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.

Definition at line 94 of file GeneticMaterial.h.

Constructor & Destructor Documentation

GeneticMaterial()

GeneticMaterial::GeneticMaterial

(

)

Definition at line 355 of file GeneticMaterial.cpp.

                                 {
  // 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
	)

Definition at line 233 of file GeneticMaterial.cpp.

                                                         {
  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

(

)

Definition at line 191 of file GeneticMaterial.cpp.

                                      {
    return GetAllele(0,1);
}

References GetAllele().

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

GetGeneticFlag()

uint32 GeneticMaterial::GetGeneticFlag

(

)

Definition at line 187 of file GeneticMaterial.cpp.

                                       {
    return GetAllele(0,0);
}

References GetAllele().

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

HeterozygosityCount()

int GeneticMaterial::HeterozygosityCount

(

)

Definition at line 328 of file GeneticMaterial.cpp.

                                         {
  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

(

)

Definition at line 317 of file GeneticMaterial.cpp.

                                       {
  // 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.

Definition at line 366 of file GeneticMaterial.cpp.

                                                  {
  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 SetAllele(), and AlleleFreq::SupplyAN().

Referenced by Vole_Population_Manager::Init().

Mutation_1()

void GeneticMaterial::Mutation_1

(

)

random allele choice

Definition at line 444 of file GeneticMaterial.cpp.

{
  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, and SetAllele().

Mutation_1ab()

void GeneticMaterial::Mutation_1ab

(

)

random allele choice a & b only

Definition at line 465 of file GeneticMaterial.cpp.

{
  // 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, and SetAllele().

Mutation_2()

void GeneticMaterial::Mutation_2

(

)

Move one allele +/-

Definition at line 481 of file GeneticMaterial.cpp.

{
  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, and SetAllele().

Mutation_3()

void GeneticMaterial::Mutation_3

(

)

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

Definition at line 510 of file GeneticMaterial.cpp.

{
  // 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, and SetAllele().

Mutation_4()

void GeneticMaterial::Mutation_4

(

)

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

Definition at line 538 of file GeneticMaterial.cpp.

{
    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(), and MutationChance.

Referenced by Vole_Female::st_Lactating().

PrintChromosome()

void GeneticMaterial::PrintChromosome	(	char *	C,
		int	Chromosome
	)

Definition at line 258 of file GeneticMaterial.cpp.

                                                            {
  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
	)

Definition at line 338 of file GeneticMaterial.cpp.

                                                                                  {
  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(), 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.

Definition at line 414 of file GeneticMaterial.cpp.

                                        {
  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.

Definition at line 394 of file GeneticMaterial.cpp.

                                         {
  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
	)

Definition at line 196 of file GeneticMaterial.cpp.

                                                                     {
  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

(

)

Definition at line 173 of file GeneticMaterial.cpp.

                                    {
    SetAllele(0,1,1);
}

References SetAllele().

Referenced by Vole_Base::SetDirectFlag().

SetGeneticFlag()

void GeneticMaterial::SetGeneticFlag

(

)

Definition at line 169 of file GeneticMaterial.cpp.

                                     {
    SetAllele(0,1,0);
}

References SetAllele().

Referenced by Vole_Base::SetGeneticFlag().

UnsetDirectFlag()

void GeneticMaterial::UnsetDirectFlag

(

)

Definition at line 182 of file GeneticMaterial.cpp.

                                      {
    SetAllele(0,0,1);
}

References SetAllele().

Referenced by Vole_Base::UnsetDirectFlag().

UnsetGeneticFlag()

void GeneticMaterial::UnsetGeneticFlag

(

)

Definition at line 178 of file GeneticMaterial.cpp.

                                       {
    SetAllele(0,0,0);
}

References SetAllele().

Referenced by Vole_Base::UnsetGeneticFlag().

Member Data Documentation

Chromosome

uint32 GeneticMaterial::Chromosome[6]

protected

Definition at line 97 of file GeneticMaterial.h.

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

---

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

• C:/Repo/ALMaSS_All/Vole/GeneticMaterial.h
• C:/Repo/ALMaSS_All/Vole/GeneticMaterial.cpp