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#include <iostream>
#include <vector>
#include "Fragment.h"
#include "commons.h"
#include "../minia/Bank.h"
#include "GraphOutput.h"
using namespace std;
#ifndef _FRAGMENT_BANK_H
#define _FRAGMENT_BANK_H
/**
* A set of indexible fragments
*/
class Fragment_Bank{
public:
// The extension types could be
// 1/ a strict sequence: any branching stops the extension
// 2/ a consensus sequence: uses minia contiging approach
// 3/ a strict graph: any branching is conserved in the graph
// 4/ a consensus graph: "small" polymorphism is merged, but "large" structures are represented.
char extension_type;
/**
* All fragments stored in the set
*/
vector<Fragment> all_fragments;
Fragment_Bank(const char type);
/**
* Free all fragments, delete the hash table
*/
~Fragment_Bank();
/**
* Read fragments from a file, and load them in the set of fragments
*/
void load_fragments(char * fragment_file);
void perform_extensions(const string prefix, int max_graph_depth,int max_nodes, parcours_t search_mode );
void format_results(const int extension_type, string prefix_name);
};
#endif // _FRAGMENT_BANK_H
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