Search Toolkit Book for CSeqVector
#include <objmgr/seq_vector.hpp>
Inheritance diagram for CSeqVector:
Collaboration diagram for CSeqVector:
Public Types | |
| typedef CBioseq_Handle::EVectorCoding | EVectorCoding |
| typedef CSeqVector_CI | const_iterator |
| typedef CMutex | TMutex |
| typedef TMutex::TWriteLockGuard | TMutexGuard |
| typedef CSeq_inst::TMol | TMol |
| 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 Types inherited from CSeqVectorTypes | |
| enum | ECaseConversion { eCaseConversion_none , eCaseConversion_upper , eCaseConversion_lower } |
| typedef unsigned char | TResidue |
| typedef CSeq_data::E_Choice | TCoding |
| typedef TResidue | value_type |
| typedef TSeqPos | size_type |
| typedef TSignedSeqPos | difference_type |
| typedef std::random_access_iterator_tag | iterator_category |
| typedef const TResidue * | pointer |
| typedef const TResidue & | reference |
Public Member Functions | |
| CSeqVector (void) | |
| CSeqVector (const CBioseq_Handle &bioseq, EVectorCoding coding=CBioseq_Handle::eCoding_Ncbi, ENa_strand strand=eNa_strand_unknown) | |
| CSeqVector (const CSeqMap &seqMap, CScope &scope, EVectorCoding coding=CBioseq_Handle::eCoding_Ncbi, ENa_strand strand=eNa_strand_unknown) | |
| CSeqVector (const CSeqMap &seqMap, const CTSE_Handle &top_tse, EVectorCoding coding=CBioseq_Handle::eCoding_Ncbi, ENa_strand strand=eNa_strand_unknown) | |
| CSeqVector (const CSeq_loc &loc, CScope &scope, EVectorCoding coding=CBioseq_Handle::eCoding_Ncbi, ENa_strand strand=eNa_strand_unknown) | |
| CSeqVector (const CSeq_loc &loc, const CTSE_Handle &top_tse, EVectorCoding coding=CBioseq_Handle::eCoding_Ncbi, ENa_strand strand=eNa_strand_unknown) | |
| CSeqVector (const CBioseq &bioseq, CScope *scope=0, EVectorCoding coding=CBioseq_Handle::eCoding_Ncbi, ENa_strand strand=eNa_strand_unknown) | |
| CSeqVector (const CSeqVector &vec) | |
| virtual | ~CSeqVector (void) |
| CSeqVector & | operator= (const CSeqVector &vec) |
| bool | empty (void) const |
| TSeqPos | size (void) const |
| TMutex & | GetMutex (void) const |
| Get mutex for a few non-MT-safe methods to make them MT-safe at a cost of performance. More... | |
| TResidue | operator[] (TSeqPos pos) const |
| 0-based array of residues Note: this method is not MT-safe, do not call it in parallel with other, even MT-safe method. More... | |
| bool | IsInGap (TSeqPos pos) const |
| true if sequence at 0-based position 'pos' has gap Note: this method is not MT-safe, do not call it in parallel with other, even MT-safe method. More... | |
| TSeqPos | GetGapSizeForward (TSeqPos pos) const |
| returns number of gap symbols ahead including base at position 'pos' returns 0 if the position is not in gap More... | |
| CConstRef< CSeq_literal > | GetGapSeq_literal (TSeqPos pos) const |
| returns gap Seq-literal object ref returns null if it's not a gap or an unspecified gap More... | |
| bool | CanGetRange (TSeqPos start, TSeqPos stop) const |
| Check if the sequence data is available for the interval [start, stop). More... | |
| bool | CanGetRange (const const_iterator &start, const const_iterator &stop) const |
| void | GetSeqData (TSeqPos start, TSeqPos stop, string &buffer) const |
| Fill the buffer string with the sequence data for the interval [start, stop). More... | |
| void | GetSeqData (const const_iterator &start, const const_iterator &stop, string &buffer) const |
| void | GetPackedSeqData (string &buffer, TSeqPos start=0, TSeqPos stop=kInvalidSeqPos) |
| TMol | GetSequenceType (void) const |
| bool | IsProtein (void) const |
| bool | IsNucleotide (void) const |
| CScope & | GetScope (void) const |
| const CSeqMap & | GetSeqMap (void) const |
| ENa_strand | GetStrand (void) const |
| void | SetStrand (ENa_strand strand) |
| TCoding | GetCoding (void) const |
| Target sequence coding. More... | |
| void | SetCoding (TCoding coding) |
| void | SetIupacCoding (void) |
| Set coding to either Iupacaa or Iupacna depending on molecule type. More... | |
| void | SetNcbiCoding (void) |
| Set coding to either Ncbi8aa or Ncbi8na depending on molecule type. More... | |
| void | SetCoding (EVectorCoding coding) |
| Set coding to either Iupac or Ncbi8xx. More... | |
| TResidue | GetGapChar (ECaseConversion case_cvt=eCaseConversion_none) const |
| Return gap symbol corresponding to the selected coding. More... | |
| const_iterator | begin (void) const |
| const_iterator | end (void) const |
| void | SetRandomizeAmbiguities (void) |
| Randomization of ambiguities and gaps in ncbi2na coding. More... | |
| void | SetRandomizeAmbiguities (Uint4 seed) |
| void | SetRandomizeAmbiguities (CRandom &random_gen) |
| void | SetRandomizeAmbiguities (CRef< INcbi2naRandomizer > randomizer) |
| void | SetNoAmbiguities (void) |
| 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 |
Private Member Functions | |
| void | x_InitSequenceType (void) |
| CSeqVector_CI & | x_GetIterator (TSeqPos pos) const |
| CSeqVector_CI * | x_CreateIterator (TSeqPos pos) const |
| void | x_ResetIterator (void) const |
| void | x_InitRandomizer (CRandom &random_gen) |
| void | x_GetPacked8SeqData (string &dst_str, TSeqPos src_pos, TSeqPos src_end) |
| void | x_GetPacked4naSeqData (string &dst_str, TSeqPos src_pos, TSeqPos src_end) |
| void | x_GetPacked2naSeqData (string &dst_str, TSeqPos src_pos, TSeqPos src_end) |
Private Attributes | |
| CHeapScope | m_Scope |
| CConstRef< CSeqMap > | m_SeqMap |
| CTSE_Handle | m_TSE |
| TSeqPos | m_Size |
| TMol | m_Mol |
| ENa_strand | m_Strand |
| TCoding | m_Coding |
| CRef< INcbi2naRandomizer > | m_Randomizer |
| TMutex | m_IteratorMutex |
| AutoPtr< CSeqVector_CI > | m_Iterator |
Friends | |
| class | CBioseq_Handle |
| class | CSeqVector_CI |
Additional Inherited Members | |
| 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) |
| 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... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
| Static Protected Member Functions inherited from CSeqVectorTypes | |
| static TResidue | sx_GetGapChar (TCoding coding, ECaseConversion case_cvt) |
| static const char * | sx_GetConvertTable (TCoding src, TCoding dst, bool reverse, ECaseConversion case_cvt) |
| Static Protected Attributes inherited from CSeqVectorTypes | |
| static const char | sm_TrivialTable [256] |
Detailed Description
CSeqVector –.
Provide sequence data in the selected coding
Definition at line 64 of file seq_vector.hpp.
The documentation for this class was generated from the following files:
- include/objmgr/seq_vector.hpp
- src/objmgr/seq_vector.cpp
