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

( !top_level_id ) {

( !syns->empty() ) {

top_level_id = syns->GetSeq_id_Handle(syns->begin()).GetSeqId();

( !syns->empty() ) {

top_id = syns->GetSeq_id_Handle(syns->begin()).GetSeqId();

src_from, src_len, dst_from, dst_len;

src_from, src_len, src_strand,

dst_from, dst_len, dst_strand);

dst_from = top_ref_start + shift;

src_from, src_len, src_strand,

dst_from, dst_len, dst_strand);

src_from, src_len, dst_from, dst_len;

list<CSeqMap_CI> refs;

refs.push_back(seg_it);

(refs.empty() || refs.back().GetDepth() < seg_it.

()) {

refs.push_back(seg_it);

( !refs.empty() ) {

src_from =

.GetPosition();

src_len =

.GetLength();

dst_from =

.GetRefPosition();

*

.GetRefSeqid().GetSeqId(),

dst_from, dst_len, dst_strand);

(list<CSeqMap_CI>, it, refs) {

shift =

.GetPosition() - it->GetPosition();

src_from = it->GetRefPosition() + shift;

src_len =

.GetLength();

dst_from =

.GetRefPosition();

*it->GetRefSeqid().GetSeqId(),

src_from, src_len, src_strand,

*

.GetRefSeqid().GetSeqId(),

dst_from, dst_len, dst_strand);

( !refs.empty() && refs.back().GetDepth() >= seg_it.

()) {

refs.push_back(seg_it);

seg_from, seg_len, ref_from, ref_len;

list<CSeqMap_CI> refs;

refs.push_back(seg_it);

(refs.empty() || refs.back().GetDepth() < seg_it.

()) {

refs.push_back(seg_it);

( !refs.empty() ) {

( !refs.empty() ) {

seg_from, seg_len, seg_strand,

ref_from, ref_len, ref_strand);

ref_from, ref_len, ref_strand,

seg_from, seg_len, seg_strand);

( refs.empty() ) {

ref_from, ref_len, ref_strand);

ref_from, ref_len, ref_strand,

seg_from, seg_len, seg_strand);

refs.push_back(seg_it);

syn_id->

(*syn->GetSeqId());

bioseq->

().push_back(syn_id);

( gc_assembly.

() ) {

.IsLocal() &&

.GetLocal().IsStr() &&

.GetLocal().GetStr().find(

) != string::npos;

( gc_id.

() ) {

(

.Which() ) {

.GetGenbank().IsSetGi() ?

&

.GetGenbank().GetGi() : &

.GetGenbank().GetPublic();

&

.GetGenbank().GetPublic();

.GetRefseq().IsSetGi() ?

&

.GetRefseq().GetGi() : &

.GetRefseq().GetPublic();

&

.GetRefseq().GetPublic();

.GetExternal().GetExternal() ==

) {

&

.GetExternal().GetId();

&

.GetPrivate();

( dst_id )

;

(

.Which() ) {

(

.GetGenbank().IsSetGi() && dst_id != &

.GetGenbank().GetGi()) {

(dst_id != &

.GetGenbank().GetPublic()) {

(

.GetGenbank().IsSetGpipe() ) {

(

.GetRefseq().IsSetGi() && dst_id != &

.GetRefseq().GetGi()) {

(dst_id != &

.GetRefseq().GetPublic()) {

(

.GetRefseq().IsSetGpipe() ) {

(

.GetPrivate().IsLocal())

;

(dst_id != &

.GetPrivate()) {

(dst_id != &

.GetExternal().

()) {

);

, 0, hlen, hlen);

( (*it)->IsLiteral() ) {

chr_pos += (*it)->GetLiteral().GetLength();

( !(*it)->IsLoc() ) {

(; loc_it; ++loc_it) {

( loc_it.

() )

;

( to_alias ) {

seg_pos, seg_len, seg_str,

*chr_id, chr_pos, chr_len,

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.

Seq-loc and seq-align mapper exceptions.

the sequence(s) representing this molecule in the case of 2L and 2R - the molecule is represented by ...

bool CanGetLength() const

Is the length statistic available?

TSeqPos GetLength() const

return the length of this sequence.

CScope * GetScopeOrNull(void) const

CScope & GetScope(void) const

Storage for multiple mapping ranges.

CScope_Mapper_Sequence_Info(CScope *scope)

virtual TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

Get sequence length or kInvalidSeqPos.

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

Collect all synonyms for the id including the id itself.

virtual TSeqType GetSequenceType(const CSeq_id_Handle &idh)

Get information about sequence type (nuc or prot).

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 –.

static CSeq_id_Handle GetSeq_id_Handle(const const_iterator &iter)

iterator_bool insert(const value_type &val)

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.

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.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

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.

bool IsSetStrand(void) const

Get strand.

bool IsEmpty(void) const

True if the current location is empty.

TRange GetRange(void) const

Get the range.

ENa_strand GetStrand(void) const

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

void x_InitializeAlign(const CSeq_align &map_align, const CSeq_id &to_id, const CSeq_id *from_id=nullptr)

TDstStrandMap m_DstRanges

CSeq_loc_Mapper_Options & SetMapperSequenceInfo(IMapper_Sequence_Info *seq_info)

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

IMapper_Sequence_Info * GetMapperSequenceInfo(void) const

Sequence type, length etc.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

EGCAssemblyAlias

Destination of seq-id mapping through a GC-Assembly.

EScopeFlag

Using CScope for virtual bioseqs created from GC-Assemblies.

void x_InitializeFeat(const CSeq_feat &map_feat, EFeatMapDirection dir)

EFeatMapDirection

Mapping direction used when initializing the mapper with a feature.

CSeq_loc_Mapper_Options m_MapOptions

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void x_NextMappingRange(const CSeq_id &src_id, TSeqPos &src_start, TSeqPos &src_len, ENa_strand src_strand, const CSeq_id &dst_id, TSeqPos &dst_start, TSeqPos &dst_len, ENa_strand dst_strand, const CInt_fuzz *fuzz_from=0, const CInt_fuzz *fuzz_to=0, int frame=0, TSeqPos src_bioseq_len=kInvalidSeqPos)

virtual CSeq_align_Mapper_Base * InitAlignMapper(const CSeq_align &src_align)

void x_InitGCAssembly(const CGC_Assembly &gc_assembly, EGCAssemblyAlias to_alias)

CRef< CSeq_entry > GetTSE(void) const

Create seq-entry with all parsed sequences, annotations etc.

CSeq_inst::TMol GetSequenceType(const CSeq_id &id, TGetFlags flags=0)

Get molecular type of sequence (protein/dna/rna) Return CSeq_inst::eMol_not_set if sequence is not fo...

const TSeqIds & GetTopLevelSequences(void) const

Get seq-ids for all top-level sequences in the assembly.

void x_InitializeSeqMapUp(CSeqMap_CI seg_it, const CSeq_id *top_id)

CSeq_loc_Mapper(CMappingRanges *mapping_ranges, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())

Mapping through a pre-filled CMappipngRanges.

void x_InitializeLocs(const CSeq_loc &source, const CSeq_loc &target, int src_frame=0, int dst_frame=0)

CConstRef< CSynonymsSet > GetSynonyms(const CSeq_id &id)

Get bioseq synonyms, resolving to the bioseq in this scope.

bool x_IsUCSCRandomChr(const CGC_Sequence &gc_seq, CConstRef< CSeq_id > &chr_id, TSynonyms &synonyms) const

void x_PreserveDestinationLocs(void)

CBioseq_Handle x_AddVirtualBioseq(const TSynonyms &synonyms, const CGC_Sequence &gc_seq)

void AddScope(CScope &scope, TPriority pri=kPriority_Default)

Add the scope's datasources as a single group with the given priority All data sources (data loaders ...

void x_InitializeSeqMap(const CSeqMap &seq_map, const CSeq_id *top_id, ESeqMapDirection direction)

void x_InitializeSeqMapDown(CSeqMap_CI seg_it, const CSeq_id *top_id)

void x_AddConversion(const CSeq_id &src_id, TSeqPos src_start, ENa_strand src_strand, const CSeq_id &dst_id, TSeqPos dst_start, ENa_strand dst_strand, TSeqPos length, bool ext_right, int frame, TSeqPos src_bioseq_len, TSeqPos dst_length)

void x_InitializeSeqMapSingleLevel(CSeqMap_CI seg_it, const CSeq_id *top_id, ESeqMapDirection direction)

bool GetMapSingleLevel(void) const

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

void x_InitGCSequence(const CGC_Sequence &gc_seq, EGCAssemblyAlias to_alias)

@ eGCA_Genbank

Map to GenBank alias, prefer GI.

@ eGCA_UCSC

Map to UCSC alias.

@ eGCA_Refseq

Map to RefSeq alias, prefer GI.

@ eGCA_Other

Map to 'private' seq-id.

@ eGCA_GenbankAcc

Map to GenBank alias, prefer acc.ver.

@ eGCA_RefseqAcc

Map to RefSeq alias, prefer acc.ver.

@ eCopyScope

Create a new scope for virtual bioseqs.

@ eSeqMap_Down

map from a segmented bioseq to segments

@ eSeqMap_Up

map from segments to the top level bioseq

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

TSeqPos GetBioseqLength(void) const

bool CanGetInst_Length(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

TInst_Length GetInst_Length(void) const

const CSeqMap & GetSeqMap(void) const

Get sequence map.

CConstRef< CSynonymsSet > GetSynonyms(void) const

Get the bioseq's synonyms.

SSeqMapSelector & SetLinkUsedTSE(bool link=true)

TSeqPos GetRefPosition(void) const

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

bool GetRefMinusStrand(void) const

CSeq_id_Handle GetRefSeqid(void) const

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

TSeqPos GetPosition(void) const

return position of current segment in sequence

TSeqPos GetLength(void) const

return length of current segment

size_t GetDepth(void) const

return the depth of current segment

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

void Reset(void)

Reset reference object.

TObjectType * GetPointerOrNull(void) const THROWS_NONE

Get pointer value.

position_type GetLength(void) const

static position_type GetWholeLength(void)

static TThisType GetWhole(void)

#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.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

TFrom GetFrom(void) const

Get the From member data.

const TStr & GetStr(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

const TGenbank & GetGenbank(void) const

Get the variant data.

list< CRef< CGC_Sequence > > TSeqs

const TId & GetId(void) const

Get the Id member data.

const TUnit & GetUnit(void) const

Get the variant data.

const TStructure & GetStructure(void) const

Get the Structure member data.

bool IsSingle(void) const

Check if variant Single is selected.

const TGi & GetGi(void) const

Get the Gi member data.

const TRefseq & GetRefseq(void) const

Get the variant data.

bool IsSetMols(void) const

collections of molecules for this assembly Check if a value has been assigned to Mols data member.

const TPrivate & GetPrivate(void) const

Get the variant data.

list< CRef< CGC_TypedSeqId > > TSeq_id_synonyms

bool IsAssembly_set(void) const

Check if variant Assembly_set is selected.

bool IsSetMore_assemblies(void) const

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

bool IsSetOther_sequences(void) const

On primary assembly-unit: here will be the unplaced sequences On alt-loci: list of sequences aligned/...

const TOther_sequences & GetOther_sequences(void) const

Get the Other_sequences member data.

const TPrimary_assembly & GetPrimary_assembly(void) const

Get the Primary_assembly member data.

bool IsSetStructure(void) const

locations of ordered scaffolds/components Check if a value has been assigned to Structure data member...

E_Choice Which(void) const

Which variant is currently selected.

const TExternal & GetExternal(void) const

Get the variant data.

const TSeq_id_synonyms & GetSeq_id_synonyms(void) const

Get the Seq_id_synonyms member data.

bool IsSetGi(void) const

optional since not all sequences have GIs Similarity: relationship between this synonym to main seqid...

list< CRef< CGC_TaggedSequences > > TSequences

const TAssembly_set & GetAssembly_set(void) const

Get the variant data.

const TMols & GetMols(void) const

Get the Mols member data.

list< CRef< CGC_Replicon > > TMols

bool IsSetSequences(void) const

placed: populated both on chromosome and scaffold levels unlocalized: populated on chromosome level C...

const TSequences & GetSequences(void) const

Get the Sequences member data.

bool IsUnit(void) const

Check if variant Unit is selected.

list< CRef< CGC_Assembly > > TMore_assemblies

list< CRef< CGC_Sequence > > TSet

const TSingle & GetSingle(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

const TMore_assemblies & GetMore_assemblies(void) const

Get the More_assemblies member data.

bool IsSetSeq_id_synonyms(void) const

Other known identifiers: Local / gpipe-satellite / genbank / refseq Check if a value has been assigne...

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

ENa_strand

strand of nucleic acid

TLocal & SetLocal(void)

Select the variant.

const TLocal & GetLocal(void) const

Get the variant data.

TId & SetId(void)

Assign a value to Id data member.

void SetInst(TInst &value)

Assign a value to Inst data member.

const Tdata & Get(void) const

Get the member data.

list< CRef< CDelta_seq > > Tdata

@ eRepr_virtual

no seq data

@ eMol_na

just a nucleic acid

const CharType(& source)[N]

CSeq_loc_Mapper_Options & SetOptionsScope(CSeq_loc_Mapper_Options &options, CScope *scope)

ENa_strand s_IndexToStrand(size_t idx)

bool s_IsLocalRandomChrId(const CSeq_id &id)

const CSeq_id * s_GetSeqIdAlias(const CGC_TypedSeqId &id, CSeq_loc_Mapper::EGCAssemblyAlias alias)

Uint4 GetSequenceType(const CBioseq_Handle &bsh)

Return a (corrected) set of flags identifying the sequence type.

Selector used in CSeqMap methods returning iterators.

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