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#ifndef SIMULATOR_OUTPUT_SAMPLE_LIST_SET_H_
#define SIMULATOR_OUTPUT_SAMPLE_LIST_SET_H_
#include <map>
#include <string>
#include <iostream>
#include "../../pbdata/utils.hpp"
#include "OutputSampleList.hpp"
using namespace std;
typedef map<string, OutputSampleList> OutputSampleListMap;
class OutputSampleListSet {
public:
OutputSampleListMap listMap;
vector<string> keys;
int keyLength;
int nSufficient;
int sampleSpaceSize;
int keySize;
int minSamples;
int maxSamples;
vector<int> lengths;
OutputSampleListSet(int keySizeP) {
minSamples = 500;
maxSamples = 2000;
nSufficient = 0;
keySize = keySizeP;
sampleSpaceSize = 1 << (2*keySize);
}
void Write(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) {
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));
int i;
for ( i = 0; i < lengths.size(); i++) {
out.write((char*) &lengths[i], sizeof(int));
}
}
void Read(string &inName) {
ifstream in;
CrucialOpen(inName, in, std::ios::in|std::ios::binary);
Read(in);
in.close();
}
void Read(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(string key, OutputSample &sample) {
if (listMap[key].size() < minSamples) {
if (listMap[key].size() < maxSamples) {
listMap[key].push_back(sample);
}
if (listMap[key].size() == minSamples) {
nSufficient++;
cout << nSufficient << " / " << sampleSpaceSize << endl;
}
}
}
bool Sufficient() {
return nSufficient == sampleSpaceSize;
}
void SampleRandomSample(string key, OutputSample &sample) {
if (listMap.find(key) == listMap.end()) {
cout << listMap.size() << endl;
cout <<"ERROR, " << key << " is not a sampled context." << endl;
int i;
for (i = 0; i < key.size(); i++) {
char c = toupper(key[i]);
if (c != 'A' and c != 'C' and c != 'G' and c != 'T') {
cout << "The nucleotide " << c << " is not supported." << endl;
}
}
exit(1);
}
sample = listMap[key][RandomInt(listMap[key].size())];
}
};
#endif
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