/// <summary>
/// Read parameters from json resource.
/// </summary>
private Genotype ReadParametersFromResource()
{
List <Exception> exceptions;
var simulations = FileFormat.ReadFromString <Simulations>(ReflectionUtilities.GetResourceAsString(nameOfStockResource),
out exceptions);
if (exceptions.Count > 0)
{
throw new Exception($"Invalid stock resource found. Name of resource: {nameOfStockResource}");
}
parameters = simulations.Children[0] as Genotype;
return(parameters);
}
/// <summary>
/// Default fibre diameter as a function of age, sex, time since shearing and fleece weight
/// </summary>
/// <param name="Params"></param>
/// <param name="iAgeDays"></param>
/// <param name="Repr"></param>
/// <param name="iFleeceDays"></param>
/// <param name="fGFW"></param>
/// <returns></returns>
static public double DefaultMicron(Genotype Params, int iAgeDays, GrazType.ReproType Repr, int iFleeceDays, double fGFW)
{
double fPotFleece;
if ((iFleeceDays > 0) && (fGFW > 0.0))
{
fPotFleece = DefaultFleece(Params, iAgeDays, Repr, iFleeceDays);
return(Params.MaxFleeceDiam * Math.Pow(fGFW / fPotFleece, Params.WoolC[13]));
}
else
{
return(Params.MaxFleeceDiam);
}
}
/// <summary>Construct an animal parameter set from a source parameters set.</summary>
/// <param name="srcSet">The source parameter set.</param>
public Genotype(Genotype srcSet)
{
//create a new array
for (int i = 0; i < ConceiveSigs.Length; i++)
{
ConceiveSigs[i] = new double[2];
}
CopyParams(srcSet);
if (srcSet != null)
{
Initialise();
}
}
/// <summary>
/// Read parameters from json resource.
/// </summary>
private Genotype ReadParametersFromResource()
{
Simulations simulations;
try
{
simulations = FileFormat.ReadFromString <Simulations>(ReflectionUtilities.GetResourceAsString(nameOfStockResource),
e => throw e, false);
}
catch (Exception err)
{
throw new Exception($"Invalid stock resource found. Name of resource: {nameOfStockResource}", err);
}
parameters = simulations.Children[0] as Genotype;
return(parameters);
}
/// <summary>
/// Set parentage of a genotype.
/// </summary>
/// <param name="parentBreed">The parent breed.</param>
/// <param name="proportion">The proportion of the parent.</param>
private void SetParentage(Genotype parentBreed, double proportion)
{
for (int k = 0; k <= parentBreed.FParentage.Length - 1; k++)
{
int i = 0;
while ((i < FParentage.Length) && (parentBreed.FParentage[k].sBaseBreed != FParentage[i].sBaseBreed))
{
i++;
}
if (i == FParentage.Length)
{
Array.Resize(ref FParentage, i + 1);
FParentage[i].sBaseBreed = parentBreed.FParentage[k].sBaseBreed;
FParentage[i].fPropn = 0.0;
}
FParentage[i].fPropn = FParentage[i].fPropn + proportion * parentBreed.FParentage[k].fPropn;
}
}
/// <summary>
/// Default fleece weight as a function of age, sex and time since shearing
/// </summary>
/// <param name="Params"></param>
/// <param name="iAgeDays"></param>
/// <param name="Repr"></param>
/// <param name="iFleeceDays"></param>
/// <returns></returns>
static public double DefaultFleece(Genotype Params,
int iAgeDays,
GrazType.ReproType Repr,
int iFleeceDays)
{
double Result;
double fMeanAgeFactor;
iFleeceDays = Math.Min(iFleeceDays, iAgeDays);
if ((Params.Animal == GrazType.AnimalType.Sheep) && (iFleeceDays > 0))
{
fMeanAgeFactor = 1.0 - (1.0 - Params.WoolC[5])
* (Math.Exp(-Params.WoolC[12] * (iAgeDays - iFleeceDays)) - Math.Exp(-Params.WoolC[12] * iAgeDays))
/ (Params.WoolC[12] * iFleeceDays);
Result = Params.FleeceRatio * Params.SexStdRefWt(Repr) * fMeanAgeFactor * iFleeceDays / 365.0;
}
else
{
Result = 0.0;
}
return(Result);
}
/// <summary>
/// Create a genotype cross.
/// </summary>
/// <param name="nameOfNewGenotype">Name of new genotype. Can be null.</param>
/// <param name="damBreedName">Dam breed name.</param>
/// <param name="damProportion">Proportion dam.</param>
/// <param name="sireBreedName">Sire breed name.</param>
/// <param name="sireProportion">Proportion sire.</param>
private Genotype CreateGenotypeCross(string nameOfNewGenotype,
string damBreedName, double damProportion,
string sireBreedName, double sireProportion)
{
if (damProportion + sireProportion != 1)
{
throw new Exception("When creating a cross breed the total proportions must be equal to one.");
}
var damBreed = stock.Genotypes.Get(damBreedName);
damBreed.Initialise();
var sireBreed = stock.Genotypes.Get(sireBreedName);
sireBreed.Initialise();
Genotype newGenotype = new Genotype(nameOfNewGenotype, damBreed, sireBreed, damProportion, sireProportion);
// Add the new genotype into our list.
stock.Genotypes.Add(newGenotype);
return(newGenotype);
}
/// <summary>Constructor</summary>
/// <param name="animalParameterSet"></param>
public GenotypeWrapper(Genotype animalParameterSet)
{
parameters = animalParameterSet;
Name = animalParameterSet.Name;
AnimalType = animalParameterSet.Animal.ToString();
}
/// <summary>
/// Constructor for a breed cross. Blend two animal parameter sets.
/// </summary>
/// <param name="nameOfNewGenotype">The name given to the new parameter set.</param>
/// <param name="damBreed">The dam breed.</param>
/// <param name="sireBreed">The sire breed.</param>
/// <param name="damProportion">The dam proportion.</param>
/// <param name="sireProportion">The sire proportion.</param>
/// <returns></returns>
public Genotype(string nameOfNewGenotype, Genotype damBreed, Genotype sireBreed, double damProportion, double sireProportion)
{
sEditor = damBreed.sEditor;
sEditDate = damBreed.sEditDate;
Animal = damBreed.Animal;
bDairyBreed = damBreed.bDairyBreed;
MaxYoung = damBreed.MaxYoung;
OvulationPeriod = damBreed.OvulationPeriod;
Puberty = damBreed.Puberty;
BreedSRW = damProportion * damBreed.BreedSRW + sireProportion * sireBreed.BreedSRW;
PotFleeceWt = damProportion * damBreed.PotFleeceWt + sireProportion * sireBreed.PotFleeceWt;
FDairyIntakePeak = damProportion * damBreed.FDairyIntakePeak + sireProportion * sireBreed.FDairyIntakePeak;
FleeceRatio = damProportion * damBreed.FleeceRatio + sireProportion * sireBreed.FleeceRatio;
MaxFleeceDiam = damProportion * damBreed.MaxFleeceDiam + sireProportion * sireBreed.MaxFleeceDiam;
PeakMilk = damProportion * damBreed.PeakMilk + sireProportion * sireBreed.PeakMilk;
for (int idx = 1; idx <= 2; idx++)
{
MortRate[idx] = damProportion * damBreed.MortRate[idx] + sireProportion * sireBreed.MortRate[idx];
}
for (int idx = 1; idx <= 2; idx++)
{
MortAge[idx] = damProportion * damBreed.MortAge[idx] + sireProportion * sireBreed.MortAge[idx];
}
MortIntensity = damProportion * damBreed.MortIntensity + sireProportion * sireBreed.MortIntensity;
MortCondConst = damProportion * damBreed.MortCondConst + sireProportion * sireBreed.MortCondConst;
MortWtDiff = damProportion * damBreed.MortWtDiff + sireProportion * sireBreed.MortWtDiff;
for (int idx = 0; idx < SRWScalars.Length; idx++)
{
SRWScalars[idx] = damProportion * damBreed.SRWScalars[idx] + sireProportion * sireBreed.SRWScalars[idx];
}
for (int idx = 1; idx < GrowthC.Length; idx++)
{
GrowthC[idx] = damProportion * damBreed.GrowthC[idx] + sireProportion * sireBreed.GrowthC[idx];
}
for (int idx = 1; idx < IntakeC.Length; idx++)
{
IntakeC[idx] = damProportion * damBreed.IntakeC[idx] + sireProportion * sireBreed.IntakeC[idx];
}
for (int idx = 0; idx < IntakeLactC.Length; idx++)
{
IntakeLactC[idx] = damProportion * damBreed.IntakeLactC[idx] + sireProportion * sireBreed.IntakeLactC[idx];
}
for (int idx = 1; idx < GrazeC.Length; idx++)
{
GrazeC[idx] = damProportion * damBreed.GrazeC[idx] + sireProportion * sireBreed.GrazeC[idx];
}
for (int idx = 1; idx < EfficC.Length; idx++)
{
EfficC[idx] = damProportion * damBreed.EfficC[idx] + sireProportion * sireBreed.EfficC[idx];
}
for (int idx = 1; idx < MaintC.Length; idx++)
{
MaintC[idx] = damProportion * damBreed.MaintC[idx] + sireProportion * sireBreed.MaintC[idx];
}
for (int idx = 1; idx < DgProtC.Length; idx++)
{
DgProtC[idx] = damProportion * damBreed.DgProtC[idx] + sireProportion * sireBreed.DgProtC[idx];
}
for (int idx = 1; idx < ProtC.Length; idx++)
{
ProtC[idx] = damProportion * damBreed.ProtC[idx] + sireProportion * sireBreed.ProtC[idx];
}
for (int idx = 1; idx < PregC.Length; idx++)
{
PregC[idx] = damProportion * damBreed.PregC[idx] + sireProportion * sireBreed.PregC[idx];
}
for (int idx = 1; idx < PregScale.Length; idx++)
{
PregScale[idx] = damProportion * damBreed.PregScale[idx] + sireProportion * sireBreed.PregScale[idx];
}
for (int idx = 1; idx < BirthWtScale.Length; idx++)
{
BirthWtScale[idx] = damProportion * damBreed.BirthWtScale[idx] + sireProportion * sireBreed.BirthWtScale[idx];
}
for (int idx = 1; idx < PeakLactC.Length; idx++)
{
PeakLactC[idx] = damProportion * damBreed.PeakLactC[idx] + sireProportion * sireBreed.PeakLactC[idx];
}
for (int idx = 1; idx < LactC.Length; idx++)
{
LactC[idx] = damProportion * damBreed.LactC[idx] + sireProportion * sireBreed.LactC[idx];
}
for (int idx = 1; idx < WoolC.Length; idx++)
{
WoolC[idx] = damProportion * damBreed.WoolC[idx] + sireProportion * sireBreed.WoolC[idx];
}
for (int idx = 1; idx < ChillC.Length; idx++)
{
ChillC[idx] = damProportion * damBreed.ChillC[idx] + sireProportion * sireBreed.ChillC[idx];
}
for (int idx = 1; idx < GainC.Length; idx++)
{
GainC[idx] = damProportion * damBreed.GainC[idx] + sireProportion * sireBreed.GainC[idx];
}
for (int idx = 1; idx < PhosC.Length; idx++)
{
PhosC[idx] = damProportion * damBreed.PhosC[idx] + sireProportion * sireBreed.PhosC[idx];
}
for (int idx = 1; idx < SulfC.Length; idx++)
{
SulfC[idx] = damProportion * damBreed.SulfC[idx] + sireProportion * sireBreed.SulfC[idx];
}
for (int idx = 1; idx < MethC.Length; idx++)
{
MethC[idx] = damProportion * damBreed.MethC[idx] + sireProportion * sireBreed.MethC[idx];
}
for (int idx = 1; idx < AshAlkC.Length; idx++)
{
AshAlkC[idx] = damProportion * damBreed.AshAlkC[idx] + sireProportion * sireBreed.AshAlkC[idx];
}
for (int idx = 1; idx < DayLengthConst.Length; idx++)
{
DayLengthConst[idx] = damProportion * damBreed.DayLengthConst[idx] + sireProportion * sireBreed.DayLengthConst[idx];
}
for (int idx = 0; idx < ToxaemiaSigs.Length; idx++)
{
ToxaemiaSigs[idx] = damProportion * damBreed.ToxaemiaSigs[idx] + sireProportion * sireBreed.ToxaemiaSigs[idx];
}
for (int idx = 0; idx < DystokiaSigs.Length; idx++)
{
DystokiaSigs[idx] = damProportion * damBreed.DystokiaSigs[idx] + sireProportion * sireBreed.DystokiaSigs[idx];
}
for (int idx = 0; idx < ExposureConsts.Length; idx++)
{
ExposureConsts[idx] = damProportion * damBreed.ExposureConsts[idx] + sireProportion * sireBreed.ExposureConsts[idx];
}
FertWtDiff = damProportion * damBreed.FertWtDiff + sireProportion * sireBreed.FertWtDiff;
SelfWeanPropn = damProportion * damBreed.SelfWeanPropn + sireProportion * sireBreed.SelfWeanPropn;
for (int i = 0; i < ConceiveSigs.Length; i++)
{
ConceiveSigs[i] = new double[2];
}
for (int idx = 1; idx < ConceiveSigs.Length; idx++)
{
for (int Jdx = 0; Jdx < ConceiveSigs[idx].Length; Jdx++)
{
ConceiveSigs[idx][Jdx] = damProportion * damBreed.ConceiveSigs[idx][Jdx] + sireProportion * sireBreed.ConceiveSigs[idx][Jdx];
}
}
for (int idx = 0; idx <= FParentage.Length - 1; idx++)
{
FParentage[idx].fPropn = 0.0;
}
SetParentage(damBreed, damProportion);
SetParentage(sireBreed, sireProportion);
if (!string.IsNullOrEmpty(nameOfNewGenotype))
{
Name = nameOfNewGenotype;
}
else if (FParentage.Length == 1)
{
Name = FParentage[0].sBaseBreed;
}
else if (FParentage.Length > 1)
{
int iDecPlaces = 0;
for (int Idx = 0; Idx <= FParentage.Length - 1; Idx++)
{
if ((FParentage[Idx].fPropn > 0.0005) && (FParentage[Idx].fPropn <= 0.05))
{
iDecPlaces = 1;
}
}
Name = "";
for (int Idx = 0; Idx <= FParentage.Length - 1; Idx++)
{
if (FParentage[Idx].fPropn > 0.0005)
{
if (Name != "")
{
Name = Name + ", ";
}
Name = Name + FParentage[Idx].sBaseBreed + " "
+ String.Format("{0:0." + new String('0', iDecPlaces) + "}", 100.0 * FParentage[Idx].fPropn) + "%";
}
}
}
}
/// <summary>
/// Copies all the animal parameters
/// </summary>
/// <param name="srcSet">Parameter set to copy from.</param>
private void CopyParams(Genotype srcSet)
{
int Idx;
Name = srcSet.Name;
DeriveParams();
Genotype prmSet = (Genotype)srcSet;
if (prmSet != null)
{
BreedSRW = prmSet.BreedSRW;
PotFleeceWt = prmSet.PotFleeceWt;
FDairyIntakePeak = prmSet.FDairyIntakePeak;
Array.Resize(ref FParentage, prmSet.FParentage.Length);
for (Idx = 0; Idx <= FParentage.Length - 1; Idx++)
{
FParentage[Idx] = prmSet.FParentage[Idx];
}
sEditor = prmSet.sEditor;
sEditDate = prmSet.sEditDate;
Animal = prmSet.Animal;
MaxYoung = prmSet.MaxYoung;
Array.Copy(prmSet.SRWScalars, SRWScalars, prmSet.SRWScalars.Length);
MaxFleeceDiam = prmSet.MaxFleeceDiam;
bDairyBreed = prmSet.bDairyBreed;
PeakMilk = prmSet.PeakMilk;
Array.Copy(prmSet.MortRate, MortRate, prmSet.MortRate.Length);
Array.Copy(prmSet.MortAge, MortAge, prmSet.MortAge.Length);
MortIntensity = prmSet.MortIntensity;
MortCondConst = prmSet.MortCondConst;
MortWtDiff = prmSet.MortWtDiff;
Array.Copy(prmSet.GrowthC, GrowthC, prmSet.GrowthC.Length);
Array.Copy(prmSet.IntakeC, IntakeC, prmSet.IntakeC.Length);
Array.Copy(prmSet.IntakeLactC, IntakeLactC, prmSet.IntakeLactC.Length);
Array.Copy(prmSet.GrazeC, GrazeC, prmSet.GrazeC.Length);
Array.Copy(prmSet.EfficC, EfficC, prmSet.EfficC.Length);
Array.Copy(prmSet.MaintC, MaintC, prmSet.MaintC.Length);
Array.Copy(prmSet.DgProtC, DgProtC, prmSet.DgProtC.Length);
Array.Copy(prmSet.ProtC, ProtC, prmSet.ProtC.Length);
Array.Copy(prmSet.PregC, PregC, prmSet.PregC.Length);
Array.Copy(prmSet.PregScale, PregScale, prmSet.PregScale.Length);
Array.Copy(prmSet.BirthWtScale, BirthWtScale, prmSet.BirthWtScale.Length);
Array.Copy(prmSet.PeakLactC, PeakLactC, prmSet.PeakLactC.Length);
Array.Copy(prmSet.LactC, LactC, prmSet.LactC.Length);
Array.Copy(prmSet.WoolC, WoolC, prmSet.WoolC.Length);
Array.Copy(prmSet.ChillC, ChillC, prmSet.ChillC.Length);
Array.Copy(prmSet.GainC, GainC, prmSet.GainC.Length);
Array.Copy(prmSet.PhosC, PhosC, prmSet.PhosC.Length);
Array.Copy(prmSet.SulfC, SulfC, prmSet.SulfC.Length);
Array.Copy(prmSet.MethC, MethC, prmSet.MethC.Length);
Array.Copy(prmSet.AshAlkC, AshAlkC, prmSet.AshAlkC.Length);
OvulationPeriod = prmSet.OvulationPeriod;
Array.Copy(prmSet.Puberty, Puberty, prmSet.Puberty.Length);
Array.Copy(prmSet.DayLengthConst, DayLengthConst, prmSet.DayLengthConst.Length);
for (int i = 0; i < prmSet.ConceiveSigs.Length; i++)
{
Array.Copy(prmSet.ConceiveSigs[i], ConceiveSigs[i], prmSet.ConceiveSigs[i].Length);
}
FertWtDiff = prmSet.FertWtDiff;
Array.Copy(prmSet.ToxaemiaSigs, ToxaemiaSigs, prmSet.ToxaemiaSigs.Length);
Array.Copy(prmSet.DystokiaSigs, DystokiaSigs, prmSet.DystokiaSigs.Length);
Array.Copy(prmSet.ExposureConsts, ExposureConsts, prmSet.ExposureConsts.Length);
SelfWeanPropn = prmSet.SelfWeanPropn;
}
}
/// <summary>Set the user specified genotypes.</summary>
/// <param name="animalParameterSet">The user specified animal parameter set.</param>
public void Add(Genotype animalParameterSet)
{
Add(new GenotypeWrapper(animalParameterSet));
}
