#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbi_system.hpp>
#include <corelib/test_boost.hpp>
#include <objtools/readers/idmapper.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Seq_point.hpp>
#include <objmgr/util/sequence.hpp>

Include dependency graph for unit_test_idmapper.cpp:

Go to the SVN repository for this file.

Functions
	USING_SCOPE (objects)

	BOOST_AUTO_TEST_CASE (Test_SimpleIdMapper)
	Test simple seq-id -> seq-id mapping, given a mapping table of seq-id -> seq-id. More...

	BOOST_AUTO_TEST_CASE (Test_SimpleLocMapper)
	Test location mapping given a context in which we only map seq-ids The goal here is to output the same location that we start with, except we change the seq-ids. More...

	BOOST_AUTO_TEST_CASE (Test_ComplexLocMapper)
	More Complex case involving mapping of location ranges that will shift positions. More...

	BOOST_AUTO_TEST_CASE (Test_EvenMoreComplexLocMapper)
	More Complex case involving mapping of location ranges that will shift positions. More...

	BOOST_AUTO_TEST_CASE (Test_BuiltinIdMapper)
	Test of built-in ID mapper This also tests the configuration-based methods as well. More...

Variables
	USING_NCBI_SCOPE

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/5]

BOOST_AUTO_TEST_CASE ( Test_BuiltinIdMapper )

Test of built-in ID mapper This also tests the configuration-based methods as well.

Definition at line 243 of file unit_test_idmapper.cpp.

References CSeq_interval_Base::GetFrom(), CSeq_id_Handle::GetGi(), CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), CSeq_loc_Base::GetInt(), CSeq_interval_Base::GetTo(), GI_CONST, CIdMapper::Map(), CSeq_loc::SetId(), and CSeq_loc::SetInt().

◆ BOOST_AUTO_TEST_CASE() [2/5]

BOOST_AUTO_TEST_CASE ( Test_ComplexLocMapper )

More Complex case involving mapping of location ranges that will shift positions.

Definition at line 115 of file unit_test_idmapper.cpp.

References CIdMapper::AddMapping(), CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CIdMapper::Map(), CSeq_loc::SetId(), CSeq_loc::SetInt(), and CSeq_loc::SetPnt().

◆ BOOST_AUTO_TEST_CASE() [3/5]

BOOST_AUTO_TEST_CASE ( Test_EvenMoreComplexLocMapper )

More Complex case involving mapping of location ranges that will shift positions.

Definition at line 152 of file unit_test_idmapper.cpp.

References CIdMapper::AddMapping(), CSeq_loc_Base::e_Packed_int, CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSeq_id_Handle(), CIdMapper::Map(), CRef< C, Locker >::Reset(), CSeq_loc::SetId(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().

◆ BOOST_AUTO_TEST_CASE() [4/5]

BOOST_AUTO_TEST_CASE ( Test_SimpleIdMapper )

Test simple seq-id -> seq-id mapping, given a mapping table of seq-id -> seq-id.

Definition at line 57 of file unit_test_idmapper.cpp.

References CIdMapper::AddMapping(), CSeq_id_Handle::GetHandle(), and CIdMapper::Map().

◆ BOOST_AUTO_TEST_CASE() [5/5]

BOOST_AUTO_TEST_CASE ( Test_SimpleLocMapper )

Test location mapping given a context in which we only map seq-ids The goal here is to output the same location that we start with, except we change the seq-ids.

Definition at line 86 of file unit_test_idmapper.cpp.

References CIdMapper::AddMapping(), CSeq_interval_Base::GetFrom(), CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), CSeq_loc_Base::GetInt(), CSeq_interval_Base::GetTo(), CIdMapper::Map(), CSeq_loc::SetId(), and CSeq_loc::SetInt().

◆ USING_SCOPE()

USING_SCOPE ( objects )

Variable Documentation

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 49 of file unit_test_idmapper.cpp.

Functions

Variables