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

( GetErrCode() ) {

eUnsupported:

;

eOtherError:

;

annot_copy->

(**annot);

entry.

().push_back(annot_copy);

( gc_assembly.

() ) {

(

.IsLoc() ) {

(delta_loc.

()) {

(tagged_seq.

().size() == 1) {

( it_id.

() ) {

);

(synonyms.

(struct_syn) != synonyms.

()) {

entry = parent_entry;

annot_copy->

(**annot);

entry->

().push_back(annot_copy);

syn_id->

(*syn->GetSeqId());

bioseq->

().push_back(syn_id);

bioseq->

().SetExt().SetDelta(

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.

@Seq_descr.hpp User-defined methods of the data storage class.

void SetDescr(CSeq_descr &value)

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

SQLRETURN desc_copy(TDS_DESC *dest, TDS_DESC *src)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

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

Set object to copy of another one.

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

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

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

void x_ParseGCSequence(const CGC_Sequence &gc_seq, const CGC_Sequence *parent_seq, CRef< CSeq_entry > parent_entry, CRef< CSeq_id > override_id)

CGC_Assembly_Parser(const CGC_Assembly &assembly, TParserFlags flags=fDefault)

Parse the assembly, convert it to seq-entry, collect additional information (top-level sequences etc)...

void x_InitSeq_entry(CRef< CSeq_entry > entry, CRef< CSeq_entry > parent)

void x_CopyData(const CGC_AssemblyDesc &assm_desc, CSeq_entry &entry)

void x_AddBioseq(CRef< CSeq_entry > parent_entry, const TSeqIds &synonyms, const CGC_Sequence &gc_seq)

virtual ~CGC_Assembly_Parser(void)

void x_ParseGCAssembly(const CGC_Assembly &gc_assembly, CRef< CSeq_entry > parent_entry)

@ fIgnoreLocalIds

Do not add local private and external ids to bioseqs.

@ fIgnoreAnnots

Do not add annotations to seq-entries and bioseqs.

@ fIgnoreExternalIds

Do not add external ids to bioseqs.

@ fIgnoreDescr

Do not add descriptions to seq-entries and bioseqs.

@ fSkipDuplicates

Skip duplicate sequences (all synonyms are checked).

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.

const TGenbank & GetGenbank(void) const

Get the variant data.

bool IsSetGpipe(void) const

the gpipe accession Check if a value has been assigned to Gpipe data member.

list< CRef< CSeq_annot > > TAnnot

const TDescr & GetDescr(void) const

Get the Descr member data.

list< CRef< CGC_Sequence > > TSeqs

const TId & GetId(void) const

Get the Id member data.

bool IsSetDescr(void) const

Various attributes assigned at this level: biosrc, comments, publications...

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.

list< CRef< CSeq_annot > > TAnnot

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetAnnot(void) const

in alt-loci units - contain alignment of this sequence to the primary unit Check if a value has been ...

bool IsSetDesc(void) const

descriptors live in a shared data block Check if a value has been assigned to Desc data member.

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 TDesc & GetDesc(void) const

Get the Desc member data.

const TOther_sequences & GetOther_sequences(void) const

Get the Other_sequences member data.

bool IsSetAnnot(void) const

Feature annotation; Contains Pseudo Autosomal regions on chromosomes and scaffolds in the following f...

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.

const TSeqs & GetSeqs(void) const

Get the Seqs member data.

const TAnnot & GetAnnot(void) const

Get the Annot 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.

bool IsSetDesc(void) const

descriptors live in a shared data block Check if a value has been assigned to Desc data member.

const TMols & GetMols(void) const

Get the Mols member data.

bool IsSetDescr(void) const

Various attributes assigned at this level: biosrc, comments, publications...

list< CRef< CGC_Replicon > > TMols

bool IsSetSequences(void) const

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

const TDescr & GetDescr(void) const

Get the Descr member data.

const TGpipe & GetGpipe(void) const

Get the Gpipe member data.

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 TPublic & GetPublic(void) const

Get the Public member data.

const TSet & GetSet(void) const

Get the variant data.

const TMore_assemblies & GetMore_assemblies(void) const

Get the More_assemblies member data.

const TAnnot & GetAnnot(void) const

Get the Annot 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.

@ eState_placed

exist only within a replicon. placed sequences on higher sequence

const TId & GetId(void) const

Get the Id member data.

const TWhole & GetWhole(void) const

Get the variant data.

TFrom GetFrom(void) const

Get the From member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsLocal(void) const

Check if variant Local is selected.

const TInt & GetInt(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

const TSet & GetSet(void) const

Get the variant data.

void SetLevel(TLevel value)

Assign a value to Level data member.

void SetClass(TClass value)

Assign a value to Class data member.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

TLevel GetLevel(void) const

Get the Level member data.

@ eClass_segset

segmented sequence + parts

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

const Tdata & Get(void) const

Get the member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

const Tdata & Get(void) const

Get the member data.

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_virtual

no seq data

@ eMol_na

just a nucleic acid

Definition of all error codes used in objmgr libraries (xobjmgr.lib, xobjutil.lib and others).

Int4 delta(size_t dimension_, const Int4 *score_)

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