NCBI C++ ToolKit
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PSIBlastOptions Struct Reference

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Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should be transfered elsewhere. More...

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

Public Attributes

Int4 pseudo_count
 Pseudocount constant. More...
 
double inclusion_ethresh
 Minimum evalue for inclusion in PSSM calculation. More...
 
Boolean use_best_alignment
 If set to TRUE, use the best alignment when multiple HSPs are found in a query-subject alignment (i.e. More...
 
Boolean nsg_compatibility_mode
 Compatibility option for the NCBI's structure group (note nsg_ prefix, stands for NCBI's structure group). More...
 
double impala_scaling_factor
 Scaling factor as used in IMPALA to do the matrix rescaling. More...
 
Boolean ignore_unaligned_positions
 This turns off a validation for the multiple sequence alignment in the PSSM engine for unaligned positions. More...
 

Detailed Description

Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should be transfered elsewhere.

Definition at line 496 of file blast_options.h.

Member Data Documentation

◆ ignore_unaligned_positions

Boolean PSIBlastOptions::ignore_unaligned_positions

This turns off a validation for the multiple sequence alignment in the PSSM engine for unaligned positions.

Needed when a multiple sequence alignment is provided on the command line (e.g.: -in_msa option).

Definition at line 549 of file blast_options.h.

Referenced by PSIBlastOptionsNew(), and PSICreatePssmWithDiagnostics().

◆ impala_scaling_factor

double PSIBlastOptions::impala_scaling_factor

Scaling factor as used in IMPALA to do the matrix rescaling.

Default value of 1.0 means not to use it. Makemat/formatrpsdb set this value to 100 by default, Kappa_RedoAlignmentCore uses 32. Provided so that the NCBI structure group can create scaled PSSMs as the output of the PSSM engine. Do not change this unless you know what you are doing.

Definition at line 543 of file blast_options.h.

Referenced by CdPssmInput::CdPssmInput(), CPSIBlastOptions::DebugDump(), PSIBlastOptionsNew(), PSICreatePssmFromCDD(), PSICreatePssmWithDiagnostics(), SU_PSSMInput::SU_PSSMInput(), and CPssmEngine::x_PSIMatrix2Asn1().

◆ inclusion_ethresh

double PSIBlastOptions::inclusion_ethresh

◆ nsg_compatibility_mode

Boolean PSIBlastOptions::nsg_compatibility_mode

Compatibility option for the NCBI's structure group (note nsg_ prefix, stands for NCBI's structure group).

When set to true, the PSSM engine will function in the same way the C toolkit PSSM engine did in the structure group's cddumper application. This option should be set to FALSE by default as it enables the following behavior in the PSSM engine:

1) Ignores the query sequence (on certain stages of PSSM creation only)
2) Skips validation of multiple sequence alignment data
3) Disables assertions and validation in _PSICheckSequenceWeights
4) If no aligned sequences are provided in the multiple sequence
alignment, NULL PSSM frequency ratios are returned and the PSSM is built
based on the underlying substitution matrix.

Do not set this to TRUE unless you know what you are doing.

Definition at line 535 of file blast_options.h.

Referenced by BOOST_AUTO_TEST_CASE(), CdPssmInput::CdPssmInput(), CPSIBlastOptions::DebugDump(), CBlastOptionsLocal::GetIgnoreMsaMaster(), PSIBlastOptionsNew(), PSICreatePssmWithDiagnostics(), CBlastOptionsLocal::SetIgnoreMsaMaster(), SU_PSSMInput::SU_PSSMInput(), and CPsiBlastArgs::x_CreatePssmFromMsa().

◆ pseudo_count

Int4 PSIBlastOptions::pseudo_count

◆ use_best_alignment

Boolean PSIBlastOptions::use_best_alignment

If set to TRUE, use the best alignment when multiple HSPs are found in a query-subject alignment (i.e.

: HSP with the lowest e-value), else use all HSPs in a query-subject alignment. This option does not apply to the PSSM engine, it applies to the processing of pairwise sequence alignments to build a multiple sequence alignment structure

See also
CPsiBlastInputData (to be implemented)

Definition at line 517 of file blast_options.h.

Referenced by BOOST_AUTO_TEST_CASE(), CPSIBlastOptions::DebugDump(), PSIBlastOptionsNew(), and SU_PSSMInput::SU_PSSMInput().


The documentation for this struct was generated from the following file:
Modified on Fri Jul 19 17:12:01 2024 by modify_doxy.py rev. 669887