GeneticMaterial1616 Class Reference

#include <GeneticMaterial.h>

Public Member Functions
	GeneticMaterial1616 ()
void	SetAllele (unsigned int locus, uint32 value, unsigned int Chromo)
uint32	GetAllele (unsigned int locus, unsigned int Chromo)
void	PrintChromosome (char *C, unsigned int Chromosome)
void	SetGeneticFlag ()
void	SetDirectFlag ()
void	UnsetGeneticFlag ()
void	UnsetDirectFlag ()
uint32	GetGeneticFlag ()
uint32	GetDirectFlag ()
int	HomozygosityCount ()
int	HeterozygosityCount ()
void	Recombine (GeneticMaterial1616 *Gene1, GeneticMaterial1616 *Gene2)
void	Initiation (AlleleFreq1616 *Al)
void	Mutation_1 ()
void	Mutation_2 ()
void	Mutation_3 ()

Protected Attributes
uint32	Chromosome [4]

Constructor & Destructor Documentation

GeneticMaterial1616()

GeneticMaterial1616::GeneticMaterial1616

(

)

                                         {
  // ensure zeros in all loci
  for ( int i = 0; i < 4; i++ ) Chromosome[ i ] = 0;
}

References Chromosome.

Member Function Documentation

GetAllele()

uint32 GeneticMaterial1616::GetAllele	(	unsigned int	locus,
		unsigned int	Chromo
	)

                                                                               {
    // This is for 32 bit machines, 64bit is easier
    // locus must be 0 to 15
    //Chromo must be either 0 or 1
    // These debug tests below are costly so turn off in release code
    #ifdef __GENDEBUG
        if (Chromo>1) {
            g_msg->Warn( "Chromo > 1 in GeneticMaterial1616 - get allele", NULL );
            exit( 0 );
        }
        if (locus>15) {
            g_msg->Warn( "locus > 15 in GeneticMaterial1616 - get allele", NULL );
            exit( 0 );
        }
    #endif
 
    uint32 segment=((Chromo<<1) | ((locus & 0x08)>>3)); // locates on which segment in the comosome we are in
    uint32 allele=0x0F & (Chromosome[segment]>>((locus & 0x07)<<2)); //Locates the allele and shifts it down to the first postition to read
    return allele;
}

References Chromosome, g_msg, and MapErrorMsg::Warn().

Referenced by GetDirectFlag(), GetGeneticFlag(), HeterozygosityCount(), HomozygosityCount(), Mutation_2(), Mutation_3(), PrintChromosome(), and Recombine().

GetDirectFlag()

uint32 GeneticMaterial1616::GetDirectFlag

(

)

                                          {
    return GetAllele(0,1);
}

References GetAllele().

GetGeneticFlag()

uint32 GeneticMaterial1616::GetGeneticFlag

(

)

                                           {
    return GetAllele(0,0);
}

References GetAllele().

HeterozygosityCount()

int GeneticMaterial1616::HeterozygosityCount

(

)

                                             {
  int heterozyg = 0;
  for ( int i = 0; i < 16; i++ ) {
    if ( GetAllele( i, 0 ) != GetAllele( i, 1 ) ) heterozyg++;
  }
  return heterozyg;
}

References GetAllele().

HomozygosityCount()

int GeneticMaterial1616::HomozygosityCount

(

)

                                           {
  // OK OK there is an easy way to do this by calling HeterozygosityCount and
  // subtracting this from 32, but just is case that little bit of saved time is useful:
  int homozyg=0;
  for ( int i = 0; i < 16; i++ ) {
    if ( GetAllele( i, 0 ) == GetAllele( i, 1 ) ) homozyg++;
  }
  return homozyg;
}

References GetAllele().

Initiation()

void GeneticMaterial1616::Initiation

(

AlleleFreq1616 *

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++ ) {
   // if ( l < 16 ) c = 0; else c = 2;
 
    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 AlleleFreq1616::SupplyAN().

Mutation_1()

void GeneticMaterial1616::Mutation_1

(

)

random allele choice

{
    if (MutationChance != 0)
    {
  for ( int i = 0; i < 16; i++ )
  {
    if ( g_rand_uni_fnc() < MutationChance ) // one chance in Mutation Chance
    {
      SetAllele( i, g_random_fnc( 16 ), g_random_fnc( 2 ) );
    }
  }
    }
}

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

Mutation_2()

void GeneticMaterial1616::Mutation_2

(

)

Move one allele + and 16 becomes 0

{
    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 int strand = g_random_fnc( 2 ); // kromosom 0 or 1
      unsigned int allele = GetAllele( i, strand );
      allele++;
      allele&=0x0f; //and with 1111 - allels curls up 15 -> 0
      SetAllele( i, allele, strand );
    }
  }
}
}

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

Mutation_3()

void GeneticMaterial1616::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
      unsigned allele = GetAllele( i, strand );
      //if (strand == 1) allele++; else allele--;
      if ( g_random_fnc( 2 ) == 1 ) allele++; else allele--;
 
      //For mutations less than 0 and more than 15 the mutation should result in 1 or 14
 
      if (allele > 0x0f) // Test to see if mutation to negative or above 15
      {
          allele |= 0x1C;
          if(allele > 0x01C) { allele &= 0x01;}
          else allele >>=1;
          //allele|= 0xF0; // (240) Sets neg to 0, and 16 to 15 -> to avoid curling up
          //allele = (~allele);
      }
 
      SetAllele( i, allele, strand );
    }
  }
}
}

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

PrintChromosome()

void GeneticMaterial1616::PrintChromosome	(	char *	C,
		unsigned int	Chromosome
	)

                                                                         {
  for ( int i = 0; i < 16; i++ ) {
    uint32 allele = GetAllele( i, Chromo );
    switch ( allele ) {
      case 0:
        C[ i ] = 'a';
      break;
      case 1:
        C[ i ] = 'b';
      break;
      case 2:
        C[ i ] = 'c';
      break;
      case 3:
        C[ i ] = 'd';
      break;
      case 4:
        C[ i ] = 'e';
      break;
      case 5:
        C[ i ] = 'f';
      break;
      case 6:
        C[ i ] = 'g';
      break;
      case 7:
        C[ i ] = 'h';
      break;
      case 8:
        C[ i ] = 'i';
      break;
      case 9:
        C[ i ] = 'j';
      break;
      case 10:
        C[ i ] = 'k';
      break;
      case 11:
        C[ i ] = 'l';
      break;
      case 12:
        C[ i ] = 'm';
      break;
      case 13:
        C[ i ] = 'n';
      break;
      case 14:
        C[ i ] = 'o';
      break;
      case 15:
        C[ i ] = 'p';
      break;
    }
  }
  C[ 16 ] = 0;
}

References GetAllele().

Recombine()

void GeneticMaterial1616::Recombine	(	GeneticMaterial1616 *	Gene1,
		GeneticMaterial1616 *	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 GeneticMaterial1616::SetAllele	(	unsigned int	locus,
		uint32	value,
		unsigned int	Chromo
	)

                                                                                           {
    // This is for 32 bit machines, 64bit is easier
    // locus must be 0 to 15
    //Chromo must be either 0 or 1
    // These debug tests below are costly so turn off in release code
    #ifdef __GENDEBUG
        if (Chromo>1) {
            g_msg->Warn( "Chromo > 1 in GeneticMaterial1616 - set allele", NULL );
            exit( 0 );
        }
        if (locus>15) {
            g_msg->Warn( "locus > 15 in GeneticMaterial1616 - set allele", NULL );
            exit( 0 );
        }
    #endif
 
    uint32 segment=((Chromo<<1) | ((locus & 0x08)>>3));
    uint32 mask = 0x0F; //0000 1111F
    // Need to shift the mask over the correct allele
    mask=mask<<((locus&7)<<2);
    value = value & 0x0f; // make sure there was no extra stuff added!
    // create the value mask
    value = value << ((locus&7)<<2);
    Chromosome[ segment ] &= ~mask; // get rid of the current info
    Chromosome[ segment ] |= value; // write the value
}

References Chromosome, g_msg, and MapErrorMsg::Warn().

Referenced by Initiation(), Mutation_1(), Mutation_2(), Mutation_3(), Recombine(), SetDirectFlag(), SetGeneticFlag(), UnsetDirectFlag(), and UnsetGeneticFlag().

SetDirectFlag()

void GeneticMaterial1616::SetDirectFlag

(

)

                                        {
    SetAllele(0,1,1);
}

References SetAllele().

SetGeneticFlag()

void GeneticMaterial1616::SetGeneticFlag

(

)

                                         {
    SetAllele(0,1,0);
}

References SetAllele().

UnsetDirectFlag()

void GeneticMaterial1616::UnsetDirectFlag

(

)

                                          {
    SetAllele(0,0,1);
}

References SetAllele().

UnsetGeneticFlag()

void GeneticMaterial1616::UnsetGeneticFlag

(

)

                                           {
    SetAllele(0,0,0);
}

References SetAllele().

Member Data Documentation

Chromosome

uint32 GeneticMaterial1616::Chromosome[4]

protected

Referenced by GeneticMaterial1616(), 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