DynamicProgrammingPairwiseAlignerJob Class

Base class for all aligner algorithms. Provides storage and read/write operations for the grid.

Inheritance Hierarchy

SystemObject
Bio.Algorithms.AlignmentDynamicProgrammingPairwiseAlignerJob
Bio.Algorithms.AlignmentPairwiseOverlapSimpleAlignmentJob

Namespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)

Syntax

C++

Copy

public abstract class DynamicProgrammingPairwiseAlignerJob

Public MustInherit Class DynamicProgrammingPairwiseAlignerJob

public ref class DynamicProgrammingPairwiseAlignerJob abstract

[<AbstractClassAttribute>]
type DynamicProgrammingPairwiseAlignerJob =  class end

The DynamicProgrammingPairwiseAlignerJob type exposes the following members.

Constructors

	Name	Description
	DynamicProgrammingPairwiseAlignerJob	Initializes a new instance of the DynamicProgrammingPairwiseAlignerJob class

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Methods

	Name	Description
	Align	Launches the alignment algorithm
	ComputeBlock	Forward pass for the block. Assumes the blocks to the top and right have already been processed.
	ComputeBlockAffine	Implementation of the linear programming model for the block using the affine gap cost model
	ComputeBlockSimple	Implementation of the linear programming model for the block using the simple gap cost model
	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
	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.
	ComputeTraceBlock	Computes the traceback pointers for the block. Assumes the grid cache has been already filled during the forward pass
	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.
	InitializeCacheAffine	Initializes grid cache for the affine alignment.
	InitializeCacheAffineZero	Initializes grid cache for the affine alignment. Sets the boundary weights to zero.
	InitializeCacheSimple	Initializes grid cache for the simple alignment.
	InitializeCacheSimpleZero	Initializes grid cache for the simple alignment. Sets the boundary weights to zero.
	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
	SetBoundaryCondition	Sets the boundary values tor traceback
	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

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Fields

	Name	Description
	gapCode	Signifies gap in aligned sequence (stored as int[]) during trace back.
	gridStride	Base class for alignment implementation. Provides building blocks for alignments using either simple or affine gap models.
	optScore

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Reference

Bio.Algorithms.Alignment Namespace