BlastRPSAuxInfo Struct Reference

Search Toolkit Book for BlastRPSAuxInfo

information derived from RPS blast '.aux' file More...

#include <algo/blast/core/blast_rps.h>

Public Attributes
char *	orig_score_matrix
	score matrix used to derive PSSMs More...
Int4	gap_open_penalty
	gap open penalty used in deriving PSSMs More...
Int4	gap_extend_penalty
	gap extend penalty used in deriving PSSMs More...
double	ungapped_k
	ungapped Karlin value for orig_score_matrix (not used) More...
double	ungapped_h
	ungapped Karlin value for orig_score_matrix (not used) More...
Int4	max_db_seq_length
	maximum DB sequence length (not used) More...
Int4	db_length
	RPS DB search space (not used) More...
double	scale_factor
	the PSSMs are scaled by this amount, and so all scores and all cutoff values must be similarly scaled during the search More...
double *	karlin_k
	one Karlin value for each DB sequence More...

Detailed Description

information derived from RPS blast '.aux' file

Definition at line 100 of file blast_rps.h.

Member Data Documentation

db_length

Int4 BlastRPSAuxInfo::db_length

RPS DB search space (not used)

Definition at line 109 of file blast_rps.h.

gap_extend_penalty

Int4 BlastRPSAuxInfo::gap_extend_penalty

gap extend penalty used in deriving PSSMs

Definition at line 103 of file blast_rps.h.

Referenced by CBlastRPSAuxInfo::CBlastRPSAuxInfo().

gap_open_penalty

Int4 BlastRPSAuxInfo::gap_open_penalty

gap open penalty used in deriving PSSMs

Definition at line 102 of file blast_rps.h.

Referenced by CBlastRPSAuxInfo::CBlastRPSAuxInfo().

karlin_k

double* BlastRPSAuxInfo::karlin_k

one Karlin value for each DB sequence

Definition at line 113 of file blast_rps.h.

Referenced by CBlastRPSAuxInfo::CBlastRPSAuxInfo(), s_RPSComputeTraceback(), and CBlastRPSAuxInfo::x_DoDestroy().

max_db_seq_length

Int4 BlastRPSAuxInfo::max_db_seq_length

maximum DB sequence length (not used)

Definition at line 108 of file blast_rps.h.

orig_score_matrix

char* BlastRPSAuxInfo::orig_score_matrix

score matrix used to derive PSSMs

Definition at line 101 of file blast_rps.h.

Referenced by CBlastRPSAuxInfo::CBlastRPSAuxInfo(), and CBlastRPSAuxInfo::x_DoDestroy().

scale_factor

double BlastRPSAuxInfo::scale_factor

the PSSMs are scaled by this amount, and so all scores and all cutoff values must be similarly scaled during the search

Definition at line 110 of file blast_rps.h.

Referenced by CBlastRPSAuxInfo::CBlastRPSAuxInfo().

ungapped_h

double BlastRPSAuxInfo::ungapped_h

ungapped Karlin value for orig_score_matrix (not used)

Definition at line 106 of file blast_rps.h.

ungapped_k

double BlastRPSAuxInfo::ungapped_k

ungapped Karlin value for orig_score_matrix (not used)

Definition at line 104 of file blast_rps.h.

---

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

• include/algo/blast/core/blast_rps.h