#ifndef H_EXTRACTUSERCT
#define H_EXTRACTUSERCT

#include <vector>
#include <string>
#include <utility>


#include "Motifs/interloop.h"
#include "Motifs/hairpinloop.h"
#include "Motifs/helix.h"
#include "Motifs/multiloop.h"
#include "Motifs/pseudoknot.h"
#include "rna.h"
#include "structure.h"
#include "solinteraction.h"

bool find_bp_with_i_at_first (std::vector < std::pair < unsigned int, unsigned int > > v, unsigned int i);

bool find_bp_with_i_at_second (std::vector < std::pair < unsigned int, unsigned int > > v, unsigned int i);

void extract_ct(const std::string CTfile, const std::vector < Rna >& rnaList_,
                std::vector< std::pair < std::pair < unsigned int, unsigned int >, std::pair < unsigned int, unsigned int > > >& ctAppTwoS_,
                std::vector< std::pair < std::pair < unsigned int, unsigned int >, std::pair < unsigned int, unsigned int > > >& ctAppTwoW_,
                std::vector< std::pair < unsigned int, unsigned int > >& ctAppS_,
                std::vector< std::pair < unsigned int, unsigned int > >& ctAppW_,
                std::vector< std::pair < unsigned int, unsigned int > >& ctSingleS_,
                std::vector< std::pair < unsigned int, unsigned int > >& ctSingleW_,
                std::vector < Interloop * >& ctIntLoopS_, std::vector < Interloop * >& ctIntLoopW_,
                std::vector < Hairpinloop * >& ctHairLoopS_, std::vector < Hairpinloop * >& ctHairLoopW_,
                std::vector < Helix * >& ctHelixS_, std::vector < Helix * >& ctHelixW_,
                std::vector < Multiloop * >& ctMultiLoopS_, std::vector < Multiloop * >& ctMultiLoopW_,
                std::vector < Pseudoknot * >& ctPseudoS_, std::vector < Pseudoknot * >& ctPseudoW_);


#endif