/// <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="SmithWatermanGotohWindowedAffine"/> class with the specified parameters.
/// </summary>
/// <param name="gapCostFunction">The gap cost function to use.</param>
/// <param name="affineGapWindowSize">Specifies the affinity gap window size.</param>
public SmithWatermanGotohWindowedAffine(AbstractAffineGapCost gapCostFunction, int affineGapWindowSize)
: this(gapCostFunction, new SubCostRange5ToMinus3(), 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)
{
}