Ludovic PLATON / IRSOM

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Ludovic PLATON
3875beab 1 parent 7431e16e

Add new feature element in Featurer, remove KMER6

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Showing 3 changed files with 170 additions and 161 deletions
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......@@ -10,161 +10,170 @@
#include "data/data_basic.h"
namespace feature{
class Feature : public data::Data_basic{
protected:
virtual void init(const Data_basic *db);
public:
static const std::string TYPE;
static const std::string ENTRY_TYPE;
Feature(std::string name):data::Data_basic(name){}
Feature(const data::Data_basic *db):data::Data_basic(db){this->init(db);}
virtual ~Feature(){}
virtual float dist(feature::Feature *a)=0;
std::string to_dict()=0;
std::string to_csv()=0;
virtual std::string getID(){
return this->TYPE;
}
virtual data::Data_basic *clone()=0;
std::string getEntry_name() const;
};
class SeqLength: public feature::Feature{
protected:
int l;
void init(const Data_basic *db);
public:
static const std::string TYPE;
static const std::string ENTRY_TYPE;
static callable::Callable<data::Data_basic*,data::Data_basic*> *get_callable();
int getL() const;
SeqLength(const entry::Sequence &s):
feature::Feature(s.getName()),l(s.getLength()){}
SeqLength(const std::string &name,const int &seql):
feature::Feature(name),l(seql){}
SeqLength(const data::Data_basic *db):feature::Feature(db){this->init(db);}
~SeqLength(){}
float dist(Feature *a);
data::Data_basic *clone();
std::string to_dict();
std::string to_csv();
std::string getID(){
return this->TYPE;
}
};
class Kmer: public feature::Feature{
protected:
unsigned int k;
std::unordered_map<std::string,float> kmer;
void init(const Data_basic *db);
public:
static const std::string TYPE;
static const std::string ENTRY_TYPE;
static callable::Callable<data::Data_basic*,data::Data_basic*> *get_callable(const unsigned int &k);
Kmer(entry::Sequence &s, const unsigned int &k);
Kmer(const std::string &name,
const unsigned int &k, const std::unordered_map<std::string,float> kmer):
feature::Feature(name),
k(k),kmer(kmer){}
Kmer(const data::Data_basic *db):feature::Feature(db){this->init(db);}
~Kmer(){}
float dist(feature::Feature *a);
unsigned int getK() const;
std::unordered_map<std::string, float> getKmer() const;
data::Data_basic *clone();
std::string to_dict();
std::string to_csv();
std::string getID(){
return this->TYPE;
}
};
class ORF: public feature::Feature{
protected:
static const std::vector<std::string> START;
static const std::vector<std::string> END;
static bool in_start(const std::string &c);
static bool in_end(const std::string &c);
unsigned int length;
float coverage;
/*
class Feature : public data::Data_basic{
protected:
virtual void init(const Data_basic *db);
public:
static const std::string TYPE;
static const std::string ENTRY_TYPE;
Feature(std::string name):data::Data_basic(name){}
Feature(const data::Data_basic *db):data::Data_basic(db){this->init(db);}
virtual ~Feature(){}
virtual float dist(feature::Feature *a)=0;
std::string to_dict()=0;
std::string to_csv()=0;
virtual std::string getID(){
return this->TYPE;
}
virtual data::Data_basic *clone()=0;
std::string getEntry_name() const;
};
class SeqLength: public feature::Feature{
protected:
int l;
void init(const Data_basic *db);
public:
static const std::string TYPE;
static const std::string ENTRY_TYPE;
static callable::Callable<data::Data_basic*,data::Data_basic*> *get_callable();
int getL() const;
SeqLength(const entry::Sequence &s):
feature::Feature(s.getName()),l(s.getLength()){}
SeqLength(const std::string &name,const int &seql):
feature::Feature(name),l(seql){}
SeqLength(const data::Data_basic *db):feature::Feature(db){this->init(db);}
~SeqLength(){}
float dist(Feature *a);
data::Data_basic *clone();
std::string to_dict();
std::string to_csv();
std::string getID(){
return this->TYPE;
}
};
class Kmer: public feature::Feature{
protected:
unsigned int k;
std::unordered_map<std::string,float> kmer;
void init(const Data_basic *db);
public:
static const std::string TYPE;
static const std::string ENTRY_TYPE;
static callable::Callable<data::Data_basic*,data::Data_basic*> *get_callable(const unsigned int &k);
Kmer(entry::Sequence &s, const unsigned int &k);
Kmer(const std::string &name,
const unsigned int &k, const std::unordered_map<std::string,float> kmer):
feature::Feature(name),
k(k),kmer(kmer){}
Kmer(const data::Data_basic *db):feature::Feature(db){this->init(db);}
~Kmer(){}
float dist(feature::Feature *a);
unsigned int getK() const;
std::unordered_map<std::string, float> getKmer() const;
data::Data_basic *clone();
std::string to_dict();
std::string to_csv();
std::string getID(){
return this->TYPE;
}
};
class ORF: public feature::Feature{
protected:
static const std::vector<std::string> START;
static const std::vector<std::string> END;
static bool in_start(const std::string &c);
static bool in_end(const std::string &c);
unsigned int length;
float coverage;
float start_mean;
float start_std;
float end_mean;
float end_std;
/*
float start_center, start_std;
float end_center, end_std;
*/
void init(const Data_basic *db);
public:
static const std::string TYPE;
static const std::string ENTRY_TYPE;
static callable::Callable<data::Data_basic*,data::Data_basic*> *get_callable();
~ORF(){}
ORF(const entry::Sequence &s);
ORF(const std::string &name,
const unsigned int &length, const float &coverage):
feature::Feature(name),
length(length),coverage(coverage){}
ORF(const data::Data_basic *db):feature::Feature(db){this->init(db);}
float dist(feature::Feature *a);
data::Data_basic *clone();
std::string to_dict();
std::string to_csv();
std::string getID(){
return this->TYPE;
}
float getCoverage() const;
float getStart_center() const;
float getStart_std() const;
float getEnd_center() const;
float getEnd_std() const;
unsigned int getMax_length() const;
unsigned int getLength() const;
};
class CodonPosition: public feature::Feature{
protected:
float position[4];
void init(const Data_basic *db);
public:
static const std::string TYPE;
static const std::string ENTRY_TYPE;
static callable::Callable<data::Data_basic*,data::Data_basic*> *get_callable();
~CodonPosition(){}
CodonPosition(const entry::Sequence &s);
CodonPosition(const std::string &name,
const float (&position)[4]):
feature::Feature(name){
std::copy(std::begin(position),std::end(position),std::begin(this->position));
}
CodonPosition(const data::Data_basic *db):feature::Feature(db){this->init(db);}
const float *getPosition();
float dist(Feature *a);
data::Data_basic *clone();
std::string to_dict();
std::string to_csv();
std::string getID(){
return this->TYPE;
}
};
void init(const Data_basic *db);
public:
static const std::string TYPE;
static const std::string ENTRY_TYPE;
static callable::Callable<data::Data_basic*,data::Data_basic*> *get_callable();
~ORF(){}
ORF(const entry::Sequence &s);
ORF(const std::string &name,
const unsigned int &length, const float &coverage):
feature::Feature(name),
length(length),coverage(coverage){}
ORF(const data::Data_basic *db):feature::Feature(db){this->init(db);}
float dist(feature::Feature *a);
data::Data_basic *clone();
std::string to_dict();
std::string to_csv();
std::string getID(){
return this->TYPE;
}
float getCoverage() const;
float getStart_center() const;
float getStart_std() const;
float getEnd_center() const;
float getEnd_std() const;
unsigned int getMax_length() const;
unsigned int getLength() const;
};
class CodonBiases: public feature::Feature{
protected:
float position[4] = {0,0,0,0};
float composition[4] = {0,0,0,0};
void init(const Data_basic *db);
public:
static const std::string TYPE;
static const std::string ENTRY_TYPE;
static callable::Callable<data::Data_basic*,data::Data_basic*> *get_callable();
~CodonBiases();
CodonBiases(const entry::Sequence &s);
CodonBiases(
const std::string &name,
const float (&position)[4],
const float (&composition)[4]):
feature::Feature(name){
std::copy(std::begin(position),std::end(position),std::begin(this->position));
std::copy(std::begin(composition),std::end(composition),std::begin(this->composition));
}
CodonBiases(const data::Data_basic *db):feature::Feature(db){this->init(db);}
const float *getPosition();
float dist(Feature *a);
data::Data_basic *clone();
std::string to_dict();
std::string to_csv();
std::string getID(){
return this->TYPE;
}
};
}
#endif // FEATURE_H
......
......@@ -57,10 +57,10 @@ int main(int argc, char* argv[])
ds["KMER3"] = tmp_ds;
create_feature_maker(kmer,feature::Kmer::TYPE+std::to_string(6),tmp_ds,&re);
kmer = static_cast<feature::Feature_callable*>(feature::Kmer::get_callable(6));
tmp_ds = new data::Data_Store_Map(output+"KMER6.txt");
ds["KMER6"] = tmp_ds;
create_feature_maker(kmer,feature::Kmer::TYPE+std::to_string(6),tmp_ds,&re);
// kmer = static_cast<feature::Feature_callable*>(feature::Kmer::get_callable(6));
// tmp_ds = new data::Data_Store_Map(output+"KMER6.txt");
// ds["KMER6"] = tmp_ds;
// create_feature_maker(kmer,feature::Kmer::TYPE+std::to_string(6),tmp_ds,&re);
/* *********** ORF *********************/
/* ORF callable */
......@@ -70,12 +70,12 @@ int main(int argc, char* argv[])
ds["ORF"] = tmp_ds;
create_feature_maker(orf,feature::ORF::TYPE,tmp_ds,&re);
/* *********** Codon Position ***************/
/* *********** Codon Biases ***************/
feature::Feature_callable *cp = static_cast<feature::Feature_callable*>(feature::CodonPosition::get_callable());
tmp_ds = new data::Data_Store_Map(output+"CP.txt");
ds["CP"] = tmp_ds;
create_feature_maker(cp,feature::CodonPosition::TYPE,tmp_ds,&re);
feature::Feature_callable *cb = static_cast<feature::Feature_callable*>(feature::CodonBiases::get_callable());
tmp_ds = new data::Data_Store_Map(output+"CB.txt");
ds["CB"] = tmp_ds;
create_feature_maker(cb,feature::CodonBiases::TYPE,tmp_ds,&re);
/* *********** Fasta reader *************/
......