Initializes a new instance of the MUMmerAligner class. Constructor for all the pairwise aligner (NeedlemanWunsch, SmithWaterman, Overlap). Sets default similarity matrix and gap penalty. Users will typically reset these using parameters specific to their particular sequences and needs.

Gets or sets a value indicating whether Ambiguous matches are allowed or not.

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

Gets the description of the Aligner. Intended to be filled in by classes deriving from DynamicProgrammingPairwiseAligner class with the exact details of the Alignment algorithm.

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 or sets the length of MUM.

Gets or sets a value indicating whether MaxMatch option should be enabled or not. If this property is set to true, then mums are generated irrespective of uniqueness in query and reference sequences. By default this property is set to false, indicating that matches are unique in reference sequence only.

Gets the list of MUMs after applying Longest Increasing Subsequence algorithm to order and merge MUMs, for each query sequence.

Gets the name of the Aligner. Intended to be filled in by classes deriving from DynamicProgrammingPairwiseAligner class with the exact name of the Alignment algorithm.

Gets or sets the pair wise aligner which will be executed by end of Mummer.

Gets or sets similarity matrix for use in alignment algorithms.

Gets or sets a value indicating whether the Boolean value indicating whether MUMs generated are to be stored or not. Set to false by default. Note: Storing MUMs incur memory overhead.

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 reference sequence with query sequences using the affine gap model (gap open and gap extension penalties) and returns the best alignment found.

Align the list of input sequences using a simple constant penalty gap model.

Align the reference sequence and query sequences using an affine gap model.

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.