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#include <string.h>
#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
//#include "read_coherence_mapsembler/couple.h"
#include "commons.h"
#include "../minia/Bank.h"
#include "../minia/Kmer.h"
#include "../minia/Hash16.h"
#include "../minia/Set.h"
#include "../minia/Pool.h"
#include "../minia/Bloom.h"
#include "../minia/Debloom.h"
#include "../minia/Utils.h"
#include "../minia/SortingCount.h"
#include "../minia/Terminator.h"
#include "GraphOutput.h"
#include "IterativeExtensions.h"
#ifndef _FRAGMENT_H
#define _FRAGMENT_H
/**
* A fragment designes a sequence together with its comment and some coverage information.
* A fragment stores reads mapped on itself
**/
class Fragment{
public:
/**
* the initial sequence
*/
string fragment_sequence; // the fragment to be kmer-coherency-tested
/**
* the eventual comment of the fragment (from fasta or fastq file)
*/
string fragment_comment; // the comment of the fragment to be kmer-coherency-tested
/**
* vector of left extrem kmers kmers
*/
vector<string> left_extrem_kmers;
/**
* vector of right extrem kmers kmers
*/
vector<string> right_extrem_kmers;
/**
* Stores the initial sequence
*/
Fragment(string fragment_sequence);
bool isPalindromic();
void set_comment(string fragment_comment);
void add_left_extreme_kmer (string left_extrem_kmer);
void add_right_extreme_kmer (string right_extrem_kmer);
void perform_extension(const string prefix, int max_graph_depth, const char extension_type, int max_nodes, parcours_t search_mode);
void fragment_output_graph(GraphOutput graph);
void fragment_output_sequence(int index, string output_res, bool erase);
bool is_left_kmer (const int left_extrem_kmer_id);
bool is_right_kmer (const int right_extrem_kmer_id);
/**
* delete the hash table and free the fragment sequence
*/
~Fragment();
};
#endif //_FRAGMENT_H
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