| PairwiseSequenceAligner Class |
Base class for our pair-wise sequence aligners. This implements the core shared
portions of the Smith-Waterman and Needleman-Wunsch aligners.
Inheritance HierarchySystemObject
Bio.Algorithms.AlignmentPairwiseSequenceAligner
Bio.Algorithms.AlignmentNeedlemanWunschAligner
Bio.Algorithms.AlignmentSmithWatermanAligner
Bio.Algorithms.AlignmentPairwiseSequenceAligner
Bio.Algorithms.AlignmentNeedlemanWunschAligner
Bio.Algorithms.AlignmentSmithWatermanAligner
Namespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe PairwiseSequenceAligner type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | PairwiseSequenceAligner |
Default constructor
|
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 current Alignment algorithm used.
This is a overridden property from the abstract parent.
|
| 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
|
| GapOpenCost |
Gets or sets value of GapOpenCost
The GapOpenCost is the cost of inserting a gap character into
a sequence.
|
| 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.
|
| Name |
Gets the name of the current Alignment algorithm used.
This is a overridden property from the abstract parent.
|
| 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.
|
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.
|
| 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.
|
| 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) |
AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty),
and returns the best alignment found.
|
| AlignSimple(ISequence, ISequence) |
AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty),
and returns the best alignment found.
|
| 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.
|
| CreateAlignmentFromCell |
This takes a specific starting location in the scoring matrix and generates
an alignment from it using the traceback scores.
|
| CreateTracebackTable |
This is step (2) in the dynamic programming model - to fill in the scoring matrix
and calculate the traceback entries. This is algorithm specific and so is left
as an abstract method.
|
| 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.) |
| Initialize |
This is step (1) in the dynamic programming model - to initialize the default values
for the scoring matrix and traceback tables.
|
| MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) |
| ToString | Returns a string that represents the current object. (Inherited from Object.) |
| TracebackIsComplete |
This method is used to determine when the traceback step is complete.
It is algorithm specific.
|
Fields| Name | Description | |
|---|---|---|
 | _gap |
The gap character being used for the shared alphabet between the reference and query sequence.
|
| _sequence1 |
Original sequence
|
| _sequence2 |
Original sequence #2
|
| Cols |
Columns in ScoreTable
|
| h_Gap_Length |
This array keeps track of the length of gaps up to a point along the horizontal axis.
Only used with the affine gap model
|
| QuerySequence |
The query sequence being aligned (sequence #2)
|
| ReferenceSequence |
The reference sequence being aligned (sequence #1)
|
| Rows |
Rows in ScoreTable
|
| ScoreTable |
Generated score table - this is filled in with the scoring matrix when debugging
|
| Traceback |
Traceback table built during the matrix creation step
|
| usingAffineGapModel |
A variable to keep track of whether the traceback table was constructed with an affine gap model.
|
| v_Gap_Length |
This array keeps track of the length of gaps up to a point along the vertical axis.
nly used with the affine gap model.
|
See Also