#include <ttquanti_double.h>

Inheritance diagram for TTQuanti:

Collaboration diagram for TTQuanti:

Public Member Functions
	TTQuanti ()
	TTQuanti (const TTQuanti &T)
	~TTQuanti ()
virtual void	init ()
	Called to allocate the trait's genotypic sequences.
virtual void	init_sequence ()
	Called at the start of each replicate, sets the initial genotypes.
virtual void	reset ()
	Called at the end of each simulation/replicate, deallocates sequence memory.
virtual void	inherit (TTrait mother, TTrait father)
	Inheritance procedure, creates a new trait from mother's and father's traits.
virtual void	mutate ()
	Mutation procedure, perform mutations on the genes sequence.
virtual void *	set_trait (void *value)
	Called to set the phenotypic to a particular value or to give context-dependant value(s) to the trait.
virtual void	set_sequence (void **seq)
	Called to set the sequence pointer to an existing trait.
virtual void	set_value ()
	Tells the trait to set its phenotype from genotype, should be used instead of getValue().
virtual void *	getValue ()
	Genotype to phenotype mapper.
virtual trait_t	get_type () const
	type accessor.
virtual void **	get_sequence () const
	sequence accessor.
virtual void *	get_allele (int loc, int all) const
	Called to read one allele value at a particular locus.
virtual void	show_up ()
	Writes some info to stdout.
virtual TTQuanti *	clone ()
	Returns a copy of itself.
virtual TTQuanti &	operator= (const TTrait &T)
	Copies the complete state of the trait from right to left side of the operator, sequence data included.
virtual bool	operator== (const TTrait &T)
	Checks for parameters equivalence, not genetic equivalence.
virtual bool	operator!= (const TTrait &T)
double	get_genotype (unsigned int trait)
virtual void	store_data (BinaryStorageBuffer *saver)
	Interface to store the component data (e.g. gene values) into a binary buffer.
virtual bool	retrieve_data (BinaryStorageBuffer *reader)
	Interface to retrieve the same data from the binary buffer.
void	set_proto (TProtoQuanti *proto)
void	set_nb_locus (unsigned int val)
void	set_nb_traits (unsigned int val)
void	set_seq_length (unsigned int val)
void	set_genomic_mutation_rate (double val)
void	set_init_value (double *val, bool doInit)
void	set_init_value (double *val)
void	set_mutation_fptr (double (TProtoQuanti::val)(void))
void	set_inherit_fptr (void(TProtoQuanti::val)(double , double **))
void	set_eVariance (double var)
Private Attributes
double **	sequence
double *	_phenotypes
unsigned int	_nb_locus
unsigned int	_nb_traits
unsigned int	_seq_length
double	_genomic_mutation_rate
double *	_init_value
bool	_doInitMutation
double	_eVariance
TProtoQuanti *	_myProto
double (TProtoQuanti::	_getMutationValues )(void)
void(TProtoQuanti::*	_inherit )(double , double *)

Detailed Description

Definition at line 54 of file ttquanti_double.h.

Constructor & Destructor Documentation

TTQuanti::TTQuanti ( ) [inline]

Definition at line 58 of file ttquanti_double.h.

Referenced by clone().

              : sequence(0),_phenotypes(0),_nb_locus(0),_nb_traits(0),_seq_length(0),
                _genomic_mutation_rate(0),_init_value(0),_doInitMutation(1),_myProto(0),
                _getMutationValues(0), _inherit(0),_eVariance(0)
  { }

TTQuanti::TTQuanti ( const TTQuanti & T ) [inline]

Definition at line 63 of file ttquanti_double.h.

References _nb_traits, and _phenotypes.

                                : sequence(0),_nb_locus(T._nb_locus),_nb_traits(T._nb_traits),
    _seq_length(T._seq_length),_genomic_mutation_rate(T._genomic_mutation_rate),_init_value(T._init_value),
    _doInitMutation(T._doInitMutation),_myProto(T._myProto),_getMutationValues(T._getMutationValues),
    _inherit(T._inherit),_eVariance(T._eVariance)
  {
      _phenotypes = new double [_nb_traits];
  }

TTQuanti::~TTQuanti ( ) [inline]

Definition at line 71 of file ttquanti_double.h.

References reset().

{reset();}

Member Function Documentation

virtual TTQuanti* TTQuanti::clone ( ) [inline, virtual]

Returns a copy of itself.

Note: call the copy constructor of the trait which should only copy the parameters values not the complete state of the trait (i.e. shallow copy). The copy of the sequence data is made through the assignement operator!

Implements TTrait.

Definition at line 87 of file ttquanti_double.h.

References TTQuanti().

{return new TTQuanti(*this);}

virtual void* TTQuanti::get_allele	(	int	loc,
		int	all
	)		const `[inline, virtual]`

Called to read one allele value at a particular locus.

Returns:: the allelic value at position 'all' at locus 'loc'

Parameters:

loc	locus position in the sequence
all	which allele we want to read the value from

Implements TTrait.

Definition at line 85 of file ttquanti_double.h.

References _seq_length, and sequence.

{return (loc < (int)_seq_length && all < 2 ? (void*)&sequence[all][loc] : 0);}

double TTQuanti::get_genotype ( unsigned int trait )

Definition at line 1065 of file ttquanti_double.cc.

{
  unsigned int loc;
  double genotype = 0;
  
  for(unsigned int j = 0; j < _nb_locus; ++j) {
    loc = j * _nb_traits + trait;
    genotype += sequence[0][loc] + sequence[1][loc];
  } 
  return genotype;
}

virtual void** TTQuanti::get_sequence ( ) const [inline, virtual]

sequence accessor.

Returns:: the sequence pointer

Implements TTrait.

Definition at line 84 of file ttquanti_double.h.

References sequence.

{return (void**)sequence;}

virtual trait_t TTQuanti::get_type ( ) const [inline, virtual]

type accessor.

Returns:: the trait's type

Implements TTrait.

Definition at line 83 of file ttquanti_double.h.

References QUANT.

{return QUANT;}

virtual void* TTQuanti::getValue ( ) [inline, virtual]

Genotype to phenotype mapper.

Returns:: the phenotype computed from the genotype

Implements TTrait.

Definition at line 82 of file ttquanti_double.h.

References _phenotypes.

{return _phenotypes;}

void TTQuanti::inherit	(	TTrait *	mother,
		TTrait *	father
	)		`[inline, virtual]`

Inheritance procedure, creates a new trait from mother's and father's traits.

Parameters:

mother	the mother's trait
father	the father's trait

Implements TTrait.

Definition at line 1006 of file ttquanti_double.cc.

{
  double** mother_seq = (double**)mother->get_sequence();
  double** father_seq = (double**)father->get_sequence();
  
  (_myProto->* _inherit) (sequence[0], mother_seq);
  
  (_myProto->* _inherit) (sequence[1], father_seq);
}

void TTQuanti::init ( ) [inline, virtual]

Called to allocate the trait's genotypic sequences.

Called each time a new Individual is created (Individual::init())

Implements TTrait.

Definition at line 949 of file ttquanti_double.cc.

{  
  sequence = new double*[2];
  sequence[0] = new double [_seq_length];
  sequence[1] = new double [_seq_length];
  if(!_phenotypes) _phenotypes = new double [_nb_traits];
}

void TTQuanti::init_sequence ( ) [inline, virtual]

Called at the start of each replicate, sets the initial genotypes.

Called by Individual::create().

Implements TTrait.

Definition at line 959 of file ttquanti_double.cc.

{
  unsigned int pos;
  
  for(unsigned int i = 0; i < _nb_locus; i++) {
    pos = i * _nb_traits;
    for(unsigned int j = 0; j < _nb_traits; j++) {
      sequence[0][pos] = _init_value[j]; 
      sequence[1][pos] = _init_value[j]; 
      pos++;
    }
  }
  
  if(_doInitMutation) {

    double *mut1, *mut2;

    for(unsigned int i = 0; i < _nb_locus; i++) {
      pos = i * _nb_traits;
      mut1 = (_myProto->*_getMutationValues)();
      mut2 = (_myProto->*_getMutationValues)();
      for(unsigned int j = 0; j < _nb_traits; j++) {
        sequence[0][pos] += mut1[j]; 
        sequence[1][pos] += mut2[j]; 
        pos++;
      }
    }
  }
  
}

void TTQuanti::mutate ( ) [inline, virtual]

Mutation procedure, perform mutations on the genes sequence.

Implements TTrait.

Definition at line 1018 of file ttquanti_double.cc.

{
  unsigned int NbMut = (unsigned int)RAND::Poisson(_genomic_mutation_rate);
  unsigned int mut_locus, mut_all, pos;
  double *effects;
  
  while(NbMut != 0) {
    mut_locus = RAND::Uniform(_nb_locus);
    //    cout<<"TTQuanti::mutate:: new mutation at <"<<mut_locus<<">"<<flush;
    effects = (_myProto->*_getMutationValues)();
    //    cout<<", new effects "<<effects[0]<<" "<<effects[1]<<flush;
    mut_all = RAND::RandBool();
    //    message(" at all %i\n",mut_all);
    pos = mut_locus*_nb_traits;
    for(unsigned int i = 0; i < _nb_traits; i++)
      sequence[mut_all][pos + i] += effects[i];
    
    NbMut--; 
  }
  
}

bool TTQuanti::operator!= ( const TTrait & T ) [virtual]

Implements TTrait.

Definition at line 939 of file ttquanti_double.cc.

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

TTQuanti & TTQuanti::operator= ( const TTrait & ) [virtual]

Copies the complete state of the trait from right to left side of the operator, sequence data included.

Implements TTrait.

Definition at line 895 of file ttquanti_double.cc.

{  
  const TTQuanti& TQ = dynamic_cast<const TTQuanti&>(T);
  
  if(this != &TQ) {
    
    if( (*this) != TQ) {
      _nb_locus = TQ._nb_locus;
      _nb_traits = TQ._nb_traits;
      _seq_length = TQ._seq_length;
      _genomic_mutation_rate = TQ._genomic_mutation_rate;    
      reset();
      init();
    }
    _myProto = TQ._myProto;
    _getMutationValues = TQ._getMutationValues;
    _inherit = TQ._inherit;
    
    memcpy(sequence[0],TQ.sequence[0],_seq_length*sizeof(double));
    memcpy(sequence[1],TQ.sequence[1],_seq_length*sizeof(double));
    
    set_value();
  }
  
  return *this;
}

bool TTQuanti::operator== ( const TTrait & ) [virtual]

Checks for parameters equivalence, not genetic equivalence.

Implements TTrait.

Definition at line 924 of file ttquanti_double.cc.

{ 
  if(this->get_type().compare(T.get_type()) != 0) return false;
  
  const TTQuanti& TQ = dynamic_cast<const TTQuanti&>(T);
  
  if(this != &TQ) {
    if(_nb_locus != TQ._nb_locus) return false;
    if(_nb_traits != TQ._nb_traits) return false;
  }
  return true;
}

void TTQuanti::reset ( ) [inline, virtual]

Called at the end of each simulation/replicate, deallocates sequence memory.

Implements TTrait.

Definition at line 992 of file ttquanti_double.cc.

Referenced by set_sequence(), and ~TTQuanti().

{
  if(sequence != NULL) {
    delete [] sequence[0]; 
    delete [] sequence[1];
    delete [] sequence; 
    sequence = NULL;
  }
  if(_phenotypes != NULL) delete [] _phenotypes;
  _phenotypes = NULL;
}

virtual bool TTQuanti::retrieve_data ( BinaryStorageBuffer * reader ) [inline, virtual]

Interface to retrieve the same data from the binary buffer.

Implements StorableComponent.

Definition at line 97 of file ttquanti_double.h.

References _seq_length, BinaryStorageBuffer::read(), and sequence.

                                                             {reader->read(sequence[0],_seq_length*sizeof(double));
                                                              reader->read(sequence[1],_seq_length*sizeof(double));return true;}

void TTQuanti::set_eVariance ( double var ) [inline]

Definition at line 110 of file ttquanti_double.h.

References _eVariance.

{_eVariance = var;}

void TTQuanti::set_genomic_mutation_rate ( double val ) [inline]

Definition at line 105 of file ttquanti_double.h.

References _genomic_mutation_rate.

{_genomic_mutation_rate = val;}

void TTQuanti::set_inherit_fptr ( void(TProtoQuanti::*)(double *, double **) val ) [inline]

Definition at line 109 of file ttquanti_double.h.

References _inherit.

{_inherit = val;}

void TTQuanti::set_init_value	(	double *	val,
		bool	doInit
	)		`[inline]`

Definition at line 106 of file ttquanti_double.h.

References _doInitMutation, and _init_value.

{ _init_value = val; _doInitMutation = doInit;}

void TTQuanti::set_init_value ( double * val ) [inline]

Definition at line 107 of file ttquanti_double.h.

References _init_value.

{ _init_value = val;} //this is for the quanti_init LCE

void TTQuanti::set_mutation_fptr ( double *(TProtoQuanti::*)(void) val ) [inline]

Definition at line 108 of file ttquanti_double.h.

References _getMutationValues.

{_getMutationValues = val;}

void TTQuanti::set_nb_locus ( unsigned int val ) [inline]

Definition at line 102 of file ttquanti_double.h.

References _nb_locus.

{_nb_locus = val;}

void TTQuanti::set_nb_traits ( unsigned int val ) [inline]

Definition at line 103 of file ttquanti_double.h.

References _nb_traits.

{_nb_traits = val;}

void TTQuanti::set_proto ( TProtoQuanti * proto ) [inline]

Definition at line 101 of file ttquanti_double.h.

References _myProto.

{_myProto = proto;}

void TTQuanti::set_seq_length ( unsigned int val ) [inline]

Definition at line 104 of file ttquanti_double.h.

References _seq_length.

{_seq_length = val;}

virtual void TTQuanti::set_sequence ( void ** seq ) [inline, virtual]

Called to set the sequence pointer to an existing trait.

Parameters:

seq	the existing sequence pointer

Implements TTrait.

Definition at line 80 of file ttquanti_double.h.

References reset(), and sequence.

{reset(); sequence = (double**)seq;}

virtual void* TTQuanti::set_trait ( void * value ) [inline, virtual]

Called to set the phenotypic to a particular value or to give context-dependant value(s) to the trait.

Parameters:

value the value passed to the trait

Returns:: the argument passed

Implements TTrait.

Definition at line 79 of file ttquanti_double.h.

{return value;}

void TTQuanti::set_value ( ) [inline, virtual]

Tells the trait to set its phenotype from genotype, should be used instead of getValue().

Implements TTrait.

Definition at line 1042 of file ttquanti_double.cc.

{
  register unsigned int loc;
  
  for(unsigned int i = 0; i < _nb_traits; ++i) 
    _phenotypes[i] = 0;
  
  for(unsigned int j = 0; j < _nb_locus; ++j) {
    loc = j * _nb_traits;
    for(unsigned int i = 0; i < _nb_traits; ++i) {
      _phenotypes[i] += sequence[0][loc] + sequence[1][loc];
      loc++;
    }
  } 
  
  if(_eVariance != 0)
    for(unsigned int i = 0; i < _nb_traits; ++i) 
      _phenotypes[i] += RAND::Gaussian(_eVariance);
}

void TTQuanti::show_up ( ) [virtual]

Writes some info to stdout.

Implements TTrait.

Definition at line 1079 of file ttquanti_double.cc.

{
  message("\
          Trait's type: QUANTI\n\
          traits: %i\n\
          loci: %i\n",_nb_traits,_nb_locus);
  
  for(unsigned int i = 0; i < _nb_traits; i++)
    message("phenotype %i: %f\n",i+1,_phenotypes[i]);
  
  message("sequence: \n0:");
  unsigned int loc;
  for(unsigned int i = 0; i < _nb_traits; ++i) {
    message("\nt%i:",i+1);
    for(unsigned int j = 0; (j < _nb_locus); ++j) {
      loc = j * _nb_traits + i;
      message("%.3f,",sequence[0][loc]);
    }
  }
  message("\n1:");
  for(unsigned int i = 0; i < _nb_traits; ++i) {
    message("\nt%i:",i+1);
    for(unsigned int j = 0; (j < _nb_locus); ++j) {
      loc = j * _nb_traits + i;
      message("%.3f,",sequence[1][loc]);
    }
  }
  message("\n");
  
}

virtual void TTQuanti::store_data ( BinaryStorageBuffer * saver ) [inline, virtual]

Interface to store the component data (e.g. gene values) into a binary buffer.

Implements StorableComponent.

Definition at line 95 of file ttquanti_double.h.

References _seq_length, sequence, and BinaryStorageBuffer::store().

                                                             {saver->store(sequence[0],_seq_length*sizeof(double));
                                                              saver->store(sequence[1],_seq_length*sizeof(double));}