TTQuanti Class Reference

TTQuanti. More...

#include <ttquanti.h>

Inheritance diagram for TTQuanti:

Collaboration diagram for TTQuanti:

Public Member Functions
	TTQuanti ()
	TTQuanti (const TTQuanti &T)
virtual	~TTQuanti ()
virtual trait_t	get_type () const
virtual void	mutate ()
virtual void	inherit (const TTrait *mother, const TTrait *father)
virtual void *	set_trait (void *value)
virtual void	set_value ()
virtual void *	getValue () const
virtual double	get_additive_genotype (const unsigned int trait) const =0
virtual double	get_dominant_genotype (const unsigned int trait) const =0
virtual double	get_full_genotype (unsigned int trait)=0
virtual void	copy_sequence_block (sex_t SEX, unsigned int strand, unsigned int from_pos, unsigned int to_pos, const TTQuanti *parent)=0
virtual void	copy_sequence_1locus (sex_t SEX, unsigned int strand, unsigned int at, const TTQuanti *parent)=0
virtual void	mutate_add (unsigned int position, unsigned int allele, double value)=0
virtual void	mutate_inplace (unsigned int position, unsigned int allele, double value)=0
virtual bool	get_allele_bit (unsigned int position, unsigned int allele) const =0
virtual void	set_allele_bit (unsigned int position, unsigned int allele, bool value)=0
void	set_proto (TProtoQuanti *proto)
TProtoQuanti *	get_proto ()
double	get_phenotype (unsigned int trai)
void	set_phenotype (unsigned int trait, double value)
Public Member Functions inherited from TTrait
virtual void	init ()=0
	Called to allocate the trait's genotypic sequences. More...
virtual void	init_sequence ()=0
	Called at the start of each replicate, sets the initial genotypes. More...
virtual void	reset ()=0
	Called at the end of each simulation/replicate, deallocates sequence memory. More...
virtual void	set_sequence (void **seq)=0
	Called to set the sequence pointer to an existing trait. More...
virtual double	get_allele_value (int loc, int all) const =0
	Called to read one allele value at a particular locus. More...
virtual void	set_allele_value (unsigned int locus, unsigned int allele, double value)=0
	Called to change the allelic value at a particular locus. More...
virtual void **	get_sequence () const =0
	sequence accessor. More...
virtual void	show_up ()=0
	Writes some info to stdout. More...
virtual TTrait *	clone ()=0
	Returns a copy of itself. More...
virtual	~TTrait ()
virtual TTrait &	operator= (const TTrait &)=0
	Copies the complete state of the trait from right to left side of the operator, sequence data included. More...
virtual bool	operator== (const TTrait &)=0
	Checks for parameters equivalence, not genetic equivalence. More...
virtual bool	operator!= (const TTrait &)=0
Public Member Functions inherited from StorableComponent
virtual void	store_data (BinaryStorageBuffer *saver)=0
	Interface to store the component data (e.g. gene values) into a binary buffer. More...
virtual bool	retrieve_data (BinaryStorageBuffer *reader)=0
	Interface to retrieve the same data from the binary buffer. More...
virtual	~StorableComponent ()

Protected Attributes
double *	_phenotypes
TProtoQuanti *	_myProto

Detailed Description

TTQuanti.

Constructor & Destructor Documentation

TTQuanti() [1/2]

TTQuanti::TTQuanti ( )

inline

              : _phenotypes(0), _myProto(0)
  {
//    message("CONSTRUCTOR::TTQuanti::CONSTRUCTOR\n");
  }

TTQuanti() [2/2]

TTQuanti::TTQuanti ( const TTQuanti &  T )

inline

: _phenotypes(0), _myProto(T._myProto){}

~TTQuanti()

virtual TTQuanti::~TTQuanti ( )

inlinevirtual

{}

Member Function Documentation

copy_sequence_1locus()

virtual void TTQuanti::copy_sequence_1locus ( sex_t  SEX, unsigned int  strand, unsigned int  at, const TTQuanti *  parent  )

pure virtual

Implemented in TTQuanti_diallelic_var_pleio, TTQuanti_diallelic_full_pleio, TTQuanti_diallelic_no_pleio, TTQuanti_continuous_single, TTQuanti_continuous_no_pleio, TTQuanti_continuous_var_pleio, TTQuanti_continuous_full_pleio, TTQuanti_diallelic_no_pleio_epistasis, TTQuanti_continuous_no_pleio_epistasis, TTQuanti_diallelic_full_pleio_epistasis, TTQuanti_continuous_full_pleio_epistasis, TTQuanti_diallelic_bitstring_var_pleio, TTQuanti_diallelic_bitstring_full_pleio, and TTQuanti_diallelic_bitstring_no_pleio.

Referenced by TProtoQuanti::inherit_free().

copy_sequence_block()

virtual void TTQuanti::copy_sequence_block ( sex_t  SEX, unsigned int  strand, unsigned int  from_pos, unsigned int  to_pos, const TTQuanti *  parent  )

pure virtual

Implemented in TTQuanti_diallelic_var_pleio, TTQuanti_diallelic_full_pleio, TTQuanti_diallelic_no_pleio, TTQuanti_continuous_single, TTQuanti_continuous_no_pleio, TTQuanti_continuous_var_pleio, TTQuanti_continuous_full_pleio, TTQuanti_diallelic_no_pleio_epistasis, TTQuanti_continuous_no_pleio_epistasis, TTQuanti_diallelic_full_pleio_epistasis, TTQuanti_continuous_full_pleio_epistasis, TTQuanti_diallelic_bitstring_var_pleio, TTQuanti_diallelic_bitstring_full_pleio, and TTQuanti_diallelic_bitstring_no_pleio.

Referenced by TProtoQuanti::inherit_low().

get_additive_genotype()

virtual double TTQuanti::get_additive_genotype ( const unsigned int  trait ) const

pure virtual

Implemented in TTQuanti_diallelic_no_pleio_epistasis, TTQuanti_continuous_no_pleio_epistasis, TTQuanti_diallelic_full_pleio_epistasis, TTQuanti_continuous_full_pleio_epistasis, TTQuanti_diallelic_bitstring_var_pleio, TTQuanti_diallelic_bitstring_full_pleio, TTQuanti_diallelic_bitstring_no_pleio, TTQuanti_diallelic_var_pleio, TTQuanti_diallelic_full_pleio, TTQuanti_diallelic_no_pleio, TTQuanti_continuous_single, TTQuanti_continuous_no_pleio, TTQuanti_continuous_var_pleio, and TTQuanti_continuous_full_pleio.

Referenced by TTQuantiSH::getVaNoDominance(), TTQuantiFH::print(), and TProtoQuanti::set_genotype_value_additive().

get_allele_bit()

virtual bool TTQuanti::get_allele_bit ( unsigned int  position, unsigned int  allele  ) const

pure virtual

Implemented in TTQuanti_diallelic_bitstring, TTQuanti_diallelic, and TTQuanti_continuous.

Referenced by TTQFreqExtractor::FHwrite(), TTQuantiSH::getSNPalleleFreqInPatch(), TTQuantiSH::getVaWithDominance(), TProtoQuanti::mutate_diallelic_pleio(), TProtoQuanti::mutate_diallelic_var_pleio(), and TTQuantiFH::print().

get_dominant_genotype()

virtual double TTQuanti::get_dominant_genotype ( const unsigned int  trait ) const

pure virtual

Implemented in TTQuanti_diallelic_no_pleio_epistasis, TTQuanti_continuous_no_pleio_epistasis, TTQuanti_diallelic_full_pleio_epistasis, TTQuanti_continuous_full_pleio_epistasis, TTQuanti_diallelic_bitstring_var_pleio, TTQuanti_diallelic_bitstring_full_pleio, TTQuanti_diallelic_bitstring_no_pleio, TTQuanti_diallelic_var_pleio, TTQuanti_diallelic_full_pleio, TTQuanti_diallelic_no_pleio, TTQuanti_continuous_single, TTQuanti_continuous_no_pleio, TTQuanti_continuous_var_pleio, and TTQuanti_continuous_full_pleio.

Referenced by TProtoQuanti::set_genotype_value_dominance().

get_full_genotype()

virtual double TTQuanti::get_full_genotype ( unsigned int  trait )

pure virtual

Implemented in TTQuanti_diallelic_bitstring, TTQuanti_diallelic, and TTQuanti_continuous.

Referenced by TTQuantiSH::getVaWithDominance(), TTQuantiFH::print(), and store_quanti_trait_values().

get_phenotype()

double TTQuanti::get_phenotype

(

unsigned int

trai

)

{
  assert(trait < _myProto->get_num_traits() && _phenotypes != NULL);
 
  return _phenotypes[trait];
}

References _phenotypes.

Referenced by LCE_PhenotypeExpression::set_phenot_g1_evol(), LCE_PhenotypeExpression::set_phenot_g1_g2_evol(), LCE_PhenotypeExpression::set_phenot_g2_evol(), and LCE_PhenotypeExpression::set_phenot_no_evol().

get_proto()

TProtoQuanti* TTQuanti::get_proto ( )

inline

{return _myProto;}

References _myProto.

get_type()

virtual trait_t TTQuanti::get_type ( ) const

inlinevirtual

Implements TTrait.

{return QUANT;}

References QUANT.

Referenced by TTQuanti_continuous::operator==(), TTQuanti_diallelic::operator==(), and TTQuanti_diallelic_bitstring::operator==().

getValue()

virtual void* TTQuanti::getValue ( ) const

inlinevirtual

Implements TTrait.

{return _phenotypes;}

References _phenotypes.

Referenced by TTQuantiFH::print(), and store_quanti_trait_values().

inherit()

void TTQuanti::inherit ( const TTrait *  mother, const TTrait *  father  )

inlinevirtual

Implements TTrait.

{
  _myProto->inherit(MAL, this, (const TTQuanti*)father);
 
  _myProto->inherit(FEM, this, (const TTQuanti*)mother);
}

References _myProto, FEM, TProtoQuanti::inherit(), and MAL.

mutate()

void TTQuanti::mutate ( )

inlinevirtual

Implements TTrait.

{
  _myProto->mutate(this);
}

References _myProto, and TProtoQuanti::mutate().

mutate_add()

virtual void TTQuanti::mutate_add ( unsigned int  position, unsigned int  allele, double  value  )

pure virtual

Implemented in TTQuanti_diallelic_bitstring, TTQuanti_diallelic, and TTQuanti_continuous.

Referenced by TProtoQuanti::mutate_full_pleio(), TProtoQuanti::mutate_no_pleio(), and TProtoQuanti::mutate_var_pleio().

mutate_inplace()

virtual void TTQuanti::mutate_inplace ( unsigned int  position, unsigned int  allele, double  value  )

pure virtual

Implemented in TTQuanti_diallelic_bitstring, TTQuanti_diallelic, and TTQuanti_continuous.

Referenced by TProtoQuanti::mutate_diallelic_no_pleio(), TProtoQuanti::mutate_diallelic_pleio(), TProtoQuanti::mutate_diallelic_var_pleio(), TProtoQuanti::mutate_inplace_full_pleio(), TProtoQuanti::mutate_inplace_no_pleio(), and TProtoQuanti::mutate_inplace_var_pleio().

set_allele_bit()

virtual void TTQuanti::set_allele_bit ( unsigned int  position, unsigned int  allele, bool  value  )

pure virtual

Implemented in TTQuanti_diallelic_bitstring, TTQuanti_diallelic, and TTQuanti_continuous.

Referenced by TProtoQuanti::mutate_diallelic_pleio(), and TProtoQuanti::mutate_diallelic_var_pleio().

set_phenotype()

void TTQuanti::set_phenotype	(	unsigned int	trait,
		double	value
	)

{
  assert(trait < _myProto->get_num_traits() && _phenotypes != NULL);
 
  _phenotypes[trait] = value;
}

References _phenotypes.

Referenced by LCE_PhenotypeExpression::set_phenot_g1_evol(), LCE_PhenotypeExpression::set_phenot_g1_g2_evol(), LCE_PhenotypeExpression::set_phenot_g2_evol(), and LCE_PhenotypeExpression::set_phenot_no_evol().

set_proto()

void TTQuanti::set_proto ( TProtoQuanti *  proto )

inline

{_myProto = proto;}

References _myProto.

Referenced by TProtoQuanti::hatch().

set_trait()

virtual void* TTQuanti::set_trait ( void *  value )

inlinevirtual

Implements TTrait.

{return value;}

set_value()

void TTQuanti::set_value ( )

inlinevirtual

Implements TTrait.

{
//  cout<<" TTQuanti::set_value\n";
  for (unsigned int i = 0; i < _myProto->get_num_traits(); ++i) {
    _phenotypes[i] = _myProto->get_phenotypic_value(this, i); //(_myProto->*_myProto->_set_trait_value_func_ptr)(this, i);
  }
//  cout<<" TTQuanti::set_value::end\n";
}

References _myProto, _phenotypes, TProtoQuanti::get_num_traits(), and TProtoQuanti::get_phenotypic_value().

Referenced by TTQuantiFH::FHread(), TTQuanti_continuous::operator=(), TTQuanti_diallelic::operator=(), and TTQuanti_diallelic_bitstring::operator=().

Member Data Documentation

_myProto

TProtoQuanti* TTQuanti::_myProto

protected

Referenced by TTQuanti_diallelic_bitstring_full_pleio::copy_sequence_1locus(), TTQuanti_diallelic_bitstring_var_pleio::copy_sequence_1locus(), TTQuanti_continuous_full_pleio_epistasis::copy_sequence_1locus(), TTQuanti_diallelic_full_pleio_epistasis::copy_sequence_1locus(), TTQuanti_continuous_full_pleio::copy_sequence_1locus(), TTQuanti_continuous_var_pleio::copy_sequence_1locus(), TTQuanti_diallelic_full_pleio::copy_sequence_1locus(), TTQuanti_diallelic_var_pleio::copy_sequence_1locus(), TTQuanti_diallelic_bitstring_full_pleio::copy_sequence_block(), TTQuanti_diallelic_bitstring_var_pleio::copy_sequence_block(), TTQuanti_continuous_full_pleio_epistasis::copy_sequence_block(), TTQuanti_diallelic_full_pleio_epistasis::copy_sequence_block(), TTQuanti_continuous_no_pleio_epistasis::copy_sequence_block(), TTQuanti_diallelic_no_pleio_epistasis::copy_sequence_block(), TTQuanti_continuous_full_pleio::copy_sequence_block(), TTQuanti_continuous_var_pleio::copy_sequence_block(), TTQuanti_continuous_no_pleio::copy_sequence_block(), TTQuanti_diallelic_no_pleio::copy_sequence_block(), TTQuanti_diallelic_full_pleio::copy_sequence_block(), TTQuanti_diallelic_var_pleio::copy_sequence_block(), TTQuanti_continuous_full_pleio::get_additive_genotype(), TTQuanti_continuous_var_pleio::get_additive_genotype(), TTQuanti_continuous_no_pleio::get_additive_genotype(), TTQuanti_continuous_single::get_additive_genotype(), TTQuanti_diallelic_no_pleio::get_additive_genotype(), TTQuanti_diallelic_full_pleio::get_additive_genotype(), TTQuanti_diallelic_var_pleio::get_additive_genotype(), TTQuanti_diallelic_bitstring_no_pleio::get_additive_genotype(), TTQuanti_diallelic_bitstring_full_pleio::get_additive_genotype(), TTQuanti_diallelic_bitstring_var_pleio::get_additive_genotype(), TTQuanti_continuous_full_pleio_epistasis::get_additive_genotype(), TTQuanti_diallelic_full_pleio_epistasis::get_additive_genotype(), TTQuanti_continuous_no_pleio_epistasis::get_additive_genotype(), TTQuanti_diallelic_no_pleio_epistasis::get_additive_genotype(), TTQuanti_diallelic_bitstring::get_allele_bit(), TTQuanti_continuous::get_allele_value(), TTQuanti_diallelic::get_allele_value(), TTQuanti_diallelic_bitstring::get_allele_value(), TTQuanti_continuous_full_pleio::get_dominant_genotype(), TTQuanti_continuous_var_pleio::get_dominant_genotype(), TTQuanti_continuous_no_pleio::get_dominant_genotype(), TTQuanti_continuous_single::get_dominant_genotype(), TTQuanti_diallelic_no_pleio::get_dominant_genotype(), TTQuanti_diallelic_full_pleio::get_dominant_genotype(), TTQuanti_diallelic_var_pleio::get_dominant_genotype(), TTQuanti_diallelic_bitstring_no_pleio::get_dominant_genotype(), TTQuanti_diallelic_bitstring_full_pleio::get_dominant_genotype(), TTQuanti_diallelic_bitstring_var_pleio::get_dominant_genotype(), TTQuanti_continuous_full_pleio_epistasis::get_dominant_genotype(), TTQuanti_diallelic_full_pleio_epistasis::get_dominant_genotype(), TTQuanti_continuous_no_pleio_epistasis::get_dominant_genotype(), TTQuanti_diallelic_no_pleio_epistasis::get_dominant_genotype(), TTQuanti_continuous_full_pleio_epistasis::get_epistatic_genotype(), TTQuanti_diallelic_full_pleio_epistasis::get_epistatic_genotype(), TTQuanti_continuous_no_pleio_epistasis::get_epistatic_genotype(), TTQuanti_diallelic_no_pleio_epistasis::get_epistatic_genotype(), TTQuanti_continuous::get_full_genotype(), TTQuanti_diallelic::get_full_genotype(), TTQuanti_diallelic_bitstring::get_full_genotype(), get_proto(), TTQuanti_continuous_var_pleio::get_sequence_block_size(), TTQuanti_diallelic_var_pleio::get_sequence_block_size(), TTQuanti_diallelic_bitstring_var_pleio::get_sequence_block_size(), inherit(), TTQuanti_continuous::init(), TTQuanti_diallelic::init(), TTQuanti_diallelic_bitstring::init(), TTQuanti_continuous_full_pleio::init_sequence(), TTQuanti_continuous_var_pleio::init_sequence(), TTQuanti_continuous_no_pleio::init_sequence(), TTQuanti_diallelic_no_pleio::init_sequence(), TTQuanti_diallelic_full_pleio::init_sequence(), TTQuanti_diallelic_var_pleio::init_sequence(), TTQuanti_diallelic_bitstring_no_pleio::init_sequence(), TTQuanti_diallelic_bitstring_full_pleio::init_sequence(), TTQuanti_diallelic_bitstring_var_pleio::init_sequence(), TTQuanti_continuous_full_pleio_epistasis::init_sequence(), TTQuanti_diallelic_full_pleio_epistasis::init_sequence(), TTQuanti_continuous_no_pleio_epistasis::init_sequence(), TTQuanti_diallelic_no_pleio_epistasis::init_sequence(), mutate(), TTQuanti_continuous::operator=(), TTQuanti_diallelic::operator=(), TTQuanti_continuous::operator==(), TTQuanti_diallelic::operator==(), TTQuanti_diallelic_bitstring::operator==(), TTQuanti_continuous::retrieve_data(), TTQuanti_diallelic::retrieve_data(), TTQuanti_diallelic_bitstring::set_allele_bit(), TTQuanti_diallelic::set_allele_value(), TTQuanti_diallelic_bitstring::set_allele_value(), set_proto(), TTQuanti_continuous::set_sequence(), TTQuanti_diallelic::set_sequence(), set_value(), TTQuanti_continuous_full_pleio::show_up(), TTQuanti_continuous_var_pleio::show_up(), TTQuanti_continuous_no_pleio::show_up(), TTQuanti_diallelic_no_pleio::show_up(), TTQuanti_diallelic_full_pleio::show_up(), TTQuanti_diallelic_var_pleio::show_up(), TTQuanti_diallelic_bitstring_no_pleio::show_up(), TTQuanti_diallelic_bitstring_full_pleio::show_up(), TTQuanti_diallelic_bitstring_var_pleio::show_up(), TTQuanti_continuous_full_pleio_epistasis::show_up(), TTQuanti_diallelic_full_pleio_epistasis::show_up(), TTQuanti_continuous_no_pleio_epistasis::show_up(), TTQuanti_diallelic_no_pleio_epistasis::show_up(), TTQuanti_continuous::store_data(), and TTQuanti_diallelic::store_data().

_phenotypes

double* TTQuanti::_phenotypes

protected

Referenced by get_phenotype(), getValue(), TTQuanti_continuous::init(), TTQuanti_diallelic::init(), TTQuanti_diallelic_bitstring::init(), TTQuanti_continuous::reset(), TTQuanti_diallelic::reset(), TTQuanti_diallelic_bitstring::reset(), set_phenotype(), set_value(), TTQuanti_continuous_full_pleio::show_up(), TTQuanti_continuous_var_pleio::show_up(), TTQuanti_continuous_no_pleio::show_up(), TTQuanti_diallelic_no_pleio::show_up(), TTQuanti_diallelic_full_pleio::show_up(), TTQuanti_diallelic_var_pleio::show_up(), TTQuanti_diallelic_bitstring_no_pleio::show_up(), TTQuanti_diallelic_bitstring_full_pleio::show_up(), TTQuanti_diallelic_bitstring_var_pleio::show_up(), TTQuanti_continuous_full_pleio_epistasis::show_up(), TTQuanti_diallelic_full_pleio_epistasis::show_up(), TTQuanti_continuous_no_pleio_epistasis::show_up(), and TTQuanti_diallelic_no_pleio_epistasis::show_up().

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

• ttquanti.h
• ttquanti.cc