CGumbelParamsOptionsFactory Class Reference

Search Toolkit Book for CGumbelParamsOptionsFactory

Class used for creation of sets of input parameters. More...

#include <algo/blast/gumbel_params/gumbel_params.hpp>

Static Public Member Functions
static CRef< CGumbelParamsOptions >	CreateStandard20AAOptions (CGeneralScoreMatrix::EScoreMatrixName smat=CGeneralScoreMatrix::eBlosum62)
	Creates standard options with score matrix and residue frequenceis for 20 aa alphabet. More...
static CRef< CGumbelParamsOptions >	CreateBasicOptions (void)
	Creates standard options with no score matrix or resiudie frequencies. More...

Detailed Description

Class used for creation of sets of input parameters.

Definition at line 323 of file gumbel_params.hpp.

Member Function Documentation

CreateBasicOptions()

CRef< CGumbelParamsOptions > CGumbelParamsOptionsFactory::CreateBasicOptions ( void  )

static

Creates standard options with no score matrix or resiudie frequencies.

Returns

Gumbel params options

Definition at line 288 of file gumbel_params.cpp.

References CGumbelParamsOptions::SetGapExtension(), CGumbelParamsOptions::SetGapOpening(), CGumbelParamsOptions::SetGapped(), CGumbelParamsOptions::SetKAccuracy(), CGumbelParamsOptions::SetLambdaAccuracy(), CGumbelParamsOptions::SetMaxCalcMemory(), and CGumbelParamsOptions::SetMaxCalcTime().

Referenced by BOOST_AUTO_TEST_CASE().

CreateStandard20AAOptions()

CRef< CGumbelParamsOptions > CGumbelParamsOptionsFactory::CreateStandard20AAOptions ( CGeneralScoreMatrix::EScoreMatrixName  smat = CGeneralScoreMatrix::eBlosum62 )

static

Creates standard options with score matrix and residue frequenceis for 20 aa alphabet.

Parameters

smat	Score matrix name [in]

Returns

Gumbel params options

Definition at line 242 of file gumbel_params.cpp.

References CGumbelParamsOptions::SetGapExtension(), CGumbelParamsOptions::SetGapOpening(), CGumbelParamsOptions::SetGapped(), CGumbelParamsOptions::SetKAccuracy(), CGumbelParamsOptions::SetLambdaAccuracy(), CGumbelParamsOptions::SetMaxCalcMemory(), CGumbelParamsOptions::SetMaxCalcTime(), CGumbelParamsOptions::SetScoreMatrix(), CGumbelParamsOptions::SetSeq1ResidueProbs(), and CGumbelParamsOptions::SetSeq2ResidueProbs().

Referenced by BOOST_AUTO_TEST_CASE(), and CGumbelParamsApplication::Run().

---

The documentation for this class was generated from the following files:

• include/algo/blast/gumbel_params/gumbel_params.hpp
• src/algo/blast/gumbel_params/gumbel_params.cpp