NCBI C++ ToolKit
Functions | Variables
unit_test_autodef.cpp File Reference
#include <ncbi_pch.hpp>
#include "unit_test_autodef.hpp"
#include <corelib/ncbi_system.hpp>
#include <corelib/test_boost.hpp>
#include <objects/biblio/Id_pat.hpp>
#include <objects/biblio/Title.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/User_object.hpp>
#include <objects/medline/Medline_entry.hpp>
#include <objects/misc/sequence_macros.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seq/GIBB_mol.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objects/seq/Ref_ext.hpp>
#include <objects/seq/Map_ext.hpp>
#include <objects/seq/Seg_ext.hpp>
#include <objects/seq/Seq_gap.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seq/Seq_hist.hpp>
#include <objects/seq/Seq_hist_rec.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqblock/GB_block.hpp>
#include <objects/seqblock/EMBL_block.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/PDB_seq_id.hpp>
#include <objects/seqloc/Giimport_id.hpp>
#include <objects/seqloc/Patent_seq_id.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objtools/unit_test_util/unit_test_util.hpp>
#include <corelib/ncbiapp.hpp>
#include <objtools/edit/autodef_with_tax.hpp>
#include <serial/objostrasn.hpp>
#include <serial/objostrasnb.hpp>
#include <common/test_assert.h>
+ Include dependency graph for unit_test_autodef.cpp:

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Functions

 NCBITEST_INIT_TREE ()
 
 NCBITEST_INIT_CMDLINE (arg_desc)
 
 NCBITEST_AUTO_INIT ()
 
static CRef< CSeq_entry > BuildSequence ()
 
static CRef< CSeqdesc > AddSource (CRef< CSeq_entry > entry, string taxname)
 
static void AddTitle (CRef< CSeq_entry > entry, string defline)
 
size_t HasBoolField (const CUser_object &user, const string &field_name)
 
size_t HasStringField (const CUser_object &user, const string &field_name, const string &value)
 
size_t HasIntField (const CUser_object &user, const string &field_name, int value)
 
void CheckAutoDefOptions (const CUser_object &user, CAutoDefOptions &opts)
 
static void CheckDeflineMatches (CSeq_entry_Handle seh, CAutoDefWithTaxonomy &autodef, CRef< CAutoDefModifierCombo > mod_combo)
 
static void CheckDeflineMatches (CRef< CSeq_entry > entry, vector< CSubSource::ESubtype > subsrcs, vector< COrgMod::ESubtype > orgmods, bool init_with_descrs=false)
 
static void CheckDeflineMatches (CRef< CSeq_entry > entry, bool use_best=false, CAutoDefOptions::EFeatureListType list_type=CAutoDefOptions::eListAllFeatures, CAutoDefOptions::EMiscFeatRule misc_feat_rule=CAutoDefOptions::eNoncodingProductFeat, bool init_with_descrs=false)
 
static void CheckDeflineMatchesWithDescr (CRef< CSeq_entry > entry, bool use_best=false, CAutoDefOptions::EFeatureListType list_type=CAutoDefOptions::eListAllFeatures, CAutoDefOptions::EMiscFeatRule misc_feat_rule=CAutoDefOptions::eNoncodingProductFeat)
 
static CAutoDef::TSources s_GatherSources (const CSeq_entry &entry)
 
static void CheckDeflineMatches (CRef< CSeq_entry > entry, CSeqFeatData::ESubtype feat_to_suppress, bool init_with_descrs=false)
 
CRef< CSeq_entry > FindNucInSeqEntry (CRef< CSeq_entry > entry)
 
static void AddFeat (CRef< CSeq_feat > feat, CRef< CSeq_entry > entry)
 
static CRef< CSeq_entry > MakeProteinForNucProtSet (string id, string protein_name)
 
static CRef< CSeq_feat > MakeCDSForNucProtSet (string nuc_id, string prot_id)
 
static CRef< CSeq_feat > MakeGeneForNucProtSet (const string &nuc_id, const string &locus, const string &allele=kEmptyStr)
 
static CRef< CSeq_entry > BuildNucProtSet (const string &protein_name, const string &locus=kEmptyStr, const string &allele=kEmptyStr)
 
 BOOST_AUTO_TEST_CASE (Test_SimpleAutodef)
 
 BOOST_AUTO_TEST_CASE (Test_UnnamedPlasmid)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_476)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_630)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_169)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_374)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_155)
 
 BOOST_AUTO_TEST_CASE (Test_DocsumTitle_Popset)
 
 BOOST_AUTO_TEST_CASE (Test_DocsumTitle_Physet)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3108)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3099)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3359)
 
void TestOneOrganelleSequenceDefline (CBioSource::TGenome genome, const string &defline)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_1733)
 
void AddExon (CRef< CSeq_entry > seq, const string &number, TSeqPos start)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3386)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3410)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3395)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3439)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3488)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3486)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3496)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3458)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3679)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3848)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_2075)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_2115)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3866)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_2118)
 
 BOOST_AUTO_TEST_CASE (Test_GB_1851)
 
void s_SetProteinName (CRef< CSeq_entry > prot, const string &name)
 
CRef< CSeq_feat > s_AddCDS (CRef< CSeq_entry > np, const string &name, TSeqPos from, TSeqPos to)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3942)
 
 BOOST_AUTO_TEST_CASE (Test_GB_8927)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3926)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_2181)
 
 BOOST_AUTO_TEST_CASE (Test_GB_3949)
 
 BOOST_AUTO_TEST_CASE (Test_GB_4043)
 
 BOOST_AUTO_TEST_CASE (Test_GB_4078)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_2370)
 
 BOOST_AUTO_TEST_CASE (Test_GB_4242)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_3440)
 
 BOOST_AUTO_TEST_CASE (Test_RemovableuORF)
 
 BOOST_AUTO_TEST_CASE (Test_RemovableMobileElement)
 
 BOOST_AUTO_TEST_CASE (GB_5272)
 
 BOOST_AUTO_TEST_CASE (GB_5272a)
 
 BOOST_AUTO_TEST_CASE (GB_5272b)
 
 BOOST_AUTO_TEST_CASE (SQD_3462)
 
 BOOST_AUTO_TEST_CASE (Test_IsModifierInString)
 
 BOOST_AUTO_TEST_CASE (Test_IsUsableInDefline)
 
 BOOST_AUTO_TEST_CASE (Test_GB_5493)
 
 BOOST_AUTO_TEST_CASE (Test_TargetedLocusName)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_3602)
 
 BOOST_AUTO_TEST_CASE (Test_SB_5494)
 
 BOOST_AUTO_TEST_CASE (Test_GB_5447)
 
void MakeRegulatoryFeatureTest (const string &regulatory_class, const string &defline_interval, bool use_fake_promoters, bool keep_regulatory)
 
 BOOST_AUTO_TEST_CASE (GB_5537)
 
 BOOST_AUTO_TEST_CASE (Test_AutodefOptionsSpecifyNuclearCopyFlag)
 
 BOOST_AUTO_TEST_CASE (Test_GB_5560)
 
 BOOST_AUTO_TEST_CASE (Test_GB_5758)
 
void TestForRecomb (CRef< CSeq_entry > entry, const string &expected)
 
 BOOST_AUTO_TEST_CASE (Test_GB_5793)
 
 BOOST_AUTO_TEST_CASE (Test_GB_5765)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_3914)
 
 BOOST_AUTO_TEST_CASE (Test_CAutoDefAvailableModifier_GetOrgModLabel)
 
 BOOST_AUTO_TEST_CASE (Test_GB_5618)
 
 BOOST_AUTO_TEST_CASE (Test_GB_6375)
 
 BOOST_AUTO_TEST_CASE (Test_GB_6557)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_4185)
 
 BOOST_AUTO_TEST_CASE (Test_GB_6690)
 
 BOOST_AUTO_TEST_CASE (Test_GB_6690_WithDescr)
 
CRef< CUser_field > MkField (const string &label, const string &val)
 
 BOOST_AUTO_TEST_CASE (Test_HumanSTR)
 
 BOOST_AUTO_TEST_CASE (Test_GB_7071)
 
 BOOST_AUTO_TEST_CASE (Test_GB_7479)
 
void CheckInfluenzaDefline (const string &taxname, const string &strain, const string &serotype, const string &clone, const string &segment, const string &defline)
 
 BOOST_AUTO_TEST_CASE (Test_GB_7485)
 
 BOOST_AUTO_TEST_CASE (Test_GB_7534)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_4451)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_4529)
 
void AddProtFeat (CRef< CSeq_entry > prot, CProt_ref::EProcessed proc)
 
void TestMatPeptideListing (bool cds_is_partial, bool has_sig_peptide)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_4593)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_4607)
 
void CheckRegulatoryFeatures (const string &expected_title, bool keep_promoters, bool keep_regulatory)
 
 BOOST_AUTO_TEST_CASE (Test_SQD_4612)
 
 BOOST_AUTO_TEST_CASE (Test_GB_8547)
 
 BOOST_AUTO_TEST_CASE (Test_GB_8604)
 
CRef< CSeq_feat > MakeRegulatoryFeature (const string &reg_class, const string &comment, TSeqPos start_pos, CRef< CSeq_entry > entry)
 
CRef< CSeq_feat > MakeRptRegion (const string &rpt_type, TSeqPos start_pos, CRef< CSeq_entry > entry)
 
void TestRepeatRegion (CRef< CSeq_entry > entry, bool init_with_descrs=false)
 
 BOOST_AUTO_TEST_CASE (Test_GB_8854)
 
 BOOST_AUTO_TEST_CASE (Test_ClauseListOptions)
 

Variables

const char * sc_TestEntryCollidingLocusTags
 
static bool s_debugMode = false
 

Function Documentation

◆ AddExon()

void AddExon ( CRef< CSeq_entry >  seq,
const string &  number,
TSeqPos  start 
)

Definition at line 1006 of file unit_test_autodef.cpp.

References AddGoodImpFeat(), NStr::IsBlank(), number, CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetLocation(), CGb_qual_Base::SetQual(), CSeq_feat_Base::SetQual(), and CGb_qual_Base::SetVal().

Referenced by BOOST_AUTO_TEST_CASE().

◆ AddFeat()

static void AddFeat ( CRef< CSeq_feat >  feat,
CRef< CSeq_entry >  entry 
)
static

Definition at line 589 of file unit_test_autodef.cpp.

References CSeq_loc_Base::e_not_set, FindNucInSeqEntry(), CBioseq_Base::GetAnnot(), CBioseq_set_Base::GetAnnot(), CBioseq_Base::GetId(), CBioseq::GetLength(), CSeq_feat_Base::GetLocation(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_Base::IsSetAnnot(), CBioseq_set_Base::IsSetAnnot(), CSeq_feat_Base::IsSetLocation(), CBioseq_Base::SetAnnot(), CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CSeq_entry_Base::SetSet(), and CSeq_loc_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), BuildNucProtSet(), MakeProteinForNucProtSet(), and TestMatPeptideListing().

◆ AddProtFeat()

void AddProtFeat ( CRef< CSeq_entry >  prot,
CProt_ref::EProcessed  proc 
)

Definition at line 2905 of file unit_test_autodef.cpp.

References AddMiscFeature(), proc, prot, CSeq_feat_Base::ResetComment(), and CSeq_feat_Base::SetData().

Referenced by BOOST_AUTO_TEST_CASE(), and TestMatPeptideListing().

◆ AddSource()

static CRef<CSeqdesc> AddSource ( CRef< CSeq_entry >  entry,
string  taxname 
)
static

Definition at line 173 of file unit_test_autodef.cpp.

References CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_Base::SetDescr(), CBioseq_set_Base::SetDescr(), CBioSource_Base::SetOrg(), CSeq_entry_Base::SetSeq(), CSeq_entry_Base::SetSet(), and CSeqdesc_Base::SetSource().

Referenced by BOOST_AUTO_TEST_CASE().

◆ AddTitle()

static void AddTitle ( CRef< CSeq_entry >  entry,
string  defline 
)
static

Definition at line 187 of file unit_test_autodef.cpp.

References CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Base::GetClass(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_set_Base::IsSetClass(), CBioseq_Base::IsSetDescr(), NON_CONST_ITERATE, CBioseq_Base::SetDescr(), CBioseq_set_Base::SetDescr(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CSeqdesc_Base::SetTitle().

Referenced by BOOST_AUTO_TEST_CASE(), CheckInfluenzaDefline(), CheckRegulatoryFeatures(), MakeRegulatoryFeatureTest(), TestForRecomb(), TestMatPeptideListing(), and TestOneOrganelleSequenceDefline().

◆ BOOST_AUTO_TEST_CASE() [1/79]

BOOST_AUTO_TEST_CASE ( GB_5272  )

Definition at line 1888 of file unit_test_autodef.cpp.

References AddFeat(), AddSource(), AddTitle(), BuildNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), nuc, CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

◆ BOOST_AUTO_TEST_CASE() [2/79]

BOOST_AUTO_TEST_CASE ( GB_5272a  )

Definition at line 1904 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), AddFeat(), AddSource(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), BuildNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CSeqFeatData::eSubtype_gene, GetCDSFromGoodNucProtSet(), CObjectManager::GetInstance(), CSeq_feat_Base::GetLocation(), GetNucleotideSequenceFromGoodNucProtSet(), MakeCDSForGoodNucProtSet(), MakeProteinForGoodNucProtSet(), nuc, s_GatherSources(), CBioseq_Base::SetAnnot(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CAutoDef::SuppressFeature().

◆ BOOST_AUTO_TEST_CASE() [3/79]

BOOST_AUTO_TEST_CASE ( GB_5272b  )

Definition at line 1972 of file unit_test_autodef.cpp.

References AddFeat(), AddSource(), AddTitle(), BuildNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), GetNucleotideSequenceFromGoodNucProtSet(), MakeCDSForGoodNucProtSet(), MakeProteinForGoodNucProtSet(), nuc, CBioseq_Base::SetAnnot(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

◆ BOOST_AUTO_TEST_CASE() [4/79]

BOOST_AUTO_TEST_CASE ( GB_5537  )

Definition at line 2249 of file unit_test_autodef.cpp.

References kEmptyStr, and MakeRegulatoryFeatureTest().

◆ BOOST_AUTO_TEST_CASE() [5/79]

BOOST_AUTO_TEST_CASE ( SQD_3462  )

Definition at line 2004 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), AddMiscFeature(), AddSource(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), BuildNucProtSet(), CheckDeflineMatches(), eExtreme_Biological, COrgMod_Base::eSubtype_isolate, GetCDSFromGoodNucProtSet(), CObjectManager::GetInstance(), GetNucleotideSequenceFromGoodNucProtSet(), nuc, CSeq_feat_Base::ResetComment(), s_GatherSources(), CSeq_feat_Base::SetData(), CAutoDef::SetKeepExons(), CAutoDef::SetKeepIntrons(), CSeq_feat_Base::SetLocation(), SetOrgMod(), and CSeq_feat_Base::SetQual().

◆ BOOST_AUTO_TEST_CASE() [6/79]

BOOST_AUTO_TEST_CASE ( Test_AutodefOptionsSpecifyNuclearCopyFlag  )

Definition at line 2278 of file unit_test_autodef.cpp.

References CBioSource_Base::eGenome_mitochondrion, HasStringField(), CAutoDefOptions::MakeUserObject(), and CAutoDefOptions::SetNuclearCopyFlag().

◆ BOOST_AUTO_TEST_CASE() [7/79]

BOOST_AUTO_TEST_CASE ( Test_CAutoDefAvailableModifier_GetOrgModLabel  )

Definition at line 2424 of file unit_test_autodef.cpp.

References COrgMod_Base::eSubtype_acronym, COrgMod_Base::eSubtype_anamorph, COrgMod_Base::eSubtype_authority, COrgMod_Base::eSubtype_biotype, COrgMod_Base::eSubtype_biovar, COrgMod_Base::eSubtype_breed, COrgMod_Base::eSubtype_chemovar, COrgMod_Base::eSubtype_cultivar, COrgMod_Base::eSubtype_culture_collection, COrgMod_Base::eSubtype_ecotype, COrgMod_Base::eSubtype_forma, COrgMod_Base::eSubtype_group, COrgMod_Base::eSubtype_isolate, COrgMod_Base::eSubtype_pathovar, COrgMod_Base::eSubtype_serogroup, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_serovar, COrgMod_Base::eSubtype_strain, COrgMod_Base::eSubtype_subgroup, COrgMod_Base::eSubtype_substrain, COrgMod_Base::eSubtype_subtype, COrgMod_Base::eSubtype_synonym, COrgMod_Base::eSubtype_teleomorph, COrgMod_Base::eSubtype_type, COrgMod_Base::eSubtype_variety, and CAutoDefAvailableModifier::GetOrgModLabel().

◆ BOOST_AUTO_TEST_CASE() [8/79]

BOOST_AUTO_TEST_CASE ( Test_ClauseListOptions  )

Definition at line 3166 of file unit_test_autodef.cpp.

References AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CAutoDefOptions::eCompleteGenome, CAutoDefOptions::eCompleteSequence, CAutoDefOptions::ePartialGenome, CAutoDefOptions::ePartialSequence, and CAutoDefOptions::eWholeGenomeShotgunSequence.

◆ BOOST_AUTO_TEST_CASE() [9/79]

BOOST_AUTO_TEST_CASE ( Test_DocsumTitle_Physet  )

Definition at line 884 of file unit_test_autodef.cpp.

References AddTitle(), BuildGoodNucProtSet(), ChangeId(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CBioseq_set_Base::eClass_pop_set, GetNucleotideSequenceFromGoodNucProtSet(), SetTaxname(), and SetTaxon().

◆ BOOST_AUTO_TEST_CASE() [10/79]

BOOST_AUTO_TEST_CASE ( Test_DocsumTitle_Popset  )

Definition at line 841 of file unit_test_autodef.cpp.

References AddTitle(), BuildGoodNucProtSet(), ChangeId(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CBioseq_set_Base::eClass_pop_set, COrgMod_Base::eSubtype_isolate, GetNucleotideSequenceFromGoodNucProtSet(), SetOrgMod(), SetTaxname(), and SetTaxon().

◆ BOOST_AUTO_TEST_CASE() [11/79]

BOOST_AUTO_TEST_CASE ( Test_GB_1851  )

Definition at line 1320 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CAutoDefOptions::eCommentFeat, CAutoDefOptions::eDelete, eExtreme_Biological, CAutoDefOptions::eListAllFeatures, CAutoDefOptions::eNoncodingProductFeat, CSeq_feat_Base::SetComment(), and CSeq_feat_Base::SetLocation().

◆ BOOST_AUTO_TEST_CASE() [12/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3099  )

Definition at line 950 of file unit_test_autodef.cpp.

References AddFeat(), AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), GetNucleotideSequenceFromGoodNucProtSet(), nuc, CSeq_feat_Base::SetData(), SetNucProtSetProductName(), and SetTaxname().

◆ BOOST_AUTO_TEST_CASE() [13/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3108  )

Definition at line 914 of file unit_test_autodef.cpp.

References AddFeat(), AddSource(), AddTitle(), BuildSequence(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CRNA_ref_Base::eType_miscRNA, CRNA_ref_Base::eType_other, CRNA_ref_Base::eType_rRNA, CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

◆ BOOST_AUTO_TEST_CASE() [14/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3359  )

Definition at line 967 of file unit_test_autodef.cpp.

References AddFeat(), AddTitle(), BuildGoodFeat(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CMolInfo_Base::eBiomol_transcribed_RNA, CSeq_inst_Base::eMol_rna, CRNA_ref_Base::eType_ncRNA, SetBiomol(), CSeq_feat_Base::SetData(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and SetTaxname().

◆ BOOST_AUTO_TEST_CASE() [15/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3386  )

Definition at line 1021 of file unit_test_autodef.cpp.

References AddExon(), AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, eExtreme_Positional, GetCDSFromGoodNucProtSet(), CSeq_feat_Base::GetLocation(), GetNucleotideSequenceFromGoodNucProtSet(), CSeq_loc::GetStart(), nuc, and CSeq_feat_Base::SetLocation().

◆ BOOST_AUTO_TEST_CASE() [16/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3395  )

Definition at line 1072 of file unit_test_autodef.cpp.

References AddGoodImpFeat(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), and CSeq_feat_Base::ResetComment().

◆ BOOST_AUTO_TEST_CASE() [17/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3410  )

Definition at line 1048 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CRNA_ref_Base::eType_miscRNA, CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

◆ BOOST_AUTO_TEST_CASE() [18/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3439  )

Definition at line 1083 of file unit_test_autodef.cpp.

References AddGoodImpFeat(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CSeq_feat_Base::ResetComment(), and SetTaxname().

◆ BOOST_AUTO_TEST_CASE() [19/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3458  )

Definition at line 1155 of file unit_test_autodef.cpp.

References AddFeat(), AddMiscFeature(), AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Positional, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eRepr_raw, GetCDSFromGoodNucProtSet(), CSeq_feat_Base::GetLocation(), GetNucleotideSequenceFromGoodNucProtSet(), CSeq_loc::GetStart(), MakeGeneForFeature(), nuc, CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_id_Base::SetLocal(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetProduct(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CObject_id_Base::SetStr().

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BOOST_AUTO_TEST_CASE ( Test_GB_3486  )

Definition at line 1107 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), and SetTaxname().

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BOOST_AUTO_TEST_CASE ( Test_GB_3488  )

Definition at line 1095 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CRNA_ref_Base::eType_rRNA, rna, and SetTaxname().

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BOOST_AUTO_TEST_CASE ( Test_GB_3496  )

Definition at line 1128 of file unit_test_autodef.cpp.

References AddFeat(), AddGoodImpFeat(), AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), MakeGeneForFeature(), nuc, prot, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetPartial().

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BOOST_AUTO_TEST_CASE ( Test_GB_3679  )

Definition at line 1191 of file unit_test_autodef.cpp.

References AddFeat(), AddMiscFeature(), AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeGeneForFeature(), nuc, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CGb_qual_Base::SetQual(), CSeq_feat_Base::SetQual(), and CGb_qual_Base::SetVal().

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BOOST_AUTO_TEST_CASE ( Test_GB_3848  )

Definition at line 1216 of file unit_test_autodef.cpp.

References AddFeat(), AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeGeneForFeature(), nuc, and CSeq_feat_Base::SetData().

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BOOST_AUTO_TEST_CASE ( Test_GB_3866  )

Definition at line 1270 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CRNA_ref_Base::eType_miscRNA, CRNA_ref_Base::eType_rRNA, rna, CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

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BOOST_AUTO_TEST_CASE ( Test_GB_3926  )

Definition at line 1451 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), eExtreme_Biological, CSubSource_Base::eSubtype_clone, COrgMod_Base::eSubtype_isolate, CRNA_ref_Base::eType_rRNA, CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), SetOrgMod(), and SetSubSource().

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BOOST_AUTO_TEST_CASE ( Test_GB_3942  )

Definition at line 1385 of file unit_test_autodef.cpp.

References AddTitle(), BuildGoodNucProtSet(), ChangeId(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CSeq_loc_mix_Base::Get(), GetCDSFromGoodNucProtSet(), CBioseq_Base::GetId(), CSeq_feat_Base::GetLocation(), CSeq_loc_Base::GetMix(), GetNucleotideSequenceFromGoodNucProtSet(), GetProteinSequenceFromGoodNucProtSet(), CSeq_entry_Base::GetSeq(), MakeMixLoc(), nuc, s_AddCDS(), s_SetProteinName(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetProduct().

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BOOST_AUTO_TEST_CASE ( Test_GB_3949  )

Definition at line 1530 of file unit_test_autodef.cpp.

References AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), COrgMod_Base::eSubtype_culture_collection, GetNucleotideSequenceFromGoodNucProtSet(), nuc, and SetOrgMod().

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BOOST_AUTO_TEST_CASE ( Test_GB_4043  )

Definition at line 1546 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), AddMiscFeature(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), BuildGoodNucProtSet(), CheckDeflineMatches(), eExtreme_Biological, CAutoDef::FindBestModifierCombo(), GetCDSFromGoodNucProtSet(), CObjectManager::GetInstance(), CSeq_loc_Base::GetInt(), CSeq_feat_Base::GetLocation(), GetNucleotideSequenceFromGoodNucProtSet(), CSeq_interval_Base::GetTo(), nuc, CSeq_feat_Base::ResetComment(), s_GatherSources(), CSeq_feat_Base::SetData(), CAutoDef::SetKeepIntrons(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetQual().

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BOOST_AUTO_TEST_CASE ( Test_GB_4078  )

Definition at line 1606 of file unit_test_autodef.cpp.

References AddFeat(), AddMiscFeature(), AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CMolInfo_Base::eBiomol_cRNA, eExtreme_Biological, CSeq_inst_Base::eMol_rna, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeGeneForFeature(), nuc, SetBiomol(), CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

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BOOST_AUTO_TEST_CASE ( Test_GB_4242  )

Definition at line 1648 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), BuildGoodSeq(), CheckDeflineMatches(), CAutoDefOptions::eDelete, CAutoDefOptions::eListAllFeatures, COrgMod_Base::eSubtype_isolate, CObjectManager::GetInstance(), ITERATE, s_GatherSources(), CAutoDef::SetFeatureListType(), CAutoDef::SetMiscFeatRule(), SetOrgMod(), and SetTaxname().

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BOOST_AUTO_TEST_CASE ( Test_GB_5447  )

Definition at line 2162 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddProtFeat(), AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Positional, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eRepr_raw, GetCDSFromGoodNucProtSet(), CSeq_feat_Base::GetLocation(), GetNucleotideSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), CSeq_loc::GetStart(), nuc, CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_id_Base::SetLocal(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetProduct(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CObject_id_Base::SetStr().

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BOOST_AUTO_TEST_CASE ( Test_GB_5493  )

Definition at line 2099 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CRNA_ref_Base::eType_other, CSeq_feat_Base::SetComment(), and CSeq_feat_Base::SetData().

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BOOST_AUTO_TEST_CASE ( Test_GB_5560  )

Definition at line 2289 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetQual().

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BOOST_AUTO_TEST_CASE ( Test_GB_5618  )

Definition at line 2454 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), AddFeat(), AddMiscFeature(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), BuildGoodSeq(), CheckDeflineMatches(), COrgMod_Base::eSubtype_isolate, CObjectManager::GetInstance(), MakeGeneForFeature(), s_GatherSources(), CAutoDef::SetKeep3UTRs(), CAutoDef::SetKeep5UTRs(), and CSeq_feat_Base::SetLocation().

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BOOST_AUTO_TEST_CASE ( Test_GB_5758  )

Definition at line 2304 of file unit_test_autodef.cpp.

References AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CSubSource_Base::eSubtype_other, and SetSubSource().

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BOOST_AUTO_TEST_CASE ( Test_GB_5765  )

Definition at line 2378 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), AddMiscFeature(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), BuildGoodSeq(), CheckDeflineMatches(), CAutoDefOptions::eListAllFeatures, CObjectManager::GetInstance(), s_GatherSources(), CAutoDef::SetCustomFeatureClause(), and CAutoDef::SetFeatureListType().

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BOOST_AUTO_TEST_CASE ( Test_GB_5793  )

Definition at line 2357 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetQual(), and TestForRecomb().

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BOOST_AUTO_TEST_CASE ( Test_GB_6375  )

Definition at line 2509 of file unit_test_autodef.cpp.

References AddExon(), AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, eExtreme_Positional, GetCDSFromGoodNucProtSet(), CSeq_feat_Base::GetLocation(), GetNucleotideSequenceFromGoodNucProtSet(), CSeq_loc::GetStart(), nuc, and CSeq_feat_Base::SetLocation().

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BOOST_AUTO_TEST_CASE ( Test_GB_6557  )

Definition at line 2542 of file unit_test_autodef.cpp.

References AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), GetNucleotideSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), nuc, and prot.

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BOOST_AUTO_TEST_CASE ( Test_GB_6690  )

Definition at line 2583 of file unit_test_autodef.cpp.

References CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), BuildGoodEcoSet(), CheckDeflineMatches(), COrgMod_Base::eSubtype_other, CSubSource_Base::eSubtype_other, CAutoDef::FindBestModifierCombo(), CObjectManager::GetInstance(), NON_CONST_ITERATE, CScope::RemoveTopLevelSeqEntry(), CBioseq_set_Base::ResetDescr(), SetOrgMod(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

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BOOST_AUTO_TEST_CASE ( Test_GB_6690_WithDescr  )

Definition at line 2628 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), AddTitle(), BuildGoodEcoSet(), CheckDeflineMatchesWithDescr(), COrgMod_Base::eSubtype_other, CSubSource_Base::eSubtype_other, CAutoDef::FindBestModifierCombo(), NON_CONST_ITERATE, CBioseq_set_Base::ResetDescr(), s_GatherSources(), SetOrgMod(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

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BOOST_AUTO_TEST_CASE ( Test_GB_7071  )

Definition at line 2708 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CSeq_feat_Base::SetComment(), and CSeq_feat_Base::SetData().

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BOOST_AUTO_TEST_CASE ( Test_GB_7479  )

Definition at line 2725 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetQual().

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BOOST_AUTO_TEST_CASE ( Test_GB_7485  )

Definition at line 2773 of file unit_test_autodef.cpp.

References CheckInfluenzaDefline().

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BOOST_AUTO_TEST_CASE ( Test_GB_7534  )

Definition at line 2796 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), AddFeat(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), CSerialObject::Assign(), BuildGoodNucProtSet(), CheckDeflineMatches(), CBioSource_Base::eGenome_chloroplast, CAutoDef::FindBestModifierCombo(), GetCDSFromGoodNucProtSet(), CSeq_feat_Base::GetData(), CObjectManager::GetInstance(), GetNucleotideSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), MakeGeneForFeature(), nuc, prot, s_GatherSources(), CSeq_feat_Base::SetData(), SetGenome(), CAutoDef::SetKeepIntrons(), SetTaxname(), and CSeq_feat_Base::SetXref().

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BOOST_AUTO_TEST_CASE ( Test_GB_8547  )

Definition at line 3039 of file unit_test_autodef.cpp.

References AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CSubSource_Base::eSubtype_segment, COrgMod_Base::eSubtype_strain, SetOrgMod(), SetSubSource(), and SetTaxname().

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BOOST_AUTO_TEST_CASE ( Test_GB_8604  )

Definition at line 3052 of file unit_test_autodef.cpp.

References AddFeat(), AddMiscFeature(), AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CProt_ref_Base::eProcessed_mature, CSeqFeatData::eSubtype_mat_peptide_aa, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProteinSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), MakeGeneForFeature(), MakemRNAForCDS(), nuc, prot, CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetPartial().

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BOOST_AUTO_TEST_CASE ( Test_GB_8854  )

Definition at line 3145 of file unit_test_autodef.cpp.

References AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), MakeRegulatoryFeature(), MakeRptRegion(), and TestRepeatRegion().

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BOOST_AUTO_TEST_CASE ( Test_GB_8927  )

Definition at line 1421 of file unit_test_autodef.cpp.

References AddTitle(), BuildGoodNucProtSet(), ChangeId(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CSeq_loc_mix_Base::Get(), GetCDSFromGoodNucProtSet(), CBioseq_Base::GetId(), CSeq_feat_Base::GetLocation(), CSeq_loc_Base::GetMix(), GetNucleotideSequenceFromGoodNucProtSet(), GetProteinSequenceFromGoodNucProtSet(), CSeq_entry_Base::GetSeq(), MakeMixLoc(), nuc, s_AddCDS(), s_SetProteinName(), SetDiv(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetProduct().

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BOOST_AUTO_TEST_CASE ( Test_HumanSTR  )

Definition at line 2679 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), CSerialObject::Assign(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), MkField(), CSeq_feat_Base::SetData(), CUser_object_Base::SetData(), CDbtag_Base::SetDb(), CSeq_feat_Base::SetDbxref(), CBioseq_Base::SetDescr(), CSeq_entry_Base::SetSeq(), CDbtag_Base::SetTag(), CUser_object_Base::SetType(), and CSeqdesc_Base::SetUser().

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BOOST_AUTO_TEST_CASE ( Test_IsModifierInString  )

Definition at line 2073 of file unit_test_autodef.cpp.

References CAutoDefModifierCombo::IsModifierInString().

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BOOST_AUTO_TEST_CASE ( Test_IsUsableInDefline  )

Definition at line 2090 of file unit_test_autodef.cpp.

References CSubSource_Base::eSubtype_collected_by, CSubSource_Base::eSubtype_plasmid_name, COrgMod_Base::eSubtype_strain, COrgMod_Base::eSubtype_variety, and CAutoDefModifierCombo::IsUsableInDefline().

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BOOST_AUTO_TEST_CASE ( Test_RemovableMobileElement  )

Definition at line 1801 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), AddMiscFeature(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CAutoDefOptions::eDelete, CAutoDefOptions::eListAllFeatures, CObjectManager::GetInstance(), s_GatherSources(), CSeq_feat_Base::SetData(), CAutoDef::SetFeatureListType(), CAutoDef::SetKeepOptionalMobileElements(), CSeq_feat_Base::SetLocation(), CAutoDef::SetMiscFeatRule(), CSeq_feat_Base::SetQual(), and CGb_qual_Base::SetVal().

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BOOST_AUTO_TEST_CASE ( Test_RemovableuORF  )

Definition at line 1737 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), AddMiscFeature(), AddSource(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), BuildNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CAutoDefOptions::eDelete, CAutoDefOptions::eListAllFeatures, CObjectManager::GetInstance(), GetNucleotideSequenceFromGoodNucProtSet(), nuc, s_GatherSources(), CSeq_feat_Base::SetData(), CAutoDef::SetFeatureListType(), CAutoDef::SetKeepuORFs(), CAutoDef::SetMiscFeatRule(), and CSeq_feat_Base::SetQual().

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BOOST_AUTO_TEST_CASE ( Test_SB_5494  )

Definition at line 2147 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CBioSource_Base::eGenome_mitochondrion, CSeq_feat_Base::SetComment(), SetGenome(), and CSeq_feat_Base::SetLocation().

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BOOST_AUTO_TEST_CASE ( Test_SimpleAutodef  )

Definition at line 733 of file unit_test_autodef.cpp.

References AddSource(), AddTitle(), BuildSequence(), CheckDeflineMatches(), and CheckDeflineMatchesWithDescr().

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BOOST_AUTO_TEST_CASE ( Test_SQD_155  )

Definition at line 825 of file unit_test_autodef.cpp.

References AddFeat(), AddSource(), AddTitle(), BuildSequence(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CSeq_feat_Base::SetComment(), and CSeq_feat_Base::SetData().

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BOOST_AUTO_TEST_CASE ( Test_SQD_169  )

Definition at line 793 of file unit_test_autodef.cpp.

References AddFeat(), AddSource(), AddTitle(), BuildSequence(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CSeq_feat_Base::SetComment(), and CSeq_feat_Base::SetData().

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BOOST_AUTO_TEST_CASE ( Test_SQD_1733  )

Definition at line 995 of file unit_test_autodef.cpp.

References CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_chloroplast, CBioSource_Base::eGenome_kinetoplast, CBioSource_Base::eGenome_leucoplast, CBioSource_Base::eGenome_mitochondrion, CBioSource_Base::eGenome_unknown, and TestOneOrganelleSequenceDefline().

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BOOST_AUTO_TEST_CASE ( Test_SQD_2075  )

Definition at line 1232 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CSeq_feat_Base::SetComment(), and CSeq_feat_Base::SetLocation().

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BOOST_AUTO_TEST_CASE ( Test_SQD_2115  )

Definition at line 1245 of file unit_test_autodef.cpp.

References AddFeat(), AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), MakeGeneForFeature(), CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetData(), CGb_qual_Base::SetQual(), CSeq_feat_Base::SetQual(), and CGb_qual_Base::SetVal().

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BOOST_AUTO_TEST_CASE ( Test_SQD_2118  )

Definition at line 1302 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CSeq_feat_Base::SetComment(), and CSeq_feat_Base::SetLocation().

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BOOST_AUTO_TEST_CASE ( Test_SQD_2181  )

Definition at line 1474 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), AddMiscFeature(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), BuildGoodNucProtSet(), CheckDeflineMatches(), CAutoDefOptions::eDelete, CAutoDefOptions::eListAllFeatures, GetCDSFromGoodNucProtSet(), CObjectManager::GetInstance(), GetNucleotideSequenceFromGoodNucProtSet(), nuc, CSeq_feat_Base::ResetComment(), s_GatherSources(), CSeq_feat_Base::SetData(), CAutoDef::SetFeatureListType(), CAutoDef::SetMiscFeatRule(), CGb_qual_Base::SetQual(), CSeq_feat_Base::SetQual(), CAutoDef::SetUseFakePromoters(), and CGb_qual_Base::SetVal().

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BOOST_AUTO_TEST_CASE ( Test_SQD_2370  )

Definition at line 1635 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), and CSeq_feat_Base::SetComment().

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BOOST_AUTO_TEST_CASE ( Test_SQD_3440  )

Definition at line 1723 of file unit_test_autodef.cpp.

References CheckAutoDefOptions(), CUser_object::eObjectType_AutodefOptions, CUser_object::GetObjectType(), CAutoDefModifierCombo::InitOptions(), CAutoDefOptions::MakeUserObject(), and CAutoDefOptions::SetUseLabels().

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BOOST_AUTO_TEST_CASE ( Test_SQD_3602  )

Definition at line 2132 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CBioSource_Base::eGenome_mitochondrion, CSeq_feat_Base::SetComment(), SetGenome(), and CSeq_feat_Base::SetLocation().

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BOOST_AUTO_TEST_CASE ( Test_SQD_374  )

Definition at line 808 of file unit_test_autodef.cpp.

References AddFeat(), AddSource(), AddTitle(), BuildSequence(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

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BOOST_AUTO_TEST_CASE ( Test_SQD_3914  )

Definition at line 2412 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CRNA_ref_Base::eType_miscRNA, CSeq_feat_Base::SetComment(), and CSeq_feat_Base::SetData().

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BOOST_AUTO_TEST_CASE ( Test_SQD_4185  )

Definition at line 2565 of file unit_test_autodef.cpp.

References AddFeat(), AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CSubSource_Base::eSubtype_segment, GetNucleotideSequenceFromGoodNucProtSet(), nuc, CSeq_feat_Base::SetData(), SetNucProtSetProductName(), SetSubSource(), and SetTaxname().

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BOOST_AUTO_TEST_CASE ( Test_SQD_4451  )

Definition at line 2863 of file unit_test_autodef.cpp.

References AddFeat(), AddSource(), AddTitle(), BuildSequence(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), eExtreme_Biological, CRNA_ref_Base::eType_miscRNA, CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

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BOOST_AUTO_TEST_CASE ( Test_SQD_4529  )

Definition at line 2882 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddSource(), AddTitle(), BuildSequence(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CAutoDefOptions::eDelete, CAutoDefOptions::eListAllFeatures, CRNA_ref_Base::eType_rRNA, CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetComment(), and CSeq_feat_Base::SetData().

◆ BOOST_AUTO_TEST_CASE() [73/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_4593  )

Definition at line 2950 of file unit_test_autodef.cpp.

References TestMatPeptideListing().

◆ BOOST_AUTO_TEST_CASE() [74/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_4607  )

Definition at line 2959 of file unit_test_autodef.cpp.

References AddMiscFeature(), AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CAutoDefOptions::eDelete, CAutoDefOptions::eListAllFeatures, and CSeq_feat_Base::SetComment().

◆ BOOST_AUTO_TEST_CASE() [75/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_4612  )

Definition at line 3031 of file unit_test_autodef.cpp.

References CheckRegulatoryFeatures().

◆ BOOST_AUTO_TEST_CASE() [76/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_476  )

Definition at line 758 of file unit_test_autodef.cpp.

References AddSource(), AddTitle(), BuildNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CBioSource_Base::eGenome_plasmid, CBioSource_Base::SetGenome(), CSeqdesc_Base::SetSource(), and CBioSource_Base::SetSubtype().

◆ BOOST_AUTO_TEST_CASE() [77/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_630  )

Definition at line 771 of file unit_test_autodef.cpp.

References AddFeat(), AddSource(), AddTitle(), BuildSequence(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetQual(), CSeqdesc_Base::SetSource(), and CBioSource_Base::SetSubtype().

◆ BOOST_AUTO_TEST_CASE() [78/79]

BOOST_AUTO_TEST_CASE ( Test_TargetedLocusName  )

Definition at line 2115 of file unit_test_autodef.cpp.

References CAutoDefOptions::GetTargetedLocusName(), HasStringField(), CAutoDefOptions::InitFromUserObject(), CAutoDefOptions::MakeUserObject(), and CAutoDefOptions::SetTargetedLocusName().

◆ BOOST_AUTO_TEST_CASE() [79/79]

BOOST_AUTO_TEST_CASE ( Test_UnnamedPlasmid  )

Definition at line 744 of file unit_test_autodef.cpp.

References AddSource(), AddTitle(), BuildSequence(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CBioSource_Base::eGenome_plasmid, CBioSource_Base::SetGenome(), CSeqdesc_Base::SetSource(), and CBioSource_Base::SetSubtype().

◆ BuildNucProtSet()

static CRef<CSeq_entry> BuildNucProtSet ( const string &  protein_name,
const string &  locus = kEmptyStr,
const string &  allele = kEmptyStr 
)
static

Definition at line 685 of file unit_test_autodef.cpp.

References AddFeat(), CMolInfo_Base::eBiomol_genomic, CBioseq_set_Base::eClass_nuc_prot, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eRepr_raw, MakeCDSForNucProtSet(), MakeGeneForNucProtSet(), MakeProteinForNucProtSet(), CMolInfo_Base::SetBiomol(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeqdesc_Base::SetMolinfo(), CSeq_entry_Base::SetSeq(), and CSeq_entry_Base::SetSet().

Referenced by BOOST_AUTO_TEST_CASE().

◆ BuildSequence()

static CRef<CSeq_entry> BuildSequence ( )
static

Definition at line 154 of file unit_test_autodef.cpp.

References CMolInfo_Base::eBiomol_genomic, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eRepr_raw, CMolInfo_Base::SetBiomol(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeqdesc_Base::SetMolinfo(), and CSeq_entry_Base::SetSeq().

Referenced by BOOST_AUTO_TEST_CASE().

◆ CheckAutoDefOptions()

void CheckAutoDefOptions ( const CUser_object &  user,
CAutoDefOptions &  opts 
)

Definition at line 276 of file unit_test_autodef.cpp.

References CAutoDefOptions::AreAnyFeaturesSuppressed(), CUser_object::eObjectType_AutodefOptions, CAutoDefOptions::GetAllowModAtEndOfTaxname(), CAutoDefOptions::GetCustomFeatureClause(), CUser_object_Base::GetData(), CAutoDefOptions::GetDoNotApplyToSp(), CAutoDefOptions::GetFeatureListType(), CAutoDefOptions::GetKeep3UTRs(), CAutoDefOptions::GetKeep5UTRs(), CAutoDefOptions::GetKeepExons(), CAutoDefOptions::GetKeepIntrons(), CAutoDefOptions::GetKeepMiscRecomb(), CAutoDefOptions::GetKeepMobileElements(), CAutoDefOptions::GetKeepRegulatoryFeatures(), CAutoDefOptions::GetKeepRepeatRegion(), CAutoDefOptions::GetKeepuORFs(), CAutoDefOptions::GetMiscFeatRule(), CUser_object::GetObjectType(), CAutoDefOptions::GetOrgMods(), CAutoDefOptions::GetSubSources(), CAutoDefOptions::GetUseFakePromoters(), CAutoDefOptions::GetUseLabels(), HasBoolField(), HasIntField(), HasStringField(), NStr::IntToString(), NStr::IsBlank(), and ITERATE.

Referenced by BOOST_AUTO_TEST_CASE(), and CheckDeflineMatches().

◆ CheckDeflineMatches() [1/4]

static void CheckDeflineMatches ( CRef< CSeq_entry >  entry,
bool  use_best = false,
CAutoDefOptions::EFeatureListType  list_type = CAutoDefOptions::eListAllFeatures,
CAutoDefOptions::EMiscFeatRule  misc_feat_rule = CAutoDefOptions::eNoncodingProductFeat,
bool  init_with_descrs = false 
)
static

Definition at line 473 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), CAutoDef::AddSources(), CScope::AddTopLevelSeqEntry(), CheckDeflineMatches(), CSeqdesc_Base::e_Source, CSeq_inst_Base::eMol_na, CAutoDef::FindBestModifierCombo(), CObjectManager::GetInstance(), CAutoDef::SetFeatureListType(), and CAutoDef::SetMiscFeatRule().

◆ CheckDeflineMatches() [2/4]

static void CheckDeflineMatches ( CRef< CSeq_entry >  entry,
CSeqFeatData::ESubtype  feat_to_suppress,
bool  init_with_descrs = false 
)
static

Definition at line 538 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), CAutoDef::AddSources(), CScope::AddTopLevelSeqEntry(), CheckDeflineMatches(), CSeqdesc_Base::e_Source, CAutoDefOptions::eListAllFeatures, CSeq_inst_Base::eMol_na, CAutoDefOptions::eNoncodingProductFeat, CAutoDef::FindBestModifierCombo(), CObjectManager::GetInstance(), CAutoDef::SetFeatureListType(), CAutoDef::SetMiscFeatRule(), and CAutoDef::SuppressFeature().

◆ CheckDeflineMatches() [3/4]

static void CheckDeflineMatches ( CRef< CSeq_entry >  entry,
vector< CSubSource::ESubtype >  subsrcs,
vector< COrgMod::ESubtype >  orgmods,
bool  init_with_descrs = false 
)
static

Definition at line 431 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), CAutoDef::AddSources(), CScope::AddTopLevelSeqEntry(), CheckDeflineMatches(), CSeqdesc_Base::e_Source, CAutoDefOptions::eDelete, CAutoDefOptions::eListAllFeatures, CSeq_inst_Base::eMol_na, CObjectManager::GetInstance(), ITERATE, CAutoDef::SetFeatureListType(), and CAutoDef::SetMiscFeatRule().

◆ CheckDeflineMatches() [4/4]

static void CheckDeflineMatches ( CSeq_entry_Handle  seh,
CAutoDefWithTaxonomy &  autodef,
CRef< CAutoDefModifierCombo >  mod_combo 
)
static

Definition at line 372 of file unit_test_autodef.cpp.

References CheckAutoDefOptions(), CSeqdesc_Base::e_Title, CSeq_inst_Base::eMol_na, CSerialObject::Equals(), CBioseq_set_Handle::GetCompleteBioseq_set(), CAutoDefWithTaxonomy::GetDocsumDefLine(), CAutoDef::GetOneDefLine(), CAutoDef::GetOptionsObject(), CBioseq_Handle::GetSeqId(), CSeq_entry_Handle::GetSet(), CSeqdesc_Base::GetTitle(), CAutoDefOptions::InitFromUserObject(), CSeq_entry_Handle::IsSet(), CAutoDefOptions::MakeUserObject(), CBioseq_set::NeedsDocsumTitle(), CAutoDef::SetOptions(), and CAutoDef::SetOptionsObject().

Referenced by BOOST_AUTO_TEST_CASE(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CheckInfluenzaDefline(), CheckRegulatoryFeatures(), MakeRegulatoryFeatureTest(), TestForRecomb(), TestMatPeptideListing(), TestOneOrganelleSequenceDefline(), and TestRepeatRegion().

◆ CheckDeflineMatchesWithDescr()

static void CheckDeflineMatchesWithDescr ( CRef< CSeq_entry >  entry,
bool  use_best = false,
CAutoDefOptions::EFeatureListType  list_type = CAutoDefOptions::eListAllFeatures,
CAutoDefOptions::EMiscFeatRule  misc_feat_rule = CAutoDefOptions::eNoncodingProductFeat 
)
static

Definition at line 513 of file unit_test_autodef.cpp.

References CheckDeflineMatches().

Referenced by BOOST_AUTO_TEST_CASE(), CheckInfluenzaDefline(), TestMatPeptideListing(), and TestOneOrganelleSequenceDefline().

◆ CheckInfluenzaDefline()

void CheckInfluenzaDefline ( const string &  taxname,
const string &  strain,
const string &  serotype,
const string &  clone,
const string &  segment,
const string &  defline 
)

Definition at line 2748 of file unit_test_autodef.cpp.

References AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CSubSource_Base::eSubtype_clone, CSubSource_Base::eSubtype_segment, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_strain, NStr::IsBlank(), SetOrgMod(), SetSubSource(), and SetTaxname().

Referenced by BOOST_AUTO_TEST_CASE().

◆ CheckRegulatoryFeatures()

void CheckRegulatoryFeatures ( const string &  expected_title,
bool  keep_promoters,
bool  keep_regulatory 
)

Definition at line 2972 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), AddMiscFeature(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), BuildGoodSeq(), CheckDeflineMatches(), CAutoDefOptions::eListAllFeatures, CAutoDef::FindBestModifierCombo(), CObjectManager::GetInstance(), CSeq_feat_Base::ResetComment(), s_GatherSources(), CSeq_feat_Base::SetData(), CAutoDef::SetFeatureListType(), CAutoDef::SetKeepRegulatoryFeatures(), CSeq_feat_Base::SetQual(), and CAutoDef::SetUseFakePromoters().

Referenced by BOOST_AUTO_TEST_CASE().

◆ FindNucInSeqEntry()

CRef<CSeq_entry> FindNucInSeqEntry ( CRef< CSeq_entry >  entry)

Definition at line 570 of file unit_test_autodef.cpp.

References ctll::empty(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), CBioseq::IsNa(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), ITERATE, and NULL.

Referenced by AddFeat().

◆ HasBoolField()

size_t HasBoolField ( const CUser_object &  user,
const string &  field_name 
)

Definition at line 215 of file unit_test_autodef.cpp.

References CUser_field_Base::C_Data::e_Bool, NStr::EqualNocase(), CUser_object_Base::GetData(), and ITERATE.

Referenced by CheckAutoDefOptions().

◆ HasIntField()

size_t HasIntField ( const CUser_object &  user,
const string &  field_name,
int  value 
)

Definition at line 255 of file unit_test_autodef.cpp.

References CUser_field_Base::C_Data::e_Int, NStr::EqualNocase(), CUser_object_Base::GetData(), ITERATE, and rapidjson::value.

Referenced by CheckAutoDefOptions().

◆ HasStringField()

size_t HasStringField ( const CUser_object &  user,
const string &  field_name,
const string &  value 
)

Definition at line 235 of file unit_test_autodef.cpp.

References CUser_field_Base::C_Data::e_Str, NStr::EqualNocase(), CUser_object_Base::GetData(), ITERATE, and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), and CheckAutoDefOptions().

◆ MakeCDSForNucProtSet()

static CRef<CSeq_feat> MakeCDSForNucProtSet ( string  nuc_id,
string  prot_id 
)
static

Definition at line 659 of file unit_test_autodef.cpp.

References CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetProduct().

Referenced by BuildNucProtSet().

◆ MakeGeneForNucProtSet()

static CRef<CSeq_feat> MakeGeneForNucProtSet ( const string &  nuc_id,
const string &  locus,
const string &  allele = kEmptyStr 
)
static

Definition at line 671 of file unit_test_autodef.cpp.

References CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

Referenced by BuildNucProtSet().

◆ MakeProteinForNucProtSet()

static CRef<CSeq_entry> MakeProteinForNucProtSet ( string  id,
string  protein_name 
)
static

Definition at line 628 of file unit_test_autodef.cpp.

References AddFeat(), CMolInfo_Base::eBiomol_peptide, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eRepr_raw, CMolInfo_Base::SetBiomol(), CSeq_feat_Base::SetData(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_id_Base::SetLocal(), CSeq_feat_Base::SetLocation(), CSeqdesc_Base::SetMolinfo(), CSeq_entry_Base::SetSeq(), and CObject_id_Base::SetStr().

Referenced by BuildNucProtSet().

◆ MakeRegulatoryFeature()

CRef<CSeq_feat> MakeRegulatoryFeature ( const string &  reg_class,
const string &  comment,
TSeqPos  start_pos,
CRef< CSeq_entry >  entry 
)

Definition at line 3091 of file unit_test_autodef.cpp.

References AddMiscFeature(), CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetQual().

Referenced by BOOST_AUTO_TEST_CASE().

◆ MakeRegulatoryFeatureTest()

void MakeRegulatoryFeatureTest ( const string &  regulatory_class,
const string &  defline_interval,
bool  use_fake_promoters,
bool  keep_regulatory 
)

Definition at line 2196 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), AddMiscFeature(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), BuildGoodNucProtSet(), CheckDeflineMatches(), CObjectManager::GetInstance(), GetNucleotideSequenceFromGoodNucProtSet(), NStr::IsBlank(), nuc, CScope::RemoveTopLevelSeqEntry(), s_GatherSources(), CSeq_feat_Base::SetData(), CAutoDef::SetKeepRegulatoryFeatures(), CSeq_feat_Base::SetQual(), and CAutoDef::SetUseFakePromoters().

Referenced by BOOST_AUTO_TEST_CASE().

◆ MakeRptRegion()

CRef<CSeq_feat> MakeRptRegion ( const string &  rpt_type,
TSeqPos  start_pos,
CRef< CSeq_entry >  entry 
)

Definition at line 3102 of file unit_test_autodef.cpp.

References AddMiscFeature(), CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetQual().

Referenced by BOOST_AUTO_TEST_CASE().

◆ MkField()

CRef<CUser_field> MkField ( const string &  label,
const string &  val 
)

Definition at line 2670 of file unit_test_autodef.cpp.

References f, label, and val.

Referenced by BOOST_AUTO_TEST_CASE().

◆ NCBITEST_AUTO_INIT()

NCBITEST_AUTO_INIT ( )

Definition at line 143 of file unit_test_autodef.cpp.

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

◆ NCBITEST_INIT_CMDLINE()

NCBITEST_INIT_CMDLINE ( arg_desc  )

Definition at line 134 of file unit_test_autodef.cpp.

◆ NCBITEST_INIT_TREE()

NCBITEST_INIT_TREE ( )

Definition at line 126 of file unit_test_autodef.cpp.

References CNcbiApplication::Instance().

◆ s_AddCDS()

CRef<CSeq_feat> s_AddCDS ( CRef< CSeq_entry >  np,
const string &  name,
TSeqPos  from,
TSeqPos  to 
)

Definition at line 1358 of file unit_test_autodef.cpp.

References CSeq_id::Assign(), CSerialObject::Assign(), ChangeId(), NStr::Find(), CBioseq_Base::GetId(), CSeq_id_Base::GetLocal(), CSeq_entry_Base::GetSeq(), CObject_id_Base::GetStr(), NStr::NumericToString(), s_SetProteinName(), CBioseq_set_Base::SetAnnot(), CSeq_id_Base::SetLocal(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetProduct(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), CObject_id_Base::SetStr(), and NStr::StringToInt().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_GatherSources()

static CAutoDef::TSources s_GatherSources ( const CSeq_entry &  entry)
static

Definition at line 522 of file unit_test_autodef.cpp.

References CScope::AddTopLevelSeqEntry(), CSeqdesc_Base::e_Source, CSeq_inst_Base::eMol_na, and CObjectManager::GetInstance().

Referenced by BOOST_AUTO_TEST_CASE(), CheckRegulatoryFeatures(), MakeRegulatoryFeatureTest(), and TestForRecomb().

◆ s_SetProteinName()

void s_SetProteinName ( CRef< CSeq_entry >  prot,
const string &  name 
)

Definition at line 1352 of file unit_test_autodef.cpp.

References prot.

Referenced by BOOST_AUTO_TEST_CASE(), and s_AddCDS().

◆ TestForRecomb()

void TestForRecomb ( CRef< CSeq_entry >  entry,
const string &  expected 
)

Definition at line 2321 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), CAutoDef::AddSources(), AddTitle(), CScope::AddTopLevelSeqEntry(), CheckDeflineMatches(), CAutoDefOptions::eListAllFeatures, expected, CObjectManager::GetInstance(), s_GatherSources(), CAutoDef::SetFeatureListType(), and CAutoDef::SetKeepMiscRecomb().

Referenced by BOOST_AUTO_TEST_CASE().

◆ TestMatPeptideListing()

void TestMatPeptideListing ( bool  cds_is_partial,
bool  has_sig_peptide 
)

Definition at line 2915 of file unit_test_autodef.cpp.

References AddFeat(), AddProtFeat(), AddTitle(), BuildGoodNucProtSet(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CAutoDefOptions::eDelete, eExtreme_Biological, CAutoDefOptions::eListAllFeatures, CProt_ref_Base::eProcessed_mature, CProt_ref_Base::eProcessed_signal_peptide, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProteinSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), MakeGeneForFeature(), nuc, prot, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetPartial().

Referenced by BOOST_AUTO_TEST_CASE().

◆ TestOneOrganelleSequenceDefline()

void TestOneOrganelleSequenceDefline ( CBioSource::TGenome  genome,
const string &  defline 
)

Definition at line 985 of file unit_test_autodef.cpp.

References AddTitle(), BuildGoodSeq(), CheckDeflineMatches(), CheckDeflineMatchesWithDescr(), CAutoDefOptions::eSequence, and SetGenome().

Referenced by BOOST_AUTO_TEST_CASE().

◆ TestRepeatRegion()

void TestRepeatRegion ( CRef< CSeq_entry >  entry,
bool  init_with_descrs = false 
)

Definition at line 3114 of file unit_test_autodef.cpp.

References CAutoDef::AddDescriptors(), CAutoDef::AddSources(), CScope::AddTopLevelSeqEntry(), CheckDeflineMatches(), CSeqdesc_Base::e_Source, CAutoDefOptions::eListAllFeatures, CSeq_inst_Base::eMol_na, CAutoDef::FindBestModifierCombo(), CObjectManager::GetInstance(), CAutoDef::SetFeatureListType(), and CAutoDef::SetKeepRepeatRegion().

Referenced by BOOST_AUTO_TEST_CASE().

Variable Documentation

◆ s_debugMode

bool s_debugMode = false
static

Definition at line 132 of file unit_test_autodef.cpp.

Referenced by NCBITEST_AUTO_INIT().

◆ sc_TestEntryCollidingLocusTags

const string sc_TestEntryCollidingLocusTags
extern

Definition at line 1156 of file unit_test_validator.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

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