CAlnSeqIdsExtract< TAlnSeqId, TIdConverter > Class Template Reference

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IAlnSeqId extracting functor. More...

#include <objtools/alnmgr/seqids_extractor.hpp>

Public Types
typedef vector< TAlnSeqIdIRef >	TIdVec

Public Member Functions
	CAlnSeqIdsExtract (void)
	CAlnSeqIdsExtract (const TIdConverter &id_conv)
void	operator() (const CSeq_align &seq_align, TIdVec &id_vec) const
	Extract ids for the alignment. More...
TAlnSeqId *	NewAlnSeqId (const CSeq_id &id) const
	Convert seq-id to TAlnSeqId. More...

Static Private Member Functions
static bool	IdVecEqual (const TIdVec &x, const TIdVec &y)

Private Attributes
TIdConverter	m_IdConv

Detailed Description

template<class TAlnSeqId, class TIdConverter = CAlnSeqIdConverter<TAlnSeqId>>
class CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >

IAlnSeqId extracting functor.

Definition at line 99 of file seqids_extractor.hpp.

Member Typedef Documentation

TIdVec

template<class TAlnSeqId , class TIdConverter = CAlnSeqIdConverter<TAlnSeqId>>

typedef vector<TAlnSeqIdIRef> CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::TIdVec

Definition at line 105 of file seqids_extractor.hpp.

Constructor & Destructor Documentation

CAlnSeqIdsExtract() [1/2]

template<class TAlnSeqId , class TIdConverter = CAlnSeqIdConverter<TAlnSeqId>>

CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::CAlnSeqIdsExtract ( void  )

inline

Definition at line 102 of file seqids_extractor.hpp.

CAlnSeqIdsExtract() [2/2]

template<class TAlnSeqId , class TIdConverter = CAlnSeqIdConverter<TAlnSeqId>>

CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::CAlnSeqIdsExtract ( const TIdConverter &  id_conv )

inline

Definition at line 103 of file seqids_extractor.hpp.

Member Function Documentation

IdVecEqual()

template<class TAlnSeqId , class TIdConverter = CAlnSeqIdConverter<TAlnSeqId>>

static bool CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::IdVecEqual ( const TIdVec &  x, const TIdVec &  y  )

inlinestaticprivate

Definition at line 329 of file seqids_extractor.hpp.

Referenced by CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()().

NewAlnSeqId()

template<class TAlnSeqId , class TIdConverter = CAlnSeqIdConverter<TAlnSeqId>>

TAlnSeqId* CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::NewAlnSeqId ( const CSeq_id &  id ) const

inline

Convert seq-id to TAlnSeqId.

Definition at line 323 of file seqids_extractor.hpp.

References CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::m_IdConv.

Referenced by CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()().

operator()()

template<class TAlnSeqId , class TIdConverter = CAlnSeqIdConverter<TAlnSeqId>>

void CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator() ( const CSeq_align &  seq_align, TIdVec &  id_vec  ) const

inline

Extract ids for the alignment.

Parameters

seq_align	Input seq-align.
id_vec	Output vector to receive ids for the alignment.

Definition at line 112 of file seqids_extractor.hpp.

References _ASSERT, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Int, e_not_set, CSeq_loc_Base::e_Pnt, CSpliced_seg_Base::eProduct_type_protein, CStd_seg_Base::GetDim(), CSparse_align_Base::GetFirst_id(), CSpliced_seg_Base::GetGenomic_id(), CStd_seg_Base::GetLoc(), CSpliced_seg_Base::GetProduct_id(), CSpliced_seg_Base::GetProduct_type(), CSparse_align_Base::GetSecond_id(), CSeq_align_Base::GetSegs(), i, CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::IdVecEqual(), ITERATE, NCBI_THROW, CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::NewAlnSeqId(), NStr::NumericToString(), prot, row, string, true, and CSeq_align::Validate().

Member Data Documentation

m_IdConv

template<class TAlnSeqId , class TIdConverter = CAlnSeqIdConverter<TAlnSeqId>>

TIdConverter CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::m_IdConv

private

Definition at line 335 of file seqids_extractor.hpp.

Referenced by CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::NewAlnSeqId().

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

• include/objtools/alnmgr/seqids_extractor.hpp