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

NCBI C++ ToolKit: CSeq_id_Textseq_Tree Class Reference

Search Toolkit Book for CSeq_id_Textseq_Tree

#include "seq_id_tree.hpp"
(Private to src/objects/seq.)

CSeq_id_Textseq_Tree (CSeq_id_Mapper *mapper, CSeq_id::E_Choice type) ~CSeq_id_Textseq_Tree (void) virtual bool Empty (void) const virtual CSeq_id_Handle FindInfo (const CSeq_id &id) const virtual CSeq_id_Handle FindOrCreate (const CSeq_id &id) virtual bool HaveMatch (const CSeq_id_Handle &id) const virtual void FindMatch (const CSeq_id_Handle &id, TSeq_id_MatchList &id_list) const virtual void FindMatchStr (const string &sid, TSeq_id_MatchList &id_list) const virtual bool Match (const CSeq_id_Handle &h1, const CSeq_id_Handle &h2) const virtual bool IsBetterVersion (const CSeq_id_Handle &h1, const CSeq_id_Handle &h2) const virtual bool HaveReverseMatch (const CSeq_id_Handle &id) const virtual void FindReverseMatch (const CSeq_id_Handle &id, TSeq_id_MatchList &id_list) virtual size_t Dump (CNcbiOstream &out, CSeq_id::E_Choice type, int details) const CSeq_id_Which_Tree (CSeq_id_Mapper *mapper) virtual ~CSeq_id_Which_Tree (void) virtual CSeq_id_Handle GetGiHandle (TGi gi) virtual void DropInfo (const CSeq_id_Info *info) 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 CSeq_id_Textseq_PlainInfo * x_FindStrInfo (const TStringMap &str_map, const string &str, CSeq_id::E_Choice type, const CTextseq_id &tid) const void x_FindMatchByAcc (TSeq_id_MatchList &id_list, const string &acc, const TVersion *ver=0) const void x_FindMatchByAcc (TSeq_id_MatchList &id_list, const string &acc, const CTextseq_id *tid) const void x_FindMatchByName (TSeq_id_MatchList &id_list, const string &name, const CTextseq_id *tid=nullptr, EAllowFields allow_fields=eAnyFields) const void x_FindRevMatchByAccPacked (TSeq_id_MatchList &id_list, const string &acc, const TVersion *ver=0) const void x_FindRevMatchByAccNonPacked (TSeq_id_MatchList &id_list, const string &acc, const TVersion *ver=0) const void x_FindRevMatchByAcc (TSeq_id_MatchList &id_list, const string &acc, const TVersion *ver=0) const void x_FindRevMatchByAcc (TSeq_id_MatchList &id_list, const string &acc, const CTextseq_id *tid) const void x_FindRevMatchByName (TSeq_id_MatchList &id_list, const string &name, const CTextseq_id *tid=0) const

Definition at line 478 of file seq_id_tree.hpp.

◆ TPackedKey ◆ TPackedMap ◆ TPackedMap_CI ◆ TPackedMap_I ◆ TPackedMapValue ◆ TStringMap ◆ TStringMapCI ◆ TStringMapValue ◆ TVersion ◆ TVersions ◆ EAllowFields ◆ CSeq_id_Textseq_Tree() ◆ ~CSeq_id_Textseq_Tree() CSeq_id_Textseq_Tree::~CSeq_id_Textseq_Tree ( void )

Definition at line 1041 of file seq_id_tree.cpp.

◆ Dump()

Implements CSeq_id_Which_Tree.

Definition at line 1633 of file seq_id_tree.cpp.

References CSeq_id_Mapper::eDumpAllIds, CSeq_id_Mapper::eDumpStatistics, GetAccession(), CSeq_id::GetTextseq_Id(), int, ITERATE, kMallocOverhead, m_ByAcc, m_ByName, m_PackedMap, out(), CSeq_id_Base::SelectionName(), ncbi::grid::netcache::search::fields::size, map_checker< Container >::size(), multimap_checker< Container >::size(), string, and sx_StringMemory().

◆ Empty() bool CSeq_id_Textseq_Tree::Empty ( void ) const virtual ◆ FindInfo()

Implements CSeq_id_Which_Tree.

Definition at line 1134 of file seq_id_tree.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), CTextseq_id_Base::GetAccession(), info, CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), CTextseq_id_Base::IsSetRelease(), ncbi::grid::netcache::search::fields::key, m_PackedMap, CSeq_id_Which_Tree::m_TreeLock, CSeq_id_Textseq_Info::Pack(), CSeq_id_Textseq_Info::ParseAcc(), s_PackTextidEnabled(), x_Check(), x_FindStrInfo(), and x_Get().

◆ FindMatch()

Reimplemented from CSeq_id_Which_Tree.

Definition at line 1438 of file seq_id_tree.cpp.

References _ASSERT, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, multimap_checker< Container >::empty(), map_checker< Container >::end(), multimap_checker< Container >::end(), eOnlyName, map_checker< Container >::find(), CTextseq_id_Base::GetAccession(), CSeq_id_Which_Tree::GetInfo(), CTextseq_id_Base::GetName(), CSeq_id::GetTextseq_Id(), info, set< Key, Compare >::insert(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), CTextseq_id_Base::IsSetRelease(), CTextseq_id_Base::IsSetVersion(), ncbi::grid::netcache::search::fields::key, map_checker< Container >::lower_bound(), multimap_checker< Container >::lower_bound(), m_ByAcc, m_ByName, m_PackedMap, CSeq_id_Which_Tree::m_TreeLock, x_Check(), x_FindMatchByAcc(), and x_FindMatchByName().

◆ FindMatchStr() ◆ FindOrCreate()

Implements CSeq_id_Which_Tree.

Definition at line 1161 of file seq_id_tree.cpp.

References _ASSERT, map_checker< Container >::end(), CTextseq_id_Base::GetAccession(), CTextseq_id_Base::GetName(), info, map_checker< Container >::insert(), multimap_checker< Container >::insert(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), CTextseq_id_Base::IsSetRelease(), ncbi::grid::netcache::search::fields::key, map_checker< Container >::lower_bound(), m_ByAcc, m_ByName, CSeq_id_Which_Tree::m_Mapper, m_PackedMap, CSeq_id_Which_Tree::m_TreeLock, CSeq_id_Textseq_Info::Pack(), CSeq_id_Textseq_Info::ParseAcc(), s_AssignSeq_id(), s_PackTextidEnabled(), x_Check(), x_FindStrInfo(), and x_Get().

◆ FindReverseMatch()

Reimplemented from CSeq_id_Which_Tree.

Definition at line 1581 of file seq_id_tree.cpp.

References multimap_checker< Container >::empty(), map_checker< Container >::end(), map_checker< Container >::find(), CTextseq_id_Base::GetAccession(), CSeq_id_Which_Tree::GetInfo(), CTextseq_id_Base::GetName(), info, set< Key, Compare >::insert(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), ncbi::grid::netcache::search::fields::key, m_ByAcc, m_PackedMap, CSeq_id_Which_Tree::m_TreeLock, x_Check(), x_FindRevMatchByAcc(), x_FindRevMatchByAccNonPacked(), x_FindRevMatchByName(), and x_Get().

◆ HaveMatch() ◆ HaveReverseMatch() ◆ IsBetterVersion() ◆ Match() ◆ x_Check() [1/2] ◆ x_Check() [2/2] ◆ x_Equals() ◆ x_Erase() ◆ x_FindMatchByAcc() [1/2] ◆ x_FindMatchByAcc() [2/2]

Definition at line 1251 of file seq_id_tree.cpp.

References _ASSERT, map_checker< Container >::empty(), map_checker< Container >::end(), multimap_checker< Container >::end(), NStr::EqualNocase(), map_checker< Container >::find(), multimap_checker< Container >::find(), CTextseq_id_Base::GetVersion(), set< Key, Compare >::insert(), CTextseq_id_Base::IsSetVersion(), ncbi::grid::netcache::search::fields::key, map_checker< Container >::lower_bound(), m_ByAcc, m_PackedMap, CSeq_id_Textseq_Info::Pack(), CSeq_id_Textseq_Info::ParseAcc(), and x_Get().

Referenced by FindMatch(), FindMatchStr(), and x_FindMatchByAcc().

◆ x_FindMatchByName()

Definition at line 1355 of file seq_id_tree.cpp.

References CSeq_id_Base::e_Swissprot, eAnyFields, multimap_checker< Container >::end(), eOnlyName, NStr::EqualNocase(), multimap_checker< Container >::find(), CTextseq_id_Base::GetRelease(), set< Key, Compare >::insert(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetRelease(), CTextseq_id_Base::IsSetVersion(), m_ByName, m_Type, x_Get(), and x_IsDefaultSwissprotRelease().

Referenced by FindMatch(), and FindMatchStr().

◆ x_FindRevMatchByAcc() [1/2] ◆ x_FindRevMatchByAcc() [2/2] ◆ x_FindRevMatchByAccNonPacked() ◆ x_FindRevMatchByAccPacked() ◆ x_FindRevMatchByName() ◆ x_FindStrInfo() [1/2] ◆ x_FindStrInfo() [2/2] ◆ x_Get() ◆ x_GetVersion() ◆ x_Unindex()

Implements CSeq_id_Which_Tree.

Definition at line 1222 of file seq_id_tree.cpp.

References _ASSERT, map_checker< Container >::empty(), map_checker< Container >::erase(), CTextseq_id_Base::GetAccession(), CSeq_id_Textseq_Info::GetKey(), CTextseq_id_Base::GetName(), info, CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), m_ByAcc, m_ByName, m_PackedMap, x_Check(), x_Erase(), and x_Get().

◆ m_ByAcc ◆ m_ByName ◆ m_PackedMap ◆ m_Type

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

src/objects/seq/seq_id_tree.hpp
src/objects/seq/seq_id_tree.cpp

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

NCBI C++ ToolKit: CSeq_id_Textseq_Tree Class Reference

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