/// <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;
}
/// <summary>
/// constructor
/// </summary>
/// <param name="costFunction">the cost function to use</param>
/// <param name="affineGapWindowSize">the size of the affine gap window to use</param>
public SmithWatermanGotohWindowedAffine(AbstractSubstitutionCost costFunction, int affineGapWindowSize)
: this(new AffineGapRange5To0Multiplier1(), costFunction, affineGapWindowSize) {}
/// <summary>
/// constructor
/// </summary>
/// <param name="costFunction">the cost function to use</param>
public SmithWatermanGotoh(AbstractSubstitutionCost costFunction)
: base(new AffineGapRange5To0Multiplier1(), costFunction, affineGapWindowSize) {}
/// <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) {}
/// <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="costFunction">the cost function to use</param>
public NeedlemanWunch(AbstractSubstitutionCost costFunction) : this(defaultGapCost, costFunction) {}
/// <summary>
/// constructor
/// </summary>
/// <param name="costG">the cost of a gap</param>
/// <param name="costFunction">the cost function to use</param>
public NeedlemanWunch(double costG, AbstractSubstitutionCost costFunction) {
gapCost = costG;
dCostFunction = costFunction;
}
/// <summary>
/// constructor
/// </summary>
/// <param name="costFunction">the cost function to use</param>
public SmithWaterman(AbstractSubstitutionCost costFunction) : this(defaultGapCost, costFunction) {}
/// <summary>
/// constructor
/// </summary>
/// <param name="costG">the cost of a gap</param>
/// <param name="costFunction">the cost function to use</param>
public SmithWaterman(double costG, AbstractSubstitutionCost costFunction) {
gapCost = costG;
dCostFunction = costFunction;
}