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CAutoDefModifierCombo Class Reference

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#include <objmgr/util/autodef_mod_combo.hpp>

+ Inheritance diagram for CAutoDefModifierCombo:
+ Collaboration diagram for CAutoDefModifierCombo:

Public Types

enum  EInfluenzaType {
  eNotInfluenza = 0 , eInfluenzaA , eInfluenzaB , eInfluenzaC ,
  eInfluenzaD
}
 
typedef vector< CSubSource::ESubtype > TSubSourceTypeVector
 
typedef vector< COrgMod::ESubtype > TOrgModTypeVector
 
typedef vector< CRef< CAutoDefSourceGroup > > TGroupListVector
 
- 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 atomic< Uint8 > TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CAutoDefModifierCombo ()
 
 CAutoDefModifierCombo (CAutoDefModifierCombo *orig)
 
 ~CAutoDefModifierCombo ()
 
void InitFromOptions (const CAutoDefOptions &options)
 
void SetOptions (const CAutoDefOptions &options)
 
void InitOptions (CAutoDefOptions &options) const
 
unsigned int GetNumGroups ()
 
unsigned int GetNumSubSources ()
 
CSubSource::ESubtype GetSubSource (unsigned int index)
 
unsigned int GetNumOrgMods ()
 
COrgMod::ESubtype GetOrgMod (unsigned int index)
 
bool HasSubSource (CSubSource::ESubtype st)
 
bool HasOrgMod (COrgMod::ESubtype st)
 
void AddSource (const CBioSource &bs, const string &feature_clauses="")
 
void AddSubsource (CSubSource::ESubtype st, bool even_if_not_uniquifying=false)
 
void AddOrgMod (COrgMod::ESubtype st, bool even_if_not_uniquifying=false)
 
void GetAvailableModifiers (CAutoDefSourceDescription::TAvailableModifierVector &modifier_list)
 
bool HasTrickyHIV ()
 
bool GetDefaultExcludeSp ()
 
void SetUseModifierLabels (bool use)
 
bool GetUseModifierLabels ()
 
void SetMaxModifiers (int max_mods)
 
int GetMaxModifiers ()
 
void SetAllowModAtEndOfTaxname (bool keep)
 
bool GetAllowModAtEndOfTaxname ()
 
void SetKeepCountryText (bool keep)
 
bool GetKeepCountryText ()
 
void SetExcludeSpOrgs (bool exclude)
 
bool GetExcludeSpOrgs ()
 
void SetExcludeCfOrgs (bool exclude)
 
bool GetExcludeCfOrgs ()
 
void SetExcludeNrOrgs (bool exclude)
 
bool GetExcludeNrOrgs ()
 
void SetExcludeAffOrgs (bool exclude)
 
bool GetExcludeAffOrgs ()
 
void SetKeepParen (bool keep)
 
bool GetKeepParen ()
 
void SetKeepAfterSemicolon (bool keep)
 
bool GetKeepAfterSemicolon ()
 
void SetHIVCloneIsolateRule (CAutoDefOptions::EHIVCloneIsolateRule rule_num)
 
CAutoDefOptions::EHIVCloneIsolateRule GetHIVCloneIsolateRule ()
 
string GetSourceDescriptionString (const CBioSource &bsrc)
 
const TGroupListVector & GetGroupList () const
 
const CAutoDefSourceDescription::TModifierVector & GetModifiers () const
 
unsigned int GetNumUnique () const
 
unsigned int GetMaxInGroup () const
 
int Compare (const CAutoDefModifierCombo &other) const
 
bool operator> (const CAutoDefModifierCombo &src) const
 
bool operator< (const CAutoDefModifierCombo &src) const
 
bool AddQual (bool IsOrgMod, int subtype, bool even_if_not_uniquifying=false)
 
bool RemoveQual (bool IsOrgMod, int subtype)
 
vector< CRef< CAutoDefModifierCombo > > ExpandByAnyPresent ()
 
bool AreFeatureClausesUnique ()
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObject & operator= (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...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. 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
 
- Public Member Functions inherited from IAutoDefCombo
virtual ~IAutoDefCombo ()
 

Static Public Member Functions

static bool IsUsableInDefline (CSubSource::ESubtype subtype)
 
static bool IsUsableInDefline (COrgMod::ESubtype subtype)
 
static bool IsModifierRequiredByDefault (bool is_orgmod, int subtype)
 
static bool IsModifierInString (const string &find_this, const string &find_in, bool ignore_at_end)
 
static EInfluenzaType GetInfluenzaType (const string &taxname)
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT 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 pair< COrgMod::ESubtype, bool > TExtraOrgMod
 
typedef map< COrgMod::ESubtype, bool > TExtraOrgMods
 
typedef pair< CSubSource::ESubtype, bool > TExtraSubSrc
 
typedef map< CSubSource::ESubtype, bool > TExtraSubSrcs
 

Private Member Functions

string x_GetSubSourceLabel (CSubSource::ESubtype st)
 
string x_GetOrgModLabel (COrgMod::ESubtype st)
 
void x_CleanUpTaxName (string &tax_name)
 
bool x_AddSubsourceString (string &source_description, const CBioSource &bsrc, CSubSource::ESubtype st)
 
bool x_AddOrgModString (string &source_description, const CBioSource &bsrc, COrgMod::ESubtype st)
 
void x_AddHIVModifiers (TExtraOrgMods &extra_orgmods, TExtraSubSrcs &extra_subsrcs, const CBioSource &bsrc)
 
void x_AddInfluenzaModifiers (TExtraOrgMods &extra_orgmods, TExtraSubSrcs &extra_subsrcs, EInfluenzaType influenza_type)
 
void x_AddRequiredSubSourceModifiers (TExtraOrgMods &extra_orgmods, TExtraSubSrcs &extra_subsrcs, const CBioSource &bsrc)
 
void x_AddTypeStrainModifiers (TExtraOrgMods &extra_orgmods, TExtraSubSrcs &extra_subsrcs, const CBioSource &bsrc)
 

Static Private Member Functions

static bool x_AddMinicircle (string &source_description, const CBioSource &bsrc)
 
static bool x_AddMinicircle (string &source_description, const string &note_text)
 
static bool x_BioSourceHasSubSrc (const CBioSource &src, CSubSource::ESubtype subtype)
 
static bool x_BioSourceHasOrgMod (const CBioSource &src, COrgMod::ESubtype subtype)
 
static bool x_SpecialHandlingForInfluenza (EInfluenzaType influenza_type, CSubSource::ESubtype subtype)
 
static bool x_SpecialHandlingForInfluenza (EInfluenzaType influenza_type, COrgMod::ESubtype subtype)
 
static bool x_HasTypeStrainComment (const CBioSource &bsrc)
 

Private Attributes

TSubSourceTypeVector m_SubSources
 
TOrgModTypeVector m_OrgMods
 
TGroupListVector m_GroupList
 
CAutoDefSourceDescription::TModifierVector m_Modifiers
 
bool m_UseModifierLabels
 
int m_MaxModifiers
 
bool m_AllowModAtEndOfTaxname
 
bool m_KeepCountryText
 
bool m_ExcludeSpOrgs
 
bool m_ExcludeCfOrgs
 
bool m_ExcludeNrOrgs
 
bool m_ExcludeAffOrgs
 
bool m_KeepParen
 
bool m_KeepAfterSemicolon
 
CAutoDefOptions::EHIVCloneIsolateRule m_HIVCloneIsolateRule
 

Additional Inherited Members

- 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 57 of file autodef_mod_combo.hpp.

Member Typedef Documentation

◆ TExtraOrgMod

typedef pair<COrgMod::ESubtype, bool> CAutoDefModifierCombo::TExtraOrgMod
private

Definition at line 185 of file autodef_mod_combo.hpp.

◆ TExtraOrgMods

typedef map<COrgMod::ESubtype, bool> CAutoDefModifierCombo::TExtraOrgMods
private

Definition at line 186 of file autodef_mod_combo.hpp.

◆ TExtraSubSrc

typedef pair<CSubSource::ESubtype, bool> CAutoDefModifierCombo::TExtraSubSrc
private

Definition at line 187 of file autodef_mod_combo.hpp.

◆ TExtraSubSrcs

typedef map<CSubSource::ESubtype, bool> CAutoDefModifierCombo::TExtraSubSrcs
private

Definition at line 188 of file autodef_mod_combo.hpp.

◆ TGroupListVector

typedef vector<CRef<CAutoDefSourceGroup> > CAutoDefModifierCombo::TGroupListVector

Definition at line 117 of file autodef_mod_combo.hpp.

◆ TOrgModTypeVector

typedef vector<COrgMod::ESubtype> CAutoDefModifierCombo::TOrgModTypeVector

Definition at line 116 of file autodef_mod_combo.hpp.

◆ TSubSourceTypeVector

typedef vector<CSubSource::ESubtype> CAutoDefModifierCombo::TSubSourceTypeVector

Definition at line 115 of file autodef_mod_combo.hpp.

Member Enumeration Documentation

◆ EInfluenzaType

enum CAutoDefModifierCombo::EInfluenzaType
Enumerator
eNotInfluenza 
eInfluenzaA 
eInfluenzaB 
eInfluenzaC 
eInfluenzaD 

Definition at line 145 of file autodef_mod_combo.hpp.

Constructor & Destructor Documentation

◆ CAutoDefModifierCombo() [1/2]

CAutoDefModifierCombo::CAutoDefModifierCombo ( )

Definition at line 51 of file autodef_mod_combo.cpp.

Referenced by ExpandByAnyPresent().

◆ CAutoDefModifierCombo() [2/2]

CAutoDefModifierCombo::CAutoDefModifierCombo ( CAutoDefModifierCombo *  orig)

Definition at line 72 of file autodef_mod_combo.cpp.

References _ASSERT, ITERATE, m_AllowModAtEndOfTaxname, m_ExcludeAffOrgs, m_ExcludeCfOrgs, m_ExcludeNrOrgs, m_ExcludeSpOrgs, m_GroupList, m_HIVCloneIsolateRule, m_KeepAfterSemicolon, m_KeepCountryText, m_KeepParen, m_MaxModifiers, m_Modifiers, m_OrgMods, m_SubSources, m_UseModifierLabels, and orig.

◆ ~CAutoDefModifierCombo()

CAutoDefModifierCombo::~CAutoDefModifierCombo ( )

Definition at line 111 of file autodef_mod_combo.cpp.

Member Function Documentation

◆ AddOrgMod()

void CAutoDefModifierCombo::AddOrgMod ( COrgMod::ESubtype  st,
bool  even_if_not_uniquifying = false 
)

Definition at line 248 of file autodef_mod_combo.cpp.

References AddQual().

Referenced by ConfigureAutodefForSeqEntry(), CAutoDef::GetAllModifierCombo(), and CAutodefJob::x_MakeChanges().

◆ AddQual()

bool CAutoDefModifierCombo::AddQual ( bool  IsOrgMod,
int  subtype,
bool  even_if_not_uniquifying = false 
)

Definition at line 1031 of file autodef_mod_combo.cpp.

References CompareAutoDefSourceGroupByStrings(), m_GroupList, m_KeepAfterSemicolon, m_Modifiers, m_OrgMods, m_SubSources, NON_CONST_ITERATE, ct::sort(), and split().

Referenced by AddOrgMod(), AddSubsource(), and InitFromOptions().

◆ AddSource()

void CAutoDefModifierCombo::AddSource ( const CBioSource &  bs,
const string &  feature_clauses = "" 
)

Definition at line 222 of file autodef_mod_combo.cpp.

References g(), and m_GroupList.

Referenced by CAutoDef::AddDescriptors(), and CAutoDef::AddSources().

◆ AddSubsource()

void CAutoDefModifierCombo::AddSubsource ( CSubSource::ESubtype  st,
bool  even_if_not_uniquifying = false 
)

Definition at line 242 of file autodef_mod_combo.cpp.

References AddQual().

Referenced by ConfigureAutodefForSeqEntry(), CAutoDef::GetAllModifierCombo(), and CAutodefJob::x_MakeChanges().

◆ AreFeatureClausesUnique()

bool CAutoDefModifierCombo::AreFeatureClausesUnique ( )

Definition at line 1108 of file autodef_mod_combo.cpp.

References NStr::Equal(), g(), ITERATE, m_GroupList, prev(), and ct::sort().

◆ Compare()

int CAutoDefModifierCombo::Compare ( const CAutoDefModifierCombo &  other) const

Definition at line 984 of file autodef_mod_combo.cpp.

References GetGroupList(), GetMaxInGroup(), GetModifiers(), GetNumUnique(), m_GroupList, and m_Modifiers.

◆ ExpandByAnyPresent()

vector< CRef< CAutoDefModifierCombo > > CAutoDefModifierCombo::ExpandByAnyPresent ( )

Definition at line 1083 of file autodef_mod_combo.cpp.

References CAutoDefModifierCombo(), and m_GroupList.

◆ GetAllowModAtEndOfTaxname()

bool CAutoDefModifierCombo::GetAllowModAtEndOfTaxname ( )
inline

Definition at line 238 of file autodef_mod_combo.hpp.

References m_AllowModAtEndOfTaxname.

◆ GetAvailableModifiers()

void CAutoDefModifierCombo::GetAvailableModifiers ( CAutoDefSourceDescription::TAvailableModifierVector &  modifier_list)

Definition at line 719 of file autodef_mod_combo.cpp.

References kNumPreferred, m_GroupList, and s_PreferredList.

Referenced by CAutoDef::GetAllModifierCombo(), CAutoDef::GetAvailableModifiers(), and CAutoDef::GetNumAvailableModifiers().

◆ GetDefaultExcludeSp()

bool CAutoDefModifierCombo::GetDefaultExcludeSp ( )

Definition at line 612 of file autodef_mod_combo.cpp.

References m_GroupList.

Referenced by CAutoDef::AddDescriptors(), and CAutoDef::AddSources().

◆ GetExcludeAffOrgs()

bool CAutoDefModifierCombo::GetExcludeAffOrgs ( )
inline

Definition at line 308 of file autodef_mod_combo.hpp.

References m_ExcludeAffOrgs.

◆ GetExcludeCfOrgs()

bool CAutoDefModifierCombo::GetExcludeCfOrgs ( )
inline

Definition at line 280 of file autodef_mod_combo.hpp.

References m_ExcludeCfOrgs.

◆ GetExcludeNrOrgs()

bool CAutoDefModifierCombo::GetExcludeNrOrgs ( )
inline

Definition at line 294 of file autodef_mod_combo.hpp.

References m_ExcludeNrOrgs.

◆ GetExcludeSpOrgs()

bool CAutoDefModifierCombo::GetExcludeSpOrgs ( )
inline

Definition at line 266 of file autodef_mod_combo.hpp.

References m_ExcludeSpOrgs.

◆ GetGroupList()

const TGroupListVector& CAutoDefModifierCombo::GetGroupList ( ) const
inline

Definition at line 119 of file autodef_mod_combo.hpp.

Referenced by Compare().

◆ GetHIVCloneIsolateRule()

CAutoDefOptions::EHIVCloneIsolateRule CAutoDefModifierCombo::GetHIVCloneIsolateRule ( )
inline

Definition at line 350 of file autodef_mod_combo.hpp.

References m_HIVCloneIsolateRule.

◆ GetInfluenzaType()

CAutoDefModifierCombo::EInfluenzaType CAutoDefModifierCombo::GetInfluenzaType ( const string &  taxname)
static

Definition at line 532 of file autodef_mod_combo.cpp.

References eInfluenzaA, eInfluenzaB, eInfluenzaC, eInfluenzaD, NStr::eNocase, eNotInfluenza, and NStr::StartsWith().

Referenced by GetSourceDescriptionString().

◆ GetKeepAfterSemicolon()

bool CAutoDefModifierCombo::GetKeepAfterSemicolon ( )
inline

Definition at line 336 of file autodef_mod_combo.hpp.

References m_KeepAfterSemicolon.

◆ GetKeepCountryText()

bool CAutoDefModifierCombo::GetKeepCountryText ( )
inline

Definition at line 252 of file autodef_mod_combo.hpp.

References m_KeepCountryText.

◆ GetKeepParen()

bool CAutoDefModifierCombo::GetKeepParen ( )
inline

Definition at line 322 of file autodef_mod_combo.hpp.

References m_KeepParen.

◆ GetMaxInGroup()

unsigned int CAutoDefModifierCombo::GetMaxInGroup ( ) const

Definition at line 967 of file autodef_mod_combo.cpp.

References ITERATE, and m_GroupList.

Referenced by Compare().

◆ GetMaxModifiers()

int CAutoDefModifierCombo::GetMaxModifiers ( )
inline

Definition at line 224 of file autodef_mod_combo.hpp.

References m_MaxModifiers.

◆ GetModifiers()

const CAutoDefSourceDescription::TModifierVector& CAutoDefModifierCombo::GetModifiers ( void  ) const
inline

Definition at line 120 of file autodef_mod_combo.hpp.

Referenced by Compare().

◆ GetNumGroups()

unsigned int CAutoDefModifierCombo::GetNumGroups ( )

Definition at line 166 of file autodef_mod_combo.cpp.

References m_GroupList.

◆ GetNumOrgMods()

unsigned int CAutoDefModifierCombo::GetNumOrgMods ( )

Definition at line 186 of file autodef_mod_combo.cpp.

References m_OrgMods.

◆ GetNumSubSources()

unsigned int CAutoDefModifierCombo::GetNumSubSources ( )

Definition at line 172 of file autodef_mod_combo.cpp.

References m_SubSources.

◆ GetNumUnique()

unsigned int CAutoDefModifierCombo::GetNumUnique ( ) const

Definition at line 954 of file autodef_mod_combo.cpp.

References ITERATE, and m_GroupList.

Referenced by Compare().

◆ GetOrgMod()

COrgMod::ESubtype CAutoDefModifierCombo::GetOrgMod ( unsigned int  index)

Definition at line 192 of file autodef_mod_combo.cpp.

References _ASSERT, and m_OrgMods.

◆ GetSourceDescriptionString()

string CAutoDefModifierCombo::GetSourceDescriptionString ( const CBioSource &  bsrc)
virtual

Implements IAutoDefCombo.

Definition at line 782 of file autodef_mod_combo.cpp.

References CBioSource_Base::CanGetOrigin(), eInfluenzaA, map_checker< Container >::end(), NStr::EndsWith(), eNotInfluenza, CBioSource_Base::eOrigin_mut, CSubSource_Base::eSubtype_clone, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_segment, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_strain, NStr::Find(), map_checker< Container >::find(), GetInfluenzaType(), COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetOrigin(), COrg_ref_Base::GetTaxname(), map_checker< Container >::insert(), NStr::IsBlank(), kNumPreferred, m_ExcludeAffOrgs, m_ExcludeCfOrgs, m_ExcludeNrOrgs, m_ExcludeSpOrgs, m_OrgMods, m_SubSources, m_UseModifierLabels, s_PreferredList, NStr::StartsWith(), x_AddHIVModifiers(), x_AddInfluenzaModifiers(), x_AddMinicircle(), x_AddOrgModString(), x_AddRequiredSubSourceModifiers(), x_AddSubsourceString(), x_AddTypeStrainModifiers(), x_BioSourceHasOrgMod(), x_BioSourceHasSubSrc(), x_CleanUpTaxName(), and x_SpecialHandlingForInfluenza().

Referenced by CAutoDef::GetOneDefLine().

◆ GetSubSource()

CSubSource::ESubtype CAutoDefModifierCombo::GetSubSource ( unsigned int  index)

Definition at line 178 of file autodef_mod_combo.cpp.

References _ASSERT, and m_SubSources.

◆ GetUseModifierLabels()

bool CAutoDefModifierCombo::GetUseModifierLabels ( )
inline

Definition at line 210 of file autodef_mod_combo.hpp.

References m_UseModifierLabels.

◆ HasOrgMod()

bool CAutoDefModifierCombo::HasOrgMod ( COrgMod::ESubtype  st)

Definition at line 211 of file autodef_mod_combo.cpp.

References m_OrgMods.

Referenced by CAutoDef::GetAllModifierCombo(), and x_AddHIVModifiers().

◆ HasSubSource()

bool CAutoDefModifierCombo::HasSubSource ( CSubSource::ESubtype  st)

Definition at line 200 of file autodef_mod_combo.cpp.

References m_SubSources.

Referenced by CAutoDef::GetAllModifierCombo(), and x_AddHIVModifiers().

◆ HasTrickyHIV()

bool CAutoDefModifierCombo::HasTrickyHIV ( )

Definition at line 464 of file autodef_mod_combo.cpp.

References m_GroupList.

◆ InitFromOptions()

void CAutoDefModifierCombo::InitFromOptions ( const CAutoDefOptions &  options)

Definition at line 116 of file autodef_mod_combo.cpp.

References AddQual(), CAutoDefOptions::GetAllowModAtEndOfTaxname(), CAutoDefOptions::GetDoNotApplyToAff(), CAutoDefOptions::GetDoNotApplyToCf(), CAutoDefOptions::GetDoNotApplyToNr(), CAutoDefOptions::GetDoNotApplyToSp(), CAutoDefOptions::GetHIVRule(), CAutoDefOptions::GetIncludeCountryText(), CAutoDefOptions::GetKeepAfterSemicolon(), CAutoDefOptions::GetLeaveParenthetical(), CAutoDefOptions::GetMaxMods(), CAutoDefOptions::GetOrgMods(), CAutoDefOptions::GetSubSources(), CAutoDefOptions::GetUseLabels(), ITERATE, m_AllowModAtEndOfTaxname, m_ExcludeAffOrgs, m_ExcludeCfOrgs, m_ExcludeNrOrgs, m_ExcludeSpOrgs, m_HIVCloneIsolateRule, m_KeepAfterSemicolon, m_KeepCountryText, m_KeepParen, m_MaxModifiers, and m_UseModifierLabels.

◆ InitOptions()

void CAutoDefModifierCombo::InitOptions ( CAutoDefOptions &  options) const

Definition at line 141 of file autodef_mod_combo.cpp.

References CAutoDefOptions::AddOrgMod(), CAutoDefOptions::AddSubSource(), ITERATE, m_AllowModAtEndOfTaxname, m_ExcludeAffOrgs, m_ExcludeCfOrgs, m_ExcludeNrOrgs, m_ExcludeSpOrgs, m_HIVCloneIsolateRule, m_KeepAfterSemicolon, m_KeepCountryText, m_KeepParen, m_MaxModifiers, m_Modifiers, m_UseModifierLabels, CAutoDefOptions::SetAllowModAtEndOfTaxname(), CAutoDefOptions::SetDoNotApplyToAff(), CAutoDefOptions::SetDoNotApplyToCf(), CAutoDefOptions::SetDoNotApplyToNr(), CAutoDefOptions::SetDoNotApplyToSp(), CAutoDefOptions::SetHIVRule(), CAutoDefOptions::SetIncludeCountryText(), CAutoDefOptions::SetKeepAfterSemicolon(), CAutoDefOptions::SetLeaveParenthetical(), CAutoDefOptions::SetMaxMods(), and CAutoDefOptions::SetUseLabels().

Referenced by BOOST_AUTO_TEST_CASE(), CAutoDef::GetOneDefLine(), and CAutoDef::SetOptions().

◆ IsModifierInString()

bool CAutoDefModifierCombo::IsModifierInString ( const string &  find_this,
const string &  find_in,
bool  ignore_at_end 
)
static

Definition at line 380 of file autodef_mod_combo.cpp.

References NStr::Find().

Referenced by BOOST_AUTO_TEST_CASE(), and x_AddOrgModString().

◆ IsModifierRequiredByDefault()

bool CAutoDefModifierCombo::IsModifierRequiredByDefault ( bool  is_orgmod,
int  subtype 
)
static

Definition at line 764 of file autodef_mod_combo.cpp.

References CSubSource_Base::eSubtype_endogenous_virus_name, CSubSource_Base::eSubtype_plasmid_name, and CSubSource_Base::eSubtype_transgenic.

◆ IsUsableInDefline() [1/2]

bool CAutoDefModifierCombo::IsUsableInDefline ( COrgMod::ESubtype  subtype)
static

Definition at line 752 of file autodef_mod_combo.cpp.

References kNumPreferred, and s_PreferredList.

◆ IsUsableInDefline() [2/2]

bool CAutoDefModifierCombo::IsUsableInDefline ( CSubSource::ESubtype  subtype)
static

Definition at line 740 of file autodef_mod_combo.cpp.

References kNumPreferred, and s_PreferredList.

Referenced by BOOST_AUTO_TEST_CASE().

◆ operator<()

bool CAutoDefModifierCombo::operator< ( const CAutoDefModifierCombo &  src) const
inline

Definition at line 131 of file autodef_mod_combo.hpp.

References Compare().

◆ operator>()

bool CAutoDefModifierCombo::operator> ( const CAutoDefModifierCombo &  src) const
inline

Definition at line 126 of file autodef_mod_combo.hpp.

References Compare().

◆ RemoveQual()

bool CAutoDefModifierCombo::RemoveQual ( bool  IsOrgMod,
int  subtype 
)

Definition at line 1072 of file autodef_mod_combo.cpp.

References m_GroupList, and NON_CONST_ITERATE.

◆ SetAllowModAtEndOfTaxname()

void CAutoDefModifierCombo::SetAllowModAtEndOfTaxname ( bool  keep)
inline

Definition at line 231 of file autodef_mod_combo.hpp.

References m_AllowModAtEndOfTaxname.

◆ SetExcludeAffOrgs()

void CAutoDefModifierCombo::SetExcludeAffOrgs ( bool  exclude)
inline

Definition at line 301 of file autodef_mod_combo.hpp.

References m_ExcludeAffOrgs.

Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().

◆ SetExcludeCfOrgs()

void CAutoDefModifierCombo::SetExcludeCfOrgs ( bool  exclude)
inline

Definition at line 273 of file autodef_mod_combo.hpp.

References m_ExcludeCfOrgs.

Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().

◆ SetExcludeNrOrgs()

void CAutoDefModifierCombo::SetExcludeNrOrgs ( bool  exclude)
inline

Definition at line 287 of file autodef_mod_combo.hpp.

References m_ExcludeNrOrgs.

Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().

◆ SetExcludeSpOrgs()

void CAutoDefModifierCombo::SetExcludeSpOrgs ( bool  exclude)
inline

Definition at line 259 of file autodef_mod_combo.hpp.

References m_ExcludeSpOrgs.

Referenced by CAutoDef::AddDescriptors(), CAutoDef::AddSources(), ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().

◆ SetHIVCloneIsolateRule()

void CAutoDefModifierCombo::SetHIVCloneIsolateRule ( CAutoDefOptions::EHIVCloneIsolateRule  rule_num)
inline

Definition at line 343 of file autodef_mod_combo.hpp.

References m_HIVCloneIsolateRule.

Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().

◆ SetKeepAfterSemicolon()

void CAutoDefModifierCombo::SetKeepAfterSemicolon ( bool  keep)
inline

Definition at line 329 of file autodef_mod_combo.hpp.

References m_KeepAfterSemicolon.

Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().

◆ SetKeepCountryText()

void CAutoDefModifierCombo::SetKeepCountryText ( bool  keep)
inline

Definition at line 245 of file autodef_mod_combo.hpp.

References m_KeepCountryText.

Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().

◆ SetKeepParen()

void CAutoDefModifierCombo::SetKeepParen ( bool  keep)
inline

Definition at line 315 of file autodef_mod_combo.hpp.

References m_KeepParen.

Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().

◆ SetMaxModifiers()

void CAutoDefModifierCombo::SetMaxModifiers ( int  max_mods)
inline

Definition at line 217 of file autodef_mod_combo.hpp.

References m_MaxModifiers.

Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().

◆ SetOptions()

void CAutoDefModifierCombo::SetOptions ( const CAutoDefOptions &  options)
inline

Definition at line 67 of file autodef_mod_combo.hpp.

Referenced by CDeflineGenerator::GenerateDefline(), CAutoDef::RegenerateDefLine(), and CMacroFunction_RefreshDefline::s_RefreshDeflineCommand().

◆ SetUseModifierLabels()

void CAutoDefModifierCombo::SetUseModifierLabels ( bool  use)
inline

Definition at line 203 of file autodef_mod_combo.hpp.

References m_UseModifierLabels.

Referenced by ConfigureAutodefForSeqEntry(), and CAutodefJob::x_MakeChanges().

◆ x_AddHIVModifiers()

void CAutoDefModifierCombo::x_AddHIVModifiers ( TExtraOrgMods &  extra_orgmods,
TExtraSubSrcs &  extra_subsrcs,
const CBioSource &  bsrc 
)
private

Definition at line 475 of file autodef_mod_combo.cpp.

References map_checker< Container >::end(), CAutoDefOptions::ePreferClone, CAutoDefOptions::ePreferIsolate, NStr::Equal(), CSubSource_Base::eSubtype_clone, CSubSource_Base::eSubtype_country, COrgMod_Base::eSubtype_isolate, COrgMod_Base::eSubtype_strain, CAutoDefOptions::eWantBoth, map_checker< Container >::find(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetTaxname(), HasOrgMod(), HasSubSource(), map_checker< Container >::insert(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetTaxname(), m_HIVCloneIsolateRule, x_BioSourceHasOrgMod(), x_BioSourceHasSubSrc(), and x_CleanUpTaxName().

Referenced by GetSourceDescriptionString().

◆ x_AddInfluenzaModifiers()

void CAutoDefModifierCombo::x_AddInfluenzaModifiers ( TExtraOrgMods &  extra_orgmods,
TExtraSubSrcs &  extra_subsrcs,
EInfluenzaType  influenza_type 
)
private

Definition at line 575 of file autodef_mod_combo.cpp.

References eInfluenzaA, eInfluenzaB, eInfluenzaC, eInfluenzaD, map_checker< Container >::end(), eNotInfluenza, CSubSource_Base::eSubtype_clone, CSubSource_Base::eSubtype_segment, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_strain, map_checker< Container >::find(), and map_checker< Container >::insert().

Referenced by GetSourceDescriptionString().

◆ x_AddMinicircle() [1/2]

bool CAutoDefModifierCombo::x_AddMinicircle ( string &  source_description,
const CBioSource &  bsrc 
)
staticprivate

Definition at line 931 of file autodef_mod_combo.cpp.

References COrgMod_Base::eSubtype_other, CSubSource_Base::eSubtype_other, COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetSubtype(), COrgName_Base::IsSetMod(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), CBioSource_Base::IsSetSubtype(), and ITERATE.

Referenced by GetSourceDescriptionString().

◆ x_AddMinicircle() [2/2]

bool CAutoDefModifierCombo::x_AddMinicircle ( string &  source_description,
const string &  note_text 
)
staticprivate

Definition at line 913 of file autodef_mod_combo.cpp.

References NStr::Find(), NStr::fSplit_Tokenize, ITERATE, NStr::Split(), t, and NStr::TruncateSpacesInPlace().

◆ x_AddOrgModString()

bool CAutoDefModifierCombo::x_AddOrgModString ( string &  source_description,
const CBioSource &  bsrc,
COrgMod::ESubtype  st 
)
private

Definition at line 415 of file autodef_mod_combo.cpp.

References COrgMod_Base::eSubtype_forma, COrgMod_Base::eSubtype_forma_specialis, COrgMod_Base::eSubtype_isolate, COrgMod_Base::eSubtype_pathovar, COrgMod_Base::eSubtype_specimen_voucher, COrgMod_Base::eSubtype_strain, COrgMod_Base::eSubtype_sub_species, COrgMod_Base::eSubtype_variety, NStr::Find(), COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), COrg_ref_Base::GetTaxname(), IsModifierInString(), COrgName_Base::IsSetMod(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), ITERATE, m_AllowModAtEndOfTaxname, m_KeepAfterSemicolon, NStr::StartsWith(), val, and x_GetOrgModLabel().

Referenced by GetSourceDescriptionString().

◆ x_AddRequiredSubSourceModifiers()

void CAutoDefModifierCombo::x_AddRequiredSubSourceModifiers ( TExtraOrgMods &  extra_orgmods,
TExtraSubSrcs &  extra_subsrcs,
const CBioSource &  bsrc 
)
private

Definition at line 623 of file autodef_mod_combo.cpp.

References map_checker< Container >::end(), CSubSource_Base::eSubtype_endogenous_virus_name, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_segment, CSubSource_Base::eSubtype_transgenic, map_checker< Container >::find(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetTaxname(), map_checker< Container >::insert(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetTaxname(), and NStr::StartsWith().

Referenced by GetSourceDescriptionString().

◆ x_AddSubsourceString()

bool CAutoDefModifierCombo::x_AddSubsourceString ( string &  source_description,
const CBioSource &  bsrc,
CSubSource::ESubtype  st 
)
private

Definition at line 341 of file autodef_mod_combo.cpp.

References NStr::EqualNocase(), CSubSource_Base::eSubtype_country, CSubSource_Base::eSubtype_plasmid_name, NStr::Find(), CBioSource_Base::GetSubtype(), NStr::IsBlank(), CBioSource_Base::IsSetSubtype(), ITERATE, m_KeepAfterSemicolon, m_KeepCountryText, val, and x_GetSubSourceLabel().

Referenced by GetSourceDescriptionString().

◆ x_AddTypeStrainModifiers()

void CAutoDefModifierCombo::x_AddTypeStrainModifiers ( TExtraOrgMods &  extra_orgmods,
TExtraSubSrcs &  extra_subsrcs,
const CBioSource &  bsrc 
)
private

Definition at line 660 of file autodef_mod_combo.cpp.

References map_checker< Container >::end(), COrgMod_Base::eSubtype_strain, map_checker< Container >::find(), map_checker< Container >::insert(), and x_HasTypeStrainComment().

Referenced by GetSourceDescriptionString().

◆ x_BioSourceHasOrgMod()

bool CAutoDefModifierCombo::x_BioSourceHasOrgMod ( const CBioSource &  src,
COrgMod::ESubtype  subtype 
)
staticprivate

Definition at line 326 of file autodef_mod_combo.cpp.

References COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), COrgName_Base::IsSetMod(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), and ITERATE.

Referenced by GetSourceDescriptionString(), and x_AddHIVModifiers().

◆ x_BioSourceHasSubSrc()

bool CAutoDefModifierCombo::x_BioSourceHasSubSrc ( const CBioSource &  src,
CSubSource::ESubtype  subtype 
)
staticprivate

Definition at line 312 of file autodef_mod_combo.cpp.

References CBioSource_Base::GetSubtype(), CBioSource_Base::IsSetSubtype(), and ITERATE.

Referenced by GetSourceDescriptionString(), and x_AddHIVModifiers().

◆ x_CleanUpTaxName()

void CAutoDefModifierCombo::x_CleanUpTaxName ( string &  tax_name)
private

Definition at line 295 of file autodef_mod_combo.cpp.

References NStr::eNocase, NStr::Equal(), NStr::Find(), m_KeepParen, and NStr::TruncateSpacesInPlace().

Referenced by GetSourceDescriptionString(), and x_AddHIVModifiers().

◆ x_GetOrgModLabel()

string CAutoDefModifierCombo::x_GetOrgModLabel ( COrgMod::ESubtype  st)
private

Definition at line 277 of file autodef_mod_combo.cpp.

References COrgMod_Base::eSubtype_nat_host, CAutoDefAvailableModifier::GetOrgModLabel(), NStr::IsBlank(), label, and m_UseModifierLabels.

Referenced by x_AddOrgModString().

◆ x_GetSubSourceLabel()

string CAutoDefModifierCombo::x_GetSubSourceLabel ( CSubSource::ESubtype  st)
private

Definition at line 254 of file autodef_mod_combo.cpp.

References CSubSource_Base::eSubtype_country, CSubSource_Base::eSubtype_endogenous_virus_name, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_segment, CSubSource_Base::eSubtype_transgenic, CAutoDefAvailableModifier::GetSubSourceLabel(), NStr::IsBlank(), label, and m_UseModifierLabels.

Referenced by x_AddSubsourceString().

◆ x_HasTypeStrainComment()

bool CAutoDefModifierCombo::x_HasTypeStrainComment ( const CBioSource &  bsrc)
staticprivate

Definition at line 644 of file autodef_mod_combo.cpp.

References COrgMod_Base::eSubtype_other, NStr::FindNoCase(), COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), COrgName_Base::IsSetMod(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), and ITERATE.

Referenced by x_AddTypeStrainModifiers().

◆ x_SpecialHandlingForInfluenza() [1/2]

bool CAutoDefModifierCombo::x_SpecialHandlingForInfluenza ( EInfluenzaType  influenza_type,
COrgMod::ESubtype  subtype 
)
staticprivate

Definition at line 560 of file autodef_mod_combo.cpp.

References eInfluenzaA, eNotInfluenza, COrgMod_Base::eSubtype_serotype, and COrgMod_Base::eSubtype_strain.

◆ x_SpecialHandlingForInfluenza() [2/2]

bool CAutoDefModifierCombo::x_SpecialHandlingForInfluenza ( EInfluenzaType  influenza_type,
CSubSource::ESubtype  subtype 
)
staticprivate

Definition at line 548 of file autodef_mod_combo.cpp.

References eNotInfluenza, CSubSource_Base::eSubtype_clone, and CSubSource_Base::eSubtype_segment.

Referenced by GetSourceDescriptionString().

Member Data Documentation

◆ m_AllowModAtEndOfTaxname

bool CAutoDefModifierCombo::m_AllowModAtEndOfTaxname
private

Definition at line 163 of file autodef_mod_combo.hpp.

Referenced by CAutoDefModifierCombo(), GetAllowModAtEndOfTaxname(), InitFromOptions(), InitOptions(), SetAllowModAtEndOfTaxname(), and x_AddOrgModString().

◆ m_ExcludeAffOrgs

bool CAutoDefModifierCombo::m_ExcludeAffOrgs
private

Definition at line 170 of file autodef_mod_combo.hpp.

Referenced by CAutoDefModifierCombo(), GetExcludeAffOrgs(), GetSourceDescriptionString(), InitFromOptions(), InitOptions(), and SetExcludeAffOrgs().

◆ m_ExcludeCfOrgs

bool CAutoDefModifierCombo::m_ExcludeCfOrgs
private

Definition at line 168 of file autodef_mod_combo.hpp.

Referenced by CAutoDefModifierCombo(), GetExcludeCfOrgs(), GetSourceDescriptionString(), InitFromOptions(), InitOptions(), and SetExcludeCfOrgs().

◆ m_ExcludeNrOrgs

bool CAutoDefModifierCombo::m_ExcludeNrOrgs
private

Definition at line 169 of file autodef_mod_combo.hpp.

Referenced by CAutoDefModifierCombo(), GetExcludeNrOrgs(), GetSourceDescriptionString(), InitFromOptions(), InitOptions(), and SetExcludeNrOrgs().

◆ m_ExcludeSpOrgs

bool CAutoDefModifierCombo::m_ExcludeSpOrgs
private

Definition at line 165 of file autodef_mod_combo.hpp.

Referenced by CAutoDefModifierCombo(), GetExcludeSpOrgs(), GetSourceDescriptionString(), InitFromOptions(), InitOptions(), and SetExcludeSpOrgs().

◆ m_GroupList

TGroupListVector CAutoDefModifierCombo::m_GroupList
private

Definition at line 158 of file autodef_mod_combo.hpp.

Referenced by AddQual(), AddSource(), AreFeatureClausesUnique(), CAutoDefModifierCombo(), Compare(), ExpandByAnyPresent(), GetAvailableModifiers(), GetDefaultExcludeSp(), GetMaxInGroup(), GetNumGroups(), GetNumUnique(), HasTrickyHIV(), and RemoveQual().

◆ m_HIVCloneIsolateRule

CAutoDefOptions::EHIVCloneIsolateRule CAutoDefModifierCombo::m_HIVCloneIsolateRule
private

Definition at line 174 of file autodef_mod_combo.hpp.

Referenced by CAutoDefModifierCombo(), GetHIVCloneIsolateRule(), InitFromOptions(), InitOptions(), SetHIVCloneIsolateRule(), and x_AddHIVModifiers().

◆ m_KeepAfterSemicolon

bool CAutoDefModifierCombo::m_KeepAfterSemicolon
private

Definition at line 173 of file autodef_mod_combo.hpp.

Referenced by AddQual(), CAutoDefModifierCombo(), GetKeepAfterSemicolon(), InitFromOptions(), InitOptions(), SetKeepAfterSemicolon(), x_AddOrgModString(), and x_AddSubsourceString().

◆ m_KeepCountryText

bool CAutoDefModifierCombo::m_KeepCountryText
private

Definition at line 164 of file autodef_mod_combo.hpp.

Referenced by CAutoDefModifierCombo(), GetKeepCountryText(), InitFromOptions(), InitOptions(), SetKeepCountryText(), and x_AddSubsourceString().

◆ m_KeepParen

bool CAutoDefModifierCombo::m_KeepParen
private

Definition at line 172 of file autodef_mod_combo.hpp.

Referenced by CAutoDefModifierCombo(), GetKeepParen(), InitFromOptions(), InitOptions(), SetKeepParen(), and x_CleanUpTaxName().

◆ m_MaxModifiers

int CAutoDefModifierCombo::m_MaxModifiers
private

Definition at line 162 of file autodef_mod_combo.hpp.

Referenced by CAutoDefModifierCombo(), GetMaxModifiers(), InitFromOptions(), InitOptions(), and SetMaxModifiers().

◆ m_Modifiers

CAutoDefSourceDescription::TModifierVector CAutoDefModifierCombo::m_Modifiers
private

Definition at line 159 of file autodef_mod_combo.hpp.

Referenced by AddQual(), CAutoDefModifierCombo(), Compare(), and InitOptions().

◆ m_OrgMods

TOrgModTypeVector CAutoDefModifierCombo::m_OrgMods
private

Definition at line 157 of file autodef_mod_combo.hpp.

Referenced by AddQual(), CAutoDefModifierCombo(), GetNumOrgMods(), GetOrgMod(), GetSourceDescriptionString(), and HasOrgMod().

◆ m_SubSources

TSubSourceTypeVector CAutoDefModifierCombo::m_SubSources
private

Definition at line 156 of file autodef_mod_combo.hpp.

Referenced by AddQual(), CAutoDefModifierCombo(), GetNumSubSources(), GetSourceDescriptionString(), GetSubSource(), and HasSubSource().

◆ m_UseModifierLabels

bool CAutoDefModifierCombo::m_UseModifierLabels
private

Definition at line 161 of file autodef_mod_combo.hpp.

Referenced by CAutoDefModifierCombo(), GetSourceDescriptionString(), GetUseModifierLabels(), InitFromOptions(), InitOptions(), SetUseModifierLabels(), x_GetOrgModLabel(), and x_GetSubSourceLabel().

The documentation for this class was generated from the following files:
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Modified on Thu Nov 30 04:57:58 2023 by modify_doxy.py rev. 669887