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

77

m_UnknownLength(unknown_len),

80

m_RefMinusStrand(

false

88

: m_Position(seg.m_Position.load()),

89

m_Length(seg.m_Length.load()),

90

m_UnknownLength(seg.m_UnknownLength),

91

m_SegType(seg.m_SegType),

92

m_ObjType(seg.m_ObjType),

93

m_RefMinusStrand(seg.m_RefMinusStrand),

94

m_RefPosition(seg.m_RefPosition),

95

m_RefObject(seg.m_RefObject)

184

m_Segments(sm.m_Segments),

185

m_Resolved(sm.m_Resolved.load()),

188

m_HasSegments(sm.m_HasSegments.load()),

189

m_Changed(sm.m_Changed),

190

m_SeqLength(sm.m_SeqLength.load())

196

it->m_RefObject =

null

;

230 switch

(ext.

Which

()) {

247 "CSeq_inst.ext.map with unset CSeq_inst.length"

);

254 "CSeq_ext::??? -- not implemented"

);

270 "CSeq_inst.repr map with unset CSeq_inst.length"

);

282 "CSeq_inst.repr of sequence without data " 283 "should be not_set"

);

287 "CSeq_inst.length of sequence without data " 308 "Invalid segment index"

);

332 "Cannot resolve "

<<seq_id<<

": null scope pointer"

);

337 "Cannot resolve "

<<seq_id<<

": unknown"

);

368 "Invalid sequence length"

);

382 if

( index <= resolved )

386 TSeqPos

seg_pos = resolved_pos;

390 "Sequence position overflow"

);

392 m_Segments

[++resolved].m_Position = resolved_pos;

393

}

while

( resolved < index );

407 if

( resolved_pos <= pos ) {

414 TSeqPos

seg_pos = resolved_pos;

418 "Sequence position overflow"

);

420 m_Segments

[++resolved].m_Position = resolved_pos;

421

}

while

( resolved_pos <= pos );

430

TSegments::const_iterator itend =

m_Segments

.begin()+resolved;

431

TSegments::const_iterator it =

524 bool

resolveExternal)

const 554 if

(

literal

.IsSetSeq_data() ) {

559 "Invalid segment type"

);

578 "Invalid segment type"

);

580 if

(

data

.IsGap() ) {

581 ERR_POST

(

"CSeqMap: gap Seq-data was split as real data"

);

617 "Cannot edit unattached sequence map"

);

621 "Bioseq is not in edit state"

);

630 if

( gap_data && !gap_data->

IsGap

() ) {

632 "SetSegmentGap: Seq-data is not gap"

);

666 bool

ref_minus_strand)

736 return CSeqMap_CI

(seg0, *

this

, index, pos);

750 "cannot remove end segment"

);

760 return CSeqMap_CI

(seg0, *

this

, index, pos);

771 "Invalid segment size"

);

783 "Invalid segment type"

);

820 return Begin

(scope);

872 size_t

maxResolveCount,

899 if

( it->m_SegType ==

type

) {

910 if

( index ==

size_t

(-1) && pos ==

GetLength

(scope) ) {

916 if

( pos_in_seg > 0 ) {

994 if

( start >= length ) {

1000 if

( stop < start || stop > length ) {

1011 bool

deeper =

true

;

1012 size_t

next_depth = 0;

1013

vector<CTSE_Handle> all_tse;

1014

vector<CTSE_Handle> parent_tse;

1015

vector<CSeq_id_Handle> next_ids;

1017

vector< AutoPtr<CInitGuard> > guards;

1047

chunks.push_back(chunk);

1055 sort

(chunks.begin(), chunks.end(), PByLoader());

1056

chunks.erase(unique(chunks.begin(), chunks.end()), chunks.end());

1057 while

( !chunks.empty() ) {

1060

load_chunks.clear();

1063 size_t

s = chunks.size();

1068 for

(

size_t i

= s;

< chunks.size(); ++

) {

1070 if

( guard.

get

() && *guard.

get

() ) {

1071

load_chunks.push_back(chunks[

]);

1072

guards.push_back(guard);

1076 if

( !load_chunks.empty() ) {

1083 if

( !next_ids.empty() ) {

1085

vector<CBioseq_Handle> seqs =

1087 _ASSERT

(seqs.size() == parent_tse.size());

1088 for

(

size_t i

= 0;

< seqs.size(); ++

) {

1093

all_tse.push_back(tse);

1094 if

( !parent_tse[

].AddUsedTSE(tse) ) {

1116 catch

(exception&) {

1141 for

(

size_t i

= 1; ; ++

) {

1167 if

( loc.

IsInt

() ) {

1169 if

( locint.

GetFrom

() == 0 &&

1190 for

(

size_t i

= 1; ; ++

) {

1361 const bool

is_unknown_len = (

1382 switch

( loc.

Which

() ) {

1411 "e_Bond is not allowed as a reference type"

);

1414 "e_Feat is not allowed as a reference type"

);

1417 "invalid reference type"

);

1424 switch

( seq.

Which

() ) {

1433 "Can not add empty Delta-seq"

);

1465 "SeqMap segment crosses split chunk boundary"

);

1469 "split chunk covers bad SeqMap segment"

);

1499 if

( single_segment && !inst.

IsSetExt

() ) {

1509 if

( single_segment && !inst.

IsSetExt

() ) {

1520

CSeg_ext::Tdata::iterator iter =

data

.begin();

1525 if

( iter ==

data

.end() ) {

1555

CDelta_ext::Tdata::iterator iter =

delta

.begin();

1559 if

( iter ==

delta

.end() ) {

User-defined methods of the data storage class.

bool IsReverse(ENa_strand s)

User-defined methods of the data storage class.

int GetSequenceClass(void) const

TSeqPos GetBioseqLength(void) const

void x_SetChangedSeqMap(void)

bool CanBeEdited(void) const

SeqMap related exceptions.

TSeqPos GetLength(void) const

TChunkId GetChunkId(void) const

const CTSE_Split_Info & GetSplitInfo(void) const

bool NotLoaded(void) const

CDataSource & GetDataSource(void) const

const CTSE_Info & GetTSE_Info(void) const

CConstRef< CBioseq_Info > FindBioseq(const CSeq_id_Handle &id) const

CConstRef< CBioseq_Info > FindMatchingBioseq(const CSeq_id_Handle &id) const

CDataLoader & GetDataLoader(void) const

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#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.

CConstRef< CSeq_id > GetSeqId(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.

TBioseqHandles GetBioseqHandles(const TIds &ids)

Get bioseq handles for all ids.

virtual void GetChunks(const TChunkSet &chunks)

vector< TChunk > TChunkSet

TSeqPos GetBioseqLength(void) const

TMol GetSequenceType(void) const

const CBioseq_Info & x_GetInfo(void) const

const CSeqMap & GetSeqMap(void) const

Get sequence map.

SSeqMapSelector & SetResolveCount(size_t res_cnt)

Set max depth of resolving seq-map.

const CSeqMap::CSegment & x_GetSegment(void) const

void AddUsedTSE(const CTSE_Handle &tse) const

SSeqMapSelector m_Selector

const TSegmentInfo & x_GetSegmentInfo(void) const

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

const CSeqMap & x_GetSeqMap(void) const

CSeqMap::ESegmentType GetType(void) const

SSeqMapSelector & SetRange(TSeqPos start, TSeqPos length)

Set range for iterator.

CSeq_id_Handle GetRefSeqid(void) const

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

size_t x_GetIndex(void) const

SSeqMapSelector & SetStrand(ENa_strand strand)

Set strand to iterate over.

TSeqPos GetPosition(void) const

return position of current segment in sequence

TSeqPos GetLength(void) const

return length of current segment

bool x_HasLimitTSE(void) const

void x_SetSubSeqMap(size_t index, CSeqMap_Delta_seqs *subMap)

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

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

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

atomic< TSeqPos > m_SeqLength

CSeqMap_CI End(CScope *scope) const

size_t CountSegmentsOfType(ESegmentType type) const

const_iterator begin(CScope *scope) const

STL style methods.

const_iterator end(CScope *scope) const

void x_GetSegmentException(size_t index) const

void x_SetSegmentData(size_t index, TSeqPos length, CSeq_data &data)

void SetSegmentGap(const CSeqMap_CI &seg, TSeqPos length)

void x_LoadObject(const CSegment &seg) const

CConstRef< CSeqMap > x_GetSubSeqMap(const CSegment &seg, CScope *scope, bool resolveExternal=false) const

const CBioseq_Info & x_GetBioseqInfo(const CSegment &seg, CScope *scope) const

void x_AddGap(TSeqPos len, bool unknown_len)

size_t x_FindSegment(TSeqPos position, CScope *scope) const

CSegment(ESegmentType seg_type=eSeqEnd, TSeqPos length=kInvalidSeqPos, bool unknown_len=false)

TSeqPos x_ResolveSegmentPosition(size_t index, CScope *scope) const

atomic< TSeqPos > m_Position

void x_SetSegmentGap(size_t index, TSeqPos length, CSeq_data *gap_data=0)

atomic< THasSegments > m_HasSegments

CSeqMap_CI BeginResolved(CScope *scope) const

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

atomic< size_t > m_Resolved

void x_SetChanged(size_t index)

CSegment & x_SetSegment(size_t index)

int x_GetSequenceClass(void) const

const CSegment & x_GetSegment(size_t index) const

const CObject * x_GetObject(const CSegment &seg) const

static CRef< CSeqMap > CreateSeqMapForSeq_loc(const CSeq_loc &loc, CScope *scope)

size_t x_GetLastEndSegmentIndex(void) const

void x_SetObject(CSegment &seg, const CObject &obj)

CSeqMap_CI Begin(CScope *scope) const

NCBI style methods.

void x_SetChunk(CSegment &seg, CTSE_Chunk_Info &chunk)

CSeqMap_CI FindSegment(TSeqPos pos, CScope *scope) const

Find segment containing the position.

vector< CSegment > m_Segments

CRef< CSeqMap > CloneFor(const CBioseq &seq) const

CSeqMap_CI FindResolved(CScope *scope, TSeqPos pos, const SSeqMapSelector &selector) 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

bool HasSegmentOfType(ESegmentType type) const

void x_AddSegment(ESegmentType type, TSeqPos len, bool unknown_len=false)

void x_StartEditing(void)

static CConstRef< CSeqMap > GetSeqMapForSeq_loc(const CSeq_loc &loc, CScope *scope)

void SetRegionInChunk(CTSE_Chunk_Info &chunk, TSeqPos pos, TSeqPos length)

void x_Add(CSeqMap *submap)

bool x_GetRefMinusStrand(const CSegment &seg) const

void LoadSeq_data(TSeqPos pos, TSeqPos len, const CSeq_data &data)

vector< CSegment > TSegments

void SetRepr(CSeq_inst::TRepr repr)

CSeqMap_CI RemoveSegment(const CSeqMap_CI &seg)

Delete segment from sequence map.

CSeqMap_CI ResolvedRangeIterator(CScope *scope, TSeqPos from, TSeqPos length, ENa_strand strand=eNa_strand_plus, size_t maxResolve=size_t(-1), TFlags flags=fDefaultFlags) const

Iterate segments in the range with specified strand coordinates.

static CRef< CSeqMap > CreateSeqMapForBioseq(const CBioseq &seq)

CConstRef< CObject > m_RefObject

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

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

CRef< CTSE_Chunk_Info > x_GetChunkToLoad(const CSegment &seg) const

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_id & x_GetRefSeqid(const CSegment &seg) const

bool x_DoUpdateSeq_inst(CSeq_inst &inst)

void x_SetSegmentRef(size_t index, TSeqPos length, const CSeq_id &ref_id, TSeqPos ref_pos, bool ref_minus_strand)

void x_AddUnloadedSeq_data(TSeqPos len)

CSegment & operator=(const CSegment &seg)

TSeqPos x_GetRefPosition(const CSegment &seg) const

void SetMol(CSeq_inst::TMol mol)

const CSeq_data & x_GetSeq_data(const CSegment &seg) const

void x_SetSeq_data(size_t index, CSeq_data &data)

size_t GetSegmentsCount(void) const

CSeqMap_CI EndResolved(CScope *scope) const

TSeqPos x_ResolveSegmentLength(size_t index, CScope *scope) const

@ eSeqData

real sequence data

@ eSeqLiteral

used only in m_ObjType for gap segments

@ eSeqRef

reference to Bioseq

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

#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.

CTempString literal(const char(&str)[Size])

Templatized initialization from a string literal.

bool IsLim(void) const

Check if variant Lim is selected.

TLim GetLim(void) const

Get the variant data.

void SetTo(TTo value)

Assign a value to To data member.

void ResetFuzz_to(void)

Reset Fuzz_to data member.

list< CRef< CSeq_interval > > Tdata

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

TStrand GetStrand(void) const

Get the Strand member data.

const TId & GetId(void) const

Get the Id member data.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

const TWhole & GetWhole(void) const

Get the variant data.

void SetId(TId &value)

Assign a value to Id data member.

bool IsSetStrand(void) const

Check if a value has been assigned to Strand data member.

TFrom GetFrom(void) const

Get the From member data.

list< CRef< CSeq_loc > > Tdata

E_Choice Which(void) const

Which variant is currently selected.

const TId & GetId(void) const

Get the Id member data.

const TId & GetId(void) const

Get the Id member data.

void SetFrom(TFrom value)

Assign a value to From data member.

TStrand GetStrand(void) const

Get the Strand member data.

const Tdata & Get(void) const

Get the member data.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

void ResetFuzz_from(void)

Reset Fuzz_from data member.

const TEquiv & GetEquiv(void) const

Get the variant data.

list< CRef< CSeq_loc > > Tdata

vector< TSeqPos > TPoints

bool IsSetStrand(void) const

Check if a value has been assigned to Strand data member.

bool IsSetStrand(void) const

Check if a value has been assigned to Strand data member.

const TPoints & GetPoints(void) const

Get the Points member data.

TStrand GetStrand(void) const

Get the Strand member data.

TTo GetTo(void) const

Get the To member data.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

void SetStrand(TStrand value)

Assign a value to Strand data member.

void ResetStrand(void)

Reset Strand data member.

const TMix & GetMix(void) const

Get the variant data.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

@ e_not_set

No variant selected.

@ e_Equiv

equivalent sets of locations

@ e_Empty

to NULL one Seq-id in a collection

@ e_Feat

indirect, through a Seq-feat

TLiteral & SetLiteral(void)

Select the variant.

TRepr GetRepr(void) const

Get the Repr member data.

void SetLength(TLength value)

Assign a value to Length data member.

const TSeg & GetSeg(void) const

Get the variant data.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

ERepr

representation class

const TInst & GetInst(void) const

Get the Inst member data.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

TLoc & SetLoc(void)

Select the variant.

void SetExt(TExt &value)

Assign a value to Ext data member.

bool IsSetMol(void) const

Check if a value has been assigned to Mol data member.

const TLiteral & GetLiteral(void) const

Get the variant data.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

TLength GetLength(void) const

Get the Length member data.

TLength GetLength(void) const

Get the Length member data.

bool IsSeg(void) const

Check if variant Seg is selected.

const TFuzz & GetFuzz(void) const

Get the Fuzz member data.

TMol GetMol(void) const

Get the Mol member data.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

bool IsSetLength(void) const

length of sequence in residues Check if a value has been assigned to Length data member.

const TExt & GetExt(void) const

Get the Ext member data.

E_Choice Which(void) const

Which variant is currently selected.

EMol

molecule class in living organism

E_Choice Which(void) const

Which variant is currently selected.

const TDelta & GetDelta(void) const

Get the variant data.

const TLoc & GetLoc(void) const

Get the variant data.

void SetRepr(TRepr value)

Assign a value to Repr data member.

bool CanGetFuzz(void) const

Check if it is safe to call GetFuzz method.

const Tdata & Get(void) const

Get the member data.

bool IsSetSeq_data(void) const

may have the data Check if a value has been assigned to Seq_data data member.

void SetLength(TLength value)

Assign a value to Length data member.

list< CRef< CDelta_seq > > Tdata

const Tdata & Get(void) const

Get the member data.

bool IsGap(void) const

Check if variant Gap is selected.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

void ResetExt(void)

Reset Ext data member.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

list< CRef< CSeq_loc > > Tdata

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

const TRef & GetRef(void) const

Get the variant data.

void ResetFuzz(void)

Reset Fuzz data member.

void ResetSeq_data(void)

Reset Seq_data data member.

void ResetSeq_data(void)

Reset Seq_data data member.

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_map

ordered map of any kind

@ eRepr_virtual

no seq data

@ e_Seg

segmented sequences

@ e_Map

ordered map of markers

@ e_Ref

hot link to another sequence (a view)

@ eMol_not_set

> cdna = rna

@ e_Literal

a piece of sequence

@ e_Loc

point to a sequence

const TYPE & Get(const CNamedParameterList *param)

constexpr auto sort(_Init &&init)

double value_type

The numeric datatype used by the parser.

Int4 delta(size_t dimension_, const Int4 *score_)

Selector used in CSeqMap methods returning iterators.

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