Blast_ForbiddenRanges Struct Reference

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An instance of Blast_ForbiddenRanges is used by the Smith-Waterman algorithm to represent ranges in the database that are not to be aligned. More...

#include <algo/blast/composition_adjustment/smith_waterman.h>

Public Attributes
int	isEmpty
	True if there are no forbidden ranges. More...
int *	numForbidden
	how many forbidden ranges at each database position More...
int **	ranges
	forbidden ranges for each database position More...
int	capacity
	length of the query sequence More...

Detailed Description

An instance of Blast_ForbiddenRanges is used by the Smith-Waterman algorithm to represent ranges in the database that are not to be aligned.

Definition at line 46 of file smith_waterman.h.

Member Data Documentation

capacity

int Blast_ForbiddenRanges::capacity

length of the query sequence

Definition at line 52 of file smith_waterman.h.

isEmpty

int Blast_ForbiddenRanges::isEmpty

True if there are no forbidden ranges.

Definition at line 47 of file smith_waterman.h.

Referenced by Blast_SmithWatermanFindStart(), and Blast_SmithWatermanScoreOnly().

numForbidden

int* Blast_ForbiddenRanges::numForbidden

how many forbidden ranges at each database position

Definition at line 48 of file smith_waterman.h.

Referenced by Blast_SmithWatermanFindStart(), and Blast_SmithWatermanScoreOnly().

ranges

int** Blast_ForbiddenRanges::ranges

forbidden ranges for each database position

Definition at line 50 of file smith_waterman.h.

Referenced by Blast_SmithWatermanFindStart(), and Blast_SmithWatermanScoreOnly().

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The documentation for this struct was generated from the following file:

• include/algo/blast/composition_adjustment/smith_waterman.h