cSequenceDatabase.h

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#ifndef _CSEQUENCEDATABASE_H
#define _CSEQUENCEDATABASE_H
 
#include <iostream>
#include <fstream>
#include <vector>
#include <string>
#include "core/utilities.h"
#include "core/cSequence.h"
 
 
using namespace std;
 
 
class cMainThread;
 
 
class cSequenceDatabase {
 
    vector<cSequence> sequences;
 
    void parseRT(bool keeprt);
 
 
public:
 
 
    cSequenceDatabase();
 
 
    void loadFromPlainTextStream(ifstream &stream, bool keeprt);
 
 
    void storeToPlainTextStream(ofstream &stream, bool keeprt);
 
 
    int size();
 
 
    cSequence& operator[](int position);
 
 
    void clear();
 
 
    void push_back(cSequence& sequence);
 
 
    void erase(int index);
 
 
    void store(ofstream& os);
 
 
    void load(ifstream& is, int fileversionpart1, int fileversionpart2, int fileversionpart3);
 
 
    void attachDecoys(bool& terminatecomputation);
 
};
 
 
#endif