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NCBI C++ ToolKit: src/objmgr/seq_vector_ci.cpp Source File

<<pos);

m_CaseConversion(eCaseConversion_none),

m_CaseConversion(eCaseConversion_none),

m_Randomizer(sv_it.m_Randomizer),

m_SeqMap(seq_vector.m_SeqMap),

m_TSE(seq_vector.m_TSE),

m_Strand(seq_vector.m_Strand),

m_Coding(seq_vector.m_Coding),

m_CaseConversion(eCaseConversion_none),

m_Randomizer(seq_vector.m_Randomizer),

m_SeqMap(seq_vector.m_SeqMap),

m_TSE(seq_vector.m_TSE),

m_Strand(seq_vector.m_Strand),

m_Coding(seq_vector.m_Coding),

m_CaseConversion(case_cvt),

m_Randomizer(seq_vector.m_Randomizer),

m_SeqMap(seq_vector.m_SeqMap),

m_TSE(seq_vector.m_TSE),

m_Coding(seq_vector.m_Coding),

m_CaseConversion(case_cvt),

m_Randomizer(seq_vector.m_Randomizer),

( stop < start ) {

( exception&

) {

( pos < m_ScannedStart || pos >

) {

(

== &sv_it ) {

(pos - cache_offset, cache_offset + 1);

randomize =

;

( cacheCoding != dataCoding &&

*

= 0;

( cacheCoding != dataCoding || reverse ||

( !

&& cacheCoding != dataCoding ) {

<<

dataCoding<<

<<cacheCoding);

( dataCoding ) {

);

);

<<dataCoding);

( cache_offset < cache_size ) {

( pos < old_pos && pos >= old_pos -

&&

<<pos);

<<pos<<

<<pos+

);

chunk_end = cache + chunk_count;

.append(cache, chunk_end);

-= chunk_count;

( chunk_end == cache_end ) {

);

<<pos<<

<<

);

);

<<pos<<

<<

);

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool IsReverse(ENa_strand s)

CScope * GetScopeOrNull(void) const

SeqVector related exceptions.

unsigned int TSeqPos

Type for sequence locations and lengths.

element_type * get(void) const

Get pointer.

void reset(element_type *p=0)

Reset will delete the old pointer, set content to the new value, and assume the ownership upon the ne...

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

void x_InitSeg(TSeqPos pos)

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.

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

const CSeq_data & GetRefData(void) const

will allow any data segments, user should check for position and strand

TSeqPos x_CacheEndPos(void) const

TSeqPos x_BackupPos(void) const

SSeqMapSelector & SetLinkUsedTSE(bool link=true)

void x_CheckBackward(void)

TSeqPos SkipGap(void)

skip current gap forward returns number of skipped gap symbols does nothing and returns 0 if current ...

void x_CheckForward(void)

TSeqPos GetPos(void) const

TSeqPos GetRefPosition(void) const

vector< CTSE_Handle > m_UsedTSEs

void x_FillCache(TSeqPos start, TSeqPos count)

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).

void x_ResizeCache(size_t size)

TSeqPos x_CacheOffset(void) const

CRef< INcbi2naRandomizer > m_Randomizer

TSeqPos GetGapSizeForward(void) const

returns number of gap symbols ahead including current symbol returns 0 if current position is not in ...

CConstRef< CSeq_literal > GetGapSeq_literal(void) const

returns gap Seq-data object ref returns null if it's not a gap or an unspecified gap

CSeqVector_CI & operator=(const CSeqVector_CI &sv_it)

void x_SetPos(TSeqPos pos)

TSeqPos x_GetSize(void) const

void SetCoding(TCoding coding)

ECaseConversion m_CaseConversion

void x_ThrowOutOfRange(void) const

bool GetRefMinusStrand(void) const

TSeqPos x_CachePos(void) const

TSeqPos GetGapSizeBackward(void) const

returns number of gap symbols before current symbol returns 0 if current position is not in gap

CSeqMap::ESegmentType GetType(void) const

bool HasZeroGapBefore(void)

true if there is zero-length gap before current position

TResidue GetGapChar(void) const

returns character representation of gap in sequence

void x_PrevCacheSeg(void)

void x_NextCacheSeg(void)

static const char * sx_GetConvertTable(TCoding src, TCoding dst, bool reverse, ECaseConversion case_cvt)

TSeqPos x_CacheSize(void) const

void x_UpdateCacheUp(TSeqPos pos)

void x_InitializeCache(void)

SSeqMapSelector & SetRange(TSeqPos start, TSeqPos length)

Set range for iterator.

CConstRef< CSeqMap > m_SeqMap

bool CanGetRange(TSeqPos start, TSeqPos stop)

Check if the sequence can be obtained for the interval [start, stop)

void SetNoAmbiguities(void)

void SetStrand(ENa_strand strand)

void x_UpdateSeg(TSeqPos pos)

TSeqPos GetRefEndPosition(void) const

SSeqMapSelector & SetStrand(ENa_strand strand)

Set strand to iterate over.

static TResidue sx_GetGapChar(TCoding coding, ECaseConversion case_cvt)

bool IsInvalid(void) const

TSeqPos GetPosition(void) const

return position of current segment in sequence

void SetRandomizeAmbiguities(void)

TSeqPos SkipGapBackward(void)

skip current gap backward returns number of skipped gap symbols does nothing and returns 0 if current...

void x_SetVector(CSeqVector &seq_vector)

TSeqPos x_BackupSize(void) const

TCoding x_GetCoding(TCoding cacheCoding, TCoding dataCoding) const

TSeqPos GetLength(void) const

return length of current segment

CConstRef< CSeq_literal > GetRefGapLiteral(void) const

return CSeq_literal with gap data, or null if either the segment is not a gap, or an unspecified gap

void x_InitRandomizer(CRandom &random_gen)

bool IsInGap(void) const

true if current position of CSeqVector_CI is inside of sequence gap

void x_UpdateCacheDown(TSeqPos pos)

bool HasZeroGapAt(TSeqPos pos, CScope *scope=0) const

Returns true if there is zero-length gap at position.

CConstRef< CSeqMap > m_SeqMap

CRef< INcbi2naRandomizer > m_Randomizer

bool CanResolveRange(CScope *scope, const SSeqMapSelector &sel) const

TSeqPos GetLength(CScope *scope) const

@ eSeqData

real sequence data

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.

ENa_strand

strand of nucleic acid

E_Choice

Choice variants.

@ e_Ncbipna

nucleic acid probabilities

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Ncbistdaa

consecutive codes for std aas

@ e_Ncbi2na

2 bit nucleic acid code

@ e_Iupacna

IUPAC 1 letter nuc acid code.

@ e_Ncbipaa

amino acid probabilities

@ e_Ncbi8na

8 bit extended nucleic acid code

@ e_Ncbi4na

4 bit nucleic acid code

@ e_Iupacaa

IUPAC 1 letter amino acid code.

@ e_Ncbi8aa

8 bit extended amino acid codes

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

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

void ThrowOutOfRangeSeq_inst(size_t pos)

static const TSeqPos kMaxPreloadBases

static const TSeqPos kCacheSize

void copy_8bit_any(DstIter dst, size_t count, const SrcCont &srcCont, size_t srcPos, const char *table, bool reverse)

void copy_4bit_any(DstIter dst, size_t count, const SrcCont &srcCont, size_t srcPos, const char *table, bool reverse)

void copy_2bit_any(DstIter dst, size_t count, const SrcCont &srcCont, size_t srcPos, const char *table, bool reverse)

Selector used in CSeqMap methods returning iterators.

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