Search Toolkit Book for CAlign_CI
#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_CI & | operator= (const CAlign_CI &iter) |
| virtual | ~CAlign_CI (void) |
| CAlign_CI & | operator++ (void) |
| Move to the next object in iterated sequence. More... | |
| CAlign_CI & | operator-- (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_CI & | begin () const |
| CAlign_CI | end () const |
| bool | operator!= (const CAlign_CI &it) const |
| const CSeq_align & | operator* (void) const |
| Mapped alignment, not the original one. More... | |
| const CSeq_align * | operator-> (void) const |
| Mapped alignment, not the original one. More... | |
| const CSeq_align & | GetOriginalSeq_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_Handle & | GetSeq_annot_Handle (void) const |
| size_t | GetSize (void) const |
| bool | MaxSearchSegmentsLimitIsReached (void) const |
| const TAnnotTypes & | GetAnnotTypes (void) const |
| const TAnnotNames & | GetAnnotNames (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_align > | m_MappedAlign |
Additional Inherited Members | |
| Public Types inherited from CAnnotTypes_CI | |
| typedef SAnnotSelector::TAnnotType | TAnnotType |
| typedef vector< SAnnotTypeSelector > | TAnnotTypes |
| typedef set< CAnnotName > | TAnnotNames |
| Protected Types inherited from CAnnotTypes_CI | |
| enum | EAtEnd { at_end } |
| typedef vector< CAnnotObject_Ref > | TAnnotSet |
| typedef TAnnotSet::const_iterator | TIterator |
| Protected Member Functions inherited from CAnnotTypes_CI | |
| bool | IsValid (void) const |
| void | Next (void) |
| void | Prev (void) |
| const CAnnotObject_Ref & | Get (void) const |
| CScope & | GetScope (void) const |
| CAnnot_Collector & | GetCollector (void) |
| const TIterator & | GetIterator (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:
- include/objmgr/align_ci.hpp
- src/objmgr/align_ci.cpp
