Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm.

Namespace:  BioSharp.Core.Bio.Alignment
Assembly:  BioSharp.Core (in BioSharp.Core.dll) Version: 0.1.3191.26120 (0.1.0.0)

Syntax

C#
public NeedlemanWunsch(
	double match,
	double replace,
	double insert,
	double delete,
	double gapExtend,
	SubstitutionMatrix subMat
)

Parameters

match
Type: System..::.Double
This gives the costs for a match operation. It is only used, if there is no entry for a certain match of two symbols in the substitution matrix (default value).
replace
Type: System..::.Double
This is like the match parameter just the default, if there is no entry in the substitution matrix object.
insert
Type: System..::.Double
The costs of a single insert operation.
delete
Type: System..::.Double
The expenses of a single delete operation.
gapExtend
Type: System..::.Double
The expenses of an extension of a existing gap (that is a previous insert or delete. If the costs for insert and delete are equal and also equal to gapExtend, no affine gap penalties will be used, which saves a significant amount of memory.
subMat
Type: BioSharp.Core.Bio.Alignment..::.SubstitutionMatrix
The substitution matrix object which gives the costs for matches and replaces.

Remarks

The alphabet of sequences to be aligned will be taken from the given substitution matrix.

See Also