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_entryBuildSequence ()
 
static CRef< CSeqdescAddSource (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_entryFindNucInSeqEntry (CRef< CSeq_entry > entry)
 
static void AddFeat (CRef< CSeq_feat > feat, CRef< CSeq_entry > entry)
 
static CRef< CSeq_entryMakeProteinForNucProtSet (string id, string protein_name)
 
static CRef< CSeq_featMakeCDSForNucProtSet (string nuc_id, string prot_id)
 
static CRef< CSeq_featMakeGeneForNucProtSet (const string &nuc_id, const string &locus, const string &allele=kEmptyStr)
 
static CRef< CSeq_entryBuildNucProtSet (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_feats_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_fieldMkField (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_featMakeRegulatoryFeature (const string &reg_class, const string &comment, TSeqPos start_pos, CRef< CSeq_entry > entry)
 
CRef< CSeq_featMakeRptRegion (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 
)

◆ AddFeat()

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

◆ AddProtFeat()

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

◆ AddSource()

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

◆ AddTitle()

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

◆ BOOST_AUTO_TEST_CASE() [1/79]

BOOST_AUTO_TEST_CASE ( GB_5272  )

◆ BOOST_AUTO_TEST_CASE() [2/79]

BOOST_AUTO_TEST_CASE ( GB_5272a  )

◆ BOOST_AUTO_TEST_CASE() [3/79]

BOOST_AUTO_TEST_CASE ( GB_5272b  )

◆ 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  )

◆ BOOST_AUTO_TEST_CASE() [6/79]

BOOST_AUTO_TEST_CASE ( Test_AutodefOptionsSpecifyNuclearCopyFlag  )

◆ BOOST_AUTO_TEST_CASE() [7/79]

BOOST_AUTO_TEST_CASE ( Test_CAutoDefAvailableModifier_GetOrgModLabel  )

◆ BOOST_AUTO_TEST_CASE() [8/79]

BOOST_AUTO_TEST_CASE ( Test_ClauseListOptions  )

◆ BOOST_AUTO_TEST_CASE() [9/79]

BOOST_AUTO_TEST_CASE ( Test_DocsumTitle_Physet  )

◆ BOOST_AUTO_TEST_CASE() [10/79]

BOOST_AUTO_TEST_CASE ( Test_DocsumTitle_Popset  )

◆ BOOST_AUTO_TEST_CASE() [11/79]

BOOST_AUTO_TEST_CASE ( Test_GB_1851  )

◆ BOOST_AUTO_TEST_CASE() [12/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3099  )

◆ BOOST_AUTO_TEST_CASE() [13/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3108  )

◆ BOOST_AUTO_TEST_CASE() [14/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3359  )

◆ BOOST_AUTO_TEST_CASE() [15/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3386  )

◆ BOOST_AUTO_TEST_CASE() [16/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3395  )

◆ BOOST_AUTO_TEST_CASE() [17/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3410  )

◆ BOOST_AUTO_TEST_CASE() [18/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3439  )

◆ BOOST_AUTO_TEST_CASE() [19/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3458  )

◆ BOOST_AUTO_TEST_CASE() [20/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3486  )

◆ BOOST_AUTO_TEST_CASE() [21/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3488  )

◆ BOOST_AUTO_TEST_CASE() [22/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3496  )

◆ BOOST_AUTO_TEST_CASE() [23/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3679  )

◆ BOOST_AUTO_TEST_CASE() [24/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3848  )

◆ BOOST_AUTO_TEST_CASE() [25/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3866  )

◆ BOOST_AUTO_TEST_CASE() [26/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3926  )

◆ BOOST_AUTO_TEST_CASE() [27/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3942  )

◆ BOOST_AUTO_TEST_CASE() [28/79]

BOOST_AUTO_TEST_CASE ( Test_GB_3949  )

◆ BOOST_AUTO_TEST_CASE() [29/79]

BOOST_AUTO_TEST_CASE ( Test_GB_4043  )

◆ BOOST_AUTO_TEST_CASE() [30/79]

BOOST_AUTO_TEST_CASE ( Test_GB_4078  )

◆ BOOST_AUTO_TEST_CASE() [31/79]

BOOST_AUTO_TEST_CASE ( Test_GB_4242  )

◆ BOOST_AUTO_TEST_CASE() [32/79]

BOOST_AUTO_TEST_CASE ( Test_GB_5447  )

◆ BOOST_AUTO_TEST_CASE() [33/79]

BOOST_AUTO_TEST_CASE ( Test_GB_5493  )

◆ BOOST_AUTO_TEST_CASE() [34/79]

BOOST_AUTO_TEST_CASE ( Test_GB_5560  )

◆ BOOST_AUTO_TEST_CASE() [35/79]

BOOST_AUTO_TEST_CASE ( Test_GB_5618  )

◆ BOOST_AUTO_TEST_CASE() [36/79]

BOOST_AUTO_TEST_CASE ( Test_GB_5758  )

◆ BOOST_AUTO_TEST_CASE() [37/79]

BOOST_AUTO_TEST_CASE ( Test_GB_5765  )

◆ BOOST_AUTO_TEST_CASE() [38/79]

BOOST_AUTO_TEST_CASE ( Test_GB_5793  )

◆ BOOST_AUTO_TEST_CASE() [39/79]

BOOST_AUTO_TEST_CASE ( Test_GB_6375  )

◆ BOOST_AUTO_TEST_CASE() [40/79]

BOOST_AUTO_TEST_CASE ( Test_GB_6557  )

◆ BOOST_AUTO_TEST_CASE() [41/79]

BOOST_AUTO_TEST_CASE ( Test_GB_6690  )

◆ BOOST_AUTO_TEST_CASE() [42/79]

BOOST_AUTO_TEST_CASE ( Test_GB_6690_WithDescr  )

◆ BOOST_AUTO_TEST_CASE() [43/79]

BOOST_AUTO_TEST_CASE ( Test_GB_7071  )

◆ BOOST_AUTO_TEST_CASE() [44/79]

BOOST_AUTO_TEST_CASE ( Test_GB_7479  )

◆ BOOST_AUTO_TEST_CASE() [45/79]

BOOST_AUTO_TEST_CASE ( Test_GB_7485  )

Definition at line 2773 of file unit_test_autodef.cpp.

References CheckInfluenzaDefline().

◆ BOOST_AUTO_TEST_CASE() [46/79]

BOOST_AUTO_TEST_CASE ( Test_GB_7534  )

◆ BOOST_AUTO_TEST_CASE() [47/79]

BOOST_AUTO_TEST_CASE ( Test_GB_8547  )

◆ BOOST_AUTO_TEST_CASE() [48/79]

BOOST_AUTO_TEST_CASE ( Test_GB_8604  )

◆ BOOST_AUTO_TEST_CASE() [49/79]

BOOST_AUTO_TEST_CASE ( Test_GB_8854  )

◆ BOOST_AUTO_TEST_CASE() [50/79]

BOOST_AUTO_TEST_CASE ( Test_GB_8927  )

◆ BOOST_AUTO_TEST_CASE() [51/79]

BOOST_AUTO_TEST_CASE ( Test_HumanSTR  )

◆ BOOST_AUTO_TEST_CASE() [52/79]

BOOST_AUTO_TEST_CASE ( Test_IsModifierInString  )

◆ BOOST_AUTO_TEST_CASE() [53/79]

BOOST_AUTO_TEST_CASE ( Test_IsUsableInDefline  )

◆ BOOST_AUTO_TEST_CASE() [54/79]

BOOST_AUTO_TEST_CASE ( Test_RemovableMobileElement  )

◆ BOOST_AUTO_TEST_CASE() [55/79]

BOOST_AUTO_TEST_CASE ( Test_RemovableuORF  )

◆ BOOST_AUTO_TEST_CASE() [56/79]

BOOST_AUTO_TEST_CASE ( Test_SB_5494  )

◆ BOOST_AUTO_TEST_CASE() [57/79]

BOOST_AUTO_TEST_CASE ( Test_SimpleAutodef  )

◆ BOOST_AUTO_TEST_CASE() [58/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_155  )

◆ BOOST_AUTO_TEST_CASE() [59/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_169  )

◆ BOOST_AUTO_TEST_CASE() [60/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_1733  )

◆ BOOST_AUTO_TEST_CASE() [61/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_2075  )

◆ BOOST_AUTO_TEST_CASE() [62/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_2115  )

◆ BOOST_AUTO_TEST_CASE() [63/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_2118  )

◆ BOOST_AUTO_TEST_CASE() [64/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_2181  )

◆ BOOST_AUTO_TEST_CASE() [65/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_2370  )

◆ BOOST_AUTO_TEST_CASE() [66/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_3440  )

◆ BOOST_AUTO_TEST_CASE() [67/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_3602  )

◆ BOOST_AUTO_TEST_CASE() [68/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_374  )

◆ BOOST_AUTO_TEST_CASE() [69/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_3914  )

◆ BOOST_AUTO_TEST_CASE() [70/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_4185  )

◆ BOOST_AUTO_TEST_CASE() [71/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_4451  )

◆ BOOST_AUTO_TEST_CASE() [72/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_4529  )

◆ 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  )

◆ 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  )

◆ BOOST_AUTO_TEST_CASE() [77/79]

BOOST_AUTO_TEST_CASE ( Test_SQD_630  )

◆ BOOST_AUTO_TEST_CASE() [78/79]

BOOST_AUTO_TEST_CASE ( Test_TargetedLocusName  )

◆ BOOST_AUTO_TEST_CASE() [79/79]

BOOST_AUTO_TEST_CASE ( Test_UnnamedPlasmid  )

◆ BuildNucProtSet()

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

◆ BuildSequence()

static CRef<CSeq_entry> BuildSequence ( )
static

◆ CheckAutoDefOptions()

void CheckAutoDefOptions ( const CUser_object user,
CAutoDefOptions opts 
)

◆ 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

◆ CheckDeflineMatches() [2/4]

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

◆ CheckDeflineMatches() [3/4]

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

◆ CheckDeflineMatches() [4/4]

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

◆ 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

◆ CheckInfluenzaDefline()

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

◆ CheckRegulatoryFeatures()

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

◆ FindNucInSeqEntry()

CRef<CSeq_entry> FindNucInSeqEntry ( CRef< CSeq_entry entry)

◆ HasBoolField()

size_t HasBoolField ( const CUser_object user,
const string field_name 
)

◆ HasIntField()

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

◆ HasStringField()

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

◆ MakeCDSForNucProtSet()

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

◆ 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

◆ MakeRegulatoryFeature()

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

◆ MakeRegulatoryFeatureTest()

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

◆ MakeRptRegion()

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

◆ 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 ( )

◆ 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 
)

◆ s_GatherSources()

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

◆ 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 
)

◆ TestMatPeptideListing()

void TestMatPeptideListing ( bool  cds_is_partial,
bool  has_sig_peptide 
)

◆ TestOneOrganelleSequenceDefline()

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

◆ TestRepeatRegion()

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

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 1132 of file unit_test_validator.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

Modified on Sun Mar 03 03:15:25 2024 by modify_doxy.py rev. 669887