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CodonData.cpp
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CodonData.cpp
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#include "CodonData.h"
#include <iostream>
#include <string>
using namespace std;
CodonData::CodonData() {
}
CodonData::CodonData(map<string, vector<int> > matches) {
m_matches = matches;
}
map<string, vector<string> >& CodonData::getAllData() {
if (m_allData.size() != 0) {
// all data was computed previously
return m_allData;
} else {
mergeData();
return m_allData;
}
}
void CodonData::mergeData() {
//std::cout << "mergeData for codon insertions ... " << std::endl;
map<string, vector<string> > allData;
for (map<string, vector<int> >::iterator it = m_matches.begin(); it != m_matches.end(); ++it) {
string codon = it->first;
//std::cout << "Codon is: " << codon << std::endl;
map<int, vector<map<string, int > > >::iterator insIt = m_insertions.begin();
for (size_t refPos = 0; refPos < it->second.size(); ++refPos) {
allData[codon].push_back(to_string(it->second[refPos]));
if (insIt != m_insertions.end() && refPos == insIt->first) {
// insert new entries into vector to represent the insertion; adjust the 'pos' entry!!
for (size_t i = 0; i < insIt->second.size(); ++i) {
string insVal = "";
if (codon == "pos") {
insVal = to_string(refPos) + "INS" + to_string(i);
} else {
if (insIt->second[i].find(codon) != insIt->second[i].end()) {
// inserted codon was observed at least once
insVal = to_string(insIt->second[i].at(codon));
} else {
insVal = to_string(0); // inserted codon was never observed
}
}
allData[codon].push_back(insVal);
}
insIt++; // go to the next insertion entry
}
}
}
m_allData = allData;
}