#include <ncbi_pch.hpp>
#include <corelib/ncbi_system.hpp>
#include <corelib/ncbiapp.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/object_manager.hpp>
#include <objects/misc/sequence_macros.hpp>
#include <objects/seqtable/SeqTable_column.hpp>
#include <corelib/test_boost.hpp>
#include <gui/packages/pkg_sequence_edit/strain_serotype_influenza.hpp>
#include <gui/packages/pkg_sequence_edit/featedit_util.hpp>
#include <gui/packages/pkg_sequence_edit/add_deflinedlg.hpp>
#include <gui/packages/pkg_sequence_edit/prefix_deflinedlg.hpp>
#include <gui/packages/pkg_sequence_edit/field_choice_panel.hpp>
#include <gui/packages/pkg_sequence_edit/miscedit_util.hpp>
#include <gui/widgets/edit/field_type_constants.hpp>
#include <gui/objutils/cmd_create_feat.hpp>
#include <gui/objutils/cmd_add_seqentry.hpp>

Include dependency graph for unit_test_pkg_seqedit.cpp:

Go to the SVN repository for this file.

Functions
	NCBITEST_AUTO_INIT ()

	NCBITEST_AUTO_FINI ()

void	ReadEntry (const string &name, CSeq_entry_Handle &seh)

	BOOST_AUTO_TEST_CASE (Test_MultipleStrains)

	BOOST_AUTO_TEST_CASE (Test_MultipleStrainsEmpty)

	BOOST_AUTO_TEST_CASE (Test_AddStrainSerotype)

	BOOST_AUTO_TEST_CASE (Test_FixInfluenzaNames)

	BOOST_AUTO_TEST_CASE (Test_ParsingNoConflicts)

	BOOST_AUTO_TEST_CASE (Test_ParsingWithConflictsUpdate)

	BOOST_AUTO_TEST_CASE (Test_ParsingWithConflictsNoUpdate)

	BOOST_AUTO_TEST_CASE (Test_SplittingStructuredCollections)

	BOOST_AUTO_TEST_CASE (Test_TrimmingOrganismNames)

	BOOST_AUTO_TEST_CASE (Test_AddrRNa)

	BOOST_AUTO_TEST_CASE (Test_AddControlRegion)

	BOOST_AUTO_TEST_CASE (Test_AddMicrosatellite)

	BOOST_AUTO_TEST_CASE (Test_AddDefLine)

	BOOST_AUTO_TEST_CASE (Test_RemoveDefLines)

	BOOST_AUTO_TEST_CASE (Test_PrefixDefline)

	BOOST_AUTO_TEST_CASE (Test_Automatch)

	BOOST_AUTO_TEST_CASE (Test_LooksLikeHeader)

CRef< CUser_object >	x_MakeDefaultTextOptions (size_t num_cols)

void	x_TestPair (CSeq_entry_Handle seh, const string &match, const string &field, const vector< string > &match_vals, const vector< string > &field_vals)

void	x_TestList (CSeq_entry_Handle seh, const string &match, const vector< string > &field_list, const vector< string > &match_vals, const vector< vector< string > > &field_vals)

Variables
	USING_NCBI_SCOPE

const char *	sc_TestEntry_multiplestrains

const char *	sc_TestEntry_mtplstrains_empty

const char *	sc_TestEntry_addstrainserotype

const char *	sc_TestEntry_fixorganismnames

const char *	sc_TestEntry_noparsing

const char *	sc_TestEntry_parsingnoconflicts

const char *	sc_TestEntry_parsingwithconflicts

const char *	sc_TestEntry_splitstructcollections

const char *	sc_TestEntry_trimorgnames

const char *	sc_TestEntry_addfeat

const char *	sc_TestEntry_adddefline

const char *	sc_TestEntry_removedeflines

const char *	sc_TestEntry_prefixtodeflines

const char *	sc_TestEntry_apply_table

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/17]

BOOST_AUTO_TEST_CASE ( Test_AddControlRegion )

Definition at line 661 of file unit_test_pkg_seqedit.cpp.

References CreateControlRegion(), eExtreme_Biological, eNa_strand_plus, CCmdComposite::Execute(), CSeq_feat_Base::GetComment(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_feat_Base::GetData(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeqFeatData_Base::GetImp(), CSeq_loc_Base::GetInt(), CImp_feat_Base::GetKey(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetPartial(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), CSeqFeatData_Base::IsImp(), CSeq_loc_Base::IsInt(), CSeq_interval::IsPartialStart(), CSeq_interval::IsPartialStop(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetLocation(), CSeq_feat_Base::IsSetPartial(), CSeq_interval_Base::IsSetStrand(), ReadEntry(), sc_TestEntry_addfeat, CSeq_feat_Base::SetLocation(), VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY, and CSeq_id_Base::Which().

◆ BOOST_AUTO_TEST_CASE() [2/17]

BOOST_AUTO_TEST_CASE ( Test_AddDefLine )

Definition at line 749 of file unit_test_pkg_seqedit.cpp.

References cmd, CountDefLineConflicts(), eExistingText_replace_old, CSeq_entry_Handle::GetCompleteSeq_entry(), ReadEntry(), sc_TestEntry_adddefline, UpdateAllDefinitionLine(), and VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.

◆ BOOST_AUTO_TEST_CASE() [3/17]

BOOST_AUTO_TEST_CASE ( Test_AddMicrosatellite )

Definition at line 703 of file unit_test_pkg_seqedit.cpp.

References CreateMicrosatellite(), eExtreme_Biological, eNa_strand_plus, CCmdComposite::Execute(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_feat_Base::GetData(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeqFeatData_Base::GetImp(), CSeq_loc_Base::GetInt(), CImp_feat_Base::GetKey(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetQual(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), CSeqFeatData_Base::IsImp(), CSeq_loc_Base::IsInt(), CSeq_interval::IsPartialStart(), CSeq_interval::IsPartialStop(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetLocation(), CSeq_feat_Base::IsSetPartial(), CSeq_interval_Base::IsSetStrand(), ReadEntry(), sc_TestEntry_addfeat, CSeq_feat_Base::SetLocation(), VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY, and CSeq_id_Base::Which().

◆ BOOST_AUTO_TEST_CASE() [4/17]

BOOST_AUTO_TEST_CASE ( Test_AddrRNa )

Definition at line 618 of file unit_test_pkg_seqedit.cpp.

References AddNamedrRna(), eExtreme_Biological, eNa_strand_plus, CRNA_ref_Base::eType_rRNA, CCmdComposite::Execute(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeq_loc_Base::GetInt(), CSeq_feat_Base::GetLocation(), CRNA_ref_Base::C_Ext::GetName(), CSeq_feat_Base::GetPartial(), CSeqFeatData_Base::GetRna(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), CRNA_ref_Base::GetType(), CSeq_loc_Base::IsInt(), CSeq_interval::IsPartialStart(), CSeq_interval::IsPartialStop(), CSeqFeatData_Base::IsRna(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetLocation(), CSeq_feat_Base::IsSetPartial(), CSeq_interval_Base::IsSetStrand(), ReadEntry(), rna, sc_TestEntry_addfeat, CSeq_feat_Base::SetLocation(), VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY, and CSeq_id_Base::Which().

◆ BOOST_AUTO_TEST_CASE() [5/17]

BOOST_AUTO_TEST_CASE ( Test_AddStrainSerotype )

Definition at line 150 of file unit_test_pkg_seqedit.cpp.

References CStrainSerotypeInfluenza::eCommandInfluenza_add, NStr::eNocase, NStr::Equal(), COrgMod_Base::eSubtype_old_name, CCmdComposite::Execute(), FOR_EACH_DBXREF_ON_ORGREF, FOR_EACH_ORGMOD_ON_BIOSOURCE, CStrainSerotypeInfluenza::GetCommand(), CSeq_entry_Handle::GetCompleteSeq_entry(), ReadEntry(), sc_TestEntry_addstrainserotype, and VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.

◆ BOOST_AUTO_TEST_CASE() [6/17]

BOOST_AUTO_TEST_CASE ( Test_Automatch )

Definition at line 2900 of file unit_test_pkg_seqedit.cpp.

References CFieldChoicePanel::AutoMatch().

◆ BOOST_AUTO_TEST_CASE() [7/17]

BOOST_AUTO_TEST_CASE ( Test_FixInfluenzaNames )

Definition at line 214 of file unit_test_pkg_seqedit.cpp.

References CStrainSerotypeInfluenza::eCommandInfluenza_fixup, NStr::eNocase, NStr::Equal(), COrgMod_Base::eSubtype_old_name, CCmdComposite::Execute(), FOR_EACH_DBXREF_ON_ORGREF, FOR_EACH_ORGMOD_ON_BIOSOURCE, CStrainSerotypeInfluenza::GetCommand(), CSeq_entry_Handle::GetCompleteSeq_entry(), ReadEntry(), sc_TestEntry_fixorganismnames, and VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.

◆ BOOST_AUTO_TEST_CASE() [8/17]

BOOST_AUTO_TEST_CASE ( Test_LooksLikeHeader )

Definition at line 2908 of file unit_test_pkg_seqedit.cpp.

References CFieldChoicePanel::LooksLikeHeader().

◆ BOOST_AUTO_TEST_CASE() [9/17]

BOOST_AUTO_TEST_CASE ( Test_MultipleStrains )

Definition at line 90 of file unit_test_pkg_seqedit.cpp.

References CStrainSerotypeInfluenza::eCommandSplitQualsAtCommas, COrgMod_Base::eSubtype_strain, CCmdComposite::Execute(), FOR_EACH_ORGMOD_ON_BIOSOURCE, CStrainSerotypeInfluenza::GetCommand(), CSeq_entry_Handle::GetCompleteSeq_entry(), ReadEntry(), sc_TestEntry_multiplestrains, and VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.

◆ BOOST_AUTO_TEST_CASE() [10/17]

BOOST_AUTO_TEST_CASE ( Test_MultipleStrainsEmpty )

Definition at line 122 of file unit_test_pkg_seqedit.cpp.

References CStrainSerotypeInfluenza::eCommandSplitQualsAtCommas, COrgMod_Base::eSubtype_strain, CCmdComposite::Execute(), FOR_EACH_ORGMOD_ON_BIOSOURCE, CStrainSerotypeInfluenza::GetCommand(), CSeq_entry_Handle::GetCompleteSeq_entry(), ReadEntry(), sc_TestEntry_mtplstrains_empty, and VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.

◆ BOOST_AUTO_TEST_CASE() [11/17]

BOOST_AUTO_TEST_CASE ( Test_ParsingNoConflicts )

Definition at line 279 of file unit_test_pkg_seqedit.cpp.

References CStrainSerotypeInfluenza::eCommandInfluenza_parse, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_strain, CCmdComposite::Execute(), FOR_EACH_ORGMOD_ON_BIOSOURCE, CStrainSerotypeInfluenza::GetCommand(), CSeq_entry_Handle::GetCompleteSeq_entry(), ReadEntry(), sc_TestEntry_parsingnoconflicts, and VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.

◆ BOOST_AUTO_TEST_CASE() [12/17]

BOOST_AUTO_TEST_CASE ( Test_ParsingWithConflictsNoUpdate )

Definition at line 363 of file unit_test_pkg_seqedit.cpp.

References CStrainSerotypeInfluenza::eCommandInfluenza_parse, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_strain, CCmdComposite::Execute(), FOR_EACH_ORGMOD_ON_BIOSOURCE, CSeq_entry_Handle::GetCompleteSeq_entry(), ReadEntry(), sc_TestEntry_parsingwithconflicts, TestCStrainSerotypeInfluenza_Parse(), and VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.

◆ BOOST_AUTO_TEST_CASE() [13/17]

BOOST_AUTO_TEST_CASE ( Test_ParsingWithConflictsUpdate )

Definition at line 314 of file unit_test_pkg_seqedit.cpp.

References CStrainSerotypeInfluenza::eCommandInfluenza_parse, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_strain, CCmdComposite::Execute(), FOR_EACH_ORGMOD_ON_BIOSOURCE, CSeq_entry_Handle::GetCompleteSeq_entry(), ReadEntry(), sc_TestEntry_parsingwithconflicts, TestCStrainSerotypeInfluenza_Parse(), and VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.

◆ BOOST_AUTO_TEST_CASE() [14/17]

BOOST_AUTO_TEST_CASE ( Test_PrefixDefline )

Definition at line 813 of file unit_test_pkg_seqedit.cpp.

References AddModToDefline(), AddModVectorToDefline(), AddOrgToDefline(), CSubSource_Base::eSubtype_haplotype, COrgMod_Base::eSubtype_isolate, COrgMod_Base::eSubtype_strain, CCmdComposite::Execute(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Base::IsSeq(), ReadEntry(), CRef< C, Locker >::Reset(), sc_TestEntry_prefixtodeflines, CCmdComposite::Unexecute(), and VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.

◆ BOOST_AUTO_TEST_CASE() [15/17]

BOOST_AUTO_TEST_CASE ( Test_RemoveDefLines )

Definition at line 782 of file unit_test_pkg_seqedit.cpp.

References CCmdComposite::Execute(), CSeq_entry_Handle::GetCompleteSeq_entry(), ReadEntry(), RemoveTitlesSeqEntry(), sc_TestEntry_removedeflines, and VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.

◆ BOOST_AUTO_TEST_CASE() [16/17]

BOOST_AUTO_TEST_CASE ( Test_SplittingStructuredCollections )

Definition at line 420 of file unit_test_pkg_seqedit.cpp.

References CStrainSerotypeInfluenza::eCommandSplitStructuredCollections, COrgMod_Base::eSubtype_bio_material, COrgMod_Base::eSubtype_culture_collection, COrgMod_Base::eSubtype_specimen_voucher, CCmdComposite::Execute(), FOR_EACH_ORGMOD_ON_BIOSOURCE, CStrainSerotypeInfluenza::GetCommand(), CSeq_entry_Handle::GetCompleteSeq_entry(), ReadEntry(), sc_TestEntry_splitstructcollections, ncbi::grid::netcache::search::fields::size, and VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.

◆ BOOST_AUTO_TEST_CASE() [17/17]

BOOST_AUTO_TEST_CASE ( Test_TrimmingOrganismNames )

Definition at line 485 of file unit_test_pkg_seqedit.cpp.

References CStrainSerotypeInfluenza::eCommandTrimOrganismNames, NStr::eNocase, NStr::Equal(), CCmdComposite::Execute(), FOR_EACH_DBXREF_ON_ORGREF, CStrainSerotypeInfluenza::GetCommand(), CSeq_entry_Handle::GetCompleteSeq_entry(), ReadEntry(), sc_TestEntry_trimorgnames, and VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.

◆ NCBITEST_AUTO_FINI()

NCBITEST_AUTO_FINI ( )

Definition at line 76 of file unit_test_pkg_seqedit.cpp.

◆ NCBITEST_AUTO_INIT()

NCBITEST_AUTO_INIT ( )

Definition at line 72 of file unit_test_pkg_seqedit.cpp.

◆ ReadEntry()

void ReadEntry	(	const string &	name,
		CSeq_entry_Handle &	seh
	)

Definition at line 80 of file unit_test_pkg_seqedit.cpp.

References CScope::AddTopLevelSeqEntry(), CObjectManager::GetInstance(), and MSerial_AsnText.

Referenced by BOOST_AUTO_TEST_CASE().

◆ x_MakeDefaultTextOptions()

CRef<CUser_object> x_MakeDefaultTextOptions ( size_t num_cols )

Definition at line 2992 of file unit_test_pkg_seqedit.cpp.

References eExistingText_replace_old, i, MakeTableMetaInfoField(), and CUser_object_Base::SetData().

Referenced by x_TestList(), and x_TestPair().

◆ x_TestList()

void x_TestList	(	CSeq_entry_Handle	seh,
		const string &	match,
		const vector< string > &	field_list,
		const vector< string > &	match_vals,
		const vector< vector< string > > &	field_vals
	)

Definition at line 3070 of file unit_test_pkg_seqedit.cpp.

References CSeq_id::eContent, NStr::Equal(), CSeq_table_Base::GetColumns(), CSeqTable_column_Base::GetData(), CSeqTable_multi_data_Base::GetId(), GetMiscTableFromSeqEntry(), CSeqTable_multi_data_Base::GetString(), CSeqTable_multi_data_Base::IsId(), kSequenceIdColLabel, match(), row, CSeqTable_column_Base::SetData(), CSeqTable_column_Base::SetHeader(), ncbi::grid::netcache::search::fields::size, table, and x_MakeDefaultTextOptions().

◆ x_TestPair()

void x_TestPair	(	CSeq_entry_Handle	seh,
		const string &	match,
		const string &	field,
		const vector< string > &	match_vals,
		const vector< string > &	field_vals
	)