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CAlign_CI Class Reference

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CAlign_CI –. More...

#include <objmgr/align_ci.hpp>

+ Inheritance diagram for CAlign_CI:
+ Collaboration diagram for CAlign_CI:

Public Member Functions

 CAlign_CI (void)
 Create an empty iterator. More...
 
 CAlign_CI (const CBioseq_Handle &bioseq)
 Create an iterator that enumerates CSeq_align objects related to the given bioseq. More...
 
 CAlign_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand=eNa_strand_unknown)
 Create an iterator that enumerates CSeq_align objects related to the given bioseq. More...
 
 CAlign_CI (const CBioseq_Handle &bioseq, const SAnnotSelector &sel)
 Create an iterator that enumerates CSeq_align objects related to the given bioseq. More...
 
 CAlign_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, const SAnnotSelector &sel)
 Create an iterator that enumerates CSeq_align objects related to the given bioseq. More...
 
 CAlign_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector &sel)
 Create an iterator that enumerates CSeq_align objects related to the given bioseq. More...
 
 CAlign_CI (CScope &scope, const CSeq_loc &loc, const SAnnotSelector &sel)
 Create an iterator that enumerates CSeq_align objects related to the given seq-loc. More...
 
 CAlign_CI (CScope &scope, const CSeq_loc &loc)
 Create an iterator that enumerates CSeq_align objects related to the given seq-loc. More...
 
 CAlign_CI (const CSeq_annot_Handle &annot)
 Create an iterator that enumerates CSeq_align objects from the annotation regardless of their location. More...
 
 CAlign_CI (const CSeq_annot_Handle &annot, const SAnnotSelector &sel)
 Create an iterator that enumerates CSeq_align objects from the annotation regardless of their location based on selection. More...
 
 CAlign_CI (const CSeq_loc &loc, const CSeq_annot_Handle &annot)
 Iterate all alignments from the seq-annot that annotate the location. More...
 
 CAlign_CI (const CSeq_loc &loc, const CSeq_annot_Handle &annot, const SAnnotSelector &sel)
 Iterate all alignments from the seq-annot that annotate the location. More...
 
 CAlign_CI (const CSeq_entry_Handle &entry)
 Create an iterator that enumerates CSeq_align objects from the seq-entry regardless of their location. More...
 
 CAlign_CI (const CSeq_entry_Handle &entry, const SAnnotSelector &sel)
 Create an iterator that enumerates CSeq_align objects from the seq-entry regardless of their location based on selection. More...
 
 CAlign_CI (const CAlign_CI &iter)
 
CAlign_CIoperator= (const CAlign_CI &iter)
 
virtual ~CAlign_CI (void)
 
CAlign_CIoperator++ (void)
 Move to the next object in iterated sequence. More...
 
CAlign_CIoperator-- (void)
 Move to the pervious object in iterated sequence. More...
 
void Rewind (void)
 Move to the first object in iterated sequence. More...
 
 DECLARE_OPERATOR_BOOL (IsValid())
 Check if iterator points to an object. More...
 
const CAlign_CIbegin () const
 
CAlign_CI end () const
 
bool operator!= (const CAlign_CI &it) const
 
const CSeq_alignoperator* (void) const
 Mapped alignment, not the original one. More...
 
const CSeq_alignoperator-> (void) const
 Mapped alignment, not the original one. More...
 
const CSeq_alignGetOriginalSeq_align (void) const
 Get original alignment. More...
 
CSeq_align_Handle GetSeq_align_Handle (void) const
 Get original alignment handle. More...
 
- Public Member Functions inherited from CAnnotTypes_CI
 CAnnotTypes_CI (void)
 
 CAnnotTypes_CI (CScope &scope)
 
 CAnnotTypes_CI (TAnnotType type, const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector *params=0)
 
 CAnnotTypes_CI (TAnnotType type, CScope &scope, const CSeq_loc &loc, const SAnnotSelector *params=0)
 
 CAnnotTypes_CI (TAnnotType type, const CSeq_annot_Handle &annot, const SAnnotSelector *params=0)
 
 CAnnotTypes_CI (TAnnotType type, const CSeq_loc &loc, const CSeq_annot_Handle &annot, const SAnnotSelector *params=0)
 
 CAnnotTypes_CI (TAnnotType type, const CSeq_entry_Handle &entry, const SAnnotSelector *params=0)
 
virtual ~CAnnotTypes_CI (void)
 
void Rewind (void)
 
CSeq_annot_Handle GetAnnot (void) const
 
const CSeq_annot_HandleGetSeq_annot_Handle (void) const
 
size_t GetSize (void) const
 
bool MaxSearchSegmentsLimitIsReached (void) const
 
const TAnnotTypesGetAnnotTypes (void) const
 
const TAnnotNamesGetAnnotNames (void) const
 
Uint8 GetCostOfLoadingInBytes (void) const
 Get collected cost of loading requested data in bytes. More...
 
double GetCostOfLoadingInSeconds (void) const
 Get collected cost of loading requested data in seconds. More...
 

Private Member Functions

CAlign_CI operator++ (int)
 
CAlign_CI operator-- (int)
 
 CAlign_CI (const CAlign_CI &it, EAtEnd)
 

Private Attributes

CConstRef< CSeq_alignm_MappedAlign
 

Additional Inherited Members

- Public Types inherited from CAnnotTypes_CI
typedef SAnnotSelector::TAnnotType TAnnotType
 
typedef vector< SAnnotTypeSelectorTAnnotTypes
 
typedef set< CAnnotNameTAnnotNames
 
- Protected Types inherited from CAnnotTypes_CI
enum  EAtEnd { at_end }
 
typedef vector< CAnnotObject_RefTAnnotSet
 
typedef TAnnotSet::const_iterator TIterator
 
- Protected Member Functions inherited from CAnnotTypes_CI
bool IsValid (void) const
 
void Next (void)
 
void Prev (void)
 
const CAnnotObject_RefGet (void) const
 
CScopeGetScope (void) const
 
CAnnot_CollectorGetCollector (void)
 
const TIteratorGetIterator (void) const
 
 CAnnotTypes_CI (const CAnnotTypes_CI &src, EAtEnd)
 
bool operator!= (const CAnnotTypes_CI &it) const
 

Detailed Description

CAlign_CI –.

Enumerate CSeq_align objects related to the specified bioseq or seq-loc

Definition at line 62 of file align_ci.hpp.


The documentation for this class was generated from the following files:
Modified on Thu May 30 12:29:41 2024 by modify_doxy.py rev. 669887