GeneticMaterial256_16 Class Reference

#include <GeneticMaterial.h>

Public Member Functions
	GeneticMaterial256_16 ()
void	SetAllele (unsigned int locus, uint32 value, unsigned int Chromo)
uint32	GetAllele (unsigned int locus, unsigned int Chromo)
void	Mutation_3 ()
void	SetGeneticFlag ()
void	SetDirectFlag ()
int	HomozygosityCount ()
int	HeterozygosityCount ()
void	UnsetGeneticFlag ()
void	UnsetDirectFlag ()
uint32	GetGeneticFlag ()
uint32	GetDirectFlag ()
void	PrintGenes ()
void	Recombine (GeneticMaterial256_16 *Gene1, GeneticMaterial256_16 *Gene2)
void	Initiation (AlleleFreq256_16 *Al)

Protected Attributes
unsigned char	Chromosome [32]

Constructor & Destructor Documentation

GeneticMaterial256_16()

GeneticMaterial256_16::GeneticMaterial256_16

(

)

                                             {
  // ensure zeros in all loci
  for ( int i = 0; i < 32; i++ ) Chromosome[ i ] = 0;
}

References Chromosome.

Member Function Documentation

GetAllele()

uint32 GeneticMaterial256_16::GetAllele	(	unsigned int	locus,
		unsigned int	Chromo
	)

                                                                                 {
    if (Chromo==1) locus +=16;
    return (uint32) Chromosome[ locus ];
}

References Chromosome.

Referenced by GetDirectFlag(), GetGeneticFlag(), Mutation_3(), and Recombine().

GetDirectFlag()

uint32 GeneticMaterial256_16::GetDirectFlag

(

)

                                            {
    return GetAllele(0,1);
}

References GetAllele().

GetGeneticFlag()

uint32 GeneticMaterial256_16::GetGeneticFlag

(

)

                                             {
    return GetAllele(0,0);
}

References GetAllele().

HeterozygosityCount()

int GeneticMaterial256_16::HeterozygosityCount ( )

inline

{ return 0; } // To add if needed

HomozygosityCount()

int GeneticMaterial256_16::HomozygosityCount ( )

inline

{ return 0; } // To add if needed

Initiation()

void GeneticMaterial256_16::Initiation

(

AlleleFreq256_16 *

Al

)

The method called to intialise genes on initiation of the simulation.
Gene frequencies are based on an external text file input read in on construction.

                                                              {
  uint32 value; //, c;
  for ( int l = 0; l < 16; l++ ) {
    int chance = g_random_fnc( 1000 );
    uint32 index = 0;
    while ( chance >= Al->SupplyAN( l, index ) ) {
      index++;
    }
    value = index;
    // set the value
    SetAllele( l, value, 0 );
    chance = g_random_fnc( 1000 );
    index = 0;
    while ( chance >= Al->SupplyAN( l, index ) ) {
      index++;
    }
    value = index;
    // set the value
    SetAllele( l, value, 1 );
  }
}

References g_random_fnc(), SetAllele(), and AlleleFreq256_16::SupplyAN().

Mutation_3()

void GeneticMaterial256_16::Mutation_3

(

)

Move one allele one up or down

{
    if (MutationChance != 0){
        for ( int i = 0; i < 16; i++ ) {
            if ( g_rand_uni_fnc() < MutationChance ) // one chance in Mutation Chance for the locus
            {
                unsigned strand = g_random_fnc( 2 ); // kromosom 0 or 1
                int allele = GetAllele( i, strand );
                if ( g_random_fnc( 2 ) == 1 ) allele++; else allele--;
                //For mutations less than 0 and more than 256 the mutation should result in 1 or g_MaxAllele-1
                if (allele > g_MaxAllele) allele-=2;
                else if (allele < 0) allele = 1;
                SetAllele( i, (uint32) allele, strand );
            }
        }
    }
}

References g_MaxAllele, g_rand_uni_fnc(), g_random_fnc(), GetAllele(), MutationChance, and SetAllele().

PrintGenes()

void GeneticMaterial256_16::PrintGenes

(

)

Recombine()

void GeneticMaterial256_16::Recombine	(	GeneticMaterial256_16 *	Gene1,
		GeneticMaterial256_16 *	Gene2
	)

                                                                                                   {
    // Is called with hers and his genes
  for ( int i = 0; i < 16; i++ ) {
    // For each locus
    // Choose which chromosome for each parent
    int g0 = g_random_fnc(2);
    int g1 = g_random_fnc(2);
    // get the two alleles
    uint32 a0 = Gene1->GetAllele( i, g0 );
    uint32 a1 = Gene2->GetAllele( i, g1 );
    //  put a0 into chromo0 & a1 to chromo1 & vice versa
    SetAllele( i, a0, 0 );
    SetAllele( i, a1, 1 );
  }
}

References g_random_fnc(), GetAllele(), and SetAllele().

SetAllele()

void GeneticMaterial256_16::SetAllele	(	unsigned int	locus,
		uint32	value,
		unsigned int	Chromo
	)

                                                                                             {
    if (Chromo==1) locus +=16;
    Chromosome[ locus ] = (unsigned char) value;
}

References Chromosome.

Referenced by Initiation(), Mutation_3(), Recombine(), SetDirectFlag(), SetGeneticFlag(), UnsetDirectFlag(), and UnsetGeneticFlag().

SetDirectFlag()

void GeneticMaterial256_16::SetDirectFlag

(

)

                                          {
    SetAllele(0,1,1);
}

References SetAllele().

SetGeneticFlag()

void GeneticMaterial256_16::SetGeneticFlag

(

)

                                           {
    SetAllele(0,1,0);
}

References SetAllele().

UnsetDirectFlag()

void GeneticMaterial256_16::UnsetDirectFlag

(

)

                                            {
    SetAllele(0,0,1);
}

References SetAllele().

UnsetGeneticFlag()

void GeneticMaterial256_16::UnsetGeneticFlag

(

)

                                             {
    SetAllele(0,0,0);
}

References SetAllele().

Member Data Documentation

Chromosome

unsigned char GeneticMaterial256_16::Chromosome[32]

protected

Referenced by GeneticMaterial256_16(), GetAllele(), and SetAllele().

---

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

• /builds/ALMaSS/ALMaSS_MIDox/Vole/GeneticMaterial.h
• /builds/ALMaSS/ALMaSS_MIDox/Vole/GeneticMaterial.cpp