GeneticMaterial Class Reference

Class for the genetic material optionally carried by animals in ALMaSS. More...

#include <GeneticMaterial.h>

Public Member Functions
	GeneticMaterial ()
void	ReadFrequencies ()
void	SetAllele (int pos, uint32 value, int Chromosome)
uint32	GetAllele (int pos, int Chromosome)
void	PrintChromosome (char *C, int Chromosome)
int	HomozygosityCount ()
int	HeterozygosityCount ()
void	Recombine (GeneticMaterial *Gen21, GeneticMaterial *Gene2)
void	Initiation (AlleleFreq *Al)
float	ScoreReproduction ()
float	ScoreHQThreshold ()
void	SetGeneticFlag ()
void	SetDirectFlag ()
void	UnsetGeneticFlag ()
void	UnsetDirectFlag ()
uint32	GetGeneticFlag ()
uint32	GetDirectFlag ()
void	Mutation_1 ()
void	Mutation_1ab ()
void	Mutation_2 ()
void	Mutation_3 ()
void	Mutation_4 ()

Protected Attributes
uint32	Chromosome [6]

Detailed Description

Class for the genetic material optionally carried by animals in ALMaSS.

Constructor & Destructor Documentation

GeneticMaterial()

GeneticMaterial::GeneticMaterial

(

)

                                 {
  // ensure zeros in all loci
  for ( int i = 0; i < 6; i++ ) Chromosome[ i ] = 0;
}

References Chromosome.

Member Function Documentation

GetAllele()

uint32 GeneticMaterial::GetAllele	(	int	pos,
		int	Chromosome
	)

                                                         {
  uint32 value;
  // Get the right chromosome
  // if Chromo==0 then 0-2, else 3-5
  Chromo *= 3; // 0 or 3
  if ( locus < 16 ) {
    // Shift it so the locus is in the last two bits
    // Does it twice because 32 bis coding for 16 loci
    value = Chromosome[ Chromo ] >> locus;
    value = ( value >> locus ) & 0x03;
  } else {
    Chromo++; // 1 or 4
    locus -= 16; // Now 0 to 16
    if ( locus >= 8 ) {
      Chromo++; // 2 or 5
      locus -= 8;
    }
    value = Chromosome[ Chromo ] >> ( locus * 4 );
    value = value & 0x0f;
  }
  return value;
}

References Chromosome.

Referenced by GetDirectFlag(), GetGeneticFlag(), HeterozygosityCount(), HomozygosityCount(), Mutation_2(), Mutation_3(), Mutation_4(), PrintChromosome(), Recombine(), Vole_Base::SupplyAllele(), and Vole_Base::SupplyMyAllele().

GetDirectFlag()

uint32 GeneticMaterial::GetDirectFlag

(

)

                                      {
    return GetAllele(0,1);
}

References GetAllele().

Referenced by Vole_Base::GetDirectFlag(), and Vole_JuvenileMale::st_BecomeSubAdult().

GetGeneticFlag()

uint32 GeneticMaterial::GetGeneticFlag

(

)

                                       {
    return GetAllele(0,0);
}

References GetAllele().

Referenced by Vole_Base::GetGeneticFlag(), and Vole_JuvenileMale::st_BecomeSubAdult().

HeterozygosityCount()

int GeneticMaterial::HeterozygosityCount

(

)

                                         {
  int heterozyg = 0;
  for ( int i = 0; i < 32; i++ ) {
    if ( GetAllele( i, 0 ) != GetAllele( i, 1 ) ) heterozyg++;
  }
  return heterozyg;
}

References GetAllele().

Referenced by Vole_Base::SupplyHeteroZyg().

HomozygosityCount()

int GeneticMaterial::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 < 32; i++ ) {
    if ( GetAllele( i, 0 ) == GetAllele( i, 1 ) ) homozyg++;
  }
  return homozyg;
}

References GetAllele().

Referenced by Vole_Base::SupplyHomoZyg().

Initiation()

void GeneticMaterial::Initiation

(

AlleleFreq *

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;
  for ( int l = 0; l < 32; l++ ) {
    //if ( l < 16 ) c = 0; else if ( l < 24 ) c = 1; else c = 2;
 
    int chance = random( 1000 );
    uint32 index = 0;
    while ( chance > Al->SupplyAN( l, index ) ) {
      index++;
    }
    value = index;
    // set the value
    SetAllele( l, value, 0 );
    chance = random( 1000 );
    index = 0;
    while ( chance > Al->SupplyAN( l, index ) ) {
      index++;
    }
    value = index;
    // set the value
    SetAllele( l, value, 1 );
  }
}

References random(), SetAllele(), and AlleleFreq::SupplyAN().

Referenced by Vole_Population_Manager::Init().

Mutation_1()

void GeneticMaterial::Mutation_1

(

)

random allele choice

{
  for ( int i = 0; i < 16; i++ ) {
    if ( g_rand_uni() < MutationChance ) // one chance in Mutation Chance
    {
      SetAllele( i, random( 4 ), random( 2 ) );
    }
  }
  for ( int i = 16; i < 32; i++ ) {
    if ( g_rand_uni() < MutationChance ) // one chance in Mutation Chance
    {
      SetAllele( i, random( 16 ), random( 2 ) );
    }
  }
}

References g_rand_uni, MutationChance, random(), and SetAllele().

Mutation_1ab()

void GeneticMaterial::Mutation_1ab

(

)

random allele choice a & b only

{
  // Only used when all loci have only two alleles!
  for ( int i = 0; i < 32; i++ ) {
    if ( g_rand_uni() < MutationChance ) // one chance in Mutation Chance
    {
      SetAllele( i, random( 2 ), random( 2 ) );
    }
  }
}

References g_rand_uni, MutationChance, random(), and SetAllele().

Mutation_2()

void GeneticMaterial::Mutation_2

(

)

Move one allele +/-

{
  for ( int i = 0; i < 16; i++ ) {
    if ( g_rand_uni() < MutationChance ) // one chance in Mutation Chance
    {
      int strand = random( 2 );
      int allele = GetAllele( i, strand );
      if ( random( 2 ) == 1 ) allele++; else allele--;
      if ( allele == -1 ) allele = 3; else if ( allele == 4 ) allele = 0;
      SetAllele( i, allele, strand );
    }
  }
  for ( int i = 16; i < 32; i++ ) {
    if ( g_rand_uni() < MutationChance ) // one chance in Mutation Chance
    {
      int strand = random( 2 );
      int allele = GetAllele( i, strand );
      if ( random( 2 ) == 1 ) allele++; else allele--;
      if ( allele == -1 ) allele = 15; else if ( allele == 16 ) allele = 0;
      SetAllele( i, allele, strand );
    }
  }
}

References g_rand_uni, GetAllele(), MutationChance, random(), and SetAllele().

Mutation_3()

void GeneticMaterial::Mutation_3

(

)

switch a<->b & c<->d

{
  // NB Only works for the first 16 loci
  for ( int i = 0; i < 16; i++ ) {
    if ( g_rand_uni() < MutationChance ) // one chance in Mutation Chance
    {
      int strand = random( 2 );
      int allele = GetAllele( i, strand );
      switch ( allele ) {
        case 0:
          allele = 1;
        break;
        case 1:
          allele = 0;
        break;
        case 2:
          allele = 3;
        break;
        case 3:
          allele = 2;
        break;
      }
      SetAllele( i, allele, strand );
    }
  }
}

References g_rand_uni, GetAllele(), MutationChance, random(), and SetAllele().

Mutation_4()

void GeneticMaterial::Mutation_4

(

)

Specially mutation of only the first locus with two options 0/1

{
    if (g_rand_uni() < MutationChance) // one chance in Mutation Chance
    {
        int strand = random(2);
        int allele = GetAllele(0, strand);
        allele = (allele + 1) && 1; // only 1 or 0 is allowed
    }
}

References g_rand_uni, GetAllele(), MutationChance, and random().

Referenced by Vole_Female::st_Lactating().

PrintChromosome()

void GeneticMaterial::PrintChromosome	(	char *	C,
		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().

ReadFrequencies()

void GeneticMaterial::ReadFrequencies

(

)

Recombine()

void GeneticMaterial::Recombine	(	GeneticMaterial *	Gen21,
		GeneticMaterial *	Gene2
	)

                                                                                  {
  for ( int i = 0; i < 32; i++ ) {
    // For each locus
    // Choose which chromosome for each parent
    int g0 = random( 2 );
    int g1 = random( 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 GetAllele(), random(), and SetAllele().

Referenced by Vole_Base::CopyMyself(), and Vole_Female::st_Lactating().

ScoreHQThreshold()

float GeneticMaterial::ScoreHQThreshold

(

)

This function can be used to alter fitness based on associated genetic codes. These are only used in population genetic research, e.g. to create hybrid zones.

                                        {
  return 1.0;
  // OLD CODE OUTDATED
  /* Ditte's Simulation Version uint32 allele0a = GetAllele(0,0); // loci 0 uint32 allele1a = GetAllele(1,0); // loci 1
  uint32 allele0b = GetAllele(0,1); // loci 0 uint32 allele1b = GetAllele(1,1); // loci 1
  // Initial rules are that if 0a and 1a are 0 & 2 or 2 & 0 then OK   (a,c)(c,a)
  // likewise they may be 1 & 3 or 3 & 1  (b,d) (d,b) // any other combination is bad // Same for loci 1 bool IsOK0=false;
  switch(allele0a) { case 0: if (allele1a==2) IsOK0=true; break; case 1: if (allele1a==3) IsOK0=true; break; case 2:
  if (allele1a==0) IsOK0=true; break; case 3: if (allele1a==1) IsOK0=true; break; default: assert(NULL); break; }
  bool IsOK1=false; switch(allele0b) { case 0: if (allele1b==2) IsOK1=true; break; case 1: if (allele1b==3) IsOK1=true; break;
  case 2: if (allele1b==0) IsOK1=true; break; case 3: if (allele1b==1) IsOK1=true; break; default: assert(NULL); break; }
  // determine the effect of the genetics // In the simple case it is good or bad
  if (IsOK0 && IsOK1) return 1.0; else return 0.9;
 
  // Lar Bach's version uint32 allele2a = GetAllele(2,0); // loci 0 uint32 allele2b = GetAllele(2,1); // loci 0
  float result= -0.5; switch (allele2a) { case 0: case 2: case 3: break; default: result+=0.5; } switch (allele2b) { case 0:
  case 2: case 3: break; default: result+=0.5; break; } return result;
  // returns -0.5 if homozygous aa, 0.5 if homozygous bb & het=0
 
  */
}

ScoreReproduction()

float GeneticMaterial::ScoreReproduction

(

)

This function can be used to alter reproductive effects based on genetic codes. These are only used in population genetic research.

                                         {
  return 1.0;
  /* OLD CODE OUTDATED uint32 allele0a = GetAllele(0,0); // loci 0 uint32 allele1a = GetAllele(1,0); // loci 1
  uint32 allele0b = GetAllele(0,1); // loci 0 uint32 allele1b = GetAllele(1,1); // loci 1
  // Initial rules are that locus 0 and 1 are ac or bd then OK // likewise they may be ca or db
  // any other combination is bad // Same for loci 1 bool IsOK0=false; switch(allele0a) { case 0:   //a
  if (allele1a==2) IsOK0=true; break; case 1:   //b if (allele1a==3) IsOK0=true; break; case 2:   //c
  if (allele1a==0) IsOK0=true; break; case 3:   //d if (allele1a==1) IsOK0=true; break; default:
  FILE* errfile=fopen("GeneticErrorFile.Txt","w"); fprintf(errfile,"Unknown Allele Number\n"); fclose(errfile); exit(10);
  break; } bool IsOK1=false; switch(allele0b) { case 0: if (allele1b==2) IsOK1=true; break; case 1:
  if (allele1b==3) IsOK1=true; break; case 2: if (allele1b==0) IsOK1=true; break; case 3: if (allele1b==1) IsOK1=true; break;
  default: FILE* errfile=fopen("GeneticErrorFile.Txt","w"); fprintf(errfile,"Unknown Allele Number\n"); fclose(errfile);
  exit(11); break; } // determine the effect of the genetics // In the simple case it is good or bad
  if (IsOK0 && IsOK1) return 1.0; else return 0.05; */
}

SetAllele()

void GeneticMaterial::SetAllele	(	int	pos,
		uint32	value,
		int	Chromosome
	)

                                                                     {
  Chromo*=3; // now 0 or 3
  uint32 mask;
  if (locus<16) {
  // Get the right chromosome
  // Create the mask
  // Does it twice because 32 bits coding for 16 loci
  mask = 0x03 << locus;
  mask = mask << locus;
  // just to make make sure it is 0-3
  value = value & 0x03;
  // create the value mask
  value = value << locus;
  value = value << locus;
  // clear the locus
  Chromosome[ Chromo ] &= ~mask;
  // write the value
  Chromosome[ Chromo ] |= value;
  } else {
    Chromo++; // now 1 or 4
    locus-=16;
    if (locus>=8) {
      Chromo++;
      locus-=8;
    }
    mask = 0x0F << (locus*4);
    value = value & 0x0f; // make sure there was no extra stuff added!
    // create the value mask
    value = value << (locus*4);
    Chromosome[ Chromo ] &= ~mask;
    // write the value
    Chromosome[ Chromo ] |= value;
    }
}

References Chromosome.

Referenced by Vole_Population_Manager::Init(), Initiation(), Mutation_1(), Mutation_1ab(), Mutation_2(), Mutation_3(), Recombine(), SetDirectFlag(), SetGeneticFlag(), UnsetDirectFlag(), and UnsetGeneticFlag().

SetDirectFlag()

void GeneticMaterial::SetDirectFlag

(

)

                                    {
    SetAllele(0,1,1);
}

References SetAllele().

Referenced by Vole_Base::SetDirectFlag().

SetGeneticFlag()

void GeneticMaterial::SetGeneticFlag

(

)

                                     {
    SetAllele(0,1,0);
}

References SetAllele().

Referenced by Vole_Base::SetGeneticFlag().

UnsetDirectFlag()

void GeneticMaterial::UnsetDirectFlag

(

)

                                      {
    SetAllele(0,0,1);
}

References SetAllele().

Referenced by Vole_Base::UnsetDirectFlag().

UnsetGeneticFlag()

void GeneticMaterial::UnsetGeneticFlag

(

)

                                       {
    SetAllele(0,0,0);
}

References SetAllele().

Referenced by Vole_Base::UnsetGeneticFlag().

Member Data Documentation

Chromosome

uint32 GeneticMaterial::Chromosome[6]

protected

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

---

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

• /builds/a1mass/almass_stable_oddox/Vole/GeneticMaterial.h
• /builds/a1mass/almass_stable_oddox/Vole/GeneticMaterial.cpp