| SmithWatermanAligner Class |
Implements the SmithWaterman algorithm for partial alignment.
See Chapter 2 in Biological Sequence Analysis; Durbin, Eddy, Krogh and Mitchison;
Cambridge Press; 1998.
Inheritance HierarchySystemObject
Bio.Algorithms.AlignmentPairwiseSequenceAligner
Bio.Algorithms.AlignmentSmithWatermanAligner
Bio.Algorithms.AlignmentPairwiseSequenceAligner
Bio.Algorithms.AlignmentSmithWatermanAligner
Namespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe SmithWatermanAligner type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | SmithWatermanAligner | Initializes a new instance of the SmithWatermanAligner class |
Properties| Name | Description | |
|---|---|---|
 | ConsensusResolver |
Gets or sets the object that will be used to compute the alignment's consensus.
(Inherited from PairwiseSequenceAligner.) |
| Description |
Gets the Description of the current Alignment algorithm used.
This is a overridden property from the abstract parent.
This property returns a simple description of what
SmithWatermanAligner class implements.
(Overrides PairwiseSequenceAlignerDescription.) |
| GapExtensionCost |
Gets or sets value of GapExtensionCost
The GapExtensionCost is the cost of extending an already existing gap.
This is only used in the affine gap model
(Inherited from PairwiseSequenceAligner.) |
| GapOpenCost |
Gets or sets value of GapOpenCost
The GapOpenCost is the cost of inserting a gap character into
a sequence.
(Inherited from PairwiseSequenceAligner.) |
| IncludeScoreTable |
True to include the score table and matrix as part of the output.
This is placed into the Metadata for the alignment. It is turned off by
default due to the expense of generating it.
(Inherited from PairwiseSequenceAligner.) |
| Name |
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
Smith-Waterman algorithm.
(Overrides PairwiseSequenceAlignerName.) |
| SimilarityMatrix |
Gets or sets value of similarity matrix
The similarity matrix determines the score for any possible pair
of symbols that are encountered at a common location across the
sequences being aligned.
(Inherited from PairwiseSequenceAligner.) |
Methods| Name | Description | |
|---|---|---|
| Align(IEnumerableISequence) |
Align aligns the set of input sequences using the affine gap model (gap open and gap extension penalties)
and returns the best alignment found.
(Inherited from PairwiseSequenceAligner.) |
| Align(ISequence, ISequence) |
Align aligns the set of input sequences using the affine gap model (gap open and gap extension penalties)
and returns the best alignment found.
(Inherited from PairwiseSequenceAligner.) |
| Align(SimilarityMatrix, Int32, Int32, ISequence, ISequence) |
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.
(Inherited from PairwiseSequenceAligner.) |
| AlignSimple(IEnumerableISequence) |
AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty),
and returns the best alignment found.
(Inherited from PairwiseSequenceAligner.) |
| AlignSimple(ISequence, ISequence) |
AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty),
and returns the best alignment found.
(Inherited from PairwiseSequenceAligner.) |
| AlignSimple(SimilarityMatrix, Int32, ISequence, ISequence) |
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.
(Inherited from PairwiseSequenceAligner.) |
| Equals | Determines whether the specified object is equal to the current object. (Inherited from Object.) |
| GetHashCode | Serves as the default hash function. (Inherited from Object.) |
| GetType | Gets the Type of the current instance. (Inherited from Object.) |
| ToString | Returns a string that represents the current object. (Inherited from Object.) |
See Also