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NCBI C++ ToolKit: include/objects/seq/seq_loc_mapper_base.hpp Source File

GoodSrcId(

&

)

;

{

m_Dst_id_Handle; }

Map_Strand(

is_set_strand,

x_Map_Fuzz(

& fuzz)

;

ext_to =

,

( rg.

() ) {

m_Ranges.push_back(offset_rg);

m_TotalRange.CombineWith(offset_rg);

GetAlign_Dense_seg_TotalRange(

)

;

GetAlign_Sparse_ToFirst(

)

;

GetAlign_Sparse_ToSecond(

)

;

GetMapSingleLevel(

)

;

GetTrimMappedLocation(

)

;

x_IsSetOption(

opt)

;

x_SetOption(

opt,

enable);

fAlign_Dense_seg_TotalRange = 1 << 0,

fAlign_Sparse_ToFirst = 0,

fAlign_Sparse_ToSecond = 1 << 1,

fMapSingleLevel = 1 << 2,

fTrimMappedLocation = 1 << 3

eSplicedRow_Prod = 0,

fFuzzOption_CStyle = 1 << 0,

fFuzzOption_RemoveLimTlOrTr = 1 << 1

fAnnotMap_Location = 1 << 0,

fAnnotMap_Product = 1 << 1,

fAnnotMap_Both = fAnnotMap_Location | fAnnotMap_Product,

fAnnotMap_RemoveNonMapping = 1 << 2,

fAnnotMap_ThrowOnFailure = 1 << 3,

fAnnotMap_Default = fAnnotMap_Both

LastIsPartial(

);

InitAlignMapper(

& src_align);

x_InitializeFeat(

& map_feat,

EFeatMapDirection dir);

x_InitializeAlign(

& map_align,

* from_id =

);

x_InitializeAlign(

& map_align,

TSynonyms& to_ids,

TSynonyms* from_ids =

);

x_InitializeAlign(

& map_align,

from_row =

(-1));

x_PreserveDestinationLocs(

);

x_NextMappingRange(

& src_id,

x_AddConversion(

& src_id,

x_MapSeq_loc(

& src_loc);

x_PushRangesToDstMix(

);

: range(rg), fuzz(fz), group(grp) {}

range < rg.

;

x_CheckSeqTypes(

& loc,

ESeqType x_ForceSeqTypes(

& loc)

;

x_InitAlign(

& diag,

to_row,

from_row);

x_InitAlign(

& denseg,

to_row,

from_row);

x_InitAlign(

& sseg,

to_row);

x_InitAlign(

& pseg,

to_row,

from_row);

TSynonyms& to_ids);

x_InitSpliced(

& spliced, ESplicedRow to_row);

x_InitSparse(

& sparse,

to_row);

x_AddExonPartsMapping(

& mapping_len,

x_MapNextRange(

& src_rg,

TRangeFuzz& src_fuzz,

TSortedMappings& mappings,

x_MapInterval(

& src_id,

TRangeFuzz orig_fuzz);

x_SetLastTruncated(

);

x_PushNullLoc(

);

strand_idx)

;

TRangeFuzz& fuzz,

x_ReverseRangeOrder(

)

;

x_IsSynonym(

&

,

TSynonyms& synonyms)

;

fTrimSplicedSegs = 1 << 0,

fKeepNonmapping = 1 << 1,

fCheckStrand = 1 << 2,

fIncludeSrcLocs = 1 << 3,

fMixedAlignsAsSpliced = 1 << 4,

fErrorOnPartial = 1 << 5

x_SetMiscFlag(EMiscFlags flag,

);

GetWidthById(

&

)

;

CollectSynonyms(

&

, TSynonyms& synonyms)

;

GetNonMappingAsNull(

);

SetLoc(

& loc);

* GetFeat(

)

;

ResetObject(

);

(x->m_Src_from != y->m_Src_from) {

x->m_Src_from < y->m_Src_from;

(x->m_Src_to != y->m_Src_to) {

x->m_Src_to > y->m_Src_to;

(x->m_Src_to != y->m_Src_to) {

x->m_Src_to > y->m_Src_to;

(x->m_Src_from != y->m_Src_from) {

x->m_Src_from < y->m_Src_from;

: m_SeqInfo(0), m_Options(0) {}

: m_SeqInfo(seq_info), m_Options(opts) {}

: m_SeqInfo(0), m_Options(opts) {}

User-defined methods of the data storage class.

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

Helper class for mapping graphs.

CMappingRange - describes a single interval to interval mapping.

Storage for multiple mapping ranges.

Default IMessage implementation: text and severity only.

Class used to map seq-alignments.

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

CSeq_loc_Mapper_Base –.

CSeq_loc_Mapper_Options –.

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const char si[8][64]

std::ofstream out("events_result.xml")

main entry point for tests

static const char * str(char *buf, int n)

CRange< Position > Map(const CRange< Position > &target, const CRange< Position > &range)

unsigned int TSeqPos

Type for sequence locations and lengths.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

EDiagSev

Severity level for the posted diagnostics.

void Write(CObjectOStream &out, TConstObjectPtr object, const CTypeRef &type)

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.

CRef< IMapper_Sequence_Info > m_SeqInfo

pair< TFuzz, TFuzz > TRangeFuzz

TDstStrandMap m_DstRanges

CSeq_loc_Mapper_Options & SetMapperSequenceInfo(IMapper_Sequence_Info *seq_info)

CSeq_loc_Mapper_Base & SetErrorOnPartial(bool value=true)

Report source range trimming as an error.

void x_SetMiscFlag(EMiscFlags flag, bool value)

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

bool operator()(const CRef< CMappingRange > &x, const CRef< CMappingRange > &y) const

set< CSeq_id_Handle > TSynonyms

virtual void CollectSynonyms(const CSeq_id_Handle &id, TSynonyms &synonyms)=0

Collect all synonyms for the id including the id itself.

ESeqType GetSeqTypeById(const CSeq_id_Handle &idh) const

Methods for getting sequence types, use cached types (m_SeqTypes) if possible.

TRangeMap::const_iterator TRangeIterator

CRef< CGraphRanges > m_GraphRanges

bool operator<(const SMappedRange &rg) const

CSeq_loc_Mapper_Base & TruncateNonmappingRanges(void)

map< CSeq_id_Handle, TRangeMap > TIdMap

EMapResult

Result of seq-annot mapping.

CSeq_id_Handle m_Dst_id_Handle

void AddRange(const TRange &rg)

const CSeq_id_Handle & GetDstIdHandle(void) const

CSeq_align::C_Segs::TDendiag TDendiag

CSeq_loc_Mapper_Options(void)

list< SMappedRange > TMappedRanges

const TIdMap & GetIdMap() const

TSeqPos GetLength(void) const

CSeq_loc_Mapper_Options & SetTrimMappedLocation(bool value=true)

ESplicedRow

Spliced-seg row indexing constants.

bool operator()(const CRef< CMappingRange > &x, const CRef< CMappingRange > &y) const

IMapper_Sequence_Info * GetMapperSequenceInfo(void) const

Sequence type, length etc.

CMappingRanges::TRangeIterator TRangeIterator

FAnnotMapFlag

Flags defining seq-annot mapping options.

virtual TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)=0

Get sequence length or kInvalidSeqPos.

bool GetTrimMappedLocation(void) const

Mapped location trimming at sequence end.

void SetSeqTypeById(const CSeq_id_Handle &idh, ESeqType seqtype) const

Methods for setting sequence types.

CSeq_loc_Mapper_Base & SetGapPreserve(void)

Whether to preserve or remove NULL sub-locations (usually indicating gaps) from the result.

EFeatMapDirection

Mapping direction used when initializing the mapper with a feature.

vector< TMappedRanges > TRangesByStrand

CRangeMultimap< CRef< CMappingRange >, TSeqPos > TRangeMap

CSeq_loc_Mapper_Options m_MapOptions

const CSeq_id_Handle & CollectSynonyms(const CSeq_id_Handle &id) const

map< CSeq_id_Handle, TDstRanges > TDstIdMap

CSeq_loc_Mapper_Base & SetMergeNone(void)

Intervals' merging mode MergeNone and MergeAbutting do not change the order of ranges in the destinat...

CSeq_loc_Mapper_Base & SetTrimSplicedSeg(bool trim)

For mapping spliced-segs only: preserve or trim starting/ending indels.

EMapOptions

Options for interpretations of locations.

void SetReverseSrc(bool value=true)

CSeq_loc_Mapper_Options & SetAlign_Sparse_ToFirst(bool value=true)

CSeq_align::C_Segs::TStd TStd

bool GoodSrcId(const CSeq_id &id) const

Check if the id is on the source sequence.

TSeqPos GetDst_from(void) const

void SetReverseDst(bool value=true)

CSeq_loc_Mapper_Options & SetAlign_Dense_seg_TotalRange(bool value=true)

EObjectType Which(void) const

Check type of the object stored in the message.

list< TRange > TDstRanges

map< CSeq_id_Handle, CSeq_id_Handle > TSynonymMap

vector< CRef< CMappingRange > > TSortedMappings

bool x_IsSetOption(int opt) const

CSeq_loc_Mapper_Base::ESeqType TSeqType

bool GetAlign_Dense_seg_TotalRange(void) const

Dense-seg mapping option.

CSeq_loc_Mapper_Base & SetMergeAbutting(void)

Merge only abutting intervals, keep overlapping.

int GetWidthById(const CSeq_id_Handle &idh) const

Get sequence width.

CMappingRange::TRange TRange

bool GetAlign_Sparse_ToFirst(void) const

Mapping direction when mapping through a sparse-seg.

CMappingRanges::TRangeMap TRangeMap

TSeqPos GetOffset(void) const

CSeq_loc_Mapper_Base & SetMergeContained(void)

Merge intervals only if one is completely covered by another.

bool GetReverseSrc(void) const

CRef< CSeq_loc > m_Dst_loc

void IncOffset(TSeqPos inc)

CSeq_loc_Mapper_Base & operator=(const CSeq_loc_Mapper_Base &)

bool x_IsSetMiscFlag(EMiscFlags flag) const

CSeq_loc_Mapper_Base & SetMergeAll(void)

Merge any abutting or overlapping intervals.

map< CSeq_id_Handle, TSeqPos > TLengthMap

bool LastIsPartial(void)

Check if the last mapping resulted in partial location (not all ranges from the original location cou...

const CMappingRanges & GetMappingRanges(void) const

Get mapping ranges.

bool GetReverseDst(void) const

bool GetReverse(void) const

CRef< CSeq_loc > m_SrcLocs

CSeq_loc_Mapper_Base & MixedAlignsAsSpliced(bool value=true)

When set to 'true' if mapped alignment has exactly one genomic and one protein row,...

CMappingRange::TRange TRange

vector< TRange > TGraphRanges

CRef< CSeq_align > x_MapSeq_align(const CSeq_align &src_align, size_t *row)

virtual TSeqType GetSequenceType(const CSeq_id_Handle &idh)=0

Get information about sequence type (nuc or prot).

CSeq_loc_Mapper_Base & SetCheckStrand(bool value=true)

Check strands before mapping a range.

CRef< CMappingRanges > m_Mappings

const TGraphRanges & GetRanges(void) const

TSeqPos GetSrc_from(void) const

CSeq_loc_Mapper_Base & SetMergeBySeg(void)

Merge only intervals from the same group.

SMappedRange(const TRange &rg, const TRangeFuzz &fz, int grp=0)

TIdMap::const_iterator TIdIterator

ESeqType GetSeqType(const CSeq_id_Handle &idh) const

CMappingRanges::TSortedMappings TSortedMappings

CSeq_id_Handle m_Src_id_Handle

map< CSeq_id_Handle, ESeqType > TSeqTypeById

const TRange & GetTotalRange(void) const

map< CSeq_id_Handle, TRangesByStrand > TRangesById

CSeq_loc_Mapper_Options & SetMapSingleLevel(bool value=true)

CSeq_loc_Mapper_Base & SetGapRemove(void)

bool GetAlign_Sparse_ToSecond(void) const

pair< TFuzz, TFuzz > TRangeFuzz

CSeq_loc_Mapper_Base & KeepNonmappingRanges(void)

Keep ranges which can not be mapped.

void x_SetOption(int opt, bool enable)

CSeq_loc_Mapper_Base(const CSeq_loc_Mapper_Base &)

CSeq_loc_Mapper_Base & IncludeSourceLocs(bool value=true)

Include source ranges in the mapped location.

vector< TDstIdMap > TDstStrandMap

CSeq_loc_Mapper_Options & SetAlign_Sparse_ToSecond(bool value=true)

CRef< CSeq_id > GetDstId(void) const

bool GetMapSingleLevel(void) const

Mapping depth when using a seq-map, a bioseq or a GC-assembly.

void SetOffset(TSeqPos offset)

CSeq_loc_Mapper_Base::TSynonyms TSynonyms

@ eMapped_Some

Some (not all) annotations were mapped.

@ eLocationToProduct

Map from the feature's location to product.

@ fAlign_Dense_seg_TotalRange

Ignore internal dense-seg structure - map each dense-seg according to the total ranges involved.

@ fTrimMappedLocation

Enable trimming of source/destination ranges at sequence end.

@ fMapSingleLevel

Flag used when mapping through a seq-map (this includes mapping through a bioseq or a GC-assembly).

@ fAlign_Sparse_ToSecond

Map to second-id.

CRef< C > Ref(C *object)

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

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

list< CRef< CStd_seg > > TStd

list< CRef< CSpliced_exon_chunk > > TParts

list< CRef< CDense_diag > > TDendiag

ENa_strand

strand of nucleic acid

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

IMessage/IMessageListener interfaces and basic implementations.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

int GetLoc(const string &acc, const string &pat, CSeq_loc &loc, CScope &scope)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

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