tek::Transposon Class Reference

Transposon class. More...

#include <transposon.hpp>

Public Types
using	param_type = TransposonParams
	Alias.

Public Member Functions
	Transposon () noexcept=default
	default constructor
	Transposon (DNA< NUM_NONSYNONYMOUS_SITES > &&non, DNA< NUM_SYNONYMOUS_SITES > &&syn) noexcept
	constructor
	Transposon (const Transposon &)=default
	copy constructor
	Transposon (Transposon &&) noexcept=default
	move constructor
template<class URBG>
void	mutate (URBG &engine) noexcept
	make one point mutation
void	speciate () noexcept
	modify species_ and NUM_SPECIES_
void	indel () noexcept
	set has_indel_
void	hyperactivate () noexcept
	set is_hyperactive_
double	activity () const noexcept
	\(a_i\); count nonsynonymous mutations and return the pre-calculated ACTIVITY_
double	transposition_rate () const noexcept
	\(u_i = u_0 \times a_i\)
uint_fast32_t	operator- (const Transposon &other) const noexcept
	Hamming distance.
double	operator* (const Transposon &other) const noexcept
	interaction coefficient between species
bool	is_far_enough_from (const Transposon &other) const noexcept
	check if distance is large enough for speciation
const DNA< NUM_NONSYNONYMOUS_SITES > &	nonsynonymous_sites () const noexcept
	getter of nonsynonymous_sites_
const DNA< NUM_SYNONYMOUS_SITES > &	synonymous_sites () const noexcept
	getter of synonymous_sites_
bool	has_indel () const noexcept
	getter of has_indel_
uint_fast32_t	species () const noexcept
	getter of species_
double	dn () const noexcept
	nonsynonymous substitution per nonsynonymous site
double	ds () const noexcept
	synonymous substitution per synonymous site
std::ostream &	write_summary (std::ostream &) const
	write summary
std::ostream &	write_fasta (std::ostream &) const
	write sequence with header in FASTA format
std::ostream &	write_metadata (std::ostream &) const
	write metadata for FASTA header
std::ostream &	write_sequence (std::ostream &) const
	write sequence

Static Public Member Functions
static bool	can_speciate () noexcept
	check if speciation is allowed under the condition
static void	INTERACTION_COEFS_clear () noexcept
	clear INTERACTION_COEFS_
static void	INTERACTION_COEFS_emplace (uint_fast32_t x, uint_fast32_t y, double coef) noexcept
	setter of INTERACTION_COEFS_
static double	INTERACTION_COEFS_get (uint_fast32_t x, uint_fast32_t y)
	getter of INTERACTION_COEFS_
static void	write_activity (std::ostream &, double alpha, unsigned int beta)
	calculate and write activity for the given alpha and beta
static void	param (const param_type &p)
	Set PARAM_.
static const param_type &	param ()
	Get PARAM_.
static void	initialize ()
	Set PARAM_ with default values;.

Static Public Attributes
static constexpr uint_fast32_t	NUM_SYNONYMOUS_SITES = LENGTH / 3u
	number of synonymous sites
static constexpr uint_fast32_t	NUM_NONSYNONYMOUS_SITES = LENGTH - NUM_SYNONYMOUS_SITES
	number of nonsynonymous sites
static constexpr double	MAX_TRANSPOSITION_RATE = 0.01
	\(u_0\), maximum transposition rate
static constexpr double	OVER_SYNONYMOUS_SITES = 1.0 / NUM_SYNONYMOUS_SITES
	reciprocal of synonymous sites
static constexpr double	OVER_NONSYNONYMOUS_SITES = 1.0 / NUM_NONSYNONYMOUS_SITES
	reciprocal of nonsynonymous sites

Static Private Member Functions
static double	calc_activity (uint_fast32_t num_mutations)

Private Attributes
DNA< NUM_NONSYNONYMOUS_SITES >	nonsynonymous_sites_
	nonsynonymous sites
DNA< NUM_SYNONYMOUS_SITES >	synonymous_sites_
	synonymous sites
bool	has_indel_ = false
	activity is zero if this is true
bool	is_hyperactive_ = false
	activity is doubled if this is true
uint_fast32_t	species_ = 0
	transposon species

Static Private Attributes
static param_type	PARAM_
	Parameters shared among instances.
static double	THRESHOLD_
	1 - TransposonParams::ALPHA
static std::array< double, NUM_NONSYNONYMOUS_SITES >	ACTIVITY_
	pre-calculated activity values
static std::atomic_uint_fast32_t	NUM_SPECIES_
	number of species; incremented by speciation
static std::unordered_map< uint_fast64_t, double >	INTERACTION_COEFS_
	interaction coefficients between species

Friends
std::ostream &	operator<< (std::ostream &ost, const Transposon &x)
	shortcut for Transposon::write_summary()

Detailed Description

Transposon class.

Member Function Documentation

calc_activity()

double tek::Transposon::calc_activity ( uint_fast32_t num_mutations )

staticprivate

\[ a = \left(\frac {1 - d - \alpha} {1 - \alpha} \right)^\beta \]

operator*()

double tek::Transposon::operator* ( const Transposon & other ) const

inlinenoexcept

interaction coefficient between species

\[ I(d) = \begin{cases} 1 & d < d_l \\ \frac {d_u - d}{d_u - d_l} & d_l \le d < d_u \\ 0 & d_u \le d \end{cases} \]

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The documentation for this class was generated from the following files:

• src/transposon.hpp
• src/transposon.cpp