),
"Invalid document format", );
SAFE_POINT( NULL != generateTask, "Invalid generate task", );
const U2DbiRef dbiRef = generateTask->getDbiRef( );
const DNAAlphabet *alp = cfg.alphabet;
SAFE_POINT( NULL != alp, "Generated sequence has invalid alphabet", );
const QString baseSeqName = cfg.getSequenceName( );
const QList<U2Sequence> seqs = generateTask->getResults( );
MultipleSequenceAlignment msa(tr( "Generated MSA" ), alp);
DbiConnection con( dbiRef, stateInfo );
for ( int sequenceNum = 0, totalSeqCount = seqs.size( ); sequenceNum < totalSeqCount;
++sequenceNum )
{
const QString seqName = ( 1 < totalSeqCount )
? ( baseSeqName + " " + QString::number( sequenceNum + 1 ) ) : baseSeqName;
// TODO: large sequences will cause out of memory error here
const QByteArray seqContent = con.dbi->getSequenceDbi( )->getSequenceData(
seqs[sequenceNum].id, U2_REGION_MAX, stateInfo );
msa->addRow( seqName, seqContent, sequenceNum);
}
MultipleSequenceAlignmentObject *alnObject = MultipleSequenceAlignmentImporter::createAlignment( source->getDbiRef( ), msa, stateInfo );
CHECK_OP( stateInfo, );
source->addObject( alnObject );
}
int main(int argc, char* argv[]) {
MSA msa(argc, argv);
return 0;
}
