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COrg_ref Class Reference

Represents ASN.1 type Org-ref defined in file seqfeat.asn

Search Toolkit Book for COrg_ref

#include <objects/seqfeat/Org_ref.hpp>

+ Inheritance diagram for COrg_ref:
+ Collaboration diagram for COrg_ref:

Public Types

enum  EOrgref_part {
  eOrgref_nothing = 0 , eOrgref_taxname = 0x0010 , eOrgref_common = 0x0040 , eOrgref_mod = 0x0800 ,
  eOrgref_db = 0x2000 , eOrgref_db_taxid = 0x0001 , eOrgref_db_all = (eOrgref_db | eOrgref_db_taxid) , eOrgref_syn = 0x4000 ,
  eOrgref_orgname = 0x0008 , eOrgref_on_name = 0x0080 , eOrgref_on_attr = 0x1000 , eOrgref_on_attr_spec = 0x00010000 ,
  eOrgref_on_attr_nofwd = 0x00040000 , eOrgref_on_attr_uncult = 0x00080000 , eOrgref_on_attr_all = (eOrgref_on_attr | eOrgref_on_attr_spec | eOrgref_on_attr_nofwd | eOrgref_on_attr_uncult) , eOrgref_on_mod = 0x0200 ,
  eOrgref_on_mod_nom = 0x00020000 , eOrgref_on_mod_oldname = 0x00100000 , eOrgref_on_mod_tm = 0x00200000 , eOrgref_on_mod_all = (eOrgref_on_mod | eOrgref_on_mod_nom | eOrgref_on_mod_oldname | eOrgref_on_mod_tm) ,
  eOrgref_on_lin = 0x0020 , eOrgref_on_gc = 0x0002 , eOrgref_on_mgc = 0x0004 , eOrgref_on_pgc = 0x0400 ,
  eOrgref_on_div = 0x0100 , eOrgref_on_all , eOrgref_all , eOrgref_all_but_syn = (eOrgref_all ^ eOrgref_syn) ,
  eOrgref_all_but_spec = (eOrgref_all ^ eOrgref_on_attr_spec) , eOrgref_default = eOrgref_all
}
 
typedef unsigned int fOrgref_parts
 
- Public Types inherited from COrg_ref_Base
enum class  E_memberIndex {
  e__allMandatory = 0 , e_taxname , e_common , e_mod ,
  e_db , e_syn , e_orgname
}
 
typedef string TTaxname
 
typedef string TCommon
 
typedef list< stringTMod
 
typedef vector< CRef< CDbtag > > TDb
 
typedef list< stringTSyn
 
typedef COrgName TOrgname
 
typedef Tparent::CMemberIndex< E_memberIndex, 7 > TmemberIndex
 
- 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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 COrg_ref (void)
 
 ~COrg_ref (void)
 
void GetLabel (string *label) const
 
TTaxId GetTaxId () const
 
TTaxId SetTaxId (TTaxId tax_id)
 
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 IsSetOrgMod (void) const
 
bool IsVarietyValid (const string &variety) const
 
bool HasValidVariety () const
 
bool IsSubspeciesValid (const string &subspecies) const
 
CRef< COrg_refMakeCommon (const COrg_ref &other) const
 
bool UpdateFromTable ()
 
void CleanForGenBank ()
 
void FilterOutParts (fOrgref_parts to_remain)
 
- Public Member Functions inherited from COrg_ref_Base
 COrg_ref_Base (void)
 
virtual ~COrg_ref_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetTaxname (void) const
 preferred formal name Check if a value has been assigned to Taxname data member. More...
 
bool CanGetTaxname (void) const
 Check if it is safe to call GetTaxname method. More...
 
void ResetTaxname (void)
 Reset Taxname data member. More...
 
const TTaxnameGetTaxname (void) const
 Get the Taxname member data. More...
 
void SetTaxname (const TTaxname &value)
 Assign a value to Taxname data member. More...
 
void SetTaxname (TTaxname &&value)
 
TTaxnameSetTaxname (void)
 Assign a value to Taxname data member. More...
 
bool IsSetCommon (void) const
 common name Check if a value has been assigned to Common data member. More...
 
bool CanGetCommon (void) const
 Check if it is safe to call GetCommon method. More...
 
void ResetCommon (void)
 Reset Common data member. More...
 
const TCommonGetCommon (void) const
 Get the Common member data. More...
 
void SetCommon (const TCommon &value)
 Assign a value to Common data member. More...
 
void SetCommon (TCommon &&value)
 
TCommonSetCommon (void)
 Assign a value to Common data member. More...
 
bool IsSetMod (void) const
 unstructured modifiers Check if a value has been assigned to Mod data member. More...
 
bool CanGetMod (void) const
 Check if it is safe to call GetMod method. More...
 
void ResetMod (void)
 Reset Mod data member. More...
 
const TModGetMod (void) const
 Get the Mod member data. More...
 
TModSetMod (void)
 Assign a value to Mod data member. More...
 
bool IsSetDb (void) const
 ids in taxonomic or culture dbases Check if a value has been assigned to Db data member. More...
 
bool CanGetDb (void) const
 Check if it is safe to call GetDb method. More...
 
void ResetDb (void)
 Reset Db data member. More...
 
const TDbGetDb (void) const
 Get the Db member data. More...
 
TDbSetDb (void)
 Assign a value to Db data member. More...
 
bool IsSetSyn (void) const
 synonyms for taxname or common Check if a value has been assigned to Syn data member. More...
 
bool CanGetSyn (void) const
 Check if it is safe to call GetSyn method. More...
 
void ResetSyn (void)
 Reset Syn data member. More...
 
const TSynGetSyn (void) const
 Get the Syn member data. More...
 
TSynSetSyn (void)
 Assign a value to Syn data member. More...
 
bool IsSetOrgname (void) const
 Check if a value has been assigned to Orgname data member. More...
 
bool CanGetOrgname (void) const
 Check if it is safe to call GetOrgname method. More...
 
void ResetOrgname (void)
 Reset Orgname data member. More...
 
const TOrgnameGetOrgname (void) const
 Get the Orgname member data. More...
 
void SetOrgname (TOrgname &value)
 Assign a value to Orgname data member. More...
 
TOrgnameSetOrgname (void)
 Assign a value to Orgname 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 CConstRef< COrg_refTableLookup (const string &taxname)
 
static const vector< string > & GetTaxnameList ()
 
- 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_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 COrg_ref_Base Tparent
 

Private Member Functions

 COrg_ref (const COrg_ref &value)
 
COrg_refoperator= (const COrg_ref &value)
 
string x_GetTaxnameAfterFirstTwoWords () const
 

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 50 of file Org_ref.hpp.

Member Typedef Documentation

◆ fOrgref_parts

typedef unsigned int COrg_ref::fOrgref_parts

Definition at line 94 of file Org_ref.hpp.

◆ Tparent

Definition at line 52 of file Org_ref.hpp.

Member Enumeration Documentation

◆ EOrgref_part

Enumerator
eOrgref_nothing 
eOrgref_taxname 
eOrgref_common 
eOrgref_mod 
eOrgref_db 
eOrgref_db_taxid 
eOrgref_db_all 
eOrgref_syn 
eOrgref_orgname 
eOrgref_on_name 
eOrgref_on_attr 
eOrgref_on_attr_spec 
eOrgref_on_attr_nofwd 
eOrgref_on_attr_uncult 
eOrgref_on_attr_all 
eOrgref_on_mod 
eOrgref_on_mod_nom 
eOrgref_on_mod_oldname 
eOrgref_on_mod_tm 
eOrgref_on_mod_all 
eOrgref_on_lin 
eOrgref_on_gc 
eOrgref_on_mgc 
eOrgref_on_pgc 
eOrgref_on_div 
eOrgref_on_all 
eOrgref_all 
eOrgref_all_but_syn 
eOrgref_all_but_spec 
eOrgref_default 

Definition at line 54 of file Org_ref.hpp.

Constructor & Destructor Documentation

◆ COrg_ref() [1/2]

COrg_ref::COrg_ref ( void  )
inline

Definition at line 156 of file Org_ref.hpp.

Referenced by MakeCommon().

◆ ~COrg_ref()

COrg_ref::~COrg_ref ( void  )

Definition at line 52 of file Org_ref.cpp.

◆ COrg_ref() [2/2]

COrg_ref::COrg_ref ( const COrg_ref value)
private

Member Function Documentation

◆ CleanForGenBank()

void COrg_ref::CleanForGenBank ( )

◆ FilterOutParts()

void COrg_ref::FilterOutParts ( fOrgref_parts  to_remain)

Definition at line 517 of file Org_ref.cpp.

References COrgName::EnableModifierForwarding(), eOrgref_all, eOrgref_common, eOrgref_db_all, eOrgref_db_taxid, eOrgref_mod, eOrgref_nothing, eOrgref_on_all, eOrgref_on_attr_all, eOrgref_on_attr_nofwd, eOrgref_on_div, eOrgref_on_gc, eOrgref_on_lin, eOrgref_on_mgc, eOrgref_on_mod, eOrgref_on_mod_nom, eOrgref_on_mod_oldname, eOrgref_on_mod_tm, eOrgref_on_name, eOrgref_on_pgc, eOrgref_syn, eOrgref_taxname, COrgMod_Base::eSubtype_old_name, COrgMod_Base::eSubtype_type_material, i, COrgName::IsModifierForwardingDisabled(), COrgName_Base::IsSetAttrib(), COrg_ref_Base::IsSetCommon(), COrg_ref_Base::IsSetDb(), COrgName_Base::IsSetDiv(), COrgName_Base::IsSetGcode(), COrgName_Base::IsSetLineage(), COrgName_Base::IsSetMgcode(), COrg_ref_Base::IsSetMod(), COrgName_Base::IsSetMod(), COrgName_Base::IsSetName(), COrg_ref_Base::IsSetOrgname(), COrgName_Base::IsSetPgcode(), COrg_ref_Base::IsSetSyn(), COrg_ref_Base::IsSetTaxname(), NO_FLAG, COrgName::RemoveModBySubtype(), COrg_ref_Base::Reset(), COrgName_Base::ResetAttrib(), COrg_ref_Base::ResetCommon(), COrg_ref_Base::ResetDb(), COrgName_Base::ResetDiv(), COrgName_Base::ResetGcode(), COrgName_Base::ResetLineage(), COrgName_Base::ResetMgcode(), COrg_ref_Base::ResetMod(), COrgName_Base::ResetMod(), COrgName_Base::ResetName(), COrgName::ResetNomenclature(), COrg_ref_Base::ResetOrgname(), COrgName_Base::ResetPgcode(), COrg_ref_Base::ResetSyn(), COrg_ref_Base::ResetTaxname(), s_taxonName, COrg_ref_Base::SetDb(), and COrg_ref_Base::SetOrgname().

◆ GetDivision()

const string & COrg_ref::GetDivision ( void  ) const

◆ GetGcode()

int COrg_ref::GetGcode ( void  ) const

◆ GetLabel()

void COrg_ref::GetLabel ( string label) const

◆ GetLineage()

const string & COrg_ref::GetLineage ( void  ) const

◆ GetMgcode()

int COrg_ref::GetMgcode ( void  ) const

◆ GetPgcode()

int COrg_ref::GetPgcode ( void  ) const

◆ GetTaxId()

TTaxId COrg_ref::GetTaxId ( void  ) const

◆ GetTaxnameList()

const vector< string > & COrg_ref::GetTaxnameList ( )
static

Definition at line 503 of file Org_ref.cpp.

References s_CommonTaxnameList, and s_InitializeOrgRefMap().

◆ HasValidVariety()

bool COrg_ref::HasValidVariety ( ) const

◆ IsSetDivision()

bool COrg_ref::IsSetDivision ( void  ) const

◆ IsSetGcode()

bool COrg_ref::IsSetGcode ( void  ) const

◆ IsSetLineage()

bool COrg_ref::IsSetLineage ( void  ) const

◆ IsSetMgcode()

bool COrg_ref::IsSetMgcode ( void  ) const

◆ IsSetOrgMod()

bool COrg_ref::IsSetOrgMod ( void  ) const

◆ IsSetPgcode()

bool COrg_ref::IsSetPgcode ( void  ) const

◆ IsSubspeciesValid()

bool COrg_ref::IsSubspeciesValid ( const string subspecies) const

◆ IsVarietyValid()

bool COrg_ref::IsVarietyValid ( const string variety) const

◆ MakeCommon()

CRef< COrg_ref > COrg_ref::MakeCommon ( const COrg_ref other) const

◆ operator=()

COrg_ref& COrg_ref::operator= ( const COrg_ref value)
private

◆ SetTaxId()

TTaxId COrg_ref::SetTaxId ( TTaxId  tax_id)

◆ TableLookup()

CConstRef< COrg_ref > COrg_ref::TableLookup ( const string taxname)
static

◆ UpdateFromTable()

bool COrg_ref::UpdateFromTable ( )

◆ x_GetTaxnameAfterFirstTwoWords()

string COrg_ref::x_GetTaxnameAfterFirstTwoWords ( ) const
private

The documentation for this class was generated from the following files:
Modified on Mon Apr 22 04:03:09 2024 by modify_doxy.py rev. 669887