| PairwiseOverlapSimpleAlignmentJob Class |
Pairwise Overlap alignment implementation using simple gap model.
Inheritance HierarchySystemObject
Bio.Algorithms.AlignmentDynamicProgrammingPairwiseAlignerJob
Bio.Algorithms.AlignmentPairwiseOverlapSimpleAlignmentJob
Bio.Algorithms.AlignmentPairwiseOverlapAffineAlignmentJob
Bio.Algorithms.AlignmentDynamicProgrammingPairwiseAlignerJob
Bio.Algorithms.AlignmentPairwiseOverlapSimpleAlignmentJob
Bio.Algorithms.AlignmentPairwiseOverlapAffineAlignmentJob
Namespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe PairwiseOverlapSimpleAlignmentJob type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | PairwiseOverlapSimpleAlignmentJob(SimilarityMatrix, Int32, ISequence, ISequence) |
Inializes a new alignment job
|
 | PairwiseOverlapSimpleAlignmentJob(SimilarityMatrix, Int32, Int32, ISequence, ISequence) |
Inializes a new alignment job
|
Methods| Name | Description | |
|---|---|---|
| Align |
Launches the alignment algorithm
(Inherited from DynamicProgrammingPairwiseAlignerJob.) |
| ComputeBlock |
Forward pass for the block.
(Overrides DynamicProgrammingPairwiseAlignerJobComputeBlock(DynamicProgrammingPairwiseAlignerJobWeightFunction, Int32, Int32, Int32, Int32).) |
| ComputeBlockAffine |
Implementation of the linear programming model for the block using the affine gap cost model
(Inherited from DynamicProgrammingPairwiseAlignerJob.) |
| ComputeBlockSimple |
Implementation of the linear programming model for the block using the simple gap cost model
(Inherited from DynamicProgrammingPairwiseAlignerJob.) |
| ComputeCornerBlock |
Computes the lower-right corner block of the grid.
Combines the forward and traceback passes for performance.
This is the only block computation that takes place for smaller-than-block alignments
(Overrides DynamicProgrammingPairwiseAlignerJobComputeCornerBlock(Int32, Int32, Int32, Int32, SByte).) |
| ComputeIntermediateBlock |
Computes weights for all blocks of the grid except the lower-right corner one.
Assumes the grid cache to the left and top of the block has already been filled.
Weights on the bottom and right edge of the block are written back to the grid.
(Overrides DynamicProgrammingPairwiseAlignerJobComputeIntermediateBlock(Int32, Int32, Int32, Int32).) |
| ComputeTraceBlock |
Computes the traceback pointers for the block.
Assumes the grid cache has been already filled during the forward pass
(Overrides DynamicProgrammingPairwiseAlignerJobComputeTraceBlock(Int32, Int32, Int32, Int32, SByte).) |
| 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.) |
| InitializeCache |
Initializes grid cache for the algorithm.
(Overrides DynamicProgrammingPairwiseAlignerJobInitializeCache.) |
| InitializeCacheAffine |
Initializes grid cache for the affine alignment.
(Inherited from DynamicProgrammingPairwiseAlignerJob.) |
| InitializeCacheAffineZero |
Initializes grid cache for the affine alignment.
Sets the boundary weights to zero.
(Inherited from DynamicProgrammingPairwiseAlignerJob.) |
| InitializeCacheSimple |
Initializes grid cache for the simple alignment.
(Inherited from DynamicProgrammingPairwiseAlignerJob.) |
| InitializeCacheSimpleZero |
Initializes grid cache for the simple alignment.
Sets the boundary weights to zero.
(Inherited from DynamicProgrammingPairwiseAlignerJob.) |
| MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) |
| PopulateFold |
Fills the fold data structure for the block from the grid cache
(Inherited from DynamicProgrammingPairwiseAlignerJob.) |
| SetBoundaryCondition |
Sets the boundary values tor traceback
(Overrides DynamicProgrammingPairwiseAlignerJobSetBoundaryCondition(SByte, Int32, Int32, Int32, Int32).) |
| ToString | Returns a string that represents the current object. (Inherited from Object.) |
| WritebackFold |
Writes the fold data structure for the block back to the grid cache
(Inherited from DynamicProgrammingPairwiseAlignerJob.) |
Fields| Name | Description | |
|---|---|---|
 | gapCode |
Signifies gap in aligned sequence (stored as int[]) during trace back.
(Inherited from DynamicProgrammingPairwiseAlignerJob.) |
 | optScore | (Inherited from DynamicProgrammingPairwiseAlignerJob.) |
See Also