/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chain">
/// Source sequence.
/// </param>
/// <param name="link">
/// Link of intervals in chain.
/// </param>
/// <returns>
/// AT skew value as <see cref="double"/>.
/// </returns>
public double Calculate(Chain chain, Link link)
{
DnaProcessor.CheckDnaAlphabet(chain.Alphabet);
var a = remotenessCalculator.Calculate(chain.GetOrCreateCongenericChain(new ValueString("A")), link);
var t = remotenessCalculator.Calculate(chain.GetOrCreateCongenericChain(new ValueString("T")), link);
return (int)(a + t) == 0 ? 0 : (a - t) / (a + t);
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chain">
/// Source sequence.
/// </param>
/// <param name="link">
/// Link of intervals in chain.
/// </param>
/// <returns>
/// G+C Ratio value as <see cref="double"/>.
/// </returns>
public double Calculate(Chain chain, Link link)
{
DnaProcessor.CheckDnaAlphabet(chain.Alphabet);
var g = remotenessCalculator.Calculate(chain.GetOrCreateCongenericChain(new ValueString("G")), link);
var c = remotenessCalculator.Calculate(chain.GetOrCreateCongenericChain(new ValueString("C")), link);
var l = remotenessCalculator.Calculate(chain, link);
return 100 * (g + c) / l;
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chain">
/// Source sequence.
/// </param>
/// <param name="link">
/// Link of intervals in chain.
/// </param>
/// <returns>
/// G+C skew value as <see cref="double"/>.
/// </returns>
public double Calculate(Chain chain, Link link)
{
DnaProcessor.CheckDnaAlphabet(chain.Alphabet);
var g = counter.Calculate(chain.GetOrCreateCongenericChain(new ValueString("G")), link);
var c = counter.Calculate(chain.GetOrCreateCongenericChain(new ValueString("C")), link);
var result = (g - c) / (g + c);
return result;
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chain">
/// Source sequence.
/// </param>
/// <param name="link">
/// Link of intervals in chain.
/// </param>
/// <returns>
/// G+C Ratio value as <see cref="double"/> .
/// </returns>
public double Calculate(Chain chain, Link link)
{
DnaProcessor.CheckDnaAlphabet(chain.Alphabet);
var g = remotenessCalculator.Calculate(chain.GetOrCreateCongenericChain(new ValueString("G")), link);
var c = remotenessCalculator.Calculate(chain.GetOrCreateCongenericChain(new ValueString("C")), link);
var a = remotenessCalculator.Calculate(chain.GetOrCreateCongenericChain(new ValueString("A")), link);
var t = remotenessCalculator.Calculate(chain.GetOrCreateCongenericChain(new ValueString("T")), link);
var result = (g + c) / (a + t);
return result;
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chain">
/// Source sequence.
/// </param>
/// <param name="link">
/// Link of intervals in chain.
/// </param>
/// <returns>
/// RY skew value as <see cref="double"/>.
/// </returns>
public double Calculate(Chain chain, Link link)
{
DnaProcessor.CheckDnaAlphabet(chain.Alphabet);
var g = counter.Calculate(chain.GetOrCreateCongenericChain(new ValueString("G")), link);
var c = counter.Calculate(chain.GetOrCreateCongenericChain(new ValueString("C")), link);
var a = counter.Calculate(chain.GetOrCreateCongenericChain(new ValueString("A")), link);
var t = counter.Calculate(chain.GetOrCreateCongenericChain(new ValueString("T")), link);
var l = counter.Calculate(chain, link);
var result = ((g + a) - (c + t)) / l;
return result;
}
