taxon1_unit_test.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbi_system.hpp>
#include <corelib/ncbiapp.hpp>
#include <objects/taxon1/taxon1.hpp>
#include <serial/serial.hpp>
#include <serial/objostr.hpp>
#include <serial/objistr.hpp>
#include <corelib/test_boost.hpp>

Include dependency graph for taxon1_unit_test.cpp:

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Functions
	USING_SCOPE (objects)
	NCBITEST_AUTO_INIT ()
	NCBITEST_INIT_CMDLINE (arg_desc)
	NCBITEST_AUTO_FINI ()
	NCBITEST_INIT_TREE ()
	BOOST_AUTO_TEST_CASE (test_tax1_init)
	BOOST_AUTO_TEST_CASE (test_tax1e_maxTaxId)
	BOOST_AUTO_TEST_CASE (test_tax1_getbyid)
	BOOST_AUTO_TEST_CASE (test_tax1m_getbyid)
static CRef< COrg_ref >	s_String2OrgRef (const string &orgref_in)
static string	s_OrgRef2String (const COrg_ref &orgref)
	BOOST_AUTO_TEST_CASE (test_tax1_getTaxIdByOrgRef)
	BOOST_AUTO_TEST_CASE (test_tax1_getTaxIdByName)
	BOOST_AUTO_TEST_CASE (test_tax1_findTaxIdByName)
	BOOST_AUTO_TEST_CASE (test_tax1_getAllTaxIdByName)
	BOOST_AUTO_TEST_CASE (test_tax1_getOrgRef)
	BOOST_AUTO_TEST_CASE (test_tax1_lookup)
	BOOST_AUTO_TEST_CASE (test_tax1m_lookup_tm)
	BOOST_AUTO_TEST_CASE (test_tax1m_lookup)
	BOOST_AUTO_TEST_CASE (test_tax1_getParent)
	BOOST_AUTO_TEST_CASE (test_tax1_getGenus)
	BOOST_AUTO_TEST_CASE (test_tax1_getChildren)
	BOOST_AUTO_TEST_CASE (test_tax1_getGCName)
	BOOST_AUTO_TEST_CASE (test_tax1_join)
	BOOST_AUTO_TEST_CASE (test_tax1_getAllNames)
	BOOST_AUTO_TEST_CASE (test_tax1_getTaxId4GI)
	BOOST_AUTO_TEST_CASE (test_tax1m_getBlastName)
	BOOST_AUTO_TEST_CASE (test_tax1e_needUpdate)
	BOOST_AUTO_TEST_CASE (test_tax1m_getRankByName)
	BOOST_AUTO_TEST_CASE (test_tax1m_getDivByName)
	BOOST_AUTO_TEST_SUITE_END ()
	Auxiliary class to convert a string into an argument count and vector. More...

Variables
	USING_NCBI_SCOPE
CTaxon1	tax1
ESerialDataFormat	format = eSerial_AsnBinary

Function Documentation

BOOST_AUTO_TEST_CASE() [1/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_findTaxIdByName

)

Definition at line 251 of file taxon1_unit_test.cpp.

References CTaxon1::FindTaxIdByName(), and tax1.

BOOST_AUTO_TEST_CASE() [2/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_getAllNames

)

Definition at line 525 of file taxon1_unit_test.cpp.

References CTaxon1::GetAllNames(), and tax1.

BOOST_AUTO_TEST_CASE() [3/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_getAllTaxIdByName

)

Definition at line 277 of file taxon1_unit_test.cpp.

References CTaxon1::GetAllTaxIdByName(), and tax1.

BOOST_AUTO_TEST_CASE() [4/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_getbyid

)

Definition at line 129 of file taxon1_unit_test.cpp.

References CTaxon1::GetById(), CTaxon2_data_Base::GetOrg(), COrg_ref_Base::GetTaxname(), CTaxon2_data_Base::IsSetOrg(), COrg_ref_Base::IsSetTaxname(), NULL, util::strcmp(), and tax1.

BOOST_AUTO_TEST_CASE() [5/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_getChildren

)

Definition at line 489 of file taxon1_unit_test.cpp.

References CTaxon1::GetChildren(), and tax1.

BOOST_AUTO_TEST_CASE() [6/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_getGCName

)

Definition at line 503 of file taxon1_unit_test.cpp.

References b, CTaxon1::GetGCName(), and tax1.

BOOST_AUTO_TEST_CASE() [7/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_getGenus

)

Definition at line 477 of file taxon1_unit_test.cpp.

References CTaxon1::GetGenus(), and tax1.

BOOST_AUTO_TEST_CASE() [8/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_getOrgRef

)

Definition at line 301 of file taxon1_unit_test.cpp.

References CTaxon1::GetOrgRef(), NULL, s_OrgRef2String(), and tax1.

BOOST_AUTO_TEST_CASE() [9/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_getParent

)

Definition at line 465 of file taxon1_unit_test.cpp.

References CTaxon1::GetParent(), and tax1.

BOOST_AUTO_TEST_CASE() [10/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_getTaxId4GI

)

Definition at line 543 of file taxon1_unit_test.cpp.

References b, GetArgs, CTaxon1::GetTaxId4GI(), GI_CONST, CNcbiApplicationAPI::Instance(), tax1, and ZERO_GI.

BOOST_AUTO_TEST_CASE() [11/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_getTaxIdByName

)

Definition at line 224 of file taxon1_unit_test.cpp.

References CTaxon1::GetTaxIdByName(), and tax1.

BOOST_AUTO_TEST_CASE() [12/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_getTaxIdByOrgRef

)

Definition at line 195 of file taxon1_unit_test.cpp.

References CTaxon1::GetTaxIdByOrgRef(), NULL, s_String2OrgRef(), and tax1.

BOOST_AUTO_TEST_CASE() [13/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_init

)

Definition at line 114 of file taxon1_unit_test.cpp.

References b, ctll::empty(), GetArgs, CTaxon1::Init(), CNcbiApplication::Instance(), CNcbiEnvironment::Set(), CNcbiApplicationAPI::SetEnvironment(), and tax1.

BOOST_AUTO_TEST_CASE() [14/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_join

)

Definition at line 516 of file taxon1_unit_test.cpp.

References CTaxon1::Join(), and tax1.

BOOST_AUTO_TEST_CASE() [15/23]

BOOST_AUTO_TEST_CASE

(

test_tax1_lookup

)

Definition at line 339 of file taxon1_unit_test.cpp.

References CTaxon2_data_Base::GetOrg(), CTaxon2_data_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), CTaxon1::Lookup(), CTaxon1::LookupMerge(), NStr::MatchesMask(), NULL, CRef< C, Locker >::Reset(), s_OrgRef2String(), s_String2OrgRef(), and tax1.

BOOST_AUTO_TEST_CASE() [16/23]

BOOST_AUTO_TEST_CASE

(

test_tax1e_maxTaxId

)

Definition at line 124 of file taxon1_unit_test.cpp.

References b, CTaxon1::GetMaxTaxId(), and tax1.

BOOST_AUTO_TEST_CASE() [17/23]

BOOST_AUTO_TEST_CASE

(

test_tax1e_needUpdate

)

Definition at line 583 of file taxon1_unit_test.cpp.

References b, CTaxon1::CheckOrgRef(), CTaxon1::eStatus_WrongCommonName, CTaxon1::eStatus_WrongDivision, CTaxon1::eStatus_WrongLineage, CTaxon1::eStatus_WrongOrgname, CConstRef< C, Locker >::GetPointer(), CTaxon1::LookupMerge(), NULL, NStr::Replace(), s_String2OrgRef(), and tax1.

BOOST_AUTO_TEST_CASE() [18/23]

BOOST_AUTO_TEST_CASE

(

test_tax1m_getBlastName

)

Definition at line 571 of file taxon1_unit_test.cpp.

References b, CTaxon1::GetBlastName(), and tax1.

BOOST_AUTO_TEST_CASE() [19/23]

BOOST_AUTO_TEST_CASE

(

test_tax1m_getbyid

)

Definition at line 160 of file taxon1_unit_test.cpp.

References CTaxon1::GetScientificName(), and tax1.

BOOST_AUTO_TEST_CASE() [20/23]

BOOST_AUTO_TEST_CASE

(

test_tax1m_getDivByName

)

Definition at line 691 of file taxon1_unit_test.cpp.

References b, CTaxon1::GetDivisionIdByName(), CTaxon1::GetDivisionName(), and tax1.

BOOST_AUTO_TEST_CASE() [21/23]

BOOST_AUTO_TEST_CASE

(

test_tax1m_getRankByName

)

Definition at line 667 of file taxon1_unit_test.cpp.

References CTaxon1::GetRankIdByName(), and tax1.

BOOST_AUTO_TEST_CASE() [22/23]

BOOST_AUTO_TEST_CASE

(

test_tax1m_lookup

)

Definition at line 426 of file taxon1_unit_test.cpp.

References CTaxon2_data_Base::GetBlast_name(), CTaxon2_data_Base::GetIs_species_level(), CTaxon2_data_Base::GetIs_uncultured(), CTaxon2_data_Base::GetOrg(), CTaxon2_data_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), CTaxon1::Lookup(), CTaxon1::LookupMerge(), NStr::MatchesMask(), NULL, CRef< C, Locker >::Reset(), s_OrgRef2String(), s_String2OrgRef(), and tax1.

BOOST_AUTO_TEST_CASE() [23/23]

BOOST_AUTO_TEST_CASE

(

test_tax1m_lookup_tm

)

Definition at line 394 of file taxon1_unit_test.cpp.

References CTaxon1::LookupMerge(), NStr::MatchesMask(), NULL, CRef< C, Locker >::Reset(), s_OrgRef2String(), s_String2OrgRef(), and tax1.

BOOST_AUTO_TEST_SUITE_END()

BOOST_AUTO_TEST_SUITE_END

(

)

Auxiliary class to convert a string into an argument count and vector.

Definition at line 3204 of file blastinput_unit_test.cpp.

NCBITEST_AUTO_FINI()

NCBITEST_AUTO_FINI

(

)

Definition at line 73 of file taxon1_unit_test.cpp.

References CTaxon1::Fini(), and tax1.

NCBITEST_AUTO_INIT()

NCBITEST_AUTO_INIT

(

)

Definition at line 55 of file taxon1_unit_test.cpp.

NCBITEST_INIT_CMDLINE()

NCBITEST_INIT_CMDLINE

(

arg_desc

)

Definition at line 61 of file taxon1_unit_test.cpp.

References CArgDescriptions::eString.

NCBITEST_INIT_TREE()

NCBITEST_INIT_TREE

(

)

Definition at line 81 of file taxon1_unit_test.cpp.

References NCBITEST_DEPENDS_ON.

s_OrgRef2String()

static string s_OrgRef2String ( const COrg_ref &  orgref )

static

Definition at line 184 of file taxon1_unit_test.cpp.

References eSerial_AsnText, and CObjectOStream::Open().

Referenced by BOOST_AUTO_TEST_CASE().

s_String2OrgRef()

static CRef< COrg_ref > s_String2OrgRef ( const string &  orgref_in )

static

Definition at line 173 of file taxon1_unit_test.cpp.

References CObjectIStream::CreateFromBuffer(), and eSerial_AsnText.

Referenced by BOOST_AUTO_TEST_CASE().

USING_SCOPE()

USING_SCOPE

(

objects

)

Variable Documentation

format

ESerialDataFormat format = eSerial_AsnBinary

Definition at line 53 of file taxon1_unit_test.cpp.

tax1

CTaxon1 tax1

Definition at line 52 of file taxon1_unit_test.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), and NCBITEST_AUTO_FINI().

USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 49 of file taxon1_unit_test.cpp.