/// <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; }