TTQuanti_diallelic_bitstring Class Reference

TTQuanti_diallelic_bitstring. More...

#include <ttquanti_bitstring.h>

Inheritance diagram for TTQuanti_diallelic_bitstring:

Collaboration diagram for TTQuanti_diallelic_bitstring:

Public Member Functions
	TTQuanti_diallelic_bitstring ()
	TTQuanti_diallelic_bitstring (const TTQuanti &T)
virtual	~TTQuanti_diallelic_bitstring ()
virtual bool	get_allele_bit (unsigned int position, unsigned int allele) const
virtual void	set_allele_bit (unsigned int position, unsigned int allele, bool value)
void	set_bit_sequence (const bitstring *inseq)
const bitstring &	get_bit_sequence (bool chromosome) const
void	inherit_free (const TTrait *mother, const TTrait *father)
virtual void	reset ()
virtual void	init ()
virtual void	set_sequence (void **seq)
virtual void **	get_sequence () const
virtual unsigned int	get_allele (int loc, int all) const
virtual double	get_allele_value (int locus, int allele) const
virtual void	set_allele_value (unsigned int locus, unsigned int allele, double value)
virtual TTQuanti_diallelic_bitstring &	operator= (const TTrait &T)
virtual bool	operator== (const TTrait &T)
virtual bool	operator!= (const TTrait &T)
virtual void	store_data (BinaryStorageBuffer *saver)
virtual bool	retrieve_data (BinaryStorageBuffer *reader)
virtual double	get_full_genotype (unsigned int trait)
virtual void	mutate_add (unsigned int position, unsigned int allele, double value)
virtual void	mutate_inplace (unsigned int position, unsigned int allele, double value)
Public Member Functions inherited from TTQuanti
	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 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
void	set_proto (TProtoQuanti *proto)
TProtoQuanti *	get_proto ()
double	get_phenotype (unsigned int trai)
void	set_phenotype (unsigned int trait, double value)
void	reset_phenotype_to_genotypic_value ()
Public Member Functions inherited from TTrait
virtual void	init_sequence ()=0
	Called at the start of each replicate, sets the initial genotypes. More...
virtual void	show_up ()=0
	Writes some info to stdout. More...
virtual TTrait *	clone ()=0
	Returns a copy of itself. More...
virtual	~TTrait ()
Public Member Functions inherited from StorableComponent
virtual	~StorableComponent ()

Protected Attributes
bitstring *	_sequence
Protected Attributes inherited from TTQuanti
double *	_phenotypes
double *	_genotypic_values
TProtoQuanti *	_myProto

Detailed Description

TTQuanti_diallelic_bitstring.

Constructor & Destructor Documentation

TTQuanti_diallelic_bitstring() [1/2]

TTQuanti_diallelic_bitstring::TTQuanti_diallelic_bitstring ( )

inline

                                  : TTQuanti(), _sequence(0)
  {}

TTQuanti_diallelic_bitstring() [2/2]

TTQuanti_diallelic_bitstring::TTQuanti_diallelic_bitstring ( const TTQuanti &  T )

inline

                                                   : TTQuanti(T), _sequence(0)
  {}

~TTQuanti_diallelic_bitstring()

virtual TTQuanti_diallelic_bitstring::~TTQuanti_diallelic_bitstring ( )

inlinevirtual

{reset();}

References reset().

Member Function Documentation

get_allele()

unsigned int TTQuanti_diallelic_bitstring::get_allele ( int  loc, int  all  ) const

virtual

Implements TTrait.

{
  assert(position < (int)_myProto->get_seq_length() && allele < 2);
 
  return _sequence[allele][position];
}

References TTQuanti::_myProto, _sequence, and TProtoQuanti::get_seq_length().

get_allele_bit()

bool TTQuanti_diallelic_bitstring::get_allele_bit ( unsigned int  position, unsigned int  allele  ) const

virtual

Implements TTQuanti.

{
  assert(position < _myProto->get_seq_length() && allele < 2);
 
  return _sequence[allele][position];
}

References _sequence.

get_allele_value()

double TTQuanti_diallelic_bitstring::get_allele_value ( int  locus, int  allele  ) const

inlinevirtual

Implements TTrait.

{
  // beware that get_diallele_value() expects a locus ID, not a sequence position!!!
 
  assert(position < (int)_myProto->get_seq_length() && all < 2);
 
  return _myProto->get_seq_diallele_value( position, (unsigned int)_sequence[all][position] );
}

References TTQuanti::_myProto, _sequence, TProtoQuanti::get_seq_diallele_value(), and TProtoQuanti::get_seq_length().

get_bit_sequence()

const bitstring& TTQuanti_diallelic_bitstring::get_bit_sequence ( bool  chromosome ) const

inline

                               {return _sequence[chromosome];}

References _sequence.

Referenced by TTQuanti_diallelic_bitstring_no_pleio::copy_sequence_1locus(), TTQuanti_diallelic_bitstring_full_pleio::copy_sequence_1locus(), TTQuanti_diallelic_bitstring_var_pleio::copy_sequence_1locus(), TTQuanti_diallelic_bitstring_no_pleio_epistasis::copy_sequence_1locus(), TTQuanti_diallelic_bitstring_full_pleio_epistasis::copy_sequence_1locus(), TTQuanti_diallelic_bitstring_no_pleio::copy_sequence_block(), TTQuanti_diallelic_bitstring_full_pleio::copy_sequence_block(), TTQuanti_diallelic_bitstring_var_pleio::copy_sequence_block(), TTQuanti_diallelic_bitstring_no_pleio_epistasis::copy_sequence_block(), and TTQuanti_diallelic_bitstring_full_pleio_epistasis::copy_sequence_block().

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get_full_genotype()

double TTQuanti_diallelic_bitstring::get_full_genotype ( unsigned int  trait )

virtual

Implements TTQuanti.

{ //returns genotypic value that includes dominance effects if any
  return _myProto->get_genotypic_value(this, trait);
}

References TTQuanti::_myProto, and TProtoQuanti::get_genotypic_value().

get_sequence()

virtual void** TTQuanti_diallelic_bitstring::get_sequence ( ) const

inlinevirtual

Implements TTrait.

                                                                    {
    error("calling TTQuanti_diallelic_bitstring::get_sequence()\n");
    return (void**)NULL;
  }

References error().

inherit_free()

void TTQuanti_diallelic_bitstring::inherit_free	(	const TTrait *	mother,
		const TTrait *	father
	)

init()

void TTQuanti_diallelic_bitstring::init ( )

inlinevirtual

Implements TTrait.

Reimplemented in TTQuanti_diallelic_bitstring_no_pleio.

{
  reset();
 
  _sequence = new bitstring [2];
  _sequence[0].reset(_myProto->get_seq_length());
  _sequence[1].reset(_myProto->get_seq_length());
 
  _phenotypes = new double [_myProto->get_num_traits()];
  _genotypic_values = new double [_myProto->get_num_traits()];
 
  memset(_phenotypes, 0.0, _myProto->get_num_traits()*sizeof(double));
  memset(_genotypic_values, 0.0, _myProto->get_num_traits()*sizeof(double));
}

References TTQuanti::_genotypic_values, TTQuanti::_myProto, TTQuanti::_phenotypes, _sequence, TProtoQuanti::get_num_traits(), TProtoQuanti::get_seq_length(), reset(), and bitstring::reset().

Referenced by TTQuanti_diallelic_bitstring_no_pleio::init(), operator=(), and set_bit_sequence().

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mutate_add()

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

inlinevirtual

Implements TTQuanti.

                               {_sequence[allele].set(position, bool(value));}

References _sequence, and bitstring::set().

mutate_inplace()

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

inlinevirtual

Implements TTQuanti.

                               {_sequence[allele].flip(position);}

References _sequence, and bitstring::flip().

operator!=()

bool TTQuanti_diallelic_bitstring::operator!= ( const TTrait &  T )

virtual

Implements TTrait.

{
  if(!((*this) == T) )
    return true;
  else
    return false;
}

operator=()

TTQuanti_diallelic_bitstring & TTQuanti_diallelic_bitstring::operator= ( const TTrait &  T )

virtual

Implements TTrait.

{
  const TTQuanti_diallelic_bitstring& TQ = dynamic_cast<const TTQuanti_diallelic_bitstring&>(T);
 
  assert(*this == TQ);  // to make sure that the sequences are of same length
 
  if(this != &TQ) {
 
    init();
 
    _sequence[0].copy(TQ._sequence[0]);
    _sequence[1].copy(TQ._sequence[1]);
 
    set_value();
  }
 
  return *this;
}

References _sequence, bitstring::copy(), init(), and TTQuanti::set_value().

operator==()

bool TTQuanti_diallelic_bitstring::operator== ( const TTrait &  T )

virtual

Implements TTrait.

    {
  if(this->get_type().compare(T.get_type()) != 0) return false;
 
  const TTQuanti_diallelic_bitstring& TQ = dynamic_cast<const TTQuanti_diallelic_bitstring&>(T);
 
  if(this != &TQ) {
    if(_myProto->get_num_locus() != TQ._myProto->get_num_locus()) return false;
    if(_myProto->get_num_traits() != TQ._myProto->get_num_traits()) return false;
    if(_myProto->get_seq_length() != TQ._myProto->get_seq_length()) return false;
    if(_myProto->get_pleiotropy_type() != TQ._myProto->get_pleiotropy_type()) return false;
  }
  return true;
    }

References TTQuanti::_myProto, TProtoQuanti::get_num_locus(), TProtoQuanti::get_num_traits(), TProtoQuanti::get_pleiotropy_type(), TProtoQuanti::get_seq_length(), TTQuanti::get_type(), and TTrait::get_type().

reset()

void TTQuanti_diallelic_bitstring::reset ( )

inlinevirtual

Implements TTrait.

{
  if(_sequence) {
    delete [] _sequence;
    _sequence = NULL;
  }
 
  if(_phenotypes) delete [] _phenotypes;
  _phenotypes = NULL;
  if(_genotypic_values) delete [] _genotypic_values;
  _genotypic_values = NULL;
 
}

References TTQuanti::_genotypic_values, TTQuanti::_phenotypes, and _sequence.

Referenced by init(), and ~TTQuanti_diallelic_bitstring().

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retrieve_data()

bool TTQuanti_diallelic_bitstring::retrieve_data ( BinaryStorageBuffer *  reader )

inlinevirtual

Implements StorableComponent.

{
  size_t wnb = _sequence[0].nb_words();
  size_t bytes = wnb * sizeof(bitstring::_ul);
  bitstring::_ul *srce = new bitstring::_ul [wnb];
 
  reader->read(srce, bytes);
  _sequence[0].set_data(srce,wnb);
 
  reader->read(srce, bytes);
  _sequence[1].set_data(srce,wnb);
 
  delete [] srce;
 
  return true;
}

References _sequence, bitstring::nb_words(), BinaryStorageBuffer::read(), and bitstring::set_data().

set_allele_bit()

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

virtual

Implements TTQuanti.

{
  assert(position < (int)_myProto->get_seq_length() && allele < 2);
 
  _sequence[allele].set(position, value); // avoiding reference
}

References TTQuanti::_myProto, _sequence, TProtoQuanti::get_seq_length(), and bitstring::set().

set_allele_value()

void TTQuanti_diallelic_bitstring::set_allele_value ( unsigned int  locus, unsigned int  allele, double  value  )

inlinevirtual

Implements TTrait.

{
//  assert(position);
  bool a = _sequence[allele][position];
  double refval1 = _myProto->get_seq_diallele_value( position, a );
  double refval2 = _myProto->get_seq_diallele_value( position, !a );
 
  if( refval1 != value && refval2 != value )
    fatal("trait quant::trying to set allele %i at position %i to value %f, which is not as set in the input allele table (%f, %f)\n",
        allele, position, value, refval1, refval2);
 
  if( refval1 != value )
    _sequence[allele].flip(position);
}

References TTQuanti::_myProto, _sequence, fatal(), bitstring::flip(), and TProtoQuanti::get_seq_diallele_value().

set_bit_sequence()

void TTQuanti_diallelic_bitstring::set_bit_sequence

(

const bitstring *

inseq

)

{
  init();
  _sequence[0].copy(inseq[0]);
  _sequence[1].copy(inseq[1]);
}

References _sequence, bitstring::copy(), and init().

set_sequence()

void TTQuanti_diallelic_bitstring::set_sequence ( void **  seq )

virtual

Implements TTrait.

{
  error("Calling TTQuanti_diallelic_bitstring::set_sequence(), should be calling TTQuanti_diallelic_bitstring::set_bit_sequence()\n");
}

References error().

store_data()

void TTQuanti_diallelic_bitstring::store_data ( BinaryStorageBuffer *  saver )

inlinevirtual

Implements StorableComponent.

{
  size_t wnb = _sequence[0].nb_words();
  size_t bytes = sizeof(bitstring::_ul);
 
  for(size_t i = 0; i < wnb; i++)
    saver->store(_sequence[0].getword_atIdx(i), bytes);
 
  for(size_t i = 0; i < wnb; i++)
    saver->store(_sequence[1].getword_atIdx(i), bytes);
}

References _sequence, bitstring::getword_atIdx(), bitstring::nb_words(), and BinaryStorageBuffer::store().

Member Data Documentation

_sequence

bitstring* TTQuanti_diallelic_bitstring::_sequence

protected

Referenced by TTQuanti_diallelic_bitstring_no_pleio::copy_sequence_1locus(), TTQuanti_diallelic_bitstring_full_pleio::copy_sequence_1locus(), TTQuanti_diallelic_bitstring_var_pleio::copy_sequence_1locus(), TTQuanti_diallelic_bitstring_no_pleio_epistasis::copy_sequence_1locus(), TTQuanti_diallelic_bitstring_full_pleio_epistasis::copy_sequence_1locus(), TTQuanti_diallelic_bitstring_no_pleio::copy_sequence_block(), TTQuanti_diallelic_bitstring_full_pleio::copy_sequence_block(), TTQuanti_diallelic_bitstring_var_pleio::copy_sequence_block(), TTQuanti_diallelic_bitstring_no_pleio_epistasis::copy_sequence_block(), TTQuanti_diallelic_bitstring_full_pleio_epistasis::copy_sequence_block(), 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_diallelic_bitstring_no_pleio_epistasis::get_additive_genotype(), TTQuanti_diallelic_bitstring_full_pleio_epistasis::get_additive_genotype(), TTQuanti_diallelic_bitstring_no_pleio::get_additive_genotype_equal_effects(), get_allele(), get_allele_bit(), get_allele_value(), get_bit_sequence(), 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_diallelic_bitstring_no_pleio_epistasis::get_dominant_genotype(), TTQuanti_diallelic_bitstring_full_pleio_epistasis::get_dominant_genotype(), init(), TTQuanti_diallelic_bitstring_no_pleio::init_sequence(), TTQuanti_diallelic_bitstring_full_pleio::init_sequence(), TTQuanti_diallelic_bitstring_var_pleio::init_sequence(), TTQuanti_diallelic_bitstring_no_pleio_epistasis::init_sequence(), TTQuanti_diallelic_bitstring_full_pleio_epistasis::init_sequence(), mutate_add(), mutate_inplace(), operator=(), reset(), retrieve_data(), set_allele_bit(), set_allele_value(), set_bit_sequence(), TTQuanti_diallelic_bitstring_no_pleio::show_up(), TTQuanti_diallelic_bitstring_full_pleio::show_up(), TTQuanti_diallelic_bitstring_var_pleio::show_up(), TTQuanti_diallelic_bitstring_no_pleio_epistasis::show_up(), TTQuanti_diallelic_bitstring_full_pleio_epistasis::show_up(), and store_data().

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

• ttquanti_bitstring.h
• ttquanti_bitstring.cc