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:

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Functions
	USING_SCOPE (objects)
	NCBITEST_INIT_CMDLINE (descrs)
bool	DumpExpected (void)
bool	Verbose (void)
CScope &	GetScope (void)
size_t	LoadAligns (CNcbiIstream &in, CAlnContainer &aligns, size_t limit=0)
CRef< TScopeAlnStats >	InitAlnStats (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

)

Definition at line 964 of file unit_test_alnmgr.cpp.

References CheckPairwiseAln(), CreateAnchoredAlnFromAln(), DumpExpected(), CAnchoredAln::GetAnchorRow(), CAnchoredAln::GetPairwiseAlns(), InitAlnStats(), int, LoadAligns(), row, and CAlnContainer::size().

BOOST_AUTO_TEST_CASE() [2/8]

BOOST_AUTO_TEST_CASE

(

s_TestAnchoredAln

)

Definition at line 688 of file unit_test_alnmgr.cpp.

References CheckPairwiseAln(), CreateAnchoredAlnFromAln(), DumpExpected(), CAnchoredAln::GetAnchorRow(), CAnchoredAln::GetPairwiseAlns(), InitAlnStats(), int, LoadAligns(), row, and CAlnContainer::size().

BOOST_AUTO_TEST_CASE() [3/8]

BOOST_AUTO_TEST_CASE

(

s_TestAnchoredAlnBuilt

)

Definition at line 726 of file unit_test_alnmgr.cpp.

References BuildAln(), CheckPairwiseAln(), CreateAnchoredAlnVec(), DumpExpected(), CAlnUserOptions::fAllowTranslocation, CAlnUserOptions::fAnchorRowFirst, CAlnUserOptions::fIgnoreInsertions, CAlnUserOptions::fTruncateOverlaps, CAlnUserOptions::fUseAnchorAsAlnSeq, CAnchoredAln::GetAnchorRow(), CAnchoredAln::GetPairwiseAlns(), InitAlnStats(), int, LoadAligns(), CAlnUserOptions::m_MergeFlags, Ref(), row, CAlnUserOptions::SetAnchorId(), and Verbose().

BOOST_AUTO_TEST_CASE() [4/8]

BOOST_AUTO_TEST_CASE

(

s_TestLoadAlign

)

Definition at line 431 of file unit_test_alnmgr.cpp.

References DumpExpected(), variation::Equals(), InitAlnStats(), ITERATE, LoadAligns(), and MSerial_AsnText.

BOOST_AUTO_TEST_CASE() [5/8]

BOOST_AUTO_TEST_CASE

(

s_TestPairwiseAln

)

Definition at line 479 of file unit_test_alnmgr.cpp.

References CheckPairwiseAln(), ConvertSeqAlignToPairwiseAln(), DumpExpected(), CPairwise_CI::eAligned, CAlnUserOptions::eBothDirections, CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fDefaultPolicy, InitAlnStats(), LoadAligns(), and row.

BOOST_AUTO_TEST_CASE() [6/8]

BOOST_AUTO_TEST_CASE

(

s_TestPairwiseAlnRanged

)

Definition at line 556 of file unit_test_alnmgr.cpp.

References CAlignRangeCollectionList< TAlnRange >::begin(), ConvertSeqAlignToPairwiseAln(), DumpExpected(), CPairwise_CI::eAligned, CAlnUserOptions::eBothDirections, CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fDefaultPolicy, flags, CPairwiseAln::GetFirstBaseWidth(), CAlignRangeCollectionList< TAlnRange >::GetFirstFrom(), CPairwiseAln::GetFirstId(), CAlignRangeCollectionList< TAlnRange >::GetFirstTo(), CAlignRangeCollectionList< TAlnRange >::GetFlags(), CPairwiseAln::GetSecondBaseWidth(), CPairwiseAln::GetSecondId(), CAlignRangeCollectionList< TAlnRange >::GetSecondPosByFirstPos(), InitAlnStats(), LoadAligns(), MSerial_AsnText, CAlignRangeCollectionList< TAlnRange >::rbegin(), row, CAlignRangeCollectionList< TAlnRange >::size(), and Verbose().

BOOST_AUTO_TEST_CASE() [7/8]

BOOST_AUTO_TEST_CASE

(

s_TestSparseAlnCoords

)

Definition at line 811 of file unit_test_alnmgr.cpp.

References BuildAln(), CheckSparseAln(), CreateAnchoredAlnVec(), DumpExpected(), CAlnUserOptions::fTruncateOverlaps, GetScope(), InitAlnStats(), LoadAligns(), CAlnUserOptions::m_MergeFlags, MSerial_AsnText, Ref(), CAlnUserOptions::SetAnchorId(), and Verbose().

BOOST_AUTO_TEST_CASE() [8/8]

BOOST_AUTO_TEST_CASE

(

s_TestSparseAlnData

)

Definition at line 882 of file unit_test_alnmgr.cpp.

References BuildAln(), CheckSparseAln(), CreateAnchoredAlnVec(), CreateSeqAlignFromAnchoredAln(), DumpExpected(), CSeq_align_Base::C_Segs::e_Denseg, CSerialObject::Equals(), CAlnUserOptions::fTruncateOverlaps, GetScope(), InitAlnStats(), LoadAligns(), CAlnUserOptions::m_MergeFlags, MSerial_AsnText, Ref(), CAlnUserOptions::SetAnchorId(), and Verbose().

CheckPairwiseAln()

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

Definition at line 142 of file unit_test_alnmgr.cpp.

References DumpExpected(), flags, CPairwiseAln::GetFirstBaseWidth(), CAlignRangeCollectionList< TAlnRange >::GetFirstFrom(), CAlignRange< Position >::GetFirstFrom(), CPairwiseAln::GetFirstId(), CAlignRangeCollectionList< TAlnRange >::GetFirstTo(), CAlignRangeCollectionList< TAlnRange >::GetFlags(), CAlignRangeCollectionList< TAlnRange >::GetInsertions(), CPairwiseAln::GetSecondBaseWidth(), CPairwiseAln::GetSecondId(), CAlignRangeCollectionList< TAlnRange >::GetSecondPosByFirstPos(), CAlignRange< Position >::IsDirect(), ITERATE, len, MSerial_AsnText, row, and Verbose().

Referenced by BOOST_AUTO_TEST_CASE().

CheckSparseAln()

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

Definition at line 253 of file unit_test_alnmgr.cpp.

References CSparseAln::AlnRangeToNativeSeqRange(), DumpExpected(), IAlnSegmentIterator::eAllSegments, COpenRange< Position >::Empty(), CSparseAln::GetAlnRange(), IAlnSegment::GetAlnRange(), CSparseAln::GetAlnSeqString(), CSparseAln::GetAnchor(), CSparseAln::GetBaseWidth(), CSparseAln::GetDim(), CRange_Base::GetFrom(), CSparseAln::GetNumRows(), IAlnSegment::GetRange(), CSparseAln::GetSeqAlnStart(), CSparseAln::GetSeqAlnStop(), CSparseAln::GetSeqId(), CSparseAln::GetSeqRange(), CSparseAln::GetSeqString(), CRange_Base::GetTo(), IAlnSegment::GetType(), COpenRange< TSeqPos >::GetWhole(), COpenRange< TSignedSeqPos >::GetWhole(), MSerial_AsnText, row, and Verbose().

Referenced by BOOST_AUTO_TEST_CASE().

DumpExpected()

bool DumpExpected

(

void

)

Definition at line 74 of file unit_test_alnmgr.cpp.

References CNcbiApplicationAPI::GetArgs(), and CNcbiApplication::Instance().

Referenced by BOOST_AUTO_TEST_CASE(), CheckPairwiseAln(), and CheckSparseAln().

GetScope()

CScope& GetScope

(

void

)

Definition at line 86 of file unit_test_alnmgr.cpp.

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

Referenced by BOOST_AUTO_TEST_CASE(), and InitAlnStats().

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
	)

Definition at line 104 of file unit_test_alnmgr.cpp.

References in(), CAlnContainer::insert(), MSerial_AsnText, and CSeq_align::Validate().

Referenced by BOOST_AUTO_TEST_CASE().

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

)

Definition at line 80 of file unit_test_alnmgr.cpp.

References CNcbiApplicationAPI::GetArgs(), and CNcbiApplication::Instance().

Referenced by BOOST_AUTO_TEST_CASE(), CheckPairwiseAln(), and CheckSparseAln().

Variable Documentation

USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 62 of file unit_test_alnmgr.cpp.