bool Analyzer::convert(Pattern& pattern, vector<string>& items, RowData& row_data){
// pattern and item size must match
if (pattern.size() != items.size()) {
return false;
}
Pattern::iterator itr_pattern = pattern.begin();
vector<string>::iterator itr_items = items.begin();
// process every element using proper element parser
// return true only if all items are proper handled
while (itr_pattern != pattern.end()) {
Element* ele = *(*itr_pattern);
string str = *itr_items;
// increase pattern itr and corresponding item itr
itr_pattern++;
itr_items++;
Data data;
if (ele->convert(str, data)) {
row_data.push_back(data);
} else {
row_data.clear();
return false;
}
}
return true;
}
Matrix clipped_Hebbian(const Pattern& Z, const Topology& W)
{
Matrix J(W.n, W.n, 0); // Create a nxn Matrix filled with 0
// clipped Hebbian Definition: Jij=Wij * Zp(i) * Zp(j)
// Redefinition:
// If there is a connection between neuron i and neuron j,
// check if neuron i and neuron j are both in pattern p
// ----------------------------
// 1. Go through all the patterns
for (Pattern::const_iterator p=Z.begin(); p!=Z.end(); ++p)
// 2. Go through all connections of the topology
for (Topology::const_iterator i=W.begin(); i!=W.end(); ++i)
{
// 3. Check if neuron 'i' is in pattern
if (find(p->begin(), p->end(), i->first)!=p->end())
// 4. If so, then check if any of the neurons connected to 'i' is in the pattern 'p' as well
for (NeuronList::const_iterator j=i->second.begin(); j!=i->second.end(); ++j)
if (find(p->begin(), p->end(), *j)!=p->end())
// If so, Jij is equal to 1
J(i->first,*j)=1;
}
return J;
}
Pattern gram::get_kmer_from_read(const uint32_t &kmer_size, const Pattern &read) {
Pattern kmer;
auto kmer_start_it = read.begin() + read.size() - kmer_size;
kmer.assign(kmer_start_it, read.end());
return kmer;
}