TTNeutralGenes_bitstring Class Reference

TTNeutralGenes_bitstring : diallelic neutral loci encoded as bitstrings. More...

#include <ttneutralgenes_bitstring.h>

Inheritance diagram for TTNeutralGenes_bitstring:

Collaboration diagram for TTNeutralGenes_bitstring:

Public Member Functions
	TTNeutralGenes_bitstring ()
	TTNeutralGenes_bitstring (const TTNeutralGenes_bitstring &T)
virtual	~TTNeutralGenes_bitstring ()
const bitstring &	get_bit_sequence (bool chromosome) const
Implementations
virtual TTNeutralGenes &	operator= (const TTrait &T)
virtual void	init ()
virtual void	init_sequence ()
virtual void	reset ()
virtual void **	get_sequence () const
virtual unsigned int	get_allele (int loc, int all) const
virtual double	get_allele_value (int loc, int all) const
virtual void	set_allele_value (unsigned int locus, unsigned int allele, double value)
virtual void	set_sequence (void **seq)
virtual void	inherit (const TTrait *mother, const TTrait *father)
virtual void	mutate ()
virtual void	show_up ()
virtual TTNeutralGenes *	clone ()
virtual void	store_data (BinaryStorageBuffer *saver)
virtual bool	retrieve_data (BinaryStorageBuffer *reader)
Public Member Functions inherited from TTNeutralGenes
	TTNeutralGenes ()
	TTNeutralGenes (const TTNeutralGenes &T)
virtual	~TTNeutralGenes ()
void	set_proto (TProtoNeutralGenes *proto)
virtual bool	operator== (const TTrait &T)
virtual bool	operator!= (const TTrait &T)
virtual void *	set_trait (void *value)
virtual trait_t	get_type () const
virtual void	set_value ()
virtual void *	getValue () const
Public Member Functions inherited from TTrait
virtual	~TTrait ()
Public Member Functions inherited from StorableComponent
virtual	~StorableComponent ()

Protected Attributes
bitstring *	_sequence
bool	_free_recombination
Protected Attributes inherited from TTNeutralGenes
TProtoNeutralGenes *	_myProto
const trait_t	_type

Private Member Functions
void	inherit_low (sex_t SEX, const TTNeutralGenes_bitstring *parent)

Detailed Description

TTNeutralGenes_bitstring : diallelic neutral loci encoded as bitstrings.

Constructor & Destructor Documentation

TTNeutralGenes_bitstring() [1/2]

TTNeutralGenes_bitstring::TTNeutralGenes_bitstring ( )

inline

    : TTNeutralGenes(), _sequence(0), _free_recombination(true) { }

Referenced by clone().

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TTNeutralGenes_bitstring() [2/2]

TTNeutralGenes_bitstring::TTNeutralGenes_bitstring ( const TTNeutralGenes_bitstring &  T )

inline

    : TTNeutralGenes(T), _sequence(0), _free_recombination(T._free_recombination) { }

~TTNeutralGenes_bitstring()

virtual TTNeutralGenes_bitstring::~TTNeutralGenes_bitstring ( )

inlinevirtual

{ reset(); }

References reset().

Member Function Documentation

clone()

virtual TTNeutralGenes* TTNeutralGenes_bitstring::clone ( )

inlinevirtual

Implements TTNeutralGenes.

{ return new TTNeutralGenes_bitstring(*this); }

References TTNeutralGenes_bitstring().

get_allele()

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

virtual

Implements TTNeutralGenes.

{
  return (unsigned int)_sequence[all][loc];
}

get_allele_value()

double TTNeutralGenes_bitstring::get_allele_value ( int  loc, int  all  ) const

virtual

Implements TTNeutralGenes.

{
  return (double)_sequence[all][loc];
}

get_bit_sequence()

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

inline

    { return _sequence[chromosome]; }

References _sequence.

Referenced by inherit(), inherit_low(), TTNeutralGenesSH::setAlleleTables(), TTNeutralGenesSH::setFstat_bitstring(), TTNeutralGenesSH::setFstatWeirCockerham_bitstring(), TTNeutralGenesSH::setHo(), and TTNeutralGenesSH::setHo2().

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get_sequence()

virtual void** TTNeutralGenes_bitstring::get_sequence ( ) const

inlinevirtual

Implements TTNeutralGenes.

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

References error().

inherit()

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

virtual

Implements TTNeutralGenes.

{
  const TTNeutralGenes_bitstring* mom = dynamic_cast<const TTNeutralGenes_bitstring*>(mother);
  const TTNeutralGenes_bitstring* dad = dynamic_cast<const TTNeutralGenes_bitstring*>(father);
 
  if (_free_recombination) {
 
    // Word-level random recombination: for each 64-bit word, generate a random mask
    // offspring = (parent_chrom_a & mask) | (parent_chrom_b & ~mask)
    size_t nwords = mom->_sequence[0].nb_words();
 
    // Mother -> offspring[FEM]
    unsigned int mom_first = RAND::RandBool();
    const bitstring& mom_seq0 = mom->get_bit_sequence(mom_first);
    const bitstring& mom_seq1 = mom->get_bit_sequence(!mom_first);
 
    for (size_t w = 0; w < nwords; w++) {
      bitstring::_ul mask = RAND::RandULong();
      bitstring::_ul result = (*mom_seq0.getword_atIdx(w) & mask) |
                              (*mom_seq1.getword_atIdx(w) & ~mask);
      *_sequence[FEM].getword_atIdx(w) = result;
    }
 
    // Father -> offspring[MAL]
    unsigned int dad_first = RAND::RandBool();
    const bitstring& dad_seq0 = dad->get_bit_sequence(dad_first);
    const bitstring& dad_seq1 = dad->get_bit_sequence(!dad_first);
 
    for (size_t w = 0; w < nwords; w++) {
      bitstring::_ul mask = RAND::RandULong();
      bitstring::_ul result = (*dad_seq0.getword_atIdx(w) & mask) |
                              (*dad_seq1.getword_atIdx(w) & ~mask);
      *_sequence[MAL].getword_atIdx(w) = result;
    }
 
  } else {
 
    // Low recombination: use crossover table from genetic map
    // Mother -> offspring[FEM]
    inherit_low(FEM, mom);
    // Father -> offspring[MAL]
    inherit_low(MAL, dad);
 
  }
}

References _sequence, FEM, get_bit_sequence(), bitstring::getword_atIdx(), MAL, bitstring::nb_words(), RAND::RandBool(), and RAND::RandULong().

inherit_low()

void TTNeutralGenes_bitstring::inherit_low ( sex_t  SEX, const TTNeutralGenes_bitstring *  parent  )

private

{
  vector< pair<unsigned int, unsigned int> > recTable =
      TProtoNeutralGenes::getGeneticMapRef().reduceJunctions(SEX, _myProto->getMapIndex());
 
  unsigned int prevLoc = 0;
 
#ifdef _REC_DEBUG_
  //number of x-overs
  unsigned int nbRec = recTable.size();
  cout << "TTNeutralGenes_bitstring::inherit_low; nb Rec = "<<nbRec - 1<<endl;
  cout << "   --sex = "<<SEX<<"\n";
#endif
 
  vector< pair<unsigned int, unsigned int> >::const_iterator xover = recTable.begin();
 
  while(xover != recTable.end()) {
 
 
    if(xover->first > prevLoc) {
 
#ifdef _REC_DEBUG_
      cout<< "   copy seq from "<<prevLoc<<" to "<<xover->first
          <<" ("<<(xover->first - prevLoc)<<" loc) on side "<<xover->second<<std::endl;
#endif
 
      const bitstring& orig = parent->get_bit_sequence((bool)xover->second);
      _sequence[SEX].copy(orig, prevLoc, xover->first);
    }
 
    prevLoc = xover->first;
    xover++;
  }
}

References bitstring::copy(), get_bit_sequence(), TTProtoWithMap::getGeneticMapRef(), and GeneticMap::reduceJunctions().

init()

void TTNeutralGenes_bitstring::init ( )

virtual

Implements TTNeutralGenes.

{
  if(_sequence != NULL)
    fatal("TTNeutralGenes_bitstring::init::_sequence is not NULL !\n");
 
  _sequence = new bitstring[2];
  _sequence[0].reset(_myProto->get_locus_num());
  _sequence[1].reset(_myProto->get_locus_num());
 
  _free_recombination = (_myProto->getRecombRate() == 0.5);
}

References fatal(), and bitstring::reset().

init_sequence()

void TTNeutralGenes_bitstring::init_sequence ( )

virtual

Implements TTNeutralGenes.

{
  if(_sequence == NULL) {
    _sequence = new bitstring[2];
    _sequence[0].reset(_myProto->get_locus_num());
    _sequence[1].reset(_myProto->get_locus_num());
  }
 
  unsigned int nloc = _myProto->get_locus_num();
 
  if(_myProto->get_init_model() == 1) {
 
    for(unsigned int i = 0; i < nloc; ++i) {
      _sequence[0][i] = RAND::RandBool();
      _sequence[1][i] = RAND::RandBool();
    }
 
  } else if (_myProto->get_init_model() == 2) {
 
    _sequence[0].reset();
    _sequence[1].reset();
    mutate();
 
  } else { // model 0: all monomorphic
 
    _sequence[0].reset();
    _sequence[1].reset();
 
  }
}

References RAND::RandBool(), and bitstring::reset().

mutate()

void TTNeutralGenes_bitstring::mutate ( )

virtual

Implements TTNeutralGenes.

{
  unsigned int NbMut = _myProto->get_num_mutations();
 
  for( ; NbMut > 0; NbMut--) {
    _sequence[RAND::RandBool()].flip(RAND::Uniform(_myProto->get_locus_num()));
  }
}

References RAND::RandBool(), and RAND::Uniform().

operator=()

TTNeutralGenes & TTNeutralGenes_bitstring::operator= ( const TTrait &  T )

virtual

Implements TTNeutralGenes.

{
  const TTNeutralGenes_bitstring& TN = dynamic_cast<const TTNeutralGenes_bitstring&>(T);
 
  if(this != &TN) {
    _myProto = TN._myProto;
    _free_recombination = TN._free_recombination;
 
    if(_sequence == NULL) init();
 
    _sequence[0].copy(TN._sequence[0]);
    _sequence[1].copy(TN._sequence[1]);
  }
 
  return *this;
}

References _free_recombination, TTNeutralGenes::_myProto, and _sequence.

reset()

void TTNeutralGenes_bitstring::reset ( )

virtual

Implements TTNeutralGenes.

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

Referenced by ~TTNeutralGenes_bitstring().

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retrieve_data()

bool TTNeutralGenes_bitstring::retrieve_data ( BinaryStorageBuffer *  reader )

virtual

Implements TTNeutralGenes.

{
  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 BinaryStorageBuffer::read().

set_allele_value()

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

virtual

Implements TTNeutralGenes.

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

set_sequence()

void TTNeutralGenes_bitstring::set_sequence ( void **  seq )

virtual

Implements TTNeutralGenes.

{
  error("calling TTNeutralGenes_bitstring::set_sequence(void**), use set_allele_value() instead\n");
}

References error().

show_up()

void TTNeutralGenes_bitstring::show_up ( )

virtual

Implements TTNeutralGenes.

{
  unsigned int nloc = _myProto->get_locus_num();
  unsigned int show = (nloc > 10 ? 10 : nloc);
 
  message("\n  Trait's type: ntrl (bitstring)\n\
       locus: %i\n\
     alleles: 2\n\
    _sequence:", nloc);
 
  for(unsigned int i = 0; i < show; i++)
    message("\n              %i %i", (int)_sequence[0][i], (int)_sequence[1][i]);
  if(nloc > 10) message("\n              ...");
  message("\n");
}

References message().

store_data()

void TTNeutralGenes_bitstring::store_data ( BinaryStorageBuffer *  saver )

virtual

Implements TTNeutralGenes.

{
  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 BinaryStorageBuffer::store().

Member Data Documentation

_free_recombination

bool TTNeutralGenes_bitstring::_free_recombination

protected

Referenced by operator=().

_sequence

bitstring* TTNeutralGenes_bitstring::_sequence

protected

Referenced by get_bit_sequence(), inherit(), and operator=().

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

• ttneutralgenes_bitstring.h
• ttneutralgenes_bitstring.cc