CDRefresher Class Reference

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#include <algo/structure/cd_utils/cuCdUpdater.hpp>

Collaboration diagram for CDRefresher:

Public Member Functions
	CDRefresher (CCdCore *cd)
TGi	refresh (CRef< CSeq_align > seqAlign, CRef< CSeq_entry > seqEntry)
bool	hasOlderVersion (CRef< CBioseq > bioseq)

Private Types
typedef map< string, CRef< CBioseq > >	AccessionBioseqMap

Private Member Functions
void	addSequences (CSeq_entry &seqEntry)
void	addSequence (CRef< CBioseq > bioseq)

Private Attributes
CCdCore *	m_cd
AccessionBioseqMap	m_accSeqMap

Detailed Description

Definition at line 55 of file cuCdUpdater.hpp.

Member Typedef Documentation

AccessionBioseqMap

typedef map<string, CRef< CBioseq > > CDRefresher::AccessionBioseqMap

private

Definition at line 66 of file cuCdUpdater.hpp.

Constructor & Destructor Documentation

CDRefresher()

CDRefresher::CDRefresher

(

CCdCore *

cd

)

Definition at line 1672 of file cuCdUpdater.cpp.

References addSequences(), and CCdd_Base::SetSequences().

Member Function Documentation

addSequence()

void CDRefresher::addSequence ( CRef< CBioseq >  bioseq )

private

Definition at line 1694 of file cuCdUpdater.cpp.

References GetAccAndVersion(), map_checker< Container >::insert(), and m_accSeqMap.

Referenced by addSequences().

addSequences()

void CDRefresher::addSequences ( CSeq_entry &  seqEntry )

private

Definition at line 1678 of file cuCdUpdater.cpp.

References addSequence(), CSeq_entry_Base::IsSet(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by CDRefresher().

hasOlderVersion()

bool CDRefresher::hasOlderVersion

(

CRef< CBioseq >

bioseq

)

Definition at line 1703 of file cuCdUpdater.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), GetAccAndVersion(), CDUpdater::getGi(), and m_accSeqMap.

Referenced by CDUpdater::pickBioseq(), and refresh().

refresh()

TGi CDRefresher::refresh	(	CRef< CSeq_align >	seqAlign,
		CRef< CSeq_entry >	seqEntry
	)

Definition at line 1722 of file cuCdUpdater.cpp.

References CCdCore::AddSequence(), CDUpdater::BioseqHasSeqId(), bmp, GetAccAndVersion(), CDUpdater::GetAllIdsFromSeqEntry(), CDUpdater::getGi(), GetNcbieaaString(), CDUpdater::GetOneBioseqFromSeqEntry(), CCdCore::GetSeqAligns(), GetSeqID(), hasOlderVersion(), i, INVALID_GI, m_accSeqMap, m_cd, and CRef< C, Locker >::NotNull().

Referenced by CDUpdater::update().

Member Data Documentation

m_accSeqMap

AccessionBioseqMap CDRefresher::m_accSeqMap

private

Definition at line 67 of file cuCdUpdater.hpp.

Referenced by addSequence(), hasOlderVersion(), and refresh().

m_cd

CCdCore* CDRefresher::m_cd

private

Definition at line 65 of file cuCdUpdater.hpp.

Referenced by refresh().

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

• include/algo/structure/cd_utils/cuCdUpdater.hpp
• src/algo/structure/cd_utils/cuCdUpdater.cpp