A RetroSearch Logo

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Search Query:

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCAutoDefModifierCombo.html below:

NCBI C++ ToolKit: CAutoDefModifierCombo Class Reference

Search Toolkit Book for CAutoDefModifierCombo

#include <objmgr/util/autodef_mod_combo.hpp>

  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 ()     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...
    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   virtual  ~IAutoDefCombo ()   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)  

Definition at line 57 of file autodef_mod_combo.hpp.

◆ TExtraOrgMod ◆ TExtraOrgMods ◆ TExtraSubSrc ◆ TExtraSubSrcs ◆ TGroupListVector ◆ TOrgModTypeVector ◆ TSubSourceTypeVector ◆ EInfluenzaType Enumerator eNotInfluenza  eInfluenzaA  eInfluenzaB  eInfluenzaC  eInfluenzaD 

Definition at line 145 of file autodef_mod_combo.hpp.

◆ CAutoDefModifierCombo() [1/2] CAutoDefModifierCombo::CAutoDefModifierCombo ( ) ◆ CAutoDefModifierCombo() [2/2]

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() ◆ AddOrgMod() ◆ 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() ◆ AddSubsource() ◆ AreFeatureClausesUnique() bool CAutoDefModifierCombo::AreFeatureClausesUnique ( ) ◆ Compare() ◆ ExpandByAnyPresent() ◆ GetAllowModAtEndOfTaxname() bool CAutoDefModifierCombo::GetAllowModAtEndOfTaxname ( ) inline ◆ GetAvailableModifiers() ◆ GetDefaultExcludeSp() bool CAutoDefModifierCombo::GetDefaultExcludeSp ( ) ◆ GetExcludeAffOrgs() bool CAutoDefModifierCombo::GetExcludeAffOrgs ( ) inline ◆ GetExcludeCfOrgs() bool CAutoDefModifierCombo::GetExcludeCfOrgs ( ) inline ◆ GetExcludeNrOrgs() bool CAutoDefModifierCombo::GetExcludeNrOrgs ( ) inline ◆ GetExcludeSpOrgs() bool CAutoDefModifierCombo::GetExcludeSpOrgs ( ) inline ◆ GetGroupList() ◆ GetHIVCloneIsolateRule() ◆ GetInfluenzaType() ◆ GetKeepAfterSemicolon() bool CAutoDefModifierCombo::GetKeepAfterSemicolon ( ) inline ◆ GetKeepCountryText() bool CAutoDefModifierCombo::GetKeepCountryText ( ) inline ◆ GetKeepParen() bool CAutoDefModifierCombo::GetKeepParen ( ) inline ◆ GetMaxInGroup() unsigned int CAutoDefModifierCombo::GetMaxInGroup ( ) const ◆ GetMaxModifiers() int CAutoDefModifierCombo::GetMaxModifiers ( ) inline ◆ GetModifiers() ◆ GetNumGroups() unsigned int CAutoDefModifierCombo::GetNumGroups ( ) ◆ GetNumOrgMods() unsigned int CAutoDefModifierCombo::GetNumOrgMods ( ) ◆ GetNumSubSources() unsigned int CAutoDefModifierCombo::GetNumSubSources ( ) ◆ GetNumUnique() unsigned int CAutoDefModifierCombo::GetNumUnique ( ) const ◆ GetOrgMod() ◆ GetSourceDescriptionString()

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, st(), 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() ◆ GetUseModifierLabels() bool CAutoDefModifierCombo::GetUseModifierLabels ( ) inline ◆ HasOrgMod() ◆ HasSubSource() ◆ HasTrickyHIV() bool CAutoDefModifierCombo::HasTrickyHIV ( ) ◆ InitFromOptions()

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() ◆ IsModifierRequiredByDefault() bool CAutoDefModifierCombo::IsModifierRequiredByDefault ( bool  is_orgmod, int  subtype  ) static ◆ IsUsableInDefline() [1/2] ◆ IsUsableInDefline() [2/2] ◆ operator<() ◆ operator>() ◆ RemoveQual() bool CAutoDefModifierCombo::RemoveQual ( bool  IsOrgMod, int  subtype  ) ◆ SetAllowModAtEndOfTaxname() void CAutoDefModifierCombo::SetAllowModAtEndOfTaxname ( bool  keep ) inline ◆ SetExcludeAffOrgs() void CAutoDefModifierCombo::SetExcludeAffOrgs ( bool  exclude ) inline ◆ SetExcludeCfOrgs() void CAutoDefModifierCombo::SetExcludeCfOrgs ( bool  exclude ) inline ◆ SetExcludeNrOrgs() void CAutoDefModifierCombo::SetExcludeNrOrgs ( bool  exclude ) inline ◆ SetExcludeSpOrgs() void CAutoDefModifierCombo::SetExcludeSpOrgs ( bool  exclude ) inline ◆ SetHIVCloneIsolateRule() ◆ SetKeepAfterSemicolon() void CAutoDefModifierCombo::SetKeepAfterSemicolon ( bool  keep ) inline ◆ SetKeepCountryText() void CAutoDefModifierCombo::SetKeepCountryText ( bool  keep ) inline ◆ SetKeepParen() void CAutoDefModifierCombo::SetKeepParen ( bool  keep ) inline ◆ SetMaxModifiers() void CAutoDefModifierCombo::SetMaxModifiers ( int  max_mods ) inline ◆ SetOptions() ◆ SetUseModifierLabels() void CAutoDefModifierCombo::SetUseModifierLabels ( bool  use ) inline ◆ x_AddHIVModifiers()

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()

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]

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] ◆ x_AddOrgModString()

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, st(), NStr::StartsWith(), val, and x_GetOrgModLabel().

Referenced by GetSourceDescriptionString().

◆ x_AddRequiredSubSourceModifiers()

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()

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, st(), val, and x_GetSubSourceLabel().

Referenced by GetSourceDescriptionString().

◆ x_AddTypeStrainModifiers() ◆ x_BioSourceHasOrgMod() ◆ x_BioSourceHasSubSrc() ◆ x_CleanUpTaxName() void CAutoDefModifierCombo::x_CleanUpTaxName ( string &  tax_name ) private ◆ x_GetOrgModLabel() ◆ x_GetSubSourceLabel() ◆ x_HasTypeStrainComment() ◆ x_SpecialHandlingForInfluenza() [1/2] ◆ x_SpecialHandlingForInfluenza() [2/2] ◆ m_AllowModAtEndOfTaxname bool CAutoDefModifierCombo::m_AllowModAtEndOfTaxname private ◆ m_ExcludeAffOrgs bool CAutoDefModifierCombo::m_ExcludeAffOrgs private ◆ m_ExcludeCfOrgs bool CAutoDefModifierCombo::m_ExcludeCfOrgs private ◆ m_ExcludeNrOrgs bool CAutoDefModifierCombo::m_ExcludeNrOrgs private ◆ m_ExcludeSpOrgs bool CAutoDefModifierCombo::m_ExcludeSpOrgs private ◆ m_GroupList

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 ◆ m_KeepAfterSemicolon bool CAutoDefModifierCombo::m_KeepAfterSemicolon private ◆ m_KeepCountryText bool CAutoDefModifierCombo::m_KeepCountryText private ◆ m_KeepParen bool CAutoDefModifierCombo::m_KeepParen private ◆ m_MaxModifiers int CAutoDefModifierCombo::m_MaxModifiers private ◆ m_Modifiers ◆ m_OrgMods ◆ m_SubSources ◆ m_UseModifierLabels bool CAutoDefModifierCombo::m_UseModifierLabels private

The documentation for this class was generated from the following files:

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4