| DynamicProgrammingPairwiseAligner Class |
Base class for dynamic programming alignment algorithms, including NeedlemanWunsch,
SmithWaterman and PairwiseOverlap.
The basic reference for this code (including NW, SW and Overlap) is Chapter 2 in
Biological Sequence Analysis; Durbin, Eddy, Krogh and Mitchison; Cambridge Press; 1998
The variable names in these classes follow the notation in Durbin et al.
Inheritance HierarchySystemObject
Bio.Algorithms.AlignmentDynamicProgrammingPairwiseAligner
Bio.Algorithms.AlignmentPairwiseOverlapAligner
Bio.Algorithms.AlignmentDynamicProgrammingPairwiseAligner
Bio.Algorithms.AlignmentPairwiseOverlapAligner
Namespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe DynamicProgrammingPairwiseAligner type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | DynamicProgrammingPairwiseAligner |
Initializes a new instance of the DynamicProgrammingPairwiseAligner class.
Constructor for all the pairwise aligner (NeedlemanWunsch, SmithWaterman, Overlap).
Sets default similarity matrix and gap penalties.
Users will typically reset these using parameters specific to their particular sequences and needs.
|
Properties| Name | Description | |
|---|---|---|
 | ConsensusResolver |
Gets or sets the object that will be used to compute the alignment's consensus.
|
| Description |
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.
|
| GapExtensionCost |
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.
|
| GapOpenCost |
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.
|
| Name |
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.
|
| SimilarityMatrix | Gets or sets similarity matrix for use in alignment algorithms. |
Methods| Name | Description | |
|---|---|---|
 | Align(IEnumerableISequence) |
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.
|
| Align(ISequence, ISequence) |
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.
|
| 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.
|
| AlignSimple(IEnumerableISequence) |
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.
|
| AlignSimple(ISequence, ISequence) |
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.
|
| 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.
|
| CreateAffineAlignmentJob |
Creates the Affine aligner job
|
| CreateSimpleAlignmentJob |
Creates the Simple aligner job
|
| Equals | Determines whether the specified object is equal to the current object. (Inherited from Object.) |
| Finalize | Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection. (Inherited from Object.) |
| GetHashCode | Serves as the default hash function. (Inherited from Object.) |
| GetType | Gets the Type of the current instance. (Inherited from Object.) |
| MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) |
| ToString | Returns a string that represents the current object. (Inherited from Object.) |
| ValidateAlignInput |
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.
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Fields| Name | Description | |
|---|---|---|
 | FirstInputSequence |
First input sequence.
|
| InternalSimilarityMatrix |
Similarity matrix for use in alignment algorithms.
|
| SecondInputSequence |
Second input sequence.
|
See Also