extract_user_ct.h
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#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 checkBasePairIndex(std::vector < std::string > v, uint l);
bool checkIndex(std::vector < std::string > v, uint l);
void addHelix(int rna1, int rna2, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_, std::vector < Helix * >& ctHelix,
std::string CTfile, int nLine, uint &nbHardCT);
void addIntLoop(int rna1, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_, std::vector < Interloop * >& ctIntLoop,
std::string CTfile, int nLine, uint &nbHardCT);
void addHairLoop(int rna1, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_, std::vector < Hairpinloop * >& ctHairLoop,
std::string CTfile, int nLine, uint &nbHardCT);
void addMultiLoop(int rna1, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_, std::vector < Multiloop * >& ctMultiLoop,
std::string CTfile, int nLine, uint &nbHardCT);
void addBp(int rna1, int rna2, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_,
std::vector< std::tuple < std::pair < uint, uint >, std::pair < uint, uint >, uint > >& ctAppTwo,
std::vector< std::tuple < uint, uint, uint > >& ctApp,
std::string CTfile, int nLine, uint &nbHardCT);
void addSingle(int rna1, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_, std::vector < std::tuple < uint, uint, uint > >& ctSingle,
std::string CTfile, int nLine, uint &nbHardCT);
void extract_ct(const std::string CTfile, const std::vector < Rna >& rnaList_,
std::vector< std::tuple < std::pair < uint, uint >, std::pair < uint, uint >, uint > >& ctAppTwo,
std::vector< std::tuple < uint, uint, uint > >& ctApp,
std::vector< std::tuple < uint, uint, uint > >& ctSingle,
std::vector < Interloop * >& ctIntLoop,
std::vector < Hairpinloop * >& ctHairLoop,
std::vector < Helix * >& ctHelix,
std::vector < Multiloop * >& ctMultiLoop,
std::vector < Pseudoknot * >& ctPseudo,
uint &nbHardCT);
#endif