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>
/// <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="costFunction">the cost function to use</param>
public SmithWatermanGotoh(AbstractSubstitutionCost costFunction)
: base(new AffineGapRange5To0Multiplier1(), costFunction, affineGapWindowSize)
{
}
public SmithWatermanGotoh(AbstractAffineGapCost gapCostFunction, AbstractSubstitutionCost costFunction) : base(gapCostFunction, costFunction, 0x7fffffff)
{
}
/// <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="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)
{
}
public SmithWaterman(double costG, AbstractSubstitutionCost costFunction)
{
GapCost = costG;
DCostFunction = costFunction;
}
public SmithWaterman(AbstractSubstitutionCost costFunction) : this(DefaultGapCost, costFunction)
{
}
public NeedlemanWunch(double costG, AbstractSubstitutionCost costFunction)
{
this.estimatedTimingConstant = 0.00018420000560581684;
this.gapCost = costG;
this.dCostFunction = costFunction;
}
public NeedlemanWunch(AbstractSubstitutionCost costFunction) : this(2.0, costFunction)
{
}
public SmithWaterman(double costG, AbstractSubstitutionCost costFunction)
{
this.gapCost = costG;
this.dCostFunction = costFunction;
}
public SmithWaterman(AbstractSubstitutionCost costFunction) : this(0.5, costFunction)
{
}
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;
}
