NCBI C++ ToolKit
Classes | Macros | Typedefs | Functions | Variables
biosource_tests.cpp File Reference
#include <ncbi_pch.hpp>
#include <sstream>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/OrgMod.hpp>
#include <objects/general/Dbtag.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/seq_vector.hpp>
#include <objects/macro/Source_qual.hpp>
#include <objects/taxon3/taxon3.hpp>
#include <util/xregexp/regexp.hpp>
#include "discrepancy_core.hpp"
+ Include dependency graph for biosource_tests.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes

class  CCompareValues< T, R >
 

Macros

#define SARS_TAX_ID   2697049
 

Typedefs

typedef list< stringTInconsistecyDescriptionList
 

Functions

 USING_SCOPE (objects)
 
bool HasCultureCollectionForATCCStrain (const COrgName::TMod &mods, const string &strain)
 
bool HasStrainForATCCCultureCollection (const COrgName::TMod &mods, const string &culture_collection)
 
static bool SetCultureCollectionFromStrain (CBioSource &src)
 
static bool MatchExceptSpaceColon (const string &a, const string &b)
 
bool HasAmplifiedWithSpeciesSpecificPrimerNote (const CBioSource &src)
 
static bool IsMissingRequiredClone (const CBioSource &biosource)
 
static bool IsSameSubtype (const CBioSource::TSubtype &first, const CBioSource::TSubtype &second)
 
static bool IsSameDb (const COrg_ref::TDb &first, const COrg_ref::TDb &second)
 
static void GetOrgnameDifferences (const COrgName &first, const COrgName &second, TInconsistecyDescriptionList &diffs)
 
static void GetOrgrefDifferences (const COrg_ref &first_org, const COrg_ref &second_org, TInconsistecyDescriptionList &diffs)
 
static void GetBiosourceDifferences (const CBioSource &first_biosrc, const CBioSource &second_biosrc, TInconsistecyDescriptionList &diffs)
 
static const CDbtagGetTaxonTag (const COrg_ref &org)
 
static bool OrgDiffers (const COrg_ref &first, const COrg_ref &second)
 
static CRef< CTaxon3_replyGetOrgRefs (vector< CRef< COrg_ref >> &orgs)
 
static bool RemoveCountryColon (CBioSource &src)
 
static bool ChangeCountryColonToComma (CBioSource &src)
 
static bool FixHumanHost (CBioSource &src)
 
static string GetSrcQual (const CBioSource &bs, int qual)
 
static bool SetEnvSampleFixAmplifiedPrimers (CBioSource &src)
 
static bool EqualPrimerSets (const CPCRPrimerSet::Tdata &a, const CPCRPrimerSet::Tdata &b)
 
static bool FindDuplicatePrimers (const CPCRReaction &a, const CPCRReaction &b)
 
static string GetOrgModName (const COrgMod &qual)
 
static string GetSubtypeName (const CSubSource &qual)
 

Variables

static constexpr CDiscrepancyCaseProps s_testcase_props_MAP_CHROMOSOME_CONFLICT = { CDiscrepancyVisitorImpl<eTestNames:: MAP_CHROMOSOME_CONFLICT >::Create, eTestTypes:: BIOSRC , eTestNames:: MAP_CHROMOSOME_CONFLICT , "MAP_CHROMOSOME_CONFLICT" , "Eukaryotic sequences with a map source qualifier should also have a chromosome source qualifier" , eDisc | eOncaller | eSmart | eFatal , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_INFLUENZA_DATE_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_DATE_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_DATE_MISMATCH , "INFLUENZA_DATE_MISMATCH" , "Influenza Strain/Collection Date Mismatch" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_INFLUENZA_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_QUALS , "INFLUENZA_QUALS" , "Influenza must have strain, host, isolation_source, country, collection_date" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_INFLUENZA_SEROTYPE = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_SEROTYPE >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_SEROTYPE , "INFLUENZA_SEROTYPE" , "Influenza A virus must have serotype" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_INFLUENZA_SEROTYPE_FORMAT = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_SEROTYPE_FORMAT >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_SEROTYPE_FORMAT , "INFLUENZA_SEROTYPE_FORMAT" , "Influenza A virus serotype must match /^H[1-9]\\d*$|^N[1-9]\\d*$|^H[1-9]\\d*N[1-9]\\d*$|^mixed$/" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_UNCULTURED_NOTES = { CDiscrepancyVisitorImpl<eTestNames:: UNCULTURED_NOTES >::Create, eTestTypes:: BIOSRC , eTestNames:: UNCULTURED_NOTES , "UNCULTURED_NOTES" , "Uncultured Notes" , eOncaller | eFatal , nullptr }
 
const string kMissingViralQualsTop = "[n] virus organism[s] [is] missing required qualifiers"
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_VIRAL_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_VIRAL_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: MISSING_VIRAL_QUALS , "MISSING_VIRAL_QUALS" , "Viruses should specify collection-date, country, and specific-host" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_ATCC_CULTURE_CONFLICT = { CDiscrepancyVisitorImpl<eTestNames:: ATCC_CULTURE_CONFLICT >::Create, eTestTypes:: BIOSRC , eTestNames:: ATCC_CULTURE_CONFLICT , "ATCC_CULTURE_CONFLICT" , "ATCC strain should also appear in culture collection" , eDisc | eOncaller , nullptr }
 
const string kAmplifiedWithSpeciesSpecificPrimers = "amplified with species-specific primers"
 
static constexpr CDiscrepancyCaseProps s_testcase_props_BACTERIA_SHOULD_NOT_HAVE_ISOLATE = { CDiscrepancyVisitorImpl<eTestNames:: BACTERIA_SHOULD_NOT_HAVE_ISOLATE >::Create, eTestTypes:: BIOSRC , eTestNames:: BACTERIA_SHOULD_NOT_HAVE_ISOLATE , "BACTERIA_SHOULD_NOT_HAVE_ISOLATE" , "Bacterial sources should not have isolate" , eDisc | eOncaller | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MAG_SHOULD_NOT_HAVE_STRAIN = { CDiscrepancyVisitorImpl<eTestNames:: MAG_SHOULD_NOT_HAVE_STRAIN >::Create, eTestTypes:: BIOSRC , eTestNames:: MAG_SHOULD_NOT_HAVE_STRAIN , "MAG_SHOULD_NOT_HAVE_STRAIN" , "Organism assembled from metagenome reads should not have strain" , eDisc | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MAG_MISSING_ISOLATE = { CDiscrepancyVisitorImpl<eTestNames:: MAG_MISSING_ISOLATE >::Create, eTestTypes:: BIOSRC , eTestNames:: MAG_MISSING_ISOLATE , "MAG_MISSING_ISOLATE" , "Organism assembled from metagenome reads should have isolate" , eDisc | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MULTISRC = { CDiscrepancyVisitorImpl<eTestNames:: MULTISRC >::Create, eTestTypes:: BIOSRC , eTestNames:: MULTISRC , "MULTISRC" , "Comma or semicolon appears in strain or isolate" , eDisc | eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MULTIPLE_CULTURE_COLLECTION = { CDiscrepancyVisitorImpl<eTestNames:: MULTIPLE_CULTURE_COLLECTION >::Create, eTestTypes:: BIOSRC , eTestNames:: MULTIPLE_CULTURE_COLLECTION , "MULTIPLE_CULTURE_COLLECTION" , "Multiple culture-collection quals" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_REQUIRED_STRAIN = { CDiscrepancyVisitorImpl<eTestNames:: REQUIRED_STRAIN >::Create, eTestTypes:: BIOSRC , eTestNames:: REQUIRED_STRAIN , "REQUIRED_STRAIN" , "Bacteria should have strain" , eDisc | eSubmitter | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_STRAIN_CULTURE_COLLECTION_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: STRAIN_CULTURE_COLLECTION_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: STRAIN_CULTURE_COLLECTION_MISMATCH , "STRAIN_CULTURE_COLLECTION_MISMATCH" , "Strain and culture-collection values conflict" , eOncaller | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_SP_NOT_UNCULTURED = { CDiscrepancyVisitorImpl<eTestNames:: SP_NOT_UNCULTURED >::Create, eTestTypes:: BIOSRC , eTestNames:: SP_NOT_UNCULTURED , "SP_NOT_UNCULTURED" , "Organism ending in sp. needs tax consult" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_FIND_STRAND_TRNAS = { CDiscrepancyVisitorImpl<eTestNames:: FIND_STRAND_TRNAS >::Create, eTestTypes:: SEQUENCE , eTestNames:: FIND_STRAND_TRNAS , "FIND_STRAND_TRNAS" , "Find tRNAs on the same strand" , eDisc , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_REQUIRED_CLONE = { CDiscrepancyVisitorImpl<eTestNames:: REQUIRED_CLONE >::Create, eTestTypes:: BIOSRC , eTestNames:: REQUIRED_CLONE , "REQUIRED_CLONE" , "Uncultured or environmental sources should have clone" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_STRAIN_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: STRAIN_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: STRAIN_TAXNAME_MISMATCH , "STRAIN_TAXNAME_MISMATCH" , "BioSources with the same strain should have the same taxname" , eDisc | eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_SPECVOUCHER_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: SPECVOUCHER_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: SPECVOUCHER_TAXNAME_MISMATCH , "SPECVOUCHER_TAXNAME_MISMATCH" , "BioSources with the same specimen voucher should have the same taxname" , eOncaller | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_CULTURE_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: CULTURE_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: CULTURE_TAXNAME_MISMATCH , "CULTURE_TAXNAME_MISMATCH" , "Test BioSources with the same culture collection but different taxname" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_BIOMATERIAL_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: BIOMATERIAL_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: BIOMATERIAL_TAXNAME_MISMATCH , "BIOMATERIAL_TAXNAME_MISMATCH" , "Test BioSources with the same biomaterial but different taxname" , eOncaller | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_ORGANELLE_ITS = { CDiscrepancyVisitorImpl<eTestNames:: ORGANELLE_ITS >::Create, eTestTypes:: SEQUENCE , eTestNames:: ORGANELLE_ITS , "ORGANELLE_ITS" , "Test Bioseqs for suspect rRNA / ITS on organelle" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_BIOSOURCE = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_BIOSOURCE >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_BIOSOURCE , "INCONSISTENT_BIOSOURCE" , "Inconsistent BioSource" , eDisc | eSubmitter | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_TAX_LOOKUP_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: TAX_LOOKUP_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: TAX_LOOKUP_MISMATCH , "TAX_LOOKUP_MISMATCH" , "Find Tax Lookup Mismatches" , eDisc , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_TAX_LOOKUP_MISSING = { CDiscrepancyVisitorImpl<eTestNames:: TAX_LOOKUP_MISSING >::Create, eTestTypes:: BIOSRC , eTestNames:: TAX_LOOKUP_MISSING , "TAX_LOOKUP_MISSING" , "Find Missing Tax Lookup" , eDisc , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_UNNECESSARY_ENVIRONMENTAL = { CDiscrepancyVisitorImpl<eTestNames:: UNNECESSARY_ENVIRONMENTAL >::Create, eTestTypes:: BIOSRC , eTestNames:: UNNECESSARY_ENVIRONMENTAL , "UNNECESSARY_ENVIRONMENTAL" , "Unnecessary environmental qualifier present" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_END_COLON_IN_COUNTRY = { CDiscrepancyVisitorImpl<eTestNames:: END_COLON_IN_COUNTRY >::Create, eTestTypes:: BIOSRC , eTestNames:: END_COLON_IN_COUNTRY , "END_COLON_IN_COUNTRY" , "Country name end with colon" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_COUNTRY_COLON = { CDiscrepancyVisitorImpl<eTestNames:: COUNTRY_COLON >::Create, eTestTypes:: BIOSRC , eTestNames:: COUNTRY_COLON , "COUNTRY_COLON" , "Country description should only have 1 colon" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_HUMAN_HOST = { CDiscrepancyVisitorImpl<eTestNames:: HUMAN_HOST >::Create, eTestTypes:: BIOSRC , eTestNames:: HUMAN_HOST , "HUMAN_HOST" , "\'Human\' in host should be \'Homo sapiens\'" , eDisc | eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_CHECK_AUTHORITY = { CDiscrepancyVisitorImpl<eTestNames:: CHECK_AUTHORITY >::Create, eTestTypes:: BIOSRC , eTestNames:: CHECK_AUTHORITY , "CHECK_AUTHORITY" , "Authority and Taxname should match first two words" , eDisc | eOncaller , nullptr }
 
static const pair< int, stringsrcqual_keywords []
 
static const size_t srcqual_keywords_sz = ArraySize(srcqual_keywords)
 
static constexpr CDiscrepancyCaseProps s_testcase_props_TRINOMIAL_SHOULD_HAVE_QUALIFIER = { CDiscrepancyVisitorImpl<eTestNames:: TRINOMIAL_SHOULD_HAVE_QUALIFIER >::Create, eTestTypes:: BIOSRC , eTestNames:: TRINOMIAL_SHOULD_HAVE_QUALIFIER , "TRINOMIAL_SHOULD_HAVE_QUALIFIER" , "Trinomial sources should have corresponding qualifier" , eDisc | eOncaller | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE = { CDiscrepancyVisitorImpl<eTestNames:: AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE >::Create, eTestTypes:: BIOSRC , eTestNames:: AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE , "AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE" , "Species-specific primers, no environmental sample" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_PRIMER = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_PRIMER >::Create, eTestTypes:: BIOSRC , eTestNames:: MISSING_PRIMER , "MISSING_PRIMER" , "Missing values in primer set" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_DUPLICATE_PRIMER_SET = { CDiscrepancyVisitorImpl<eTestNames:: DUPLICATE_PRIMER_SET >::Create, eTestTypes:: BIOSRC , eTestNames:: DUPLICATE_PRIMER_SET , "DUPLICATE_PRIMER_SET" , "Duplicate PCR primer pair" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_METAGENOMIC = { CDiscrepancyVisitorImpl<eTestNames:: METAGENOMIC >::Create, eTestTypes:: BIOSRC , eTestNames:: METAGENOMIC , "METAGENOMIC" , "Source has metagenomic qualifier" , eDisc | eOncaller | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_METAGENOME_SOURCE = { CDiscrepancyVisitorImpl<eTestNames:: METAGENOME_SOURCE >::Create, eTestTypes:: BIOSRC , eTestNames:: METAGENOME_SOURCE , "METAGENOME_SOURCE" , "Source has metagenome_source qualifier" , eDisc | eOncaller | eSmart , nullptr }
 
static const char * kDupSrc = "[n] source[s] [has] two or more qualifiers with the same value"
 
static constexpr std::initializer_list< const char * > g_aliases_DUP_SRC_QUAL = { "DUP_SRC_QUAL_DATA" }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_DUP_SRC_QUAL = { CDiscrepancyVisitorImpl<eTestNames:: DUP_SRC_QUAL >::Create, eTestTypes:: BIOSRC , eTestNames:: DUP_SRC_QUAL , "DUP_SRC_QUAL" , "Each qualifier on a source should have different value" , eDisc | eOncaller | eSmart , &g_aliases_DUP_SRC_QUAL }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_UNUSUAL_ITS = { CDiscrepancyVisitorImpl<eTestNames:: UNUSUAL_ITS >::Create, eTestTypes:: SEQUENCE , eTestNames:: UNUSUAL_ITS , "UNUSUAL_ITS" , "Test Bioseqs for unusual rRNA / ITS" , eDisc | eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_SARS_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: SARS_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: SARS_QUALS , "SARS_QUALS" , "SARS-CoV-2 isolate must have correct format" , eOncaller , nullptr }
 

Macro Definition Documentation

◆ SARS_TAX_ID

#define SARS_TAX_ID   2697049

Definition at line 2119 of file biosource_tests.cpp.

Typedef Documentation

◆ TInconsistecyDescriptionList

Definition at line 1048 of file biosource_tests.cpp.

Function Documentation

◆ ChangeCountryColonToComma()

static bool ChangeCountryColonToComma ( CBioSource src)
static

◆ EqualPrimerSets()

static bool EqualPrimerSets ( const CPCRPrimerSet::Tdata a,
const CPCRPrimerSet::Tdata b 
)
static

Definition at line 1887 of file biosource_tests.cpp.

References a, and b.

Referenced by FindDuplicatePrimers().

◆ FindDuplicatePrimers()

static bool FindDuplicatePrimers ( const CPCRReaction a,
const CPCRReaction b 
)
inlinestatic

Definition at line 1911 of file biosource_tests.cpp.

References a, b, and EqualPrimerSets().

◆ FixHumanHost()

static bool FixHumanHost ( CBioSource src)
static

◆ GetBiosourceDifferences()

static void GetBiosourceDifferences ( const CBioSource first_biosrc,
const CBioSource second_biosrc,
TInconsistecyDescriptionList diffs 
)
static

◆ GetOrgModName()

static string GetOrgModName ( const COrgMod qual)
static

◆ GetOrgnameDifferences()

static void GetOrgnameDifferences ( const COrgName first,
const COrgName second,
TInconsistecyDescriptionList diffs 
)
static

◆ GetOrgrefDifferences()

static void GetOrgrefDifferences ( const COrg_ref first_org,
const COrg_ref second_org,
TInconsistecyDescriptionList diffs 
)
static

◆ GetOrgRefs()

static CRef<CTaxon3_reply> GetOrgRefs ( vector< CRef< COrg_ref >> &  orgs)
static

◆ GetSrcQual()

static string GetSrcQual ( const CBioSource bs,
int  qual 
)
static

◆ GetSubtypeName()

static string GetSubtypeName ( const CSubSource qual)
static

◆ GetTaxonTag()

static const CDbtag* GetTaxonTag ( const COrg_ref org)
static

Definition at line 1335 of file biosource_tests.cpp.

References NStr::EqualNocase(), COrg_ref_Base::GetDb(), and COrg_ref_Base::IsSetDb().

Referenced by OrgDiffers().

◆ HasAmplifiedWithSpeciesSpecificPrimerNote()

bool HasAmplifiedWithSpeciesSpecificPrimerNote ( const CBioSource src)

◆ HasCultureCollectionForATCCStrain()

bool HasCultureCollectionForATCCStrain ( const COrgName::TMod mods,
const string strain 
)

◆ HasStrainForATCCCultureCollection()

bool HasStrainForATCCCultureCollection ( const COrgName::TMod mods,
const string culture_collection 
)

◆ IsMissingRequiredClone()

static bool IsMissingRequiredClone ( const CBioSource biosource)
static

◆ IsSameDb()

static bool IsSameDb ( const COrg_ref::TDb first,
const COrg_ref::TDb second 
)
static

Definition at line 1100 of file biosource_tests.cpp.

References first().

Referenced by GetOrgrefDifferences().

◆ IsSameSubtype()

static bool IsSameSubtype ( const CBioSource::TSubtype first,
const CBioSource::TSubtype second 
)
static

◆ MatchExceptSpaceColon()

static bool MatchExceptSpaceColon ( const string a,
const string b 
)
static

Definition at line 668 of file biosource_tests.cpp.

References a, b, and i.

◆ OrgDiffers()

static bool OrgDiffers ( const COrg_ref first,
const COrg_ref second 
)
static

◆ RemoveCountryColon()

static bool RemoveCountryColon ( CBioSource src)
static

◆ SetCultureCollectionFromStrain()

static bool SetCultureCollectionFromStrain ( CBioSource src)
static

◆ SetEnvSampleFixAmplifiedPrimers()

static bool SetEnvSampleFixAmplifiedPrimers ( CBioSource src)
static

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ g_aliases_DUP_SRC_QUAL

constexpr std::initializer_list<const char*> g_aliases_DUP_SRC_QUAL = { "DUP_SRC_QUAL_DATA" }
staticconstexpr

Definition at line 1994 of file biosource_tests.cpp.

◆ kAmplifiedWithSpeciesSpecificPrimers

const string kAmplifiedWithSpeciesSpecificPrimers = "amplified with species-specific primers"

Definition at line 447 of file biosource_tests.cpp.

Referenced by HasAmplifiedWithSpeciesSpecificPrimerNote().

◆ kDupSrc

const char* kDupSrc = "[n] source[s] [has] two or more qualifiers with the same value"
static

Definition at line 1990 of file biosource_tests.cpp.

◆ kMissingViralQualsTop

const string kMissingViralQualsTop = "[n] virus organism[s] [is] missing required qualifiers"

Definition at line 277 of file biosource_tests.cpp.

◆ s_testcase_props_AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE

constexpr CDiscrepancyCaseProps s_testcase_props_AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE = { CDiscrepancyVisitorImpl<eTestNames:: AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE >::Create, eTestTypes:: BIOSRC , eTestNames:: AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE , "AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE" , "Species-specific primers, no environmental sample" , eOncaller , nullptr }
staticconstexpr

Definition at line 1775 of file biosource_tests.cpp.

◆ s_testcase_props_ATCC_CULTURE_CONFLICT

constexpr CDiscrepancyCaseProps s_testcase_props_ATCC_CULTURE_CONFLICT = { CDiscrepancyVisitorImpl<eTestNames:: ATCC_CULTURE_CONFLICT >::Create, eTestTypes:: BIOSRC , eTestNames:: ATCC_CULTURE_CONFLICT , "ATCC_CULTURE_CONFLICT" , "ATCC strain should also appear in culture collection" , eDisc | eOncaller , nullptr }
staticconstexpr

Definition at line 375 of file biosource_tests.cpp.

◆ s_testcase_props_BACTERIA_SHOULD_NOT_HAVE_ISOLATE

constexpr CDiscrepancyCaseProps s_testcase_props_BACTERIA_SHOULD_NOT_HAVE_ISOLATE = { CDiscrepancyVisitorImpl<eTestNames:: BACTERIA_SHOULD_NOT_HAVE_ISOLATE >::Create, eTestTypes:: BIOSRC , eTestNames:: BACTERIA_SHOULD_NOT_HAVE_ISOLATE , "BACTERIA_SHOULD_NOT_HAVE_ISOLATE" , "Bacterial sources should not have isolate" , eDisc | eOncaller | eSmart , nullptr }
staticconstexpr

Definition at line 449 of file biosource_tests.cpp.

◆ s_testcase_props_BIOMATERIAL_TAXNAME_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_BIOMATERIAL_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: BIOMATERIAL_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: BIOMATERIAL_TAXNAME_MISMATCH , "BIOMATERIAL_TAXNAME_MISMATCH" , "Test BioSources with the same biomaterial but different taxname" , eOncaller | eSmart , nullptr }
staticconstexpr

Definition at line 953 of file biosource_tests.cpp.

◆ s_testcase_props_CHECK_AUTHORITY

constexpr CDiscrepancyCaseProps s_testcase_props_CHECK_AUTHORITY = { CDiscrepancyVisitorImpl<eTestNames:: CHECK_AUTHORITY >::Create, eTestTypes:: BIOSRC , eTestNames:: CHECK_AUTHORITY , "CHECK_AUTHORITY" , "Authority and Taxname should match first two words" , eDisc | eOncaller , nullptr }
staticconstexpr

Definition at line 1679 of file biosource_tests.cpp.

◆ s_testcase_props_COUNTRY_COLON

constexpr CDiscrepancyCaseProps s_testcase_props_COUNTRY_COLON = { CDiscrepancyVisitorImpl<eTestNames:: COUNTRY_COLON >::Create, eTestTypes:: BIOSRC , eTestNames:: COUNTRY_COLON , "COUNTRY_COLON" , "Country description should only have 1 colon" , eOncaller , nullptr }
staticconstexpr

Definition at line 1554 of file biosource_tests.cpp.

◆ s_testcase_props_CULTURE_TAXNAME_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_CULTURE_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: CULTURE_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: CULTURE_TAXNAME_MISMATCH , "CULTURE_TAXNAME_MISMATCH" , "Test BioSources with the same culture collection but different taxname" , eOncaller , nullptr }
staticconstexpr

Definition at line 916 of file biosource_tests.cpp.

◆ s_testcase_props_DUP_SRC_QUAL

constexpr CDiscrepancyCaseProps s_testcase_props_DUP_SRC_QUAL = { CDiscrepancyVisitorImpl<eTestNames:: DUP_SRC_QUAL >::Create, eTestTypes:: BIOSRC , eTestNames:: DUP_SRC_QUAL , "DUP_SRC_QUAL" , "Each qualifier on a source should have different value" , eDisc | eOncaller | eSmart , &g_aliases_DUP_SRC_QUAL }
staticconstexpr

Definition at line 1994 of file biosource_tests.cpp.

◆ s_testcase_props_DUPLICATE_PRIMER_SET

constexpr CDiscrepancyCaseProps s_testcase_props_DUPLICATE_PRIMER_SET = { CDiscrepancyVisitorImpl<eTestNames:: DUPLICATE_PRIMER_SET >::Create, eTestTypes:: BIOSRC , eTestNames:: DUPLICATE_PRIMER_SET , "DUPLICATE_PRIMER_SET" , "Duplicate PCR primer pair" , eOncaller , nullptr }
staticconstexpr

Definition at line 1919 of file biosource_tests.cpp.

◆ s_testcase_props_END_COLON_IN_COUNTRY

constexpr CDiscrepancyCaseProps s_testcase_props_END_COLON_IN_COUNTRY = { CDiscrepancyVisitorImpl<eTestNames:: END_COLON_IN_COUNTRY >::Create, eTestTypes:: BIOSRC , eTestNames:: END_COLON_IN_COUNTRY , "END_COLON_IN_COUNTRY" , "Country name end with colon" , eOncaller , nullptr }
staticconstexpr

Definition at line 1495 of file biosource_tests.cpp.

◆ s_testcase_props_FIND_STRAND_TRNAS

constexpr CDiscrepancyCaseProps s_testcase_props_FIND_STRAND_TRNAS = { CDiscrepancyVisitorImpl<eTestNames:: FIND_STRAND_TRNAS >::Create, eTestTypes:: SEQUENCE , eTestNames:: FIND_STRAND_TRNAS , "FIND_STRAND_TRNAS" , "Find tRNAs on the same strand" , eDisc , nullptr }
staticconstexpr

Definition at line 741 of file biosource_tests.cpp.

◆ s_testcase_props_HUMAN_HOST

constexpr CDiscrepancyCaseProps s_testcase_props_HUMAN_HOST = { CDiscrepancyVisitorImpl<eTestNames:: HUMAN_HOST >::Create, eTestTypes:: BIOSRC , eTestNames:: HUMAN_HOST , "HUMAN_HOST" , "\'Human\' in host should be \'Homo sapiens\'" , eDisc | eOncaller , nullptr }
staticconstexpr

Definition at line 1626 of file biosource_tests.cpp.

◆ s_testcase_props_INCONSISTENT_BIOSOURCE

constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_BIOSOURCE = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_BIOSOURCE >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_BIOSOURCE , "INCONSISTENT_BIOSOURCE" , "Inconsistent BioSource" , eDisc | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 1265 of file biosource_tests.cpp.

◆ s_testcase_props_INFLUENZA_DATE_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_INFLUENZA_DATE_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_DATE_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_DATE_MISMATCH , "INFLUENZA_DATE_MISMATCH" , "Influenza Strain/Collection Date Mismatch" , eOncaller , nullptr }
staticconstexpr

Definition at line 113 of file biosource_tests.cpp.

◆ s_testcase_props_INFLUENZA_QUALS

constexpr CDiscrepancyCaseProps s_testcase_props_INFLUENZA_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_QUALS , "INFLUENZA_QUALS" , "Influenza must have strain, host, isolation_source, country, collection_date" , eOncaller , nullptr }
staticconstexpr

Definition at line 165 of file biosource_tests.cpp.

◆ s_testcase_props_INFLUENZA_SEROTYPE

constexpr CDiscrepancyCaseProps s_testcase_props_INFLUENZA_SEROTYPE = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_SEROTYPE >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_SEROTYPE , "INFLUENZA_SEROTYPE" , "Influenza A virus must have serotype" , eOncaller , nullptr }
staticconstexpr

Definition at line 220 of file biosource_tests.cpp.

◆ s_testcase_props_INFLUENZA_SEROTYPE_FORMAT

constexpr CDiscrepancyCaseProps s_testcase_props_INFLUENZA_SEROTYPE_FORMAT = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_SEROTYPE_FORMAT >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_SEROTYPE_FORMAT , "INFLUENZA_SEROTYPE_FORMAT" , "Influenza A virus serotype must match /^H[1-9]\\d*$|^N[1-9]\\d*$|^H[1-9]\\d*N[1-9]\\d*$|^mixed$/" , eOncaller , nullptr }
staticconstexpr

Definition at line 241 of file biosource_tests.cpp.

◆ s_testcase_props_MAG_MISSING_ISOLATE

constexpr CDiscrepancyCaseProps s_testcase_props_MAG_MISSING_ISOLATE = { CDiscrepancyVisitorImpl<eTestNames:: MAG_MISSING_ISOLATE >::Create, eTestTypes:: BIOSRC , eTestNames:: MAG_MISSING_ISOLATE , "MAG_MISSING_ISOLATE" , "Organism assembled from metagenome reads should have isolate" , eDisc | eSmart , nullptr }
staticconstexpr

Definition at line 537 of file biosource_tests.cpp.

◆ s_testcase_props_MAG_SHOULD_NOT_HAVE_STRAIN

constexpr CDiscrepancyCaseProps s_testcase_props_MAG_SHOULD_NOT_HAVE_STRAIN = { CDiscrepancyVisitorImpl<eTestNames:: MAG_SHOULD_NOT_HAVE_STRAIN >::Create, eTestTypes:: BIOSRC , eTestNames:: MAG_SHOULD_NOT_HAVE_STRAIN , "MAG_SHOULD_NOT_HAVE_STRAIN" , "Organism assembled from metagenome reads should not have strain" , eDisc | eSmart , nullptr }
staticconstexpr

Definition at line 503 of file biosource_tests.cpp.

◆ s_testcase_props_MAP_CHROMOSOME_CONFLICT

constexpr CDiscrepancyCaseProps s_testcase_props_MAP_CHROMOSOME_CONFLICT = { CDiscrepancyVisitorImpl<eTestNames:: MAP_CHROMOSOME_CONFLICT >::Create, eTestTypes:: BIOSRC , eTestNames:: MAP_CHROMOSOME_CONFLICT , "MAP_CHROMOSOME_CONFLICT" , "Eukaryotic sequences with a map source qualifier should also have a chromosome source qualifier" , eDisc | eOncaller | eSmart | eFatal , nullptr }
staticconstexpr

Definition at line 86 of file biosource_tests.cpp.

◆ s_testcase_props_METAGENOME_SOURCE

constexpr CDiscrepancyCaseProps s_testcase_props_METAGENOME_SOURCE = { CDiscrepancyVisitorImpl<eTestNames:: METAGENOME_SOURCE >::Create, eTestTypes:: BIOSRC , eTestNames:: METAGENOME_SOURCE , "METAGENOME_SOURCE" , "Source has metagenome_source qualifier" , eDisc | eOncaller | eSmart , nullptr }
staticconstexpr

Definition at line 1959 of file biosource_tests.cpp.

◆ s_testcase_props_METAGENOMIC

constexpr CDiscrepancyCaseProps s_testcase_props_METAGENOMIC = { CDiscrepancyVisitorImpl<eTestNames:: METAGENOMIC >::Create, eTestTypes:: BIOSRC , eTestNames:: METAGENOMIC , "METAGENOMIC" , "Source has metagenomic qualifier" , eDisc | eOncaller | eSmart , nullptr }
staticconstexpr

Definition at line 1942 of file biosource_tests.cpp.

◆ s_testcase_props_MISSING_PRIMER

constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_PRIMER = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_PRIMER >::Create, eTestTypes:: BIOSRC , eTestNames:: MISSING_PRIMER , "MISSING_PRIMER" , "Missing values in primer set" , eOncaller , nullptr }
staticconstexpr

Definition at line 1849 of file biosource_tests.cpp.

◆ s_testcase_props_MISSING_VIRAL_QUALS

constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_VIRAL_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_VIRAL_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: MISSING_VIRAL_QUALS , "MISSING_VIRAL_QUALS" , "Viruses should specify collection-date, country, and specific-host" , eOncaller , nullptr }
staticconstexpr

Definition at line 279 of file biosource_tests.cpp.

◆ s_testcase_props_MULTIPLE_CULTURE_COLLECTION

constexpr CDiscrepancyCaseProps s_testcase_props_MULTIPLE_CULTURE_COLLECTION = { CDiscrepancyVisitorImpl<eTestNames:: MULTIPLE_CULTURE_COLLECTION >::Create, eTestTypes:: BIOSRC , eTestNames:: MULTIPLE_CULTURE_COLLECTION , "MULTIPLE_CULTURE_COLLECTION" , "Multiple culture-collection quals" , eOncaller , nullptr }
staticconstexpr

Definition at line 599 of file biosource_tests.cpp.

◆ s_testcase_props_MULTISRC

constexpr CDiscrepancyCaseProps s_testcase_props_MULTISRC = { CDiscrepancyVisitorImpl<eTestNames:: MULTISRC >::Create, eTestTypes:: BIOSRC , eTestNames:: MULTISRC , "MULTISRC" , "Comma or semicolon appears in strain or isolate" , eDisc | eOncaller , nullptr }
staticconstexpr

Definition at line 578 of file biosource_tests.cpp.

◆ s_testcase_props_ORGANELLE_ITS

constexpr CDiscrepancyCaseProps s_testcase_props_ORGANELLE_ITS = { CDiscrepancyVisitorImpl<eTestNames:: ORGANELLE_ITS >::Create, eTestTypes:: SEQUENCE , eTestNames:: ORGANELLE_ITS , "ORGANELLE_ITS" , "Test Bioseqs for suspect rRNA / ITS on organelle" , eOncaller , nullptr }
staticconstexpr

Definition at line 992 of file biosource_tests.cpp.

◆ s_testcase_props_REQUIRED_CLONE

constexpr CDiscrepancyCaseProps s_testcase_props_REQUIRED_CLONE = { CDiscrepancyVisitorImpl<eTestNames:: REQUIRED_CLONE >::Create, eTestTypes:: BIOSRC , eTestNames:: REQUIRED_CLONE , "REQUIRED_CLONE" , "Uncultured or environmental sources should have clone" , eOncaller , nullptr }
staticconstexpr

Definition at line 829 of file biosource_tests.cpp.

◆ s_testcase_props_REQUIRED_STRAIN

constexpr CDiscrepancyCaseProps s_testcase_props_REQUIRED_STRAIN = { CDiscrepancyVisitorImpl<eTestNames:: REQUIRED_STRAIN >::Create, eTestTypes:: BIOSRC , eTestNames:: REQUIRED_STRAIN , "REQUIRED_STRAIN" , "Bacteria should have strain" , eDisc | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 620 of file biosource_tests.cpp.

◆ s_testcase_props_SARS_QUALS

constexpr CDiscrepancyCaseProps s_testcase_props_SARS_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: SARS_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: SARS_QUALS , "SARS_QUALS" , "SARS-CoV-2 isolate must have correct format" , eOncaller , nullptr }
staticconstexpr

Definition at line 2121 of file biosource_tests.cpp.

◆ s_testcase_props_SP_NOT_UNCULTURED

constexpr CDiscrepancyCaseProps s_testcase_props_SP_NOT_UNCULTURED = { CDiscrepancyVisitorImpl<eTestNames:: SP_NOT_UNCULTURED >::Create, eTestTypes:: BIOSRC , eTestNames:: SP_NOT_UNCULTURED , "SP_NOT_UNCULTURED" , "Organism ending in sp. needs tax consult" , eOncaller , nullptr }
staticconstexpr

Definition at line 726 of file biosource_tests.cpp.

◆ s_testcase_props_SPECVOUCHER_TAXNAME_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_SPECVOUCHER_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: SPECVOUCHER_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: SPECVOUCHER_TAXNAME_MISMATCH , "SPECVOUCHER_TAXNAME_MISMATCH" , "BioSources with the same specimen voucher should have the same taxname" , eOncaller | eSmart , nullptr }
staticconstexpr

Definition at line 879 of file biosource_tests.cpp.

◆ s_testcase_props_STRAIN_CULTURE_COLLECTION_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_STRAIN_CULTURE_COLLECTION_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: STRAIN_CULTURE_COLLECTION_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: STRAIN_CULTURE_COLLECTION_MISMATCH , "STRAIN_CULTURE_COLLECTION_MISMATCH" , "Strain and culture-collection values conflict" , eOncaller | eSmart , nullptr }
staticconstexpr

Definition at line 688 of file biosource_tests.cpp.

◆ s_testcase_props_STRAIN_TAXNAME_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_STRAIN_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: STRAIN_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: STRAIN_TAXNAME_MISMATCH , "STRAIN_TAXNAME_MISMATCH" , "BioSources with the same strain should have the same taxname" , eDisc | eOncaller , nullptr }
staticconstexpr

Definition at line 841 of file biosource_tests.cpp.

◆ s_testcase_props_TAX_LOOKUP_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_TAX_LOOKUP_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: TAX_LOOKUP_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: TAX_LOOKUP_MISMATCH , "TAX_LOOKUP_MISMATCH" , "Find Tax Lookup Mismatches" , eDisc , nullptr }
staticconstexpr

Definition at line 1323 of file biosource_tests.cpp.

◆ s_testcase_props_TAX_LOOKUP_MISSING

constexpr CDiscrepancyCaseProps s_testcase_props_TAX_LOOKUP_MISSING = { CDiscrepancyVisitorImpl<eTestNames:: TAX_LOOKUP_MISSING >::Create, eTestTypes:: BIOSRC , eTestNames:: TAX_LOOKUP_MISSING , "TAX_LOOKUP_MISSING" , "Find Missing Tax Lookup" , eDisc , nullptr }
staticconstexpr

Definition at line 1403 of file biosource_tests.cpp.

◆ s_testcase_props_TRINOMIAL_SHOULD_HAVE_QUALIFIER

constexpr CDiscrepancyCaseProps s_testcase_props_TRINOMIAL_SHOULD_HAVE_QUALIFIER = { CDiscrepancyVisitorImpl<eTestNames:: TRINOMIAL_SHOULD_HAVE_QUALIFIER >::Create, eTestTypes:: BIOSRC , eTestNames:: TRINOMIAL_SHOULD_HAVE_QUALIFIER , "TRINOMIAL_SHOULD_HAVE_QUALIFIER" , "Trinomial sources should have corresponding qualifier" , eDisc | eOncaller | eSmart , nullptr }
staticconstexpr

Definition at line 1745 of file biosource_tests.cpp.

◆ s_testcase_props_UNCULTURED_NOTES

constexpr CDiscrepancyCaseProps s_testcase_props_UNCULTURED_NOTES = { CDiscrepancyVisitorImpl<eTestNames:: UNCULTURED_NOTES >::Create, eTestTypes:: BIOSRC , eTestNames:: UNCULTURED_NOTES , "UNCULTURED_NOTES" , "Uncultured Notes" , eOncaller | eFatal , nullptr }
staticconstexpr

Definition at line 260 of file biosource_tests.cpp.

◆ s_testcase_props_UNNECESSARY_ENVIRONMENTAL

constexpr CDiscrepancyCaseProps s_testcase_props_UNNECESSARY_ENVIRONMENTAL = { CDiscrepancyVisitorImpl<eTestNames:: UNNECESSARY_ENVIRONMENTAL >::Create, eTestTypes:: BIOSRC , eTestNames:: UNNECESSARY_ENVIRONMENTAL , "UNNECESSARY_ENVIRONMENTAL" , "Unnecessary environmental qualifier present" , eOncaller , nullptr }
staticconstexpr

Definition at line 1444 of file biosource_tests.cpp.

◆ s_testcase_props_UNUSUAL_ITS

constexpr CDiscrepancyCaseProps s_testcase_props_UNUSUAL_ITS = { CDiscrepancyVisitorImpl<eTestNames:: UNUSUAL_ITS >::Create, eTestTypes:: SEQUENCE , eTestNames:: UNUSUAL_ITS , "UNUSUAL_ITS" , "Test Bioseqs for unusual rRNA / ITS" , eDisc | eOncaller , nullptr }
staticconstexpr

Definition at line 2094 of file biosource_tests.cpp.

◆ srcqual_keywords

const pair<int, string> srcqual_keywords[]
static
Initial value:
= {
}
@ eSubtype_pathovar
Definition: OrgMod_.hpp:94
@ eSubtype_sub_species
Definition: OrgMod_.hpp:105
@ eSubtype_variety
Definition: OrgMod_.hpp:89
@ eSubtype_forma_specialis
Definition: OrgMod_.hpp:109

Definition at line 1722 of file biosource_tests.cpp.

◆ srcqual_keywords_sz

const size_t srcqual_keywords_sz = ArraySize(srcqual_keywords)
static

Definition at line 1730 of file biosource_tests.cpp.

Modified on Sun Apr 14 05:28:48 2024 by modify_doxy.py rev. 669887