/// <summary>
/// constructor
/// </summary>
/// <param name="gapCostFunction">the gap cost function</param>
/// <param name="costFunction">the cost function to use</param>
/// <param name="affineGapWindowSize">the size of the affine gap window to use</param>
public SmithWatermanGotohWindowedAffine(AbstractAffineGapCost gapCostFunction, AbstractSubstitutionCost costFunction,
int affineGapWindowSize)
{
gGapFunction = gapCostFunction;
dCostFunction = costFunction;
windowSize = affineGapWindowSize;
}
public SmithWatermanGotohWindowedAffine(AbstractAffineGapCost gapCostFunction, AbstractSubstitutionCost costFunction, int affineGapWindowSize)
{
this.estimatedTimingConstant = 4.5000000682193786E-05;
this.gGapFunction = gapCostFunction;
this.dCostFunction = costFunction;
this.windowSize = affineGapWindowSize;
}
/// <summary>
/// constructor
/// </summary>
/// <param name="gapCostFunction">the gap cost function</param>
/// <param name="costFunction">the cost function to use</param>
public SmithWatermanGotoh(AbstractAffineGapCost gapCostFunction, AbstractSubstitutionCost costFunction)
: base(gapCostFunction, costFunction, affineGapWindowSize)
{
}
/// <summary>
/// constructor
/// </summary>
/// <param name="gapCostFunction">the gap cost function</param>
public SmithWatermanGotoh(AbstractAffineGapCost gapCostFunction)
: base(gapCostFunction, new SubCostRange5ToMinus3(), affineGapWindowSize)
{
}
public SmithWatermanGotoh(AbstractAffineGapCost gapCostFunction, AbstractSubstitutionCost costFunction) : base(gapCostFunction, costFunction, 0x7fffffff)
{
}
public SmithWatermanGotoh(AbstractAffineGapCost gapCostFunction) : base(gapCostFunction, new SubCostRange5ToMinus3(), 0x7fffffff)
{
}
/// <summary>
/// constructor
/// </summary>
/// <param name="gapCostFunction">the gap cost function</param>
public SmithWatermanGotohWindowedAffine(AbstractAffineGapCost gapCostFunction)
: this(gapCostFunction, new SubCostRange5ToMinus3(), defaultWindowSize)
{
}
/// <summary>
/// constructor
/// </summary>
/// <param name="gapCostFunction">the gap cost function</param>
/// <param name="costFunction">the cost function to use</param>
public SmithWatermanGotohWindowedAffine(AbstractAffineGapCost gapCostFunction, AbstractSubstitutionCost costFunction)
: this(gapCostFunction, costFunction, defaultWindowSize)
{
}
