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BlastRPSAuxInfo Struct Reference

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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:
Modified on Thu Feb 29 12:17:13 2024 by modify_doxy.py rev. 669887