Motif.h
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#ifndef MOTIF_H_
#define MOTIF_H_
#include <boost/filesystem.hpp>
#include <mutex>
#include <string>
#include <vector>
using boost::filesystem::path;
using std::pair;
using std::string;
using std::vector;
class Motif; // forward declaration
typedef struct args_ {
path descfile;
string rna;
vector<Motif>& final_results;
std::mutex& posInsertionSites_mutex;
args_(path descfile_, string rna_, vector<Motif>& vector_, std::mutex& mutex_)
: descfile(descfile_), rna(rna_), final_results(vector_), posInsertionSites_mutex(mutex_)
{
}
} args_of_parallel_func;
typedef struct Comp_ {
pair<uint, uint> pos;
size_t k;
string seq_;
Comp_(pair<int, int> p) : pos(p) { k = 1 + pos.second - pos.first; }
Comp_(uint start, uint length) : k(length)
{
pos.first = start;
pos.second = start + length - 1;
}
} Component;
class Motif
{
public:
Motif();
Motif(const vector<Component>& v, string PDB);
void load_from_csv(string csv_line);
// static void build_from_desc(path descfile, string rna, vector<Motif>& final_results);
static void build_from_desc(args_of_parallel_func args);
static char is_valid_DESC(const string& descfile);
string pos_string(void) const;
string get_origin(void) const;
string get_identifier(void) const;
vector<Component> comp;
double score_;
bool reversed_;
private:
static vector<vector<Component>> find_next_ones_in(string rna, uint offset, vector<string> vc);
string atlas_id; // if source = RNAMOTIFATLAS
string PDBID; // if source = RNA3DMOTIF
bool is_model_; // Wether the motif is a model or an extracted module from a 3D structure
enum { RNA3DMOTIF = 1, RNAMOTIFATLAS = 2, CARNAVAL = 3 } source_;
};
bool is_desc_insertible(const string& descfile, const string& rna, bool verbose);
vector<Motif> load_desc_folder(const string& path, const string& rna, bool verbose);
vector<Motif> load_csv(const string& path);
// utilities to compare secondary structures:
bool operator==(const Motif& m1, const Motif& m2);
bool operator!=(const Motif& m1, const Motif& m2);
bool operator==(const Component& c1, const Component& c2);
bool operator!=(const Component& c1, const Component& c2);
#endif // MOTIF_H_