NCBI C++ ToolKit
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CBioSource Class Reference

Represents ASN.1 type BioSource defined in file seqfeat.asn

Search Toolkit Book for CBioSource

#include <objects/seqfeat/BioSource.hpp>

+ Inheritance diagram for CBioSource:
+ Collaboration diagram for CBioSource:

Public Types

typedef pair< string, stringTNameVal
 
typedef vector< TNameValTNameValList
 
- Public Types inherited from CBioSource_Base
enum  EGenome {
  eGenome_unknown = 0, eGenome_genomic = 1, eGenome_chloroplast = 2, eGenome_chromoplast = 3,
  eGenome_kinetoplast = 4, eGenome_mitochondrion = 5, eGenome_plastid = 6, eGenome_macronuclear = 7,
  eGenome_extrachrom = 8, eGenome_plasmid = 9, eGenome_transposon = 10, eGenome_insertion_seq = 11,
  eGenome_cyanelle = 12, eGenome_proviral = 13, eGenome_virion = 14, eGenome_nucleomorph = 15,
  eGenome_apicoplast = 16, eGenome_leucoplast = 17, eGenome_proplastid = 18, eGenome_endogenous_virus = 19,
  eGenome_hydrogenosome = 20, eGenome_chromosome = 21, eGenome_chromatophore = 22, eGenome_plasmid_in_mitochondrion = 23,
  eGenome_plasmid_in_plastid = 24
}
 biological context More...
 
enum  EOrigin {
  eOrigin_unknown = 0, eOrigin_natural = 1, eOrigin_natmut = 2, eOrigin_mut = 3,
  eOrigin_artificial = 4, eOrigin_synthetic = 5, eOrigin_other = 255
}
 
typedef int TGenome
 
typedef int TOrigin
 
typedef COrg_ref TOrg
 
typedef list< CRef< CSubSource > > TSubtype
 
typedef CPCRReactionSet TPcr_primers
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1, eAllocFillZero, eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CBioSource (void)
 
 ~CBioSource (void)
 
int GetGenCode (int def=1) const
 
bool IsSetTaxname (void) const
 
const stringGetTaxname (void) const
 
bool IsSetCommon (void) const
 
const stringGetCommon (void) const
 
bool IsSetLineage (void) const
 
const stringGetLineage (void) const
 
bool IsSetGcode (void) const
 
int GetGcode (void) const
 
bool IsSetMgcode (void) const
 
int GetMgcode (void) const
 
bool IsSetPgcode (void) const
 
int GetPgcode (void) const
 
bool IsSetDivision (void) const
 
const stringGetDivision (void) const
 
bool IsSetOrgname (void) const
 
const COrgNameGetOrgname (void) const
 
bool IsSetOrgMod (void) const
 
string GetRepliconName (void) const
 
string GetBioprojectType (void) const
 
string GetBioprojectLocation (void) const
 
void SetDisableStrainForwarding (bool val)
 
bool GetDisableStrainForwarding () const
 
void UpdateWithBioSample (const CBioSource &biosample, bool force, bool is_local_copy=false)
 
TFieldDiffList GetBiosampleDiffs (const CBioSource &biosample, bool is_local_copy=false) const
 
bool BiosampleDiffsOkForUpdate (const TFieldDiffList &diffs) const
 
TNameValList GetNameValPairs () const
 
void AutoFix ()
 
void RemoveCultureNotes (bool is_species_level=true)
 
bool RemoveLineageSourceNotes ()
 
bool RemoveSubSource (int subtype)
 
bool RemoveOrgMod (int subtype)
 
bool FixEnvironmentalSample ()
 
bool RemoveNullTerms ()
 
bool AllowSexQualifier () const
 
bool AllowMatingTypeQualifier () const
 
bool FixSexMatingTypeInconsistencies ()
 
bool RemoveUnexpectedViralQualifiers ()
 
bool FixGenomeForQualifiers ()
 
bool IsViral () const
 
bool HasSubtype (CSubSource::TSubtype subtype) const
 
CRef< CBioSourceMakeCommon (const CBioSource &other) const
 
- Public Member Functions inherited from CBioSource_Base
 CBioSource_Base (void)
 
virtual ~CBioSource_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetGenome (void) const
 Check if a value has been assigned to Genome data member. More...
 
bool CanGetGenome (void) const
 Check if it is safe to call GetGenome method. More...
 
void ResetGenome (void)
 Reset Genome data member. More...
 
void SetDefaultGenome (void)
 Assign default value to Genome data member. More...
 
TGenome GetGenome (void) const
 Get the Genome member data. More...
 
void SetGenome (TGenome value)
 Assign a value to Genome data member. More...
 
TGenomeSetGenome (void)
 Assign a value to Genome data member. More...
 
bool IsSetOrigin (void) const
 Check if a value has been assigned to Origin data member. More...
 
bool CanGetOrigin (void) const
 Check if it is safe to call GetOrigin method. More...
 
void ResetOrigin (void)
 Reset Origin data member. More...
 
void SetDefaultOrigin (void)
 Assign default value to Origin data member. More...
 
TOrigin GetOrigin (void) const
 Get the Origin member data. More...
 
void SetOrigin (TOrigin value)
 Assign a value to Origin data member. More...
 
TOriginSetOrigin (void)
 Assign a value to Origin data member. More...
 
bool IsSetOrg (void) const
 Check if a value has been assigned to Org data member. More...
 
bool CanGetOrg (void) const
 Check if it is safe to call GetOrg method. More...
 
void ResetOrg (void)
 Reset Org data member. More...
 
const TOrgGetOrg (void) const
 Get the Org member data. More...
 
void SetOrg (TOrg &value)
 Assign a value to Org data member. More...
 
TOrgSetOrg (void)
 Assign a value to Org data member. More...
 
bool IsSetSubtype (void) const
 Check if a value has been assigned to Subtype data member. More...
 
bool CanGetSubtype (void) const
 Check if it is safe to call GetSubtype method. More...
 
void ResetSubtype (void)
 Reset Subtype data member. More...
 
const TSubtypeGetSubtype (void) const
 Get the Subtype member data. More...
 
TSubtypeSetSubtype (void)
 Assign a value to Subtype data member. More...
 
bool IsSetIs_focus (void) const
 to distinguish biological focus Check if a value has been assigned to Is_focus data member. More...
 
bool CanGetIs_focus (void) const
 Check if value of Is_focus member is getatable. More...
 
void ResetIs_focus (void)
 Reset Is_focus data member. More...
 
void SetIs_focus (void)
 Set NULL data member (assign 'NULL' value to Is_focus data member). More...
 
bool IsSetPcr_primers (void) const
 Check if a value has been assigned to Pcr_primers data member. More...
 
bool CanGetPcr_primers (void) const
 Check if it is safe to call GetPcr_primers method. More...
 
void ResetPcr_primers (void)
 Reset Pcr_primers data member. More...
 
const TPcr_primersGetPcr_primers (void) const
 Get the Pcr_primers member data. More...
 
void SetPcr_primers (TPcr_primers &value)
 Assign a value to Pcr_primers data member. More...
 
TPcr_primersSetPcr_primers (void)
 Assign a value to Pcr_primers data member. More...
 
virtual void Reset (void)
 Reset the whole object. More...
 
- Public Member Functions inherited from CSerialObject
 CSerialObject (void)
 
virtual ~CSerialObject (void)
 
virtual const CTypeInfoGetThisTypeInfo (void) const =0
 
virtual void Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
 Set object to copy of another one. More...
 
virtual bool Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
 Check if both objects contain the same values. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
void ThrowUnassigned (TMemberIndex index) const
 
void ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const
 
bool HasNamespaceName (void) const
 Check if object data type has namespace name. More...
 
const stringGetNamespaceName (void) const
 Get namespace name. More...
 
bool HasNamespacePrefix (void) const
 Check if data type has namespace prefix. More...
 
const stringGetNamespacePrefix (void) const
 Get namespace prefix. More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Static Public Member Functions

static CBioSource::EGenome GetGenomeByOrganelle (const string &organelle, NStr::ECase use_case=NStr::eCase, bool starts_with=false)
 
static string GetOrganelleByGenome (unsigned int genome)
 
static CBioSource::EOrigin GetOriginByString (const string &origin, NStr::ECase use_case=NStr::eCase, bool starts_with=false)
 
static string GetStringFromOrigin (unsigned int origin)
 
static bool ShouldIgnoreConflict (const string &label, string src_val, string sample_val, bool is_local_copy=false)
 
static bool IsStopWord (const string &value)
 
static bool AllowSexQualifier (const string &lineage)
 
static bool AllowMatingTypeQualifier (const string &lineage)
 
static bool IsViral (const string &lineage)
 
- Static Public Member Functions inherited from CBioSource_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EGenome (void)
 Access to EGenome's attributes (values, names) as defined in spec. More...
 
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EOrigin (void)
 Access to EOrigin's attributes (values, names) as defined in spec. More...
 
- Static Public Member Functions inherited from CSerialObject
static void SetVerifyDataThread (ESerialVerifyData verify)
 
static void SetVerifyDataGlobal (ESerialVerifyData verify)
 
static string UnassignedString (void)
 
static CStringUTF8 UnassignedStringUTF8 (void)
 
static char UnassignedByte (void)
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 

Private Types

typedef CBioSource_Base Tparent
 

Private Member Functions

 CBioSource (const CBioSource &value)
 
CBioSourceoperator= (const CBioSource &value)
 
void x_ClearCoordinatedBioSampleSubSources ()
 
void x_ClearCoordinatedBioSampleOrgMods ()
 
TNameValList x_GetOrgModNameValPairs () const
 
TNameValList x_GetSubtypeNameValPairs () const
 
void x_RemoveNameElementDiffs (const CBioSource &biosample, TFieldDiffList &diff_list) const
 
bool x_ShouldIgnoreNoteForBiosample () const
 

Static Private Member Functions

static void x_InitStopWords (void)
 
static void x_RemoveStopWords (COrg_ref &org_ref)
 

Additional Inherited Members

- Static Public Attributes inherited from CSerialObject
static const char * ms_UnassignedStr = "<*unassigned*>"
 
static const char ms_UnassignedByte = char(0xcd)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 58 of file BioSource.hpp.

Member Typedef Documentation

Definition at line 126 of file BioSource.hpp.

Definition at line 127 of file BioSource.hpp.

Definition at line 60 of file BioSource.hpp.

Constructor & Destructor Documentation

CBioSource::CBioSource ( void  )
inline

Definition at line 200 of file BioSource.hpp.

Referenced by MakeCommon().

CBioSource::~CBioSource ( void  )

Definition at line 68 of file BioSource.cpp.

CBioSource::CBioSource ( const CBioSource value)
private

Member Function Documentation

bool CBioSource::AllowMatingTypeQualifier ( const string lineage)
static

Definition at line 1728 of file BioSource.cpp.

References NStr::eNocase, IsViral(), and NStr::StartsWith().

Referenced by BOOST_AUTO_TEST_CASE().

bool CBioSource::AllowMatingTypeQualifier ( ) const
bool CBioSource::AllowSexQualifier ( const string lineage)
static

Definition at line 1695 of file BioSource.cpp.

References NStr::eNocase, IsViral(), and NStr::StartsWith().

Referenced by BOOST_AUTO_TEST_CASE().

bool CBioSource::AllowSexQualifier ( ) const
void CBioSource::AutoFix ( )
bool CBioSource::BiosampleDiffsOkForUpdate ( const TFieldDiffList diffs) const

Definition at line 690 of file BioSource.cpp.

References NStr::IsBlank(), and ITERATE.

Referenced by UpdateWithBioSample().

bool CBioSource::FixEnvironmentalSample ( )
bool CBioSource::FixGenomeForQualifiers ( )
bool CBioSource::FixSexMatingTypeInconsistencies ( )
string CBioSource::GetBioprojectLocation ( void  ) const
string CBioSource::GetBioprojectType ( void  ) const
TFieldDiffList CBioSource::GetBiosampleDiffs ( const CBioSource biosample,
bool  is_local_copy = false 
) const
const string & CBioSource::GetCommon ( void  ) const
bool CBioSource::GetDisableStrainForwarding ( ) const
const string & CBioSource::GetDivision ( void  ) const
int CBioSource::GetGcode ( void  ) const
int CBioSource::GetGenCode ( int  def = 1) const
CBioSource::EGenome CBioSource::GetGenomeByOrganelle ( const string organelle,
NStr::ECase  use_case = NStr::eCase,
bool  starts_with = false 
)
static
const string & CBioSource::GetLineage ( void  ) const
int CBioSource::GetMgcode ( void  ) const
CBioSource::TNameValList CBioSource::GetNameValPairs ( ) const
string CBioSource::GetOrganelleByGenome ( unsigned int  genome)
static
const COrgName & CBioSource::GetOrgname ( void  ) const

Definition at line 410 of file BioSource.cpp.

References CBioSource_Base::GetOrg(), and COrg_ref_Base::GetOrgname().

Referenced by CSeqEntry_test_on_biosrc::AddMissingViralQualsDiscrepancies(), AllowMatingTypeQualifier(), AllowSexQualifier(), AutoFix(), CSeqEntry_test_on_biosrc_orgmod::BiosrcHasConflictingStrainAndCultureCollectionValues(), BOOST_AUTO_TEST_CASE(), CompareOrgModValue(), FixEnvironmentalSample(), GetDisableStrainForwarding(), CSeqEntry_test_on_quals::GetMultiOrgModVlus(), CTable2AsnContext::GetOrgName(), CSeqEntry_test_on_quals::GetQual2SrcIdx(), GetSeqTableFromSeqEntry(), CSeqEntryTestAndRepData::HasAmplifiedWithSpeciesSpecificPrimerNote(), CSeqEntry_test_on_biosrc_orgmod::HasMissingBacteriaStrain(), CSeqEntry_test_on_biosrc::HasMulSrc(), CSeqEntryTestAndRepData::IsBacterialIsolate(), CSeqEntry_test_on_biosrc::IsBacterialIsolate(), CSeqEntry_test_on_biosrc::IsMissingRequiredClone(), CSuspectRuleCheck::IsNonTextSourceQualPresent(), IsNonTextSourceQualPresent(), CTestAndRepData::IsOrgModPresent(), CSeqEntry_test_on_biosrc_orgmod::IsStrainInCultureCollectionForBioSource(), RemoveLineageSourceNotes(), RemoveNullTerms(), RemoveOrgMod(), RemoveUnexpectedViralQualifiers(), CSeqEntry_test_on_tax_cflts::RunTests(), s_RareConsensusNotExpected(), SetDisableStrainForwarding(), SetOrgMod(), CSrcQualProblem::x_AddValuesFromSrc(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), x_GetOrgModNameValPairs(), CSeqEntry_test_on_biosrc::x_IsMissingRequiredStrain(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetFlags(), CBioseqContext::x_SetTaxname(), x_ShouldIgnoreNoteForBiosample(), and CSrcWriter::xGatherOrgModFeat().

CBioSource::EOrigin CBioSource::GetOriginByString ( const string origin,
NStr::ECase  use_case = NStr::eCase,
bool  starts_with = false 
)
static
int CBioSource::GetPgcode ( void  ) const

Definition at line 390 of file BioSource.cpp.

References CBioSource_Base::GetOrg(), and COrg_ref::GetPgcode().

string CBioSource::GetRepliconName ( void  ) const
string CBioSource::GetStringFromOrigin ( unsigned int  origin)
static
const string & CBioSource::GetTaxname ( void  ) const

Definition at line 340 of file BioSource.cpp.

References CBioSource_Base::GetOrg(), and COrg_ref_Base::GetTaxname().

Referenced by CAddFluComments::AddBioSource(), CExportTableDlg::AddBioSource(), CUnculTaxTool::AddBioSource(), CSrcTaxnameAfterBinomialColumn::AddToBioSource(), CStrainSerotypeInfluenza::AddToInfluenzaNames(), CAppendModToOrg::ApplyToOrgMod(), BOOST_AUTO_TEST_CASE(), CSrcTaxnameAfterBinomialColumn::ClearInBioSource(), CollectBioseqsByTaxnameAndHaplotype(), CUnculturedTool::CorrectBioSource(), CSeqEntry_test_on_biosrc_orgmod::DoAuthorityAndTaxnameConflict(), CSeqEntry_test_on_biosrc::DoInfluenzaStrainAndCollectionDateMisMatch(), CSeqEntry_test_on_biosrc::FindTrinomialWithoutQualifier(), FixEnvironmentalSample(), CStrainSerotypeInfluenza::FixupOrganismNames(), GetNameValPairs(), CTable2AsnContext::GetOrgName(), GetSeqTableFromSeqEntry(), CTestAndRepData::GetSrcQualValue(), GetSrcQualValue(), CSeqEntry_test_on_biosrc_orgmod::HasMissingBacteriaStrain(), CSeqEntry_test_on_biosrc::IsMissingRequiredClone(), CStrainSerotypeInfluenza::IsParsableInfluenzaVirusName(), CGenusSpeciesFixup::ModBioSource(), RemoveLineageSourceNotes(), CSeqEntry_on_biosrc_subsrc::RunTests(), CSeqEntry_test_on_tax_cflts::RunTests(), CSeqEntry_test_on_biosrc_orgmod::RunTests(), CSeqEntry_test_on_biosrc::RunTests(), CUnculTaxTool::StandardFixes(), CSeqEntry_ONCALLER_STRAIN_TAXNAME_CONFLICT::TestOnObj(), CSeqEntry_DISC_HAPLOTYPE_MISMATCH::TestOnObj(), CBioseq_TEST_ORGANELLE_PRODUCTS::TestOnObj(), CBioseq_TEST_UNWANTED_SPACER::TestOnObj(), CBioseq_ONCALLER_HIV_RNA_INCONSISTENT::TestOnObj(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_descr::ValidateSeqDescr(), CSrcQualProblem::x_AddValuesFromSrc(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CSeqEntry_test_on_biosrc::x_HasUnnecessaryEnvironmental(), CDeflineGenerator::x_SetBioSrc(), CBioseqContext::x_SetTaxname(), CDeflineGenerator::x_SetTitleFromProtein(), CValidError_bioseq::x_ValidateStructuredCommentContext(), CSrcWriter::xGatherTaxname(), and CGff3Writer::xWriteSequenceHeader().

bool CBioSource::HasSubtype ( CSubSource::TSubtype  subtype) const
bool CBioSource::IsSetCommon ( void  ) const
bool CBioSource::IsSetDivision ( void  ) const
bool CBioSource::IsSetGcode ( void  ) const
bool CBioSource::IsSetLineage ( void  ) const
bool CBioSource::IsSetMgcode ( void  ) const
bool CBioSource::IsSetOrgMod ( void  ) const
bool CBioSource::IsSetOrgname ( void  ) const
bool CBioSource::IsSetPgcode ( void  ) const
bool CBioSource::IsSetTaxname ( void  ) const

Definition at line 335 of file BioSource.cpp.

References CBioSource_Base::GetOrg(), CBioSource_Base::IsSetOrg(), and COrg_ref_Base::IsSetTaxname().

Referenced by CAddFluComments::AddBioSource(), CExportTableDlg::AddBioSource(), CUnculTaxTool::AddBioSource(), CStrainSerotypeInfluenza::AddToInfluenzaNames(), CAppendModToOrg::ApplyToOrgMod(), CSrcTaxnameAfterBinomialColumn::ClearInBioSource(), CSeqEntry_test_on_biosrc::DoInfluenzaStrainAndCollectionDateMisMatch(), CSeqEntry_test_on_biosrc::FindTrinomialWithoutQualifier(), CStrainSerotypeInfluenza::FixupOrganismNames(), GetNameValPairs(), CTable2AsnContext::GetOrgName(), CSeqEntry_test_on_quals::GetQual2SrcIdx(), GetSeqTableFromSeqEntry(), CTestAndRepData::GetSrcQualValue(), GetSrcQualValue(), CSeqEntry_test_on_biosrc_orgmod::HasMissingBacteriaStrain(), CSeqEntry_test_on_biosrc::IsMissingRequiredClone(), CStrainSerotypeInfluenza::IsParsableInfluenzaVirusName(), CGenusSpeciesFixup::ModBioSource(), CSeqEntry_on_biosrc_subsrc::RunTests(), CSeqEntry_test_on_tax_cflts::RunTests(), CSeqEntry_test_on_biosrc_orgmod::RunTests(), CSeqEntry_test_on_biosrc::RunTests(), s_IsEmptyBioSource(), CSeqEntry_ONCALLER_STRAIN_TAXNAME_CONFLICT::TestOnObj(), CSeqEntry_DISC_HAPLOTYPE_MISMATCH::TestOnObj(), CBioseq_TEST_ORGANELLE_PRODUCTS::TestOnObj(), CBioseq_TEST_UNWANTED_SPACER::TestOnObj(), CBioseq_ONCALLER_HIV_RNA_INCONSISTENT::TestOnObj(), CStrainSerotypeInfluenza::TrimmingOrganismNames(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_descr::ValidateSeqDescr(), CSrcQualProblem::x_AddValuesFromSrc(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), x_RemoveNameElementDiffs(), CDeflineGenerator::x_SetBioSrc(), CBioseqContext::x_SetTaxname(), CDeflineGenerator::x_SetTitleFromProtein(), CValidError_bioseq::x_ValidateStructuredCommentContext(), and CSrcWriter::xGatherTaxname().

bool CBioSource::IsStopWord ( const string value)
static
bool CBioSource::IsViral ( const string lineage)
static

Definition at line 1675 of file BioSource.cpp.

References NStr::eNocase, and NStr::StartsWith().

bool CBioSource::IsViral ( ) const
CRef< CBioSource > CBioSource::MakeCommon ( const CBioSource other) const
CBioSource& CBioSource::operator= ( const CBioSource value)
private
void CBioSource::RemoveCultureNotes ( bool  is_species_level = true)
bool CBioSource::RemoveLineageSourceNotes ( )
bool CBioSource::RemoveNullTerms ( )
bool CBioSource::RemoveOrgMod ( int  subtype)
bool CBioSource::RemoveSubSource ( int  subtype)
bool CBioSource::RemoveUnexpectedViralQualifiers ( )
void CBioSource::SetDisableStrainForwarding ( bool  val)
bool CBioSource::ShouldIgnoreConflict ( const string label,
string  src_val,
string  sample_val,
bool  is_local_copy = false 
)
static
void CBioSource::UpdateWithBioSample ( const CBioSource biosample,
bool  force,
bool  is_local_copy = false 
)
void CBioSource::x_ClearCoordinatedBioSampleOrgMods ( )
private
void CBioSource::x_ClearCoordinatedBioSampleSubSources ( )
private
CBioSource::TNameValList CBioSource::x_GetOrgModNameValPairs ( ) const
private
CBioSource::TNameValList CBioSource::x_GetSubtypeNameValPairs ( ) const
private
static void CBioSource::x_InitStopWords ( void  )
staticprivate
void CBioSource::x_RemoveNameElementDiffs ( const CBioSource biosample,
TFieldDiffList diff_list 
) const
private
void CBioSource::x_RemoveStopWords ( COrg_ref org_ref)
staticprivate
bool CBioSource::x_ShouldIgnoreNoteForBiosample ( ) const
private

The documentation for this class was generated from the following files:
Modified on Sun Mar 26 18:26:23 2017 by modify_doxy.py rev. 506947