/// <summary> /// constructor /// </summary> /// <param name="gapCostFunction">the gap cost function</param> /// <param name="affineGapWindowSize">the size of the affine gap window to use</param> public SmithWatermanGotohWindowedAffine(AbstractAffineGapCost gapCostFunction, int affineGapWindowSize) : this(gapCostFunction, new SubCostRange5ToMinus3(), affineGapWindowSize) {}
/// <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="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> /// <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> public SmithWatermanGotoh(AbstractAffineGapCost gapCostFunction) : base(gapCostFunction, new SubCostRange5ToMinus3(), affineGapWindowSize) {}