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CMultiAlignerFixture Class Reference

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Fixture class initialized for each multialigner test. More...

+ Collaboration diagram for CMultiAlignerFixture:

Public Member Functions

 CMultiAlignerFixture (void)
 
 ~CMultiAlignerFixture ()
 

Static Public Member Functions

static void x_InitScope (void)
 Initialize scope. More...
 
static void x_ReadSequences (void)
 Read test sequences in FASTA format from file. More...
 
static void x_ReadAlignments (void)
 Read test MSAs from files. More...
 
static void x_ReadRpsArchive (void)
 Read test RPS-BLAST output in the archive format from file. More...
 
static void Initialize (void)
 Initialize static attributes. More...
 
static void Finalize (void)
 Release static attributes. More...
 

Public Attributes

CRef< CMultiAlignerOptionsm_Options
 
CRef< CMultiAlignerm_Aligner
 

Static Public Attributes

static CRef< CObjectManagerm_Objmgr
 
static CRef< CScopem_Scope
 
static vector< CRef< CSeq_loc > > m_Sequences
 
static CRef< CSeq_alignm_Align1
 
static CRef< CSeq_alignm_Align2
 
static CRef< CBlast4_archivem_RpsArchive
 

Detailed Description

Fixture class initialized for each multialigner test.

Definition at line 262 of file cobalt_unit_test.cpp.

Constructor & Destructor Documentation

◆ CMultiAlignerFixture()

CMultiAlignerFixture::CMultiAlignerFixture ( void  )
inline

◆ ~CMultiAlignerFixture()

CMultiAlignerFixture::~CMultiAlignerFixture ( )
inline

Definition at line 283 of file cobalt_unit_test.cpp.

References m_Aligner, m_Options, and CRef< C, Locker >::Reset().

Member Function Documentation

◆ Finalize()

static void CMultiAlignerFixture::Finalize ( void  )
inlinestatic

Release static attributes.

Definition at line 350 of file cobalt_unit_test.cpp.

References m_Align1, m_Align2, m_Objmgr, m_RpsArchive, m_Scope, m_Sequences, and CRef< C, Locker >::Reset().

Referenced by NCBITEST_AUTO_FINI().

◆ Initialize()

static void CMultiAlignerFixture::Initialize ( void  )
inlinestatic

Initialize static attributes.

Definition at line 341 of file cobalt_unit_test.cpp.

References x_InitScope(), x_ReadAlignments(), x_ReadRpsArchive(), and x_ReadSequences().

Referenced by NCBITEST_AUTO_INIT().

◆ x_InitScope()

static void CMultiAlignerFixture::x_InitScope ( void  )
inlinestatic

Initialize scope.

Definition at line 290 of file cobalt_unit_test.cpp.

References CScope::AddDefaults(), CObjectManager::GetInstance(), m_Objmgr, m_Scope, and CRef< C, Locker >::Reset().

Referenced by Initialize().

◆ x_ReadAlignments()

static void CMultiAlignerFixture::x_ReadAlignments ( void  )
inlinestatic

Read test MSAs from files.

Definition at line 311 of file cobalt_unit_test.cpp.

References m_Align1, m_Align2, m_Scope, NCBI_THROW, and ReadMsa().

Referenced by Initialize().

◆ x_ReadRpsArchive()

static void CMultiAlignerFixture::x_ReadRpsArchive ( void  )
inlinestatic

Read test RPS-BLAST output in the archive format from file.

Definition at line 330 of file cobalt_unit_test.cpp.

References m_RpsArchive, MSerial_AsnText, NCBI_THROW, and CRef< C, Locker >::Reset().

Referenced by BOOST_AUTO_TEST_CASE(), and Initialize().

◆ x_ReadSequences()

static void CMultiAlignerFixture::x_ReadSequences ( void  )
inlinestatic

Read test sequences in FASTA format from file.

Definition at line 298 of file cobalt_unit_test.cpp.

References m_Scope, m_Sequences, NCBI_THROW, and ReadFastaQueries().

Referenced by Initialize().

Member Data Documentation

◆ m_Align1

CRef< CSeq_align > CMultiAlignerFixture::m_Align1
static

Definition at line 268 of file cobalt_unit_test.cpp.

Referenced by Finalize(), and x_ReadAlignments().

◆ m_Align2

CRef< CSeq_align > CMultiAlignerFixture::m_Align2
static

Definition at line 269 of file cobalt_unit_test.cpp.

Referenced by Finalize(), and x_ReadAlignments().

◆ m_Aligner

CRef<CMultiAligner> CMultiAlignerFixture::m_Aligner

Definition at line 273 of file cobalt_unit_test.cpp.

Referenced by CMultiAlignerFixture(), and ~CMultiAlignerFixture().

◆ m_Objmgr

CRef< CObjectManager > CMultiAlignerFixture::m_Objmgr
static

Definition at line 265 of file cobalt_unit_test.cpp.

Referenced by Finalize(), and x_InitScope().

◆ m_Options

CRef<CMultiAlignerOptions> CMultiAlignerFixture::m_Options

Definition at line 272 of file cobalt_unit_test.cpp.

Referenced by CMultiAlignerFixture(), and ~CMultiAlignerFixture().

◆ m_RpsArchive

CRef< CBlast4_archive > CMultiAlignerFixture::m_RpsArchive
static

Definition at line 270 of file cobalt_unit_test.cpp.

Referenced by Finalize(), and x_ReadRpsArchive().

◆ m_Scope

CRef< CScope > CMultiAlignerFixture::m_Scope
static

Definition at line 266 of file cobalt_unit_test.cpp.

Referenced by Finalize(), x_InitScope(), x_ReadAlignments(), and x_ReadSequences().

◆ m_Sequences

vector< CRef< CSeq_loc > > CMultiAlignerFixture::m_Sequences
static

Definition at line 267 of file cobalt_unit_test.cpp.

Referenced by Finalize(), and x_ReadSequences().


The documentation for this class was generated from the following file:
Modified on Sun Apr 14 05:28:45 2024 by modify_doxy.py rev. 669887