Initializes a new instance of the PairwiseOverlapAligner class

Gets or sets the object that will be used to compute the alignment's consensus.

Gets the description of the pair-wise-Overlap algorithm used. This is a overridden property from the abstract parent. This property returns a simple description of what PairwiseOverlapAligner class implements.

Gets or sets gap extension penalty for use in alignment algorithms. Not used for alignments using a linear gap penalty. For alignments using an affine gap, this is the penalty to extend an existing gap. This is a negative number, for example GapExtensionCost = -2, not +2.

Gets or sets gap open penalty for use in alignment algorithms. For alignments using a linear gap penalty, this is the gap penalty. For alignments using an affine gap, this is the penalty to open a new gap. This is a negative number, for example GapOpenCost = -8, not +8.

Gets the name of the current Alignment algorithm used. This is a overridden property from the abstract parent. This property returns the Name of our algorithm i.e pair-wise-Overlap algorithm.

Gets or sets similarity matrix for use in alignment algorithms.

Aligns two sequences using the affine gap metric, a gap open penalty and a gap extension penalty. This method uses the existing gap open and extension penalties and similarity matrix. Set these using GapOpenCost, GapExtensionCost and SimilarityMatrix properties before calling this method.

Aligns two sequences using the affine gap metric, a gap open penalty and a gap extension penalty. This method uses the existing gap open and extension penalties and similarity matrix. Set these using GapOpenCost, GapExtensionCost and SimilarityMatrix properties before calling this method.

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.

Aligns two sequences using a linear gap parameter, using existing gap open cost and similarity matrix. Set these using GapOpenCost and SimilarityMatrix properties before calling this method.

Aligns two sequences using a linear gap parameter, using existing gap open cost and similarity matrix. Set these using GapOpenCost and SimilarityMatrix properties before calling this method.

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.

Creates the Affine aligner job

Creates the Simple aligner job

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.

Creates a shallow copy of the current Object.

Returns a string that represents the current object.

Validates input sequences and gap penalties. Checks that input sequences use the same alphabet. Checks that each symbol in the input sequences exists in the similarity matrix. Checks that gap penalties are less than or equal to 0. Throws exception if sequences fail these checks. Writes warning to ApplicationLog if gap penalty or penalties are positive.

First input sequence.

Similarity matrix for use in alignment algorithms.

Second input sequence.