public void DefineChromosomePositions(double dBetweenMarkers = 0.5, long numberOfLocii = 11)
{
List <int> numberOfLoci = null;
//go over all chromosome and define the position according to each marker dBetweenMarkers=0.5 . ex: 0 , 0.5, 1.5 ...
//each chromosome begin at 0 cm the position of loci
if (OrganismType.Random == this.type)
{
numberOfLoci = new List <int>();
foreach (Dictionary <int, string> dic in rawGeneticData)
{
numberOfLoci.Add(Convert.ToInt32(dic[2]));
}
}
int idLocus = 0;
for (int iChr = 0; iChr < nChr; iChr++)
{
if (OrganismType.Random == this.type)
{
numberOfLocii = numberOfLoci[iChr];
}
double posPrev = -0.5;
for (int jOnChr = 0; jOnChr < numberOfLocii; jOnChr++)
{
if (posPrev < go.Chromosome[iChr].LenGenetcM)
{
Position pos = new Position();
pos.Chromosome = go.Chromosome[iChr];
pos.PositionChrGenetic = posPrev;
pos.PositionChrGenetic += dBetweenMarkers;
posPrev = pos.PositionChrGenetic;
Locus locus = new Locus(jOnChr, pos);
idLocus++;
locus.Id = idLocus;
go.Chromosome[iChr].Locus.Add(locus);
}
}
}
}
/// <summary>
/// Create the genetic organism object via teh input data
/// </summary>
/// <param name="data"></param>
private void buildGenomeOrganizm(List <Dictionary <int, string> > data)
{
var db = DatabaseProvider.GetDatabase();
db.GenomeOrganization = new GenomeOrganization();
db.GenomeOrganization.Chromosome = new List <Chromosome>();
int markerId = 0;
var chrDic = new Dictionary <int, List <Locus> >();
foreach (Dictionary <int, string> row in data)
{
//get the chr number
string chrNum = row[1].Substring(2);
int chrNumber = Convert.ToInt32(chrNum);
//get the position of the marker
double genPosition = Convert.ToDouble(row[2]);
//set the position
Position p = new Position();
p.PositionChrGenetic = genPosition;
if (chrDic.ContainsKey(chrNumber))
{
//This is case we have the chromosome
List <Locus> markerList;
chrDic.TryGetValue(chrNumber, out markerList);
//same chromosome - as the first one from the list
p.Chromosome = markerList[0].Position.Chromosome;
Locus l = new Locus(markerId, p);
l.FullName = row[0];
markerList.Add(l);
markerId++;
//add to the current chr
}
else
{
List <Locus> markerList = new List <Locus>();
chrDic.Add(chrNumber, markerList);
p.Chromosome = new Chromosome();
p.Chromosome.Name = chrNumber.ToString();
Locus l = new Locus(markerId, p);
l.FullName = row[0];
markerList.Add(l);
//add new chromosome
markerId++;
}
}
foreach (KeyValuePair <int, List <Locus> > entry in chrDic)
{
Chromosome ch = new Chromosome();
ch.Id = entry.Key;
ch.Locus = entry.Value;
var maxChrLen = ch.Locus.Max(x => x.Position.PositionChrGenetic);
ch.LenGenetcM = maxChrLen;
db.GenomeOrganization.addChr(ch);
}
}
/// <summary>
/// This is method defines the location of the loci on the chromosome
/// </summary>
/// <param name="dBetweenMarkers_set"></param>
/// <param name="nMarkersGrouped"></param>
/// <param name="dMarkersGrouped"></param>
/// <param name="indexAnimal"></param>
public void DefineChromosomePositions(double dBetweenMarkers_set, long nMarkersGrouped, double dMarkersGrouped, int indexAnimal)
{
int index = 1;
double coorPrev = 0.0, d, coorStartOnCurrentChr = 0.0, dBetweenMarkers = 2.0;
long j, nMarkersMax, nOnChr = 11;
if (dBetweenMarkers_set > 0)
{
//distance between markers
dBetweenMarkers = dBetweenMarkers_set;
}
if (index == 0)
{
//amount of markers
nMarkersMax = nChr * nOnChr;
}
else
{
//amount of markers
nMarkersMax = nChr * (int)(500 / dBetweenMarkers);
}
for (int i = 0; i < nChr; i++)
{
if (index == 0)
{
d = go.Chromosome[i].LenGenetcM / (nOnChr - 1);
}
else
{
d = dBetweenMarkers;
nOnChr = (int)(go.Chromosome[i].LenGenetcM / d) + 1;
}
//Line 195 is this correct
if (go.Chromosome[i].Id > 1)
{
coorPrev = coorPrev + 1000 - d;
}
else
{
coorPrev = -d;
}
for (j = 0; j < nOnChr; j++)
{
Locus loci = new Locus();
//default location
loci.Position.Chromosome = go.Chromosome[i];
loci.Position.PositionChrGenetic = coorPrev + d;
if (j > 1 && j <= dMarkersGrouped)
{
loci.Position.PositionChrGenetic = coorPrev + dMarkersGrouped;
}
if (j == 1)
{
coorStartOnCurrentChr = loci.Position.PositionChrGenetic;
}
if (j == nOnChr)
{
loci.Position.PositionChrGenetic = coorStartOnCurrentChr + go.Chromosome[i].LenGenetcM;
}
//Line 215 not clear
// go.Chromosome[i]loci.Position.PositionChrGenetic - coorStartOnCurrentChr;
loci.Name = "loc_" + j;
loci.Id = i;
coorPrev = loci.Position.PositionChrGenetic;
go.Chromosome[i].Locus.Add(loci);
}
}
}
