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BlastExtensionOptions Struct Reference

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Options used for gapped extension These include: a. More...

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

Public Attributes

double gap_x_dropoff
 X-dropoff value for gapped extension (in bits) More...
 
double gap_x_dropoff_final
 X-dropoff value for the final gapped extension (in bits) More...
 
EBlastPrelimGapExt ePrelimGapExt
 type of preliminary gapped extension (normally) for calculating score. More...
 
EBlastTbackExt eTbackExt
 type of traceback extension. More...
 
Int4 compositionBasedStats
 mode of compositional adjustment to use; if zero then compositional adjustment is not used More...
 
Int4 unifiedP
 Indicates unified P values to be used in blastp or tblastn. More...
 
Int4 max_mismatches
 Maximum number of mismatches allowed for Jumper. More...
 
Int4 mismatch_window
 Widnow for counting mismatches for Jumper. More...
 
EBlastProgramType program_number
 indicates blastn, blastp, etc. More...
 

Detailed Description

Options used for gapped extension These include: a.

Penalties for various types of gapping; b. Drop-off values for the extension algorithms tree exploration; c. Parameters identifying what kind of extension algorithm(s) should be used.

Definition at line 335 of file blast_options.h.

Member Data Documentation

◆ compositionBasedStats

Int4 BlastExtensionOptions::compositionBasedStats

◆ ePrelimGapExt

EBlastPrelimGapExt BlastExtensionOptions::ePrelimGapExt

◆ eTbackExt

EBlastTbackExt BlastExtensionOptions::eTbackExt

◆ gap_x_dropoff

double BlastExtensionOptions::gap_x_dropoff

◆ gap_x_dropoff_final

double BlastExtensionOptions::gap_x_dropoff_final

◆ max_mismatches

Int4 BlastExtensionOptions::max_mismatches

Maximum number of mismatches allowed for Jumper.

Definition at line 347 of file blast_options.h.

Referenced by BLAST_GapAlignStructNew(), CBlastOptionsLocal::GetMaxMismatches(), and CBlastOptionsLocal::SetMaxMismatches().

◆ mismatch_window

Int4 BlastExtensionOptions::mismatch_window

Widnow for counting mismatches for Jumper.

Definition at line 349 of file blast_options.h.

Referenced by BLAST_GapAlignStructNew(), CBlastOptionsLocal::GetMismatchWindow(), and CBlastOptionsLocal::SetMismatchWindow().

◆ program_number

EBlastProgramType BlastExtensionOptions::program_number

indicates blastn, blastp, etc.

Definition at line 351 of file blast_options.h.

Referenced by CBlastOptionsLocal::SetProgram().

◆ unifiedP

Int4 BlastExtensionOptions::unifiedP

Indicates unified P values to be used in blastp or tblastn.

Definition at line 345 of file blast_options.h.

Referenced by Blast_RedoAlignmentCore_MT(), CBlastOptionsLocal::GetUnifiedP(), and CBlastOptionsLocal::SetUnifiedP().


The documentation for this struct was generated from the following file:
Modified on Sun Jun 23 05:22:35 2024 by modify_doxy.py rev. 669887