Align aligns the set of input sequences using the affine gap model (gap open and gap extension penalties) and returns the best alignment found.

Align aligns the set of input sequences using the affine gap model (gap open and gap extension penalties) and returns the best alignment found.

Pairwise alignment of two sequences using an affine gap penalty. The various algorithms in derived classes (NeedlemanWunsch, SmithWaterman, and PairwiseOverlap) all use this general engine for alignment with an affine gap penalty.

AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty), and returns the best alignment found.

AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty), and returns the best alignment found.

Pairwise alignment of two sequences using a linear gap penalty. The various algorithms in derived classes (NeedlemanWunsch, SmithWaterman, and PairwiseOverlap) all use this general engine for alignment with a linear gap penalty.

This takes a specific starting location in the scoring matrix and generates an alignment from it using the traceback scores.

This is step (2) in the dynamic programming model - to fill in the scoring matrix and calculate the traceback entries. This is algorithm specific and so is left as an abstract method.

Determines whether the specified object is equal to the current object.

Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection.

Serves as the default hash function.

Gets the Type of the current instance.

This is step (1) in the dynamic programming model - to initialize the default values for the scoring matrix and traceback tables.

Creates a shallow copy of the current Object.

Returns a string that represents the current object.

This method is used to determine when the traceback step is complete. It is algorithm specific.