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#ifndef SIMULATOR_OUTPUT_SAMPLE_LIST_SET_H_
#define SIMULATOR_OUTPUT_SAMPLE_LIST_SET_H_
#include <iostream>
#include <map>
#include <string>
#include <alignment/simulator/OutputSampleList.hpp>
#include <pbdata/utils.hpp>
typedef std::map<std::string, OutputSampleList> OutputSampleListMap;
class OutputSampleListSet
{
public:
OutputSampleListMap listMap;
std::vector<std::string> keys;
int keyLength;
int nSufficient;
int sampleSpaceSize;
int keySize;
int minSamples;
int maxSamples;
std::vector<int> lengths;
OutputSampleListSet(int keySizeP)
{
minSamples = 500;
maxSamples = 2000;
nSufficient = 0;
keySize = keySizeP;
sampleSpaceSize = 1 << (2 * keySize);
}
void Write(std::ofstream &out)
{
// Say how many elements to write.
OutputSampleListMap::iterator mapIt;
int setSize = listMap.size();
out.write((char *)&setSize, sizeof(int));
int keySize = 0;
// Say how large each element is.
if (listMap.size() > 0) {
keySize = listMap.begin()->first.size();
}
out.write((char *)&keySize, sizeof(int));
for (mapIt = listMap.begin(); mapIt != listMap.end(); ++mapIt) {
std::string mapItKey = mapIt->first;
out.write((char *)mapItKey.c_str(), sizeof(char) * mapItKey.size());
mapIt->second.Write(out);
}
int numLengths = lengths.size();
out.write((char *)&numLengths, sizeof(int));
for (size_t i = 0; i < lengths.size(); i++) {
out.write((char *)&lengths[i], sizeof(int));
}
}
void Read(std::string &inName)
{
std::ifstream in;
CrucialOpen(inName, in, std::ios::in | std::ios::binary);
Read(in);
in.close();
}
void Read(std::ifstream &in)
{
int setSize;
in.read((char *)&setSize, sizeof(int));
in.read((char *)&keyLength, sizeof(int));
if (keyLength == 0 or setSize == 0) {
return;
}
char *key = ProtectedNew<char>(keyLength + 1);
key[keyLength] = '\0';
int i;
for (i = 0; i < setSize; i++) {
in.read(key, sizeof(char) * keyLength);
listMap[key].Read(in);
}
int numLengths;
in.read((char *)&numLengths, sizeof(int));
if (numLengths > 0) {
lengths.resize(numLengths);
}
for (i = 0; i < numLengths; i++) {
in.read((char *)&lengths[i], sizeof(int));
}
if (key) {
delete[] key;
key = NULL;
}
}
void AppendOutputSample(std::string key, OutputSample &sample)
{
if (static_cast<int>(listMap[key].size()) < minSamples) {
if (static_cast<int>(listMap[key].size()) < maxSamples) {
listMap[key].push_back(sample);
}
if (static_cast<int>(listMap[key].size()) == minSamples) {
nSufficient++;
std::cout << nSufficient << " / " << sampleSpaceSize << std::endl;
}
}
}
bool Sufficient() { return nSufficient == sampleSpaceSize; }
void SampleRandomSample(std::string key, OutputSample &sample)
{
if (listMap.find(key) == listMap.end()) {
std::cout << listMap.size() << std::endl;
std::cout << "ERROR, " << key << " is not a sampled context." << std::endl;
for (size_t i = 0; i < key.size(); i++) {
char c = toupper(key[i]);
if (c != 'A' and c != 'C' and c != 'G' and c != 'T') {
std::cout << "The nucleotide " << c << " is not supported." << std::endl;
}
}
std::exit(EXIT_FAILURE);
}
sample = listMap[key][RandomInt(listMap[key].size())];
}
};
#endif
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