public void CanSample()
{
var d = new Poisson(0.3);
d.Sample();
}
/// <summary>
/// Run example
/// </summary>
/// <a href="http://en.wikipedia.org/wiki/Poisson_distribution">Poisson distribution</a>
public void Run()
{
// 1. Initialize the new instance of the Poisson distribution class with parameter Lambda = 1
var poisson = new Poisson(1);
Console.WriteLine(@"1. Initialize the new instance of the Poisson distribution class with parameter Lambda = {0}", poisson.Lambda);
Console.WriteLine();
// 2. Distributuion properties:
Console.WriteLine(@"2. {0} distributuion properties:", poisson);
// Cumulative distribution function
Console.WriteLine(@"{0} - Сumulative distribution at location '3'", poisson.CumulativeDistribution(3).ToString(" #0.00000;-#0.00000"));
// Probability density
Console.WriteLine(@"{0} - Probability mass at location '3'", poisson.Probability(3).ToString(" #0.00000;-#0.00000"));
// Log probability density
Console.WriteLine(@"{0} - Log probability mass at location '3'", poisson.ProbabilityLn(3).ToString(" #0.00000;-#0.00000"));
// Entropy
Console.WriteLine(@"{0} - Entropy", poisson.Entropy.ToString(" #0.00000;-#0.00000"));
// Largest element in the domain
Console.WriteLine(@"{0} - Largest element in the domain", poisson.Maximum.ToString(" #0.00000;-#0.00000"));
// Smallest element in the domain
Console.WriteLine(@"{0} - Smallest element in the domain", poisson.Minimum.ToString(" #0.00000;-#0.00000"));
// Mean
Console.WriteLine(@"{0} - Mean", poisson.Mean.ToString(" #0.00000;-#0.00000"));
// Median
Console.WriteLine(@"{0} - Median", poisson.Median.ToString(" #0.00000;-#0.00000"));
// Mode
Console.WriteLine(@"{0} - Mode", poisson.Mode.ToString(" #0.00000;-#0.00000"));
// Variance
Console.WriteLine(@"{0} - Variance", poisson.Variance.ToString(" #0.00000;-#0.00000"));
// Standard deviation
Console.WriteLine(@"{0} - Standard deviation", poisson.StdDev.ToString(" #0.00000;-#0.00000"));
// Skewness
Console.WriteLine(@"{0} - Skewness", poisson.Skewness.ToString(" #0.00000;-#0.00000"));
Console.WriteLine();
// 3. Generate 10 samples of the Poisson distribution
Console.WriteLine(@"3. Generate 10 samples of the Poisson distribution");
for (var i = 0; i < 10; i++)
{
Console.Write(poisson.Sample().ToString("N05") + @" ");
}
Console.WriteLine();
Console.WriteLine();
// 4. Generate 100000 samples of the Poisson(1) distribution and display histogram
Console.WriteLine(@"4. Generate 100000 samples of the Poisson(1) distribution and display histogram");
var data = new double[100000];
for (var i = 0; i < data.Length; i++)
{
data[i] = poisson.Sample();
}
ConsoleHelper.DisplayHistogram(data);
Console.WriteLine();
// 5. Generate 100000 samples of the Poisson(4) distribution and display histogram
Console.WriteLine(@"5. Generate 100000 samples of the Poisson(4) distribution and display histogram");
poisson.Lambda = 4;
for (var i = 0; i < data.Length; i++)
{
data[i] = poisson.Sample();
}
ConsoleHelper.DisplayHistogram(data);
Console.WriteLine();
// 6. Generate 100000 samples of the Poisson(10) distribution and display histogram
Console.WriteLine(@"6. Generate 100000 samples of the Poisson(10) distribution and display histogram");
poisson.Lambda = 10;
for (var i = 0; i < data.Length; i++)
{
data[i] = poisson.Sample();
}
ConsoleHelper.DisplayHistogram(data);
}
public static void GenerateShortReadsFromDonorGenome(string donorGenomeFile, string readsFile, int readLength, double coverage, long limit)
{
Poisson poisson = new Poisson(coverage / readLength) { RandomSource = new MersenneTwister() };
using (var donorFile = File.OpenRead(donorGenomeFile))
using (var file = File.Open(readsFile, FileMode.Create))
{
var writer = new BinaryWriter(file);
var reader = new BinaryReader(donorFile);
writer.Write(readLength);
for (long donorIndex = 0, numReads = 0; donorIndex <= donorFile.Length - readLength && numReads < limit; donorIndex++)
{
var numReadsAtPos = poisson.Sample();
numReads += numReadsAtPos;
if (numReadsAtPos > 0)
{
donorFile.Seek(donorIndex, SeekOrigin.Begin);
var chars = reader.ReadChars(readLength);
string read = new string(chars);
DnaSequence dna = DnaSequence.CreateGenomeFromString(read);
for (int i = 0; i < numReadsAtPos; i++)
writer.Write(dna.Bytes);
}
}
}
}
