NCBI C++ ToolKit
Functions | Variables
unit_test_alnmgr.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/test_boost.hpp>
#include <serial/objistr.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/general/Object_id.hpp>
#include <objtools/alnmgr/aln_user_options.hpp>
#include <objtools/alnmgr/aln_asn_reader.hpp>
#include <objtools/alnmgr/aln_container.hpp>
#include <objtools/alnmgr/aln_tests.hpp>
#include <objtools/alnmgr/aln_stats.hpp>
#include <objtools/alnmgr/pairwise_aln.hpp>
#include <objtools/alnmgr/aln_serial.hpp>
#include <objtools/alnmgr/sparse_aln.hpp>
#include <objtools/alnmgr/aln_converters.hpp>
#include <objtools/alnmgr/aln_builders.hpp>
#include <objtools/alnmgr/sparse_ci.hpp>
#include <objtools/alnmgr/aln_generators.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <common/test_assert.h>
+ Include dependency graph for unit_test_alnmgr.cpp:

Go to the source code of this file.

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Functions

 USING_SCOPE (objects)
 
 NCBITEST_INIT_CMDLINE (descrs)
 
bool DumpExpected (void)
 
bool Verbose (void)
 
CScopeGetScope (void)
 
size_t LoadAligns (CNcbiIstream &in, CAlnContainer &aligns, size_t limit=0)
 
CRef< TScopeAlnStatsInitAlnStats (const CAlnContainer &aligns, unique_ptr< TScopeAlnIdMap > &aln_id_map)
 
void CheckPairwiseAln (CNcbiIstream &in_exp, const CPairwiseAln &pw, size_t aln_idx, int anchor, int row)
 
void CheckSparseAln (CNcbiIstream &in_exp, const CSparseAln &sparse, bool check_sequence)
 
 BOOST_AUTO_TEST_CASE (s_TestLoadAlign)
 
 BOOST_AUTO_TEST_CASE (s_TestPairwiseAln)
 
 BOOST_AUTO_TEST_CASE (s_TestPairwiseAlnRanged)
 
 BOOST_AUTO_TEST_CASE (s_TestAnchoredAln)
 
 BOOST_AUTO_TEST_CASE (s_TestAnchoredAlnBuilt)
 
 BOOST_AUTO_TEST_CASE (s_TestSparseAlnCoords)
 
 BOOST_AUTO_TEST_CASE (s_TestSparseAlnData)
 
 BOOST_AUTO_TEST_CASE (s_TestAlnTypes)
 

Variables

 USING_NCBI_SCOPE
 

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/8]

BOOST_AUTO_TEST_CASE ( s_TestAlnTypes  )

◆ BOOST_AUTO_TEST_CASE() [2/8]

BOOST_AUTO_TEST_CASE ( s_TestAnchoredAln  )

◆ BOOST_AUTO_TEST_CASE() [3/8]

BOOST_AUTO_TEST_CASE ( s_TestAnchoredAlnBuilt  )

◆ BOOST_AUTO_TEST_CASE() [4/8]

BOOST_AUTO_TEST_CASE ( s_TestLoadAlign  )

◆ BOOST_AUTO_TEST_CASE() [5/8]

BOOST_AUTO_TEST_CASE ( s_TestPairwiseAln  )

◆ BOOST_AUTO_TEST_CASE() [6/8]

BOOST_AUTO_TEST_CASE ( s_TestPairwiseAlnRanged  )

◆ BOOST_AUTO_TEST_CASE() [7/8]

BOOST_AUTO_TEST_CASE ( s_TestSparseAlnCoords  )

◆ BOOST_AUTO_TEST_CASE() [8/8]

BOOST_AUTO_TEST_CASE ( s_TestSparseAlnData  )

◆ CheckPairwiseAln()

void CheckPairwiseAln ( CNcbiIstream in_exp,
const CPairwiseAln pw,
size_t  aln_idx,
int  anchor,
int  row 
)

◆ CheckSparseAln()

void CheckSparseAln ( CNcbiIstream in_exp,
const CSparseAln sparse,
bool  check_sequence 
)

◆ DumpExpected()

bool DumpExpected ( void  )

◆ GetScope()

CScope& GetScope ( void  )

◆ InitAlnStats()

CRef<TScopeAlnStats> InitAlnStats ( const CAlnContainer aligns,
unique_ptr< TScopeAlnIdMap > &  aln_id_map 
)

Definition at line 128 of file unit_test_alnmgr.cpp.

References GetScope(), ITERATE, and CAlnContainer::size().

Referenced by BOOST_AUTO_TEST_CASE().

◆ LoadAligns()

size_t LoadAligns ( CNcbiIstream in,
CAlnContainer aligns,
size_t  limit = 0 
)

◆ NCBITEST_INIT_CMDLINE()

NCBITEST_INIT_CMDLINE ( descrs  )

Definition at line 67 of file unit_test_alnmgr.cpp.

◆ USING_SCOPE()

USING_SCOPE ( objects  )

◆ Verbose()

bool Verbose ( void  )

Variable Documentation

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 62 of file unit_test_alnmgr.cpp.

Modified on Fri Jan 05 07:25:33 2024 by modify_doxy.py rev. 669887