void DNASequenceGenerator::evaluateBaseContent(const MultipleSequenceAlignment& ma, QMap<char, qreal>& result) {
QList< QMap<char, qreal> > rowsContents;
foreach(const MultipleSequenceAlignmentRow& row, ma->getMsaRows()) {
QMap<char, qreal> rowContent;
evaluate(row->getData(), rowContent);
rowsContents.append(rowContent);
}
QListIterator< QMap<char, qreal> > listIter(rowsContents);
while (listIter.hasNext()) {
const QMap<char, qreal>& cm = listIter.next();
QMapIterator<char, qreal> mapIter(cm);
while (mapIter.hasNext()) {
mapIter.next();
char ch = mapIter.key();
qreal freq = mapIter.value();
if (!result.keys().contains(ch)) {
result.insertMulti(ch, freq);
} else {
result[ch] += freq;
}
}
}
int rowsNum = ma->getNumRows();
QMutableMapIterator<char, qreal> i(result);
while (i.hasNext()) {
i.next();
i.value() /= rowsNum;
}
}
void convertMAlignment2SecVect(SeqVect& sv, const MultipleSequenceAlignment& ma, bool fixAlpha) {
sv.Clear();
MuscleContext *ctx = getMuscleContext();
ctx->fillUidsVectors(ma->getNumRows());
unsigned i=0;
unsigned seq_count = 0;
foreach(const MultipleSequenceAlignmentRow& row, ma->getMsaRows()) {
Seq *ptrSeq = new Seq();
QByteArray name = row->getName().toLocal8Bit();
ptrSeq->FromString(row->getCore().constData(), name.constData());
//stripping gaps, original Seq::StripGaps fails on MSVC9
Seq::iterator newEnd = std::remove(ptrSeq->begin(), ptrSeq->end(), U2Msa::GAP_CHAR);
ptrSeq->erase(newEnd, ptrSeq->end());
if (ptrSeq->Length()!=0) {
ctx->tmp_uIds[seq_count] = ctx->input_uIds[i];
sv.push_back(ptrSeq);
seq_count++;
}
i++;
}
if (fixAlpha) {
sv.FixAlpha();
}
}