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

sx_GetGapChar(TCoding coding,

ECaseConversion case_cvt);

* sx_GetConvertTable(TCoding src, TCoding dst,

ECaseConversion case_cvt);

sm_TrivialTable[256];

GetBufferSize(

)

;

* GetBufferPtr(

)

;

* GetBufferEnd(

)

;

TCoding GetCoding(

)

;

SetCoding(TCoding coding);

SetRandomizeAmbiguities(

);

SetRandomizeAmbiguities(

);

SetRandomizeAmbiguities(

& random_gen);

SetNoAmbiguities(

);

& GetCurrentSeqMap_CI()

;

IsInGap(

)

;

GetGapSizeForward(

)

;

GetGapSizeBackward(

)

;

SkipGapBackward(

);

HasZeroGapBefore(

);

x_GetSize(

)

;

x_InitializeCache(

);

x_ResizeCache(

);

x_SwapCache(

);

x_UpdateCacheUp(

pos);

x_UpdateCacheDown(

pos);

x_UpdateSeg(

pos);

x_IncSeg(

);

x_DecSeg(

);

x_CheckForward(

);

x_CheckBackward(

);

x_InitRandomizer(

& random_gen);

x_NextCacheSeg(

);

x_PrevCacheSeg(

);

x_CachePos(

)

;

x_CacheSize(

)

;

x_CacheEndPos(

)

;

x_BackupPos(

)

;

x_BackupSize(

)

;

x_BackupEndPos(

)

;

x_CacheOffset(

)

;

x_ResetCache(

);

x_ResetBackup(

);

x_ThrowOutOfRange(

)

;

( !

(*

) ) {

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

special temporary holder for return value from postfix operators

bool operator<(const CEquivRange &A, const CEquivRange &B)

bool operator==(const CEquivRange &A, const CEquivRange &B)

objects::CSeqVectorTypes::TResidue TResidue

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

element_type * get(void) const

Get pointer.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

CVect2< NCBI_PROMOTE(int,U) > operator*(int v1, const CVect2< U > &v2)

CExpression operator>=(CREATED, time_point)

CExpression operator<=(time_point, CREATED)

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...

bool IsValid(const CSeq_point &pt, CScope *scope)

Checks that point >= 0 and point < length of Bioseq.

CSeqVector_CI & SetPos(TSeqPos pos)

virtual void RandomizeData(char *buffer, size_t count, TSeqPos pos)=0

Convert count unpacked bases in buffer 4na -> 2na with randomization.

const char * GetBufferPtr(void) const

Get pointer to current char in the buffer.

ENa_strand GetStrand(void) const

CTempValue(value_type value)

CSeq_data::E_Choice TCoding

TSeqPos x_CacheEndPos(void) const

TSeqPos x_BackupPos(void) const

bool operator>(const CSeqVector_CI &iter) const

TSignedSeqPos difference_type

CTempValue operator--(int)

TResidue operator*(void) const

const TResidue & reference

CSeqVector_CI & operator++(void)

TSeqPos GetPos(void) const

vector< CTSE_Handle > m_UsedTSEs

TCoding GetCoding(void) const

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

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

const char * GetBufferEnd(size_t size) const

Get pointer to current position+size.

TSeqPos x_CacheOffset(void) const

CSeqVector_CI & operator+=(TSeqPos value)

CRef< INcbi2naRandomizer > m_Randomizer

void x_SetPos(TSeqPos pos)

bool operator>=(const CSeqVector_CI &iter) const

ECaseConversion m_CaseConversion

bool operator!=(const CSeqVector_CI &iter) const

void x_ThrowOutOfRange(void) const

value_type operator*(void) const

TSeqPos x_CachePos(void) const

TSeqPos GetBufferSize(void) const

Get number of chars from current position to the current buffer end.

DECLARE_OPERATOR_BOOL(IsValid())

CSeqMap::ESegmentType GetType(void) const

AutoArray< char > TCacheData

CTempValue operator++(int)

Restricted postfix operators.

TResidue GetGapChar(void) const

returns character representation of gap in sequence

void x_PrevCacheSeg(void)

void x_NextCacheSeg(void)

CSeqVector_CI operator-(const CSeqVector_CI &iter, TSeqPos value)

TSeqPos x_BackupEndPos(void) const

TSeqPos x_CacheSize(void) const

bool operator<(const CSeqVector_CI &iter) const

CConstRef< CSeqMap > m_SeqMap

CSeqVector_CI & operator--(void)

bool operator<=(const CSeqVector_CI &iter) const

CSeqVector_CI operator+(const CSeqVector_CI &iter, TSeqPos value)

static TResidue sx_GetGapChar(TCoding coding, ECaseConversion case_cvt)

TSeqPos x_BackupSize(void) const

TCoding x_GetCoding(TCoding cacheCoding, TCoding dataCoding) const

bool operator==(const CSeqVector_CI &iter) const

const CSeqMap_CI & GetCurrentSeqMap_CI() const

bool IsInGap(void) const

true if current position of CSeqVector_CI is inside of sequence gap

CSeqVector_CI & operator-=(TSeqPos value)

std::random_access_iterator_tag iterator_category

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.

bool operator!=(const CNCBI_IPAddr &lhs, unsigned int rhs)

#define NCBI_XOBJMGR_EXPORT

ENa_strand

strand of nucleic acid

E_Choice

Choice variants.

@ e_not_set

No variant selected.

CNcbiMatrix< T > & operator+=(CNcbiMatrix< T > &, const CNcbiMatrix< U > &)

global addition: matrix += matrix

CNcbiMatrix< T > & operator-=(CNcbiMatrix< T > &, const CNcbiMatrix< U > &)

global subtraction: matrix -= matrix

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

const GenericPointer< typename T::ValueType > T2 value

S & operator--(CNetRef< S > &r, int)

bool operator>(const typename tree< T, tree_node_allocator >::iterator_base &one, const typename tree< T, tree_node_allocator >::iterator_base &two)

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