NCBI C++ ToolKit
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CPssmCreateTestFixture Class Reference

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This class exists merely to call private methods in CPsiBlastInputData and CPssmEngine. More...

#include "pssm_test_util.hpp"
(Private to src/algo/blast/unit_tests/api.)

Static Public Member Functions

static string x_ErrorCodeToString (int error_code)
 Gets error strings from a CPssmEngine private method. More...
 
static void x_GetSubjectSequence (const objects::CDense_seg &ds, objects::CScope &scope, string &sequence_data)
 Gets Subject sequence from a CPsiBlastInputData private method. More...
 
static unsigned char * x_GuardProteinQuery (const unsigned char *query, unsigned int query_length)
 Accesses CPssmEngine private method. More...
 
static unsigned int GetNumAlignedSequences (const CPsiBlastInputData &input)
 Accesses CPsiBlastInputData private method. More...
 

Detailed Description

This class exists merely to call private methods in CPsiBlastInputData and CPssmEngine.

Both clases declare this one as a friend.

Definition at line 56 of file pssm_test_util.hpp.

Member Function Documentation

◆ GetNumAlignedSequences()

static unsigned int CPssmCreateTestFixture::GetNumAlignedSequences ( const CPsiBlastInputData input)
inlinestatic

Accesses CPsiBlastInputData private method.

Returns the number of sequences that make up the multiple sequence alignment

Parameters
inputInstance of CPsiBlastInputData

Definition at line 96 of file pssm_test_util.hpp.

References input().

Referenced by BOOST_AUTO_TEST_CASE().

◆ x_ErrorCodeToString()

static string CPssmCreateTestFixture::x_ErrorCodeToString ( int  error_code)
inlinestatic

Gets error strings from a CPssmEngine private method.

Parameters
error_codeinput integer code

Definition at line 61 of file pssm_test_util.hpp.

References CPssmEngine::x_ErrorCodeToString().

Referenced by BOOST_AUTO_TEST_CASE().

◆ x_GetSubjectSequence()

static void CPssmCreateTestFixture::x_GetSubjectSequence ( const objects::CDense_seg &  ds,
objects::CScope &  scope,
string sequence_data 
)
inlinestatic

Gets Subject sequence from a CPsiBlastInputData private method.

Parameters
dsalignment input
scopeallos fetching of sequence
sequence_datareturn value for sequence.

Definition at line 71 of file pssm_test_util.hpp.

References CPsiBlastInputData::x_GetSubjectSequence().

Referenced by BOOST_AUTO_TEST_CASE().

◆ x_GuardProteinQuery()

static unsigned char* CPssmCreateTestFixture::x_GuardProteinQuery ( const unsigned char *  query,
unsigned int  query_length 
)
inlinestatic

Accesses CPssmEngine private method.

Copies query sequence and adds protein sentinel bytes at the beginning and at the end of the sequence.

Parameters
querysequence to copy [in]
query_lengthlength of the sequence above [in]
Exceptions
CBlastExceptionif does not have enough memory
Returns
copy of query guarded by protein sentinel bytes

Definition at line 85 of file pssm_test_util.hpp.

References query, and CPssmEngine::x_GuardProteinQuery().

Referenced by BOOST_AUTO_TEST_CASE().


The documentation for this class was generated from the following file:
Modified on Mon Jun 17 05:06:06 2024 by modify_doxy.py rev. 669887