Launches the alignment algorithm

Forward pass for the block. Assumes the blocks to the top and right have already been processed.

Implementation of the linear programming model for the block using the affine gap cost model

Implementation of the linear programming model for the block using the simple gap cost model

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

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.

Computes the traceback pointers for the block. Assumes the grid cache has been already filled during the forward pass

Determines whether the specified object is equal to the current object.

Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection.

Serves as the default hash function.

Gets the Type of the current instance.

Initializes grid cache for the algorithm.

Initializes grid cache for the affine alignment.

Initializes grid cache for the affine alignment. Sets the boundary weights to zero.

Initializes grid cache for the simple alignment.

Initializes grid cache for the simple alignment. Sets the boundary weights to zero.

Creates a shallow copy of the current Object.

Fills the fold data structure for the block from the grid cache

Sets the boundary values tor traceback

Returns a string that represents the current object.

Writes the fold data structure for the block back to the grid cache