/// <summary>
/// Initializes a new instance of the <see cref="SmithWatermanGotohWindowedAffine"/> class with the specified parameters.
/// </summary>
/// <param name="gapCostFunction">The gap cost function to use.</param>
/// <param name="costFunction">The substitution cost function to use.</param>
/// <param name="affineGapWindowSize">Specifies the affinity gap window size.</param>
public SmithWatermanGotohWindowedAffine(AbstractAffineGapCost gapCostFunction, AbstractSubstitutionCost costFunction, int affineGapWindowSize)
{
this.estimatedTimingConstant = 4.5000000682193786E-05;
this.gGapFunction = gapCostFunction;
this.dCostFunction = costFunction;
this.windowSize = affineGapWindowSize;
}
/// <summary>
/// Initializes a new instance of the <see cref="NeedlemanWunch"/> class, using the parameters specified.
/// </summary>
/// <param name="costG">The gap cost value.</param>
/// <param name="costFunction">The substitution cost function to use.</param>
public NeedlemanWunch(double costG, AbstractSubstitutionCost costFunction)
{
this.estimatedTimingConstant = 0.00018420000560581684;
this.gapCost = costG;
this.dCostFunction = costFunction;
}
/// <summary>
/// Initializes a new instance of the <see cref="NeedlemanWunch"/> class, using the substitution cost function specified.
/// </summary>
/// <param name="costFunction">The substitution cost function to use.</param>
public NeedlemanWunch(AbstractSubstitutionCost costFunction)
: this(2.0, costFunction)
{
}
/// <summary>
/// Initializes a new instance of the <see cref="SmithWaterman"/> class with the specified gap cost and cost function
/// </summary>
/// <param name="costG">The gap cost.</param>
/// <param name="costFunction">The cost function to use.</param>
public SmithWaterman(double costG, AbstractSubstitutionCost costFunction)
{
this.gapCost = costG;
this.dCostFunction = costFunction;
}
/// <summary>
/// Initializes a new instance of the <see cref="SmithWaterman"/> class, using the cost function specified.
/// </summary>
/// <param name="costFunction">The cost function to use.</param>
public SmithWaterman(AbstractSubstitutionCost costFunction)
: this(0.5, costFunction)
{
}
/// <summary>
/// Initializes a new instance of the <see cref="SmithWatermanGotohWindowedAffine"/> class with the specified parameters.
/// </summary>
/// <param name="affineGapWindowSize">The affinity gap window size.</param>
/// <param name="costFunction">The substitution cost function to use.</param>
public SmithWatermanGotohWindowedAffine(AbstractSubstitutionCost costFunction, int affineGapWindowSize)
: this(new AffineGapRange5To0Multiplier1(), costFunction, affineGapWindowSize)
{
}
/// <summary>
/// Initializes a new instance of the <see cref="SmithWatermanGotohWindowedAffine"/> class with the specified parameters.
/// </summary>
/// <param name="gapCostFunction">The gap cost function to use.</param>
/// <param name="costFunction">The substitution cost function to use.</param>
public SmithWatermanGotohWindowedAffine(AbstractAffineGapCost gapCostFunction, AbstractSubstitutionCost costFunction)
: this(gapCostFunction, costFunction, 100)
{
}
