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NCBI C++ ToolKit: src/objtools/readers/idmapper_gcassembly.cpp Source File

& alias_scope)

& alias_scope)

( src_id.

() ) {

txt_id = &acc_id.

();

txt_id = &acc_id.

();

txt_id = &acc_id.

();

txt_id = &acc_id.

();

txt_id = &acc_id.

();

& alias_scope)

((*it)->Which()) {

( (*it)->GetGenbank().IsSetGpipe() ) {

(map_to ==

&& (*it)->GetGenbank().IsSetGi()) {

( (*it)->GetRefseq().IsSetGpipe() ) {

(map_to ==

&& (*it)->GetRefseq().IsSetGi()) {

(map_to ==

&&

(*it)->GetExternal().GetExternal() ==

) {

((*it)->Which()) {

((*it)->GetPrivate().IsLocal()) {

(*it)->GetPrivate().GetLocal().GetStr();

.

(

+ s);

&

= (*it)->GetExternal().GetId();

+

(

.IsLocal() &&

.GetLocal().IsStr() &&

.GetLocal().GetStr().find(

) != string::npos &&

bioseq->

().push_back(chr_lcl);

bioseq->

().push_back(lcl);

( ; id_iter; ++id_iter) {

[idh].dest_mapper = mapper;

& alias_scope)

map_to, alias_scope);

& alias_scope)

map_to, alias_scope);

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.

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.

void x_AddUnversionedMapping(const CSeq_id &src_id, const CSeq_id_Handle &dst_id)

void AddAliasMappings(const CGC_Assembly &assm, EAliasMapping mapping, const string &alias_scope=kEmptyStr)

EAliasMapping

Mapping destination type.

@ eUCSC

External UCSC id.

@ eGenBankAcc

GenBank accession.

@ eAccVer

Find versioned accession.

@ eRefSeqAcc

RefSeq accession.

virtual CSeq_id_Handle Map(const CSeq_id_Handle &)

void x_AddAccessionMapping(const CSeq_id &id)

CIdMapperGCAssembly(CScope &scope, const CGC_Assembly &assm, EAliasMapping mapping, const string &alias_scope=kEmptyStr)

Establish mappings based on a GC-Assembly.

void x_AddAliasMappings(const CGC_Assembly &seq, EAliasMapping mapping, const string &alias_scope)

virtual CSeq_id_Handle Map(const CSeq_id_Handle &)

Map a single given CSeq_id_Handle to another.

static std::string MapErrorString(const CSeq_id_Handle &)

virtual void AddMapping(const CSeq_id_Handle &from, const CSeq_id_Handle &to)

Add a mapping to the internal mapping table.

Template class for iteration on objects of class C (non-medifiable version)

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

#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.

#define MSerial_AsnText

I/O stream manipulators –.

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

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

CSeq_id & Set(const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)

Reassign based on flat specifications; arguments interpreted as with constructors.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

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

Add bioseq, return bioseq handle.

@ eSeqMap_Down

map from a segmented bioseq to segments

@ eSeqMap_Up

map from segments to the top level bioseq

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string PrintableString(const CTempString str, TPrintableMode mode=fNewLine_Quote|fNonAscii_Passthru)

Get a printable version of the specified string.

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

Check if a string starts with a specified prefix value.

@ fNewLine_Quote

Display "\n" instead of actual linebreak.

TStr & SetStr(void)

Select the variant.

bool IsSetGpipe(void) const

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

list< CRef< CGC_Sequence > > TSeqs

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.

bool IsSetMols(void) const

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

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...

const TSeq_id_synonyms & GetSeq_id_synonyms(void) const

Get the Seq_id_synonyms member data.

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 TSequence & GetSequence(void) const

Get the Sequence 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.

bool IsSetSeq_id_synonyms(void) const

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

list< CRef< CGC_TaggedSequences > > TOther_sequences

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

TNamed_annot_track & SetNamed_annot_track(void)

Select the variant.

TEmbl & SetEmbl(void)

Select the variant.

TOther & SetOther(void)

Select the variant.

void ResetVersion(void)

Reset Version data member.

TTpe & SetTpe(void)

Select the variant.

TTpg & SetTpg(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

void ResetRelease(void)

Reset Release data member.

TPir & SetPir(void)

Select the variant.

TTpd & SetTpd(void)

Select the variant.

TGpipe & SetGpipe(void)

Select the variant.

TDdbj & SetDdbj(void)

Select the variant.

TLocal & SetLocal(void)

Select the variant.

void ResetName(void)

Reset Name data member.

TPrf & SetPrf(void)

Select the variant.

TGenbank & SetGenbank(void)

Select the variant.

TSwissprot & SetSwissprot(void)

Select the variant.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Gpipe

Internal NCBI genome pipeline processing ID.

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_Named_annot_track

Internal named annotation tracking ID.

@ e_Tpg

Third Party Annot/Seq Genbank.

TId & SetId(void)

Assign a value to Id data member.

void SetInst(TInst &value)

Assign a value to Inst data member.

@ eRepr_delta

sequence made by changes (delta) to others

@ eMol_na

just a nucleic acid

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