/*Notes -
* DefineChromosomeLength - Should be run first to define the length since the next method assumes that the length was already defined (DefineChromosomePositions).
*
*/
#region Constructor
/// <summary>
/// The default nChr is 3 and the organism type is drosophila
/// </summary>
/// <param name="_nChr"></param>
/// <param name="_type"></param>
public DataGeneratorPresentor(int _nChr = 3, OrganismType _type = OrganismType.Drosophila)
{
go = new GenomeOrganization();
nChr = _nChr;
type = _type;
database = DatabaseProvider.GetDatabase();
database.GenomeOrganization = go;
}
/// <summary>
/// This method defines the length of the chromosomes
/// difine global parameters:
/// go=Genome organisation
/// nChr=number of chromosoms
/// </summary>
public void DefineChromosomeLength()
{
go.Chromosome = new List <Chromosome>();
switch (type)
{
case OrganismType.Drosophila:
go = genereateDrosophila(go, nChr);
break;
default:
go = randomOrganism(go, nChr);
break;
}
}
private GenomeOrganization genereateDrosophila(GenomeOrganization go, int nChr)
{
//see https://en.wikipedia.org/wiki/Drosophila_melanogaster
//we consider only siple case (like in human):
// diploid,
// first chromosome is X (male has only one, he has also Y),
// no recombination in males,
// three chromosomes: X, 2, 3 (short fouth is ignored)
//indeed, drosophyla can be triploid and tetraploid (with XXX and XXXX (may also 1 or more Y) for females; X and XX)
double coef = 1;
int drosophilaConst1 = 75, drosophilaConst2 = 107, drosophilaConst3 = 110;
Chromosome ch = new Chromosome
{
Name = "1",
LenGenetcM = drosophilaConst1 * coef,
BRecInFemales = true,
BGender = false
};
go.addChr(ch);
Chromosome ch1 = new Chromosome
{
Id = 1,
Name = "2",
LenGenetcM = drosophilaConst2 * coef,
BRecInFemales = true,
BGender = false
};
go.addChr(ch1);
Chromosome ch2 = new Chromosome
{
Id = 2,
Name = "3",
LenGenetcM = drosophilaConst3 * coef,
BRecInFemales = true,
BGender = false
};
go.addChr(ch2);
return(go);
}
private GenomeOrganization randomOrganism(GenomeOrganization go, int nChr)
{
double coef = 1;
List <int> chrLength = new List <int>();
foreach (Dictionary <int, string> dic in rawGeneticData)
{
chrLength.Add(Convert.ToInt32(dic[1]));
}
for (int i = 0; i < nChr; i++)
{
Chromosome ch = new Chromosome();
ch.Name = Convert.ToString(i);
ch.LenGenetcM = coef * chrLength[i];
go.addChr(ch);
}
return(go);
}
/// <summary>
/// This method defines the length of the chromosomes
/// </summary>
public void DefineChromosomeLength()
{
switch (type)
{
case OrganismType.Drosophila:
go = genereateDrosophila(go, nChr);
break;
case OrganismType.PseudoWheat:
go = generatePseudoWheat(go, nChr);
break;
default:
//error organisim is not supported
break;
}
}
private GenomeOrganization genereateDrosophila(GenomeOrganization go, int nChr)
{
double coef = 1;
int drosophilaConst1 = 75, drosophilaConst2 = 107, drosophilaConst3 = 110;
Chromosome ch = new Chromosome
{
Id = 0,
LenGenetcM = drosophilaConst1 * coef,
BRecInFemales = true,
BGender = true
};
go.Chromosome.Add(ch);
Chromosome ch1 = new Chromosome
{
Id = 1,
LenGenetcM = drosophilaConst2 * coef,
BRecInFemales = true,
BGender = true
};
go.Chromosome.Add(ch1);
Chromosome ch2 = new Chromosome
{
Id = 3,
LenGenetcM = drosophilaConst3 * coef,
BRecInFemales = true,
BGender = true
};
go.Chromosome.Add(ch2);
return(go);
}
private GenomeOrganization generatePseudoWheat(GenomeOrganization go, int nChr)
{
return(go);
}
/*Notes -
* DefineChromosomeLength - Should be run first to define the length since the next method assumes that the length was already defined (DefineChromosomePositions).
*
*/
//My First Commit
#region Constructor
public DataGeneratorController(int _nChr, OrganismType _type)
{
go = new GenomeOrganization();
nChr = _nChr;
type = _type;
}