/// <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="NeedlemanWunch"/> class, using the parameters specified. /// </summary> /// <param name="costG">The gap cost value.</param> /// <param name="costFunction">The substitution cost function to use.</param> public NeedlemanWunch(double costG, AbstractSubstitutionCost costFunction) { this.estimatedTimingConstant = 0.00018420000560581684; this.gapCost = costG; this.dCostFunction = costFunction; }
/// <summary> /// Initializes a new instance of the <see cref="NeedlemanWunch"/> class, using the substitution cost function specified. /// </summary> /// <param name="costFunction">The substitution cost function to use.</param> public NeedlemanWunch(AbstractSubstitutionCost costFunction) : this(2.0, costFunction) { }
/// <summary> /// Initializes a new instance of the <see cref="SmithWaterman"/> class with the specified gap cost and cost function /// </summary> /// <param name="costG">The gap cost.</param> /// <param name="costFunction">The cost function to use.</param> public SmithWaterman(double costG, AbstractSubstitutionCost costFunction) { this.gapCost = costG; this.dCostFunction = costFunction; }
/// <summary> /// Initializes a new instance of the <see cref="SmithWaterman"/> class, using the cost function specified. /// </summary> /// <param name="costFunction">The cost function to use.</param> public SmithWaterman(AbstractSubstitutionCost costFunction) : this(0.5, costFunction) { }
/// <summary> /// Initializes a new instance of the <see cref="SmithWatermanGotohWindowedAffine"/> class with the specified parameters. /// </summary> /// <param name="affineGapWindowSize">The affinity gap window size.</param> /// <param name="costFunction">The substitution cost function to use.</param> public SmithWatermanGotohWindowedAffine(AbstractSubstitutionCost costFunction, int affineGapWindowSize) : this(new AffineGapRange5To0Multiplier1(), costFunction, 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) { }