Search Toolkit Book for CSeqMap
#include <objmgr/seq_map.hpp>
Inheritance diagram for CSeqMap:
Collaboration diagram for CSeqMap:
Classes | |
| class | CSegment |
| class | SPosLessSegment |
Public Types | |
| enum | ESegmentType { eSeqGap , eSeqData , eSeqSubMap , eSeqRef , eSeqEnd , eSeqChunk , eSeqLiteral } |
| enum | EFlags { fFindData = (1<<0) , fFindGap = (1<<1) , fFindLeafRef = (1<<2) , fFindInnerRef = (1<<3) , fFindExactLevel = (1<<4) , fIgnoreUnresolved = (1<<5) , fByFeaturePolicy = (1<<6) , fBySequenceClass = (1<<7) , fFindRef = (fFindLeafRef | fFindInnerRef) , fFindAny = fFindData | fFindGap | fFindRef , fFindAnyLeaf = fFindData | fFindGap | fFindLeafRef , fDefaultFlags = fFindAnyLeaf } |
| Segment type flags. More... | |
| typedef CSeq_inst::TMol | TMol |
| typedef CSeqMap_CI | const_iterator |
| typedef int | TFlags |
| Public Types inherited from CObject | |
| enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
| Control filling of newly allocated memory. More... | |
| typedef CObjectCounterLocker | TLockerType |
| Default locker type for CRef. More... | |
| typedef atomic< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
Public Member Functions | |
| ~CSeqMap (void) | |
| size_t | GetSegmentsCount (void) const |
| TSeqPos | GetLength (CScope *scope) const |
| TMol | GetMol (void) const |
| const_iterator | begin (CScope *scope) const |
| STL style methods. More... | |
| const_iterator | end (CScope *scope) const |
| CSeqMap_CI | Begin (CScope *scope) const |
| NCBI style methods. More... | |
| CSeqMap_CI | End (CScope *scope) const |
| CSeqMap_CI | FindSegment (TSeqPos pos, CScope *scope) const |
| Find segment containing the position. More... | |
| CSeqMap_CI | BeginResolved (CScope *scope) const |
| CSeqMap_CI | BeginResolved (CScope *scope, const SSeqMapSelector &selector) const |
| CSeqMap_CI | EndResolved (CScope *scope) const |
| CSeqMap_CI | EndResolved (CScope *scope, const SSeqMapSelector &selector) const |
| CSeqMap_CI | FindResolved (CScope *scope, TSeqPos pos, const SSeqMapSelector &selector) const |
| CSeqMap_CI | ResolvedRangeIterator (CScope *scope, TSeqPos from, TSeqPos length, ENa_strand strand=eNa_strand_plus, size_t maxResolve=size_t(-1), TFlags flags=fDefaultFlags) const |
| Iterate segments in the range with specified strand coordinates. More... | |
| bool | HasSegmentOfType (ESegmentType type) const |
| size_t | CountSegmentsOfType (ESegmentType type) const |
| bool | CanResolveRange (CScope *scope, const SSeqMapSelector &sel) const |
| bool | CanResolveRange (CScope *scope, TSeqPos from, TSeqPos length, ENa_strand strand=eNa_strand_plus, size_t maxResolve=size_t(-1), TFlags flags=fDefaultFlags) const |
| CRef< CSeqMap > | CloneFor (const CBioseq &seq) const |
| CSeqMap (const CSeqMap &sm) | |
| void | SetRegionInChunk (CTSE_Chunk_Info &chunk, TSeqPos pos, TSeqPos length) |
| void | LoadSeq_data (TSeqPos pos, TSeqPos len, const CSeq_data &data) |
| void | SetSegmentGap (const CSeqMap_CI &seg, TSeqPos length) |
| void | SetSegmentGap (const CSeqMap_CI &seg, TSeqPos length, CSeq_data &gap_data) |
| void | SetSegmentData (const CSeqMap_CI &seg, TSeqPos length, CSeq_data &data) |
| void | SetSegmentRef (const CSeqMap_CI &seg, TSeqPos length, const CSeq_id_Handle &ref_id, TSeqPos ref_pos, bool ref_minus_strand) |
| CSeqMap_CI | InsertSegmentGap (const CSeqMap_CI &seg, TSeqPos length) |
| Insert new gap into sequence map. More... | |
| CSeqMap_CI | RemoveSegment (const CSeqMap_CI &seg) |
| Delete segment from sequence map. More... | |
| void | SetRepr (CSeq_inst::TRepr repr) |
| void | ResetRepr (void) |
| void | SetMol (CSeq_inst::TMol mol) |
| void | ResetMol (void) |
| bool | HasZeroGapAt (TSeqPos pos, CScope *scope=0) const |
| Returns true if there is zero-length gap at position. More... | |
| Public Member Functions inherited from CObject | |
| CObject (void) | |
| Constructor. More... | |
| CObject (const CObject &src) | |
| Copy constructor. More... | |
| virtual | ~CObject (void) |
| Destructor. More... | |
| CObject & | operator= (const CObject &src) THROWS_NONE |
| Assignment operator. More... | |
| bool | CanBeDeleted (void) const THROWS_NONE |
| Check if object can be deleted. More... | |
| bool | IsAllocatedInPool (void) const THROWS_NONE |
| Check if object is allocated in memory pool (not system heap) More... | |
| bool | Referenced (void) const THROWS_NONE |
| Check if object is referenced. More... | |
| bool | ReferencedOnlyOnce (void) const THROWS_NONE |
| Check if object is referenced only once. More... | |
| void | AddReference (void) const |
| Add reference to object. More... | |
| void | RemoveReference (void) const |
| Remove reference to object. More... | |
| void | ReleaseReference (void) const |
| Remove reference without deleting object. More... | |
| virtual void | DoNotDeleteThisObject (void) |
| Mark this object as not allocated in heap – do not delete this object. More... | |
| virtual void | DoDeleteThisObject (void) |
| Mark this object as allocated in heap – object can be deleted. More... | |
| void * | operator new (size_t size) |
| Define new operator for memory allocation. More... | |
| void * | operator new[] (size_t size) |
| Define new[] operator for 'array' memory allocation. More... | |
| void | operator delete (void *ptr) |
| Define delete operator for memory deallocation. More... | |
| void | operator delete[] (void *ptr) |
| Define delete[] operator for memory deallocation. More... | |
| void * | operator new (size_t size, void *place) |
| Define new operator. More... | |
| void | operator delete (void *ptr, void *place) |
| Define delete operator. More... | |
| void * | operator new (size_t size, CObjectMemoryPool *place) |
| Define new operator using memory pool. More... | |
| void | operator delete (void *ptr, CObjectMemoryPool *place) |
| Define delete operator. More... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More... | |
| Public Member Functions inherited from CDebugDumpable | |
| CDebugDumpable (void) | |
| virtual | ~CDebugDumpable (void) |
| void | DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const |
| void | DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const |
| void | DumpToConsole (void) const |
Static Public Member Functions | |
| static CRef< CSeqMap > | CreateSeqMapForBioseq (const CBioseq &seq) |
| static CRef< CSeqMap > | CreateSeqMapForSeq_loc (const CSeq_loc &loc, CScope *scope) |
| static CConstRef< CSeqMap > | GetSeqMapForSeq_loc (const CSeq_loc &loc, CScope *scope) |
| Static Public Member Functions inherited from CObject | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
| Define method to throw null pointer exception. More... | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
| static EAllocFillMode | GetAllocFillMode (void) |
| static void | SetAllocFillMode (EAllocFillMode mode) |
| static void | SetAllocFillMode (const string &value) |
| Set mode from configuration parameter value. More... | |
| Static Public Member Functions inherited from CDebugDumpable | |
| static void | EnableDebugDump (bool on) |
Protected Types | |
| typedef vector< CSegment > | TSegments |
| typedef Uint1 | THasSegments |
| typedef bool | TChanged |
Protected Attributes | |
| CBioseq_Info * | m_Bioseq |
| vector< CSegment > | m_Segments |
| atomic< size_t > | m_Resolved |
| CRef< CObject > | m_Delta |
| TMol | m_Mol |
| atomic< THasSegments > | m_HasSegments |
| TChanged | m_Changed |
| atomic< TSeqPos > | m_SeqLength |
| CMutex | m_SeqMap_Mtx |
Private Member Functions | |
| void | ResolveAll (void) const |
| CSeqMap & | operator= (const CSeqMap &) |
Friends | |
| class | CSegment |
| class | SPosLessSegment |
| class | CSeqMap_SeqPoss |
| class | CBioseq_Info |
| class | CSeqMap_CI |
| class | CSeqMap_CI_SegmentInfo |
Additional Inherited Members | |
| Static Public Attributes inherited from CObject | |
| static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
| Define possible object states. More... | |
| static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
| Heap signature was found. More... | |
| static const TCount | eCounterBitsPlaceMask |
| Mask for 'in heap' state flags. More... | |
| static const int | eCounterStep = 1 << 2 |
| Skip over the "in heap" bits. More... | |
| static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
| Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
| static const TCount | eCounterStateMask |
| Valid object, and object in heap. More... | |
Detailed Description
CSeqMap –.
Formal sequence map – to describe sequence parts in general – location and type only, without providing real data
Definition at line 92 of file seq_map.hpp.
The documentation for this class was generated from the following files:
- include/objmgr/seq_map.hpp
- src/objmgr/seq_map.cpp
