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#ifndef __KMERCOUNTER__
#define __KMERCOUNTER__
#include <vector>
#include <map>
#include <string>
#include <set>
#include "sequenceUtil.hpp"
using namespace std;
struct eqstr {
bool operator()(const kmer_int_type_t& kmer_val_a, const kmer_int_type_t& kmer_val_b) const {
return( kmer_val_a == kmer_val_b);
}
};
struct hashme {
kmer_int_type_t operator() (const kmer_int_type_t& kmer_val) const {
return(kmer_val);
}
};
#ifdef __GOOGLE__
// #warning "******** using GOOGLE SPARSEHASH for Kmer graph *********"
#include <google/sparse_hash_map>
using google::sparse_hash_map;
typedef sparse_hash_map<kmer_int_type_t, unsigned int, hashme, eqstr> Kmer_counter_map;
typedef sparse_hash_map<kmer_int_type_t, unsigned int, hashme, eqstr>::iterator Kmer_counter_map_iterator;
typedef sparse_hash_map<kmer_int_type_t, unsigned int, hashme, eqstr>::const_iterator Kmer_counter_map_const_iterator;
#elif defined(__SUNPRO_CC) // Solaris Studio compiler
#include <hash_map>
typedef std::hash_map<kmer_int_type_t,unsigned int, hashme, eqstr> Kmer_counter_map;
typedef std::hash_map<kmer_int_type_t,unsigned int, hashme, eqstr>::iterator Kmer_counter_map_iterator;
typedef std::hash_map<kmer_int_type_t,unsigned int, hashme, eqstr>::const_iterator Kmer_counter_map_const_iterator;
#else
#include <ext/hash_map>
typedef __gnu_cxx::hash_map<kmer_int_type_t,unsigned int, hashme, eqstr> Kmer_counter_map;
typedef __gnu_cxx::hash_map<kmer_int_type_t,unsigned int, hashme, eqstr>::iterator Kmer_counter_map_iterator;
typedef __gnu_cxx::hash_map<kmer_int_type_t,unsigned int, hashme, eqstr>::const_iterator Kmer_counter_map_const_iterator;
#endif
typedef pair<kmer_int_type_t,unsigned int> Kmer_Occurence_Pair;
class KmerCounter {
public:
KmerCounter() {};
KmerCounter(unsigned int kmer_length, bool is_ds=false);
unsigned int get_kmer_length();
unsigned long size();
void add_sequence(string& sequence, unsigned int cov=1);
bool add_kmer (kmer_int_type_t, unsigned int count);
bool add_kmer (string kmer, unsigned int count);
void describe_kmers();
void dump_kmers_to_file(string& outfilename);
//vector<Kmer_counter_map_iterator> get_kmers_sort_descending_counts();
vector<Kmer_Occurence_Pair> get_kmers_sort_descending_counts();
Kmer_counter_map_iterator find_kmer(kmer_int_type_t kmer_val);
bool kmer_exists(string kmer);
bool kmer_exists(kmer_int_type_t kmer_val);
unsigned int get_kmer_count(string kmer);
unsigned int get_kmer_count(kmer_int_type_t kmer_val);
string describe_kmer(string& kmer);
string get_kmer_string(kmer_int_type_t kmer_val);
kmer_int_type_t get_kmer_intval(string kmer);
bool prune_kmer(string kmer); // remove kmer from map
bool prune_kmer(kmer_int_type_t kmer_val);
bool prune_some_kmers(unsigned int min_count, float min_entropy, bool prune_error_kmers, float min_ratio_non_error);
bool prune_branched_kmers();
void prune_kmers_min_count(unsigned int count);
void prune_kmers_min_entropy(float min_entropy);
bool clear_kmer(kmer_int_type_t kmer_val);
// methods return kmers sorted descending by count.
//vector<string> get_reverse_kmer_candidates(string& kmer);
vector<Kmer_Occurence_Pair> get_reverse_kmer_candidates(kmer_int_type_t seed_kmer);
//vector<string> get_forward_kmer_candidates(string& kmer);
vector<Kmer_Occurence_Pair> get_forward_kmer_candidates(kmer_int_type_t seed_kmer);
// methods return kmers unsorted, in order G,A,T,C
//vector<string> get_reverse_kmer_candidates_unsorted(string& kmer);
vector<Kmer_Occurence_Pair> get_reverse_kmer_candidates_unsorted(kmer_int_type_t seed_kmer, bool getZeros);
//vector<string> get_forward_kmer_candidates_unsorted(string& kmer);
vector<Kmer_Occurence_Pair> get_forward_kmer_candidates_unsorted(kmer_int_type_t seed_kmer, bool getZeros);
// get the simple list of the 4 possible kmer extensions.
kmer_int_type_t* get_forward_kmer_candidates_noLookup(kmer_int_type_t seed_kmer, kmer_int_type_t forward_kmer_array_size_4 [4]);
kmer_int_type_t* get_reverse_kmer_candidates_noLookup(kmer_int_type_t seed_kmer, kmer_int_type_t reverse_kmer_array_size_4 [4]);
bool prune_kmer_extensions( float min_ratio_non_error);
const Kmer_counter_map& get_kmer_counter_map() const;
private:
unsigned int _kmer_length;
Kmer_counter_map _kmer_counter;
bool _DS_MODE;
};
class Kmer_visitor {
public:
Kmer_visitor(unsigned int kmer_length, bool is_ds);
void add (kmer_int_type_t kmer);
bool exists (kmer_int_type_t kmer);
void erase (kmer_int_type_t kmer);
void clear();
unsigned int size();
private:
unsigned int _kmer_length;
bool _DS_MODE;
set<kmer_int_type_t> _set;
};
class Sort_kmer_by_count_desc {
public:
Sort_kmer_by_count_desc(KmerCounter *kcounter);
bool operator() (const Kmer_counter_map_iterator& i, const Kmer_counter_map_iterator& j);
bool operator() (const Kmer_Occurence_Pair& i, const Kmer_Occurence_Pair& j);
bool operator() (const kmer_int_type_t& val_i, const kmer_int_type_t& val_j);
bool operator() (const string& i, const string& j);
private:
KmerCounter *kcounter;
};
#endif
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