public async void ReadDataGenotype(string path)
{
Cursor.Current = Cursors.WaitCursor;
var rawData = await Task.Run(() => readFileGenData(path));
Cursor.Current = Cursors.Default;
List <Dictionary <int, string> > filteredData = new List <Dictionary <int, string> >();
// filter out the locus that are not in the both files
//iterate over all the raw data and filter only the ones that are both
if (rawData == null)
{
MessageBox.Show("Genotype file is not in correct format.\nExample:\nmarkerName\t010101010", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
List <Locus> LocusList = new List <Locus>();
db = DatabaseProvider.GetDatabase();
lock (db)
{
//in filterd data we removed the markers that are not found in the map
foreach (Dictionary <int, string> dic in rawData)
{
var locus = findLocus(db.GenomeOrganization.Chromosome, dic[0]);
if (locus != null)
{
filteredData.Add(dic);
LocusList.Add(locus);
}
}
if (filteredData.Count == 0)
{
MessageBox.Show("Cannot find any Genotypes in the Genetic Map,\nPlease reload the Genetic map with a relevant ogranism.", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
errorMessage = ErrorMessage.BadGeneticMap;
return;
}
var population = Regex.Split(filteredData[0][1], string.Empty);
if (population[0] == "")
{
population = population.Skip(1).ToArray();
}
if (population[population.Length - 1] == "")
{
Array.Resize(ref population, population.Length - 1);
}
if (db.SubData.Count == 0)
{
for (int i = 0; i < population.Length; i++)
{
//create classes at first use
DataIndividualsAndTraits individualsAndTraits = new DataIndividualsAndTraits();
db.SubData.Add(individualsAndTraits);
db.SubData[i].Genotype = new int[1, filteredData.Count];
db.SubData[i].GenotypeOk = new bool[1, filteredData.Count];
db.SubData[i].Locus = LocusList;
}
}
else
{
//already created just need to define the size
for (int i = 0; i < population.Length; i++)
{
db.SubData[i].Genotype = new int[1, filteredData.Count];
db.SubData[i].GenotypeOk = new bool[1, filteredData.Count];
db.SubData[i].Locus = LocusList;
}
}
int subIndex = 0;
foreach (Dictionary <int, string> dic in filteredData)
{
var pop = Regex.Split(dic[1], string.Empty);
if (pop[0] == "")
{
pop = pop.Skip(1).ToArray();
}
if (pop[pop.Length - 1] == "")
{
Array.Resize(ref pop, pop.Length - 1);
}
int offSetIndex = 0;
foreach (DataIndividualsAndTraits indiv in db.SubData)
{
if (pop[offSetIndex].Equals("-"))
{
//missing data - need to add another state to go with 1 is true ,0 false , -1 missing
indiv.Genotype[0, subIndex] = -1;
indiv.GenotypeOk[0, subIndex] = false;
}
else if (pop[offSetIndex].Equals("1"))
{
// data is 1
indiv.Genotype[0, subIndex] = 1;
indiv.GenotypeOk[0, subIndex] = true;
}
else if (pop[offSetIndex].Equals("0"))
{
//data is 0
indiv.Genotype[0, subIndex] = 0;
indiv.GenotypeOk[0, subIndex] = false;
}
offSetIndex = (offSetIndex + 1) % pop.Length;
}
subIndex = (subIndex + 1) % filteredData.Count;
}
}
}
public async void ReadDataPhenotype(string path)
{
Cursor.Current = Cursors.WaitCursor;
var rawData = await Task.Run(() => readPhenData(path));
Cursor.Current = Cursors.Default;
if (rawData == null)
{
MessageBox.Show("Phenotype file is not in correct format.\nExample:tc111\t0.25\t0.21...", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
//create list of traits
List <Trait> tempListTraits = new List <Trait>();
//get full names of the traits
for (int i = 0; i < rawData.Count; i++)
{
string traitName;
rawData[i].TryGetValue(0, out traitName);
Trait t = new Trait();
t.Id = i;
t.NameFull = traitName;
tempListTraits.Add(t);
}
string tempValue = null;
for (int i = 0; i < rawData.Count; i++)
{
//iterate and remove all the trait names since we dont need them anymore
rawData[i].Remove(0);
rawData[i].TryGetValue(rawData[i].Count, out tempValue);
if (tempValue.Equals(""))
{
rawData[i].Remove(rawData[i].Count);
}
}
db = DatabaseProvider.GetDatabase();
lock (db)
{
if (db.SubData.Count == 0)
{
for (int i = 0; i < rawData[0].Count; i++)
{
//assign all the individuals the same traits from file
DataIndividualsAndTraits individualsAndTraits = new DataIndividualsAndTraits();
individualsAndTraits.Trait = tempListTraits;
db.SubData.Add(individualsAndTraits);
}
}
else
{
for (int i = 0; i < rawData[0].Count; i++)
{
//data already exists thus need to add it the traits
db.SubData[i].Trait = tempListTraits;
}
}
//init all arrays
for (int j = 0; j < rawData[0].Count; j++)
{
db.SubData[j].TraitValueOk = new bool[1, rawData.Count];
db.SubData[j].TraitValue = new float[1, rawData.Count];
}
int traitCounter = 0;
int dicCounter = 1;
foreach (Dictionary <int, string> dic in rawData)
{
for (int i = 0; i < db.SubData.Count; i++)
{
string tempVal = dic[dicCounter];
if (tempVal.Equals("$") || tempVal.Equals(""))
{
//missing data
db.SubData[i].TraitValueOk[0, traitCounter] = false;
db.SubData[i].TraitValue[0, traitCounter] = 0;
}
else
{
db.SubData[i].TraitValueOk[0, traitCounter] = true;
float val = float.Parse(tempVal);
db.SubData[i].TraitValue[0, traitCounter] = val;
}
dicCounter++;
dicCounter = dicCounter % 117;
if (dicCounter == 0)
{
dicCounter = 1;
}
}
traitCounter++;
}
}
}
