MAPGD/allele_8h_source.html

 /* synonym for population? */


 #ifndef ALLELE_STAT_H

 #define ALLELE_STAT_H


 #include <iostream>

 #include <iomanip>

 #include <cfloat>

 #include <sstream>

 #include <vector>


 #include "typedef.h"

 #include "base.h"

 #include "data.h"


 class Allele : public Indexed_data {

 private:

     void read(std::istream& str);

     void write(std::ostream& str) const;

     static const Registration registered;

     static Data * create(const std::vector <std::string> & Columns){

         return new Allele();

     };

 public:

 //  void write_binary (std::ostream& out) const;

 //  void read_binary (std::istream& in);


     char delim;


     count_t excluded;

     bool pooled;


     Allele();       //


     float_t freq;


     gt_t ref;

     gt_t minor;

     gt_t major;

     gt_t e1;

     gt_t e2;


     float_t error;


     float_t null_error;

     float_t null_error2;

     count_t coverage;

     float_t efc;


     float_t ll, monoll, hwell;


     float_t MM;

     float_t Mm;

     float_t mm;


     count_t N;

     float_t f;

     float_t h;


     float_t gof;


     Allele & operator=(const Allele &);


     Allele(std::vector<std::string>) : Allele() {};


     /*(0){}

     {

         std::cerr << "done!\n";

     };*/

     std::string header(void) const;

     static const std::string table_name;

     static const std::string file_name;

     static const bool binary;

     size_t size(void) const;


     const std::string get_file_name(void) const;

     const std::string get_table_name(void) const;

     const bool get_binary(void) const;


     const std::string sql_header(void) const;

     const std::string sql_column_names(void) const;

     const std::string sql_values(void) const;

 };


 #endif

Allele::null_error2
float_t null_error2
error rate assuming Minor allele monomorphism.
Definition: allele.h:50

Allele::e2
gt_t e2
identity of error2.
Definition: allele.h:45

Allele::binary
static const bool binary
Default file extension.
Definition: allele.h:79

Allele::sql_column_names
const std::string sql_column_names(void) const
Returns the column names in the SQL table.
Definition: allele.cc:205

Allele::excluded
count_t excluded
A count of the number of samples that were excluded due to filtering criteria.
Definition: allele.h:34

Allele::table_name
static const std::string table_name
The destination table in the database.
Definition: allele.h:77

Allele::header
std::string header(void) const
returns first two lines of a file.
Definition: allele.cc:193

Allele::efc
float_t efc
number of 'effective' chromosomes in the sample.
Definition: allele.h:52

Allele::f
float_t f
HW statistic.
Definition: allele.h:61

Allele::write
void write(std::ostream &str) const
! the write function must be ? by the child class.
Definition: allele.cc:93

Allele::pooled
bool pooled
Inferred from pooled or labeled sequencing?
Definition: allele.h:35

Allele::size
size_t size(void) const
The size of the class in bytes.
Definition: allele.cc:197

Allele::minor
gt_t minor
identity of minor allele.
Definition: allele.h:42

Allele::error
float_t error
ml error rate.
Definition: allele.h:47

Indexed_data
Data which has an absolute position.
Definition: data.h:144

Allele::e1
gt_t e1
identity of error1
Definition: allele.h:44

Allele::null_error
float_t null_error
error rate assuming Major allele monomorphism.
Definition: allele.h:49

Allele::coverage
count_t coverage
population coverage.
Definition: allele.h:51

Allele::N
count_t N
number of individual at the site.
Definition: allele.h:60

Allele::h
float_t h
heterozygosity.
Definition: allele.h:62

Allele::get_binary
const bool get_binary(void) const
Returns the destination table name.
Definition: allele.cc:273

Allele::gof
float_t gof
gof statistic.
Definition: allele.h:64

Allele::sql_values
const std::string sql_values(void) const
Returns a string to insert values in an SQL table.
Definition: allele.cc:209

Allele::get_table_name
const std::string get_table_name(void) const
Returns the destination table name.
Definition: allele.cc:268

Allele::sql_header
const std::string sql_header(void) const
Returns a string to create an SQL table.
Definition: allele.cc:201

Allele::freq
float_t freq
frequency of major allele.
Definition: allele.h:39

Allele::Mm
float_t Mm
frequency of genotype Mm in the population.
Definition: allele.h:57

Allele::hwell
float_t hwell
log likelihoods.
Definition: allele.h:54

Allele::file_name
static const std::string file_name
Default file extension.
Definition: allele.h:78

Allele::MM
float_t MM
frequency of genotype MM in the population.
Definition: allele.h:56

Allele::operator=
Allele & operator=(const Allele &)
use the = operator to assign Allele.
Definition: allele.cc:164

Allele::get_file_name
const std::string get_file_name(void) const
Returns the default file extension.
Definition: allele.cc:263

Registration
A class which registers a child of Data in Data::new_data_.
Definition: data.h:222

Data
A class which can be written as flat text file or into an SQL database.
Definition: data.h:34

Allele::read
void read(std::istream &str)
The read function must be defined in the child class.
Definition: allele.cc:36

Allele::major
gt_t major
identity major allele.
Definition: allele.h:43

Allele::ref
gt_t ref
identity of ref allele.
Definition: allele.h:41

Allele::delim
char delim
the delimiter used when reading/writing the class in text mode.
Definition: allele.h:27

Allele
Summary statistics from the allele command.
Definition: allele.h:19

Allele::mm
float_t mm
frequency of genotype mm in the population.
Definition: allele.h:58

Allele::Allele
Allele(std::vector< std::string >)
Instance of constructor required by Data, but Allele doesn't actually need the vector to initialize...
Definition: allele.h:70