CAutoInitDesc< _T > Class Template Reference

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CSourceModParser. More...

Inheritance diagram for CAutoInitDesc< _T >:

Collaboration diagram for CAutoInitDesc< _T >:

Public Member Functions
	CAutoInitDesc (CSeq_descr &descr, CSeqdesc::E_Choice which)
	CAutoInitDesc (CBioseq &bioseq, CSeqdesc::E_Choice which)
	CAutoInitDesc (CBioseq_set &bioset, CSeqdesc::E_Choice which)
	CAutoInitDesc (_T &obj)
_T *	operator-> ()
_T &	operator* ()

Protected Member Functions
void	_getfromdesc ()
void	_getfromdesc ()
void	_getfromdesc ()
void	_getfromdesc ()
Protected Member Functions inherited from CAutoAddDesc
	CAutoAddDesc (CSeq_descr &descr, CSeqdesc::E_Choice which)
const CSeqdesc &	Get () const
CSeqdesc &	Set (bool skip_lookup=false)
bool	IsNull () const
void	Erase ()

Protected Attributes
_T *	m_ptr
CRef< CBioseq >	m_bioseq
CRef< CBioseq_set >	m_bioset
Protected Attributes inherited from CAutoAddDesc
CSeqdesc::E_Choice	m_which
CRef< CSeq_descr >	m_descr
CRef< CSeqdesc >	m_desc

Additional Inherited Members
Static Protected Member Functions inherited from CAutoAddDesc
static CRef< CSeqdesc >	LocateDesc (const CSeq_descr &descr, CSeqdesc::E_Choice which)
static bool	EraseDesc (CSeq_descr &descr, CSeqdesc::E_Choice which)

Detailed Description

template<class _T>
class CAutoInitDesc< _T >

CSourceModParser.

Class for parsing source modifiers, as found in (Sequin-targeted) FASTA files.

Some flat interchange formats (notably FASTA) limit annotations to a single definition/title line per sequence, so NCBI developed a convention for allowing them to contain bracketed modifiers of the form [key=value], as documented at https://www.ncbi.nlm.nih.gov/Sequin/modifiers.html .

Definition at line 373 of file source_mod_parser.cpp.

Constructor & Destructor Documentation

CAutoInitDesc() [1/4]

template<class _T >

CAutoInitDesc< _T >::CAutoInitDesc ( CSeq_descr &  descr, CSeqdesc::E_Choice  which  )

inline

Definition at line 444 of file source_mod_parser.cpp.

CAutoInitDesc() [2/4]

template<class _T >

CAutoInitDesc< _T >::CAutoInitDesc ( CBioseq &  bioseq, CSeqdesc::E_Choice  which  )

inline

Definition at line 452 of file source_mod_parser.cpp.

References CAutoAddDesc::m_descr, and CRef< C, Locker >::Reset().

CAutoInitDesc() [3/4]

template<class _T >

CAutoInitDesc< _T >::CAutoInitDesc ( CBioseq_set &  bioset, CSeqdesc::E_Choice  which  )

inline

Definition at line 462 of file source_mod_parser.cpp.

References CAutoAddDesc::m_descr, and CRef< C, Locker >::Reset().

CAutoInitDesc() [4/4]

template<class _T >

CAutoInitDesc< _T >::CAutoInitDesc ( _T &  obj )

inline

Definition at line 473 of file source_mod_parser.cpp.

References CAutoAddDesc::m_descr, and CRef< C, Locker >::Reset().

Member Function Documentation

_getfromdesc() [1/4]

template<class _T >

void CAutoInitDesc< _T >::_getfromdesc ( )

protected

_getfromdesc() [2/4]

void CAutoInitDesc< CBioSource >::_getfromdesc ( )

protected

Definition at line 509 of file source_mod_parser.cpp.

_getfromdesc() [3/4]

void CAutoInitDesc< CMolInfo >::_getfromdesc ( )

protected

Definition at line 515 of file source_mod_parser.cpp.

_getfromdesc() [4/4]

void CAutoInitDesc< CGB_block >::_getfromdesc ( )

protected

Definition at line 521 of file source_mod_parser.cpp.

operator*()

template<class _T >

_T & CAutoInitDesc< _T >::operator* ( void  )

inline

Definition at line 482 of file source_mod_parser.cpp.

operator->()

template<class _T >

_T * CAutoInitDesc< _T >::operator-> ( void  )

inline

Definition at line 489 of file source_mod_parser.cpp.

References CSeqdesc_Base::e_not_set.

Member Data Documentation

m_bioseq

template<class _T >

CRef<CBioseq> CAutoInitDesc< _T >::m_bioseq

mutableprotected

Definition at line 385 of file source_mod_parser.cpp.

m_bioset

template<class _T >

CRef<CBioseq_set> CAutoInitDesc< _T >::m_bioset

mutableprotected

Definition at line 386 of file source_mod_parser.cpp.

m_ptr

template<class _T >

_T* CAutoInitDesc< _T >::m_ptr

protected

Definition at line 383 of file source_mod_parser.cpp.

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

• src/objtools/readers/source_mod_parser.hpp
• src/objtools/readers/source_mod_parser.cpp