void merge_sub_vectors(std::vector<std::vector<T> >& dst, const std::vector<std::vector<T> >& src)
{
if (dst.size() < src.size()) {
dst.resize(src.size());
}
typename std::vector<std::vector<T> >::iterator dst_it = dst.begin();
typename std::vector<std::vector<T> >::const_iterator src_it = src.begin();
while (src_it != src.end()) {
merge_vectors(*dst_it++, *src_it++);
}
}
/*
Merges two VectorSiteContainers into a single VectorSiteContainer
*/
shared_ptr<VectorSiteContainer> merge_vscs(shared_ptr<VectorSiteContainer> s1, shared_ptr<VectorSiteContainer> s2)
throw (AlphabetMismatchException, Exception)
{
if (s1->getAlphabet()->getAlphabetType() != s2->getAlphabet()->getAlphabetType())
throw AlphabetMismatchException("SiteContainerTools::merge.", s1->getAlphabet(), s2->getAlphabet());
auto alphabet = s1->getAlphabet();
const int unknown_char = alphabet->getUnknownCharacterCode();
size_t l1 = s1->getNumberOfSites();
size_t l2 = s2->getNumberOfSites();
auto n1 = s1->getSequencesNames();
auto n2 = s2->getSequencesNames();
vector<string> allnames = merge_vectors(n1, n2);
unique_ptr<VectorSequenceContainer> tmp_container(new VectorSequenceContainer(alphabet));
for (auto &n : allnames) {
vector<int> seqvec1;
vector<int> seqvec2;
seqvec1.reserve(l1+l2);
seqvec2.reserve(l2);
if (s1->hasSequence(n)) {
auto tmpvec = s1->getSequence(n).getContent();
seqvec1.insert( seqvec1.end(), tmpvec.begin(), tmpvec.end());
}
else {
vector<int> tmpvec(l1, unknown_char);
seqvec1.insert( seqvec1.end(), tmpvec.begin(), tmpvec.end());
}
if (s2->hasSequence(n)) {
auto tmpvec = s2->getSequence(n).getContent();
seqvec2.insert( seqvec2.end(), tmpvec.begin(), tmpvec.end());
}
else {
vector<int> tmpvec(l2, unknown_char);
seqvec2.insert( seqvec2.end(), tmpvec.begin(), tmpvec.end());
}
seqvec1.insert(seqvec1.end(), seqvec2.begin(), seqvec2.end());
unique_ptr<BasicSequence> seq(new BasicSequence(n, seqvec1, alphabet));
tmp_container->addSequence(*seq, false);
}
auto output = make_shared<VectorSiteContainer>(*tmp_container);
return output;
}
