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NCBI C++ ToolKit: include/objmgr/seq_vector.hpp Source File

(

)

;

& GetMutex(

)

;

IsInGap(

pos)

;

GetPackedSeqData(

&

,

IsProtein(

)

;

IsNucleotide(

)

;

& GetSeqMap(

)

;

GetCoding(

)

;

SetCoding(

coding);

SetIupacCoding(

);

SetNcbiCoding(

);

SetRandomizeAmbiguities(

);

SetRandomizeAmbiguities(

);

SetRandomizeAmbiguities(

& random_gen);

SetNoAmbiguities(

);

x_ResetIterator(

)

;

x_GetPacked8SeqData(

& dst_str,

x_GetPacked4naSeqData(

& dst_str,

x_GetPacked2naSeqData(

& dst_str,

RandomizeData(

*

,

kRandomizerPosMask = 0x3f,

kRandomDataSize = kRandomizerPosMask + 1,

m_FixedTable[16];

m_RandomTable[16][kRandomDataSize];

User-defined methods of the data storage class.

bool GetSeqData(ParserPtr pp, const DataBlk &entry, CBioseq &bioseq, Int4 nodetype, unsigned char *seqconv, Uint1 seq_data_type)

unsigned int TSeqPos

Type for sequence locations and lengths.

element_type * get(void) const

Get pointer.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

EVectorCoding

CSeqVector constructor flags.

@ eCoding_Ncbi

Set coding to binary coding (Ncbi4na or Ncbistdaa)

CSeqVector_CI & SetPos(TSeqPos pos)

TSeqPos GetPos(void) const

static TResidue sx_GetGapChar(TCoding coding, ECaseConversion case_cvt)

void x_InitRandomizer(CRandom &random_gen)

bool IsInGap(void) const

true if current position of CSeqVector_CI is inside of sequence gap

ENa_strand GetStrand(void) const

AutoPtr< CSeqVector_CI > m_Iterator

TCoding GetCoding(void) const

Target sequence coding.

friend class CSeqVector_CI

bool IsInGap(TSeqPos pos) const

true if sequence at 0-based position 'pos' has gap Note: this method is not MT-safe,...

bool CanGetRange(TSeqPos start, TSeqPos stop) const

Check if the sequence data is available for the interval [start, stop).

const CSeqMap & GetSeqMap(void) const

CConstRef< CSeqMap > m_SeqMap

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

CBioseq_Handle::EVectorCoding EVectorCoding

CSeqVector_CI & x_GetIterator(TSeqPos pos) const

CRef< INcbi2naRandomizer > m_Randomizer

void x_InitSequenceType(void)

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,...

TMutex::TWriteLockGuard TMutexGuard

CSeqVector_CI * x_CreateIterator(TSeqPos pos) const

TMutex & GetMutex(void) const

Get mutex for a few non-MT-safe methods to make them MT-safe at a cost of performance.

bool IsProtein(void) const

CSeqVector_CI const_iterator

const_iterator begin(void) const

bool IsNucleotide(void) const

const_iterator end(void) const

TMol GetSequenceType(void) const

CScope & GetScope(void) const

TResidue GetGapChar(ECaseConversion case_cvt=eCaseConversion_none) const

Return gap symbol corresponding to the selected coding.

CObject & operator=(const CObject &src) THROWS_NONE

Assignment operator.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XOBJMGR_EXPORT

ENa_strand

strand of nucleic acid

E_Choice

Choice variants.

EMol

molecule class in living organism

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::SIZE size

Uint4 GetSequenceType(const CBioseq_Handle &bsh)

Return a (corrected) set of flags identifying the sequence type.

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