include/algo/structure/cd_utils/cuCdAnnotation.hpp File Reference

#include <map>
#include <vector>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbiexpt.hpp>
#include <corelib/ncbiapp.hpp>
#include <objects/cdd/Cdd.hpp>
#include <objects/cdd/Cdd_book_ref.hpp>
#include <objects/cdd/Align_annot.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <algo/structure/cd_utils/cuCdCore.hpp>

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Classes
class	CCdAnnotationInfo
Typedefs
typedef pair< unsigned int, unsigned int >	FromToPair
typedef map< unsigned int, vector< FromToPair > >	CdAnnotMap
typedef CdAnnotMap::iterator	CdAnnotMapIt
typedef CdAnnotMap::const_iterator	CdAnnotMapCit
typedef CdAnnotMap::value_type	CdAnnotMapVT
typedef map< unsigned int, vector< unsigned int > >	CdAnnotPosMap
typedef CdAnnotPosMap::iterator	CdAnnotPosMapIt
typedef CdAnnotPosMap::const_iterator	CdAnnotPosMapCit
typedef CdAnnotPosMap::value_type	CdAnnotPosMapVT
Functions
	USING_SCOPE (objects)
bool	IsCommentEvidenceInAlignAnnot (const CAlign_annot &feature)
bool	IsStructureEvidenceInAlignAnnot (const CAlign_annot &feature)
bool	IsReferenceEvidenceInAlignAnnot (const CAlign_annot &feature)
bool	IsBookRefEvidenceInAlignAnnot (const CAlign_annot &feature)
bool	IsSeqfeatEvidenceInAlignAnnot (const CAlign_annot &feature)
string	GetAlignAnnotDescription (const CAlign_annot &feature)
unsigned int	GetAlignAnnotFromToPairs (const CAlign_annot &feature, vector< FromToPair > &pairs)
unsigned int	GetAlignAnnotEvidenceFromToPairs (const CAlign_annot &feature, vector< FromToPair > &pairs)
unsigned int	GetAlignAnnotPositions (const CAlign_annot &feature, vector< unsigned int > &positions)
unsigned int	GetAlignAnnotEvidencePositions (const CAlign_annot &feature, vector< unsigned int > &positions)
string	CAlignAnnotToString (const CRef< CAlign_annot > &feature, bool includeFromTo, bool includeEvidence, bool hyphenateFromTo=true)
string	CAlignAnnotToString (const CAlign_annot &feature, bool includeFromTo, bool includeEvidence, bool hyphenateFromTo=true)
string	CAlignAnnotToASNString (const CRef< CAlign_annot > &feature, bool includeEvidence)
string	CAlignAnnotToASNString (const CAlign_annot &feature, bool includeEvidence)

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Typedef Documentation

typedef map<unsigned int, vector<FromToPair> > CdAnnotMap

Definition at line 62 of file cuCdAnnotation.hpp.

typedef CdAnnotMap::const_iterator CdAnnotMapCit

Definition at line 64 of file cuCdAnnotation.hpp.

typedef CdAnnotMap::iterator CdAnnotMapIt

Definition at line 63 of file cuCdAnnotation.hpp.

typedef CdAnnotMap::value_type CdAnnotMapVT

Definition at line 65 of file cuCdAnnotation.hpp.

typedef map<unsigned int, vector<unsigned int> > CdAnnotPosMap

Definition at line 71 of file cuCdAnnotation.hpp.

typedef CdAnnotPosMap::const_iterator CdAnnotPosMapCit

Definition at line 73 of file cuCdAnnotation.hpp.

typedef CdAnnotPosMap::iterator CdAnnotPosMapIt

Definition at line 72 of file cuCdAnnotation.hpp.

typedef CdAnnotPosMap::value_type CdAnnotPosMapVT

Definition at line 74 of file cuCdAnnotation.hpp.

typedef pair<unsigned int, unsigned int> FromToPair

Definition at line 57 of file cuCdAnnotation.hpp.

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Function Documentation

string CAlignAnnotToASNString (  const CAlign_annot &  feature, bool  includeEvidence )

Definition at line 416 of file cuCdAnnotation.cpp.

string CAlignAnnotToASNString (  const CRef< CAlign_annot > &  feature, bool  includeEvidence )

Definition at line 408 of file cuCdAnnotation.cpp. Referenced by CAlignAnnotToASNString().

string CAlignAnnotToString (  const CAlign_annot &  feature, bool  includeFromTo, bool  includeEvidence, bool  hyphenateFromTo = true )

Definition at line 315 of file cuCdAnnotation.cpp. References CAlign_annot_Base::GetDescription(), CAlign_annot_Base::IsSetDescription(), and kEmptyStr.

string CAlignAnnotToString (  const CRef< CAlign_annot > &  feature, bool  includeFromTo, bool  includeEvidence, bool  hyphenateFromTo = true )

Definition at line 221 of file cuCdAnnotation.cpp. Referenced by CAlignAnnotToString().

string GetAlignAnnotDescription (  const CAlign_annot &  feature  )

Definition at line 306 of file cuCdAnnotation.cpp. References CAlign_annot_Base::GetDescription(), CAlign_annot_Base::IsSetDescription(), and kEmptyStr.

unsigned int GetAlignAnnotEvidenceFromToPairs (  const CAlign_annot &  feature, vector< FromToPair > &  pairs )

Definition at line 111 of file cuCdAnnotation.cpp. References CAlign_annot_Base::GetEvidence(), and CAlign_annot_Base::IsSetEvidence(). Referenced by GetAlignAnnotEvidencePositions().

unsigned int GetAlignAnnotEvidencePositions (  const CAlign_annot &  feature, vector< unsigned int > &  positions )

Definition at line 174 of file cuCdAnnotation.cpp. References AppendPairToPositions(), and GetAlignAnnotEvidenceFromToPairs().

unsigned int GetAlignAnnotFromToPairs (  const CAlign_annot &  feature, vector< FromToPair > &  pairs )

Definition at line 67 of file cuCdAnnotation.cpp. Referenced by GetAlignAnnotPositions(), CCdAnnotationInfo::GetEvidencePositions(), and CCdAnnotationInfo::Initialize().

unsigned int GetAlignAnnotPositions (  const CAlign_annot &  feature, vector< unsigned int > &  positions )

Definition at line 162 of file cuCdAnnotation.cpp. References AppendPairToPositions(), and GetAlignAnnotFromToPairs().

bool IsBookRefEvidenceInAlignAnnot (  const CAlign_annot &  feature  )

Definition at line 298 of file cuCdAnnotation.cpp. References CFeature_evidence_Base::e_Book_ref, and IsEvidenceTypeInAlignAnnot().

bool IsCommentEvidenceInAlignAnnot (  const CAlign_annot &  feature  )

Definition at line 286 of file cuCdAnnotation.cpp. References CFeature_evidence_Base::e_Comment, and IsEvidenceTypeInAlignAnnot().

bool IsReferenceEvidenceInAlignAnnot (  const CAlign_annot &  feature  )

Definition at line 294 of file cuCdAnnotation.cpp. References CFeature_evidence_Base::e_Reference, and IsEvidenceTypeInAlignAnnot().

bool IsSeqfeatEvidenceInAlignAnnot (  const CAlign_annot &  feature  )

Definition at line 302 of file cuCdAnnotation.cpp. References CFeature_evidence_Base::e_Seqfeat, and IsEvidenceTypeInAlignAnnot().

bool IsStructureEvidenceInAlignAnnot (  const CAlign_annot &  feature  )

Definition at line 290 of file cuCdAnnotation.cpp. References CFeature_evidence_Base::e_Bsannot, and IsEvidenceTypeInAlignAnnot().

USING_SCOPE (  objects   )

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