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

m_MinusStrand(

),

m_LinkUsedTSE(

),

m_Flags(

::fDefaultFlags),

m_MinusStrand(

),

m_LinkUsedTSE(

),

m_MaxResolveCount(resolve_count),

( !minusStrand ) {

m_FeaturePolicyWasApplied(

)

m_FeaturePolicyWasApplied(

)

m_SearchPos(range.GetFrom()),

m_SearchEnd(range.GetToOpen()),

m_FeaturePolicyWasApplied(

)

m_FeaturePolicyWasApplied(

)

m_SearchPos(range.GetFrom()),

m_SearchEnd(range.GetToOpen()),

m_FeaturePolicyWasApplied(

)

m_Stack(1, base.m_Stack.back()),

m_FeaturePolicyWasApplied(

)

( &

.x_GetSeqMap() != &seqmap ||

.x_GetIndex() != index ) {

);

.m_LevelRangePos = 0;

.m_MinusStrand = 0;

);

);

);

);

);

);

);

);

( !

.InRange() ) {

(

*

(

.m_SeqMap->x_GetObject(seg)));

( !resolveExternal ) {

& seq_id =

.m_SeqMap->x_GetRefSeqid(seg);

( (

.size() & 63) == 0 ) {

(

=

(

.size())-2;

>= 0; --

) {

);

.m_SeqMap = seqMap;

.m_LevelRangePos = from;

.m_LevelRangeEnd = from + length;

(

.m_LevelRangeEnd <

.m_LevelRangePos) {

);

.m_MinusStrand = minusStrand;

findOffset = !minusStrand? pos: length - 1 - pos;

(

.m_Index ==

(-1) ) {

.m_Index = !minusStrand?

( pos >= length ) {

( !minusStrand ) {

.m_LevelRangeEnd ) {

.m_LevelRangeEnd);

.m_LevelRangePos ) {

.m_LevelRangePos);

= search_pos > level_pos? search_pos - level_pos: 0;

}

(

() );

end_offset = search_end < level_end? level_end - search_end: 0;

& seq_id =

.m_SeqMap->x_GetRefSeqid(seg);

sx_AdjustSelector(selector),

m_SeqMap(&bioseq.SetSeqMap())

sx_AdjustSelector(selector),

m_SeqMap(&bioseq.SetSeqMap())

sx_AdjustSelector(selector),

sx_AdjustSelector(selector),

ref_minus_strand)

*

, ref_length, ref_id, ref_pos, ref_minus_strand);

(length, gap_data);

CSeqMap_CI::operator=(it);

ref_minus_strand)

*

, ref_length, ref_id, ref_pos, ref_minus_strand);

CSeqMap_CI::operator=(it);

CSeqMap_CI::operator=(it);

CSeqMap_CI::operator=(it);

( src_coding ) {

+

( seq_data_coding ) {

+

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

SeqMap related exceptions.

Non-const iterator over CSeqMap (allows to edit the sequence).

CBioseq_Handle GetBioseqHandle(const CSeq_id &id) const

Get Bioseq handle from this TSE.

static unsigned char depth[2 *(256+1+29)+1]

unsigned int TSeqPos

Type for sequence locations and lengths.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define NCBI_THROW(exception_class, err_code, message)

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

const string AsFastaString(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

EFeatureFetchPolicy GetFeatureFetchPolicy(void) const

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

const CTSE_Handle & GetTSE_Handle(void) const

EFeatureFetchPolicy

Feature fetch policy describes when to look for features on sequence segments.

const CSeqMap & GetSeqMap(void) const

Get sequence map.

ESequenceClass GetSequenceClass(void) const

@ eFeatureFetchPolicy_default

@ eFeatureFetchPolicy_only_near

CSeqMap_I & Remove(void)

Remove current segment.

TSeqPos x_GetLevelRealPos(void) const

CSeqMap_I & InsertRef(const CSeq_id_Handle &ref_id, TSeqPos ref_pos, TSeqPos ref_length, bool ref_minus_strand=false)

Insert reference. On return the iterator points to the new segment.

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

int x_GetSequenceClass(void) const

SSeqMapSelector & SetResolveCount(size_t res_cnt)

Set max depth of resolving seq-map.

size_t GetResolveCount(void) const

const CSeqMap::CSegment & x_GetSegment(void) const

const CSeq_data & GetRefData(void) const

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

void x_Select(const CConstRef< CSeqMap > &seqMap, const SSeqMapSelector &selector, TSeqPos pos)

bool CanResolve(void) const

void AddUsedTSE(const CTSE_Handle &tse) const

bool Next(bool resolveExternal=true)

go to next/next segment, return false if no more segments if no_resolve_current == true,...

SSeqMapSelector & SetLinkUsedTSE(bool link=true)

TSeqPos x_GetTopOffset(void) const

TSeqPos x_CalcLength(void) const

void GetSequence(string &buffer, CSeqUtil::ECoding buffer_coding) const

Get current sequence as a string with the selected encoding.

SSeqMapSelector m_Selector

TSeqPos GetRefPosition(void) const

void SetSeq_data(TSeqPos length, CSeq_data &data)

Change current segment to data.

SSeqMapSelector & SetPosition(TSeqPos pos)

Find segment containing the position.

CSeqMap_I & InsertGap(TSeqPos length, CSeq_data *gap_data=0)

Insert gap. On return the iterator points to the new segment.

const TSegmentInfo & x_GetSegmentInfo(void) const

const CSeq_data & GetData(void) const

will allow only regular data segments (whole, plus strand)

void SetRef(const CSeq_id_Handle &ref_id, TSeqPos ref_pos, TSeqPos ref_length, bool ref_minus_strand=false)

Change current segment to reference.

CScope * GetScope(void) const

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

void SetSequence(const string &buffer, CSeqUtil::ECoding buffer_coding, CSeq_data::E_Choice seq_data_coding)

Set sequence data.

CConstRef< CSeqMap > m_SeqMap

const CTSE_Handle & x_GetLimitTSE(CScope *scope=0) const

TSeqPos x_GetTopOffset(void) const

const CSeqMap::CSegment & x_GetSegment(void) const

TSeqPos GetRefPosition(void) const

bool x_RefTSEMatch(const CSeqMap::CSegment &seg) const

const CSeqMap & x_GetSeqMap(void) const

void SetGap(TSeqPos length, CSeq_data *gap_data=0)

Change current segment to gap.

bool GetRefMinusStrand(void) const

CSeqMap_I & InsertData(TSeqPos length, CSeq_data &data)

Insert data. On return the iterator points to the new segment.

bool x_CanResolve(const CSeqMap::CSegment &seg) const

CBioseq_Handle x_GetBioseq(const CSeq_id &seq_id) const

void x_UpdateLength(void)

SSeqMapSelector & SetLimitTSE(const CSeq_entry_Handle &tse)

Limit TSE to resolve references.

bool m_FeaturePolicyWasApplied

void SetFlags(TFlags flags)

CSeq_id_Handle GetRefSeqid(void) const

The following function makes sense only when the segment is a reference to another seq.

bool IsUnknownLength(void) const

return true if current segment is a gap of unknown length

SSeqMapSelector::TFlags TFlags

static SSeqMapSelector sx_AdjustSelector(const SSeqMapSelector &selector)

bool x_Move(bool minusStrand, CScope *scope)

TFlags GetFlags(void) const

vector< CTSE_Handle > * m_UsedTSEs

bool x_Push(TSeqPos offset, bool resolveExternal)

TSeqPos x_GetLevelRealEnd(void) const

TSeqPos GetPosition(void) const

return position of current segment in sequence

int x_GetSequenceClass(void) const

TSeqPos GetLength(void) const

return length of current segment

bool x_HasLimitTSE(void) const

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 SetSegmentRef(const CSeqMap_CI &seg, TSeqPos length, const CSeq_id_Handle &ref_id, TSeqPos ref_pos, bool ref_minus_strand)

void SetSegmentGap(const CSeqMap_CI &seg, TSeqPos length)

size_t x_FindSegment(TSeqPos position, CScope *scope) const

atomic< TSeqPos > m_Position

CConstRef< CSeq_literal > x_GetSeq_literal(const CSegment &seg) const

int x_GetSequenceClass(void) const

const CSegment & x_GetSegment(size_t index) const

size_t x_GetLastEndSegmentIndex(void) const

TSeqPos x_GetSegmentLength(size_t index, CScope *scope) const

size_t x_GetFirstEndSegmentIndex(void) const

TSeqPos x_GetSegmentPosition(size_t index, CScope *scope) const

TSeqPos x_GetSegmentEndPosition(size_t index, CScope *scope) const

CSeqMap_CI RemoveSegment(const CSeqMap_CI &seg)

Delete segment from sequence map.

void SetSegmentData(const CSeqMap_CI &seg, TSeqPos length, CSeq_data &data)

CSeqMap_CI InsertSegmentGap(const CSeqMap_CI &seg, TSeqPos length)

Insert new gap into sequence map.

atomic< TSeqPos > m_Length

TSeqPos GetLength(CScope *scope) const

const CSeq_data & x_GetSeq_data(const CSegment &seg) const

@ eSeqData

real sequence data

@ eSeqRef

reference to Bioseq

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

int8_t Int1

1-byte (8-bit) signed 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.

TFrom GetFrom(void) const

Get the From member data.

E_Choice

Choice variants.

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

#define CODING_PACK_CASE(coding)

#define CODING_UNPACK_CASE(coding)

Selector used in CSeqMap methods returning iterators.

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