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BlastScoringParameters Struct Reference

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Scoring parameters block Contains scoring-related information that is actually used for the blast search. More...

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

+ Collaboration diagram for BlastScoringParameters:

Public Attributes

BlastScoringOptionsoptions
 User-provided values for these params. More...
 
Int2 reward
 Reward for a match. More...
 
Int2 penalty
 Penalty for a mismatch. More...
 
Int4 gap_open
 Extra penalty for starting a gap (scaled version) More...
 
Int4 gap_extend
 Penalty for each gap residue (scaled version) More...
 
Int4 shift_pen
 Penalty for shifting a frame in out-of-frame gapping (scaled version) More...
 
double scale_factor
 multiplier for all cutoff scores More...
 

Detailed Description

Scoring parameters block Contains scoring-related information that is actually used for the blast search.

Definition at line 199 of file blast_parameters.h.

Member Data Documentation

◆ gap_extend

Int4 BlastScoringParameters::gap_extend

◆ gap_open

Int4 BlastScoringParameters::gap_open

◆ options

BlastScoringOptions* BlastScoringParameters::options

◆ penalty

Int2 BlastScoringParameters::penalty

◆ reward

Int2 BlastScoringParameters::reward

◆ scale_factor

double BlastScoringParameters::scale_factor

◆ shift_pen

Int4 BlastScoringParameters::shift_pen

Penalty for shifting a frame in out-of-frame gapping (scaled version)

Definition at line 205 of file blast_parameters.h.

Referenced by BlastScoringParametersNew(), CBlastScoringParameters::DebugDump(), printBlastScoringParameters(), s_OutOfFrameAlignWithTraceback(), s_OutOfFrameGappedAlign(), and s_RPSComputeTraceback().


The documentation for this struct was generated from the following file:
Modified on Sun Apr 14 05:29:11 2024 by modify_doxy.py rev. 669887