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NCBI C++ ToolKit: src/misc/discrepancy/report_object.cpp Source File

(seq_feat.GetData().IsGene()) {

& gene = seq_feat.GetData().GetGene();

* gene = seq_feat.GetGeneXref();

rval = prot_ref.

().front();

(prot_seq_feat && prot_seq_feat->

().

()) {

(seq_feat.

().

() && !

.empty() && (string::npos != (pos =

.find(

)))) {

=

;

&& (string::npos != (pos =

.find(

)))) {

(

.find(

) == 0 ||

.find(

) == 0) {

(

& it : seq_id_ls) {

score = it->BaseBestRankScore();

(best_score > score) {

pnt.

().Assign(*best_id);

interval.

().Assign(*best_id);

(loc.

()) {

(

& it : loc.

().Set()) {

(

& it : loc.

().Set()) {

rval =

+

+ product +

+

+

+ locus_tag;

(

!= string::npos) {

(

!= string::npos) {

(m != string::npos) {

(

!= string::npos) {

(

!= string::npos) {

(m != string::npos) {

(

!= string::npos) {

(

!= string::npos) {

(

!= string::npos) {

(sd.

())

ostringstream result_strm;

(bioseq_set_class) {

result_strm <<

;

result_strm <<

;

;

result_strm << seq_id_str;

( ! direct_child_ci ) {

result_strm <<

;

( direct_child_ci->

() ) {

result_strm << seq_id_str;

result_strm.str();

User-defined methods of the data storage class.

void GetDate(string *label, bool year_only=false) const

Append a standardized string representation of the date to the label.

void GetLabel(string *label) const

string GetFeatureType() const override

CRef< CDiscrepancyContext::CRefNode > m_Ref

string GetLocusTag() const override

string GetLocation() const override

string GetProductName() const override

static string GetTextObjectDescription(const CSeq_feat &seq_feat, CScope &scope)

void GetLabel(string *label) const

bool GetLabel(string *label, TLabelFlags flags=0, ELabelVersion version=eLabel_DefaultVersion) const override

Append a label to "label" based on content.

ESubtype GetSubtype(void) const

string GetKey(EVocabulary vocab=eVocabulary_full) const

namespace ncbi::objects::

const CProt_ref * GetProtXref(void) const

get protein (if present) from Seq-feat.xref list

static const char location[]

#define ENUM_METHOD_NAME(EnumName)

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

string GetLabel(const CSeq_id &id)

@ eContent

Untagged human-readable accession or the like.

void SetPacked_int(TPacked_int &v)

void SetPacked_pnt(TPacked_pnt &v)

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

Override Assign() to incorporate cache invalidation.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

CMappedFeat GetBestOverlappingFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype need_subtype, sequence::EOverlapType overlap_type, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

@ fFGL_Content

Include its content if there is any.

@ eOverlap_Contains

2nd contains 1st extremes

const CSeq_feat * GetCDSForProduct(const CBioseq &product, CScope *scope)

Get the encoding CDS feature of a given protein sequence.

CBioseq_Handle GetBioseqFromSeqLoc(const CSeq_loc &loc, CScope &scope, CScope::EGetBioseqFlag flag=CScope::eGetBioseq_Loaded)

Retrieve the Bioseq Handle from a location.

CConstRef< CSeq_feat > GetGeneForFeature(const CSeq_feat &feat, CScope &scope)

Finds gene for feature, but obeys SeqFeatXref directives.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

#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 IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static const char label[]

bool IsSetOrg(void) const

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

const TOrg & GetOrg(void) const

Get the Org member data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool CanGetLocus(void) const

Check if it is safe to call GetLocus method.

bool CanGetLocus_tag(void) const

Check if it is safe to call GetLocus_tag method.

bool CanGetDesc(void) const

Check if it is safe to call GetDesc method.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

bool IsStr(void) const

Check if variant Str is selected.

bool CanGetClass(void) const

Check if it is safe to call GetClass method.

const TClass & GetClass(void) const

Get the Class member data.

const TStr & GetStr(void) const

Get the variant data.

const TType & GetType(void) const

Get the Type member data.

bool CanGetCommon(void) const

Check if it is safe to call GetCommon method.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

const TCommon & GetCommon(void) const

Get the Common member data.

bool CanGetTaxname(void) const

Check if it is safe to call GetTaxname method.

const TName & GetName(void) const

Get the Name member data.

bool CanGetName(void) const

Check if it is safe to call GetName method.

const TPub & GetPub(void) const

Get the variant data.

bool IsProt(void) const

Check if variant Prot is selected.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsPub(void) const

Check if variant Pub is selected.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsBiosrc(void) const

Check if variant Biosrc is selected.

const TGene & GetGene(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsRna(void) const

Check if variant Rna is selected.

void SetId(TId &value)

Assign a value to Id data member.

bool IsSetId(void) const

WARNING: this used to be optional Check if a value has been assigned to Id data member.

const TId & GetId(void) const

Get the Id member data.

bool IsSetA(void) const

connection to a least one residue Check if a value has been assigned to A data member.

void SetId(TId &value)

Assign a value to Id data member.

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.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

bool IsSetId(void) const

WARNING: this used to be optional Check if a value has been assigned to Id data member.

bool IsSetId(void) const

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

bool IsSetB(void) const

other end may not be available Check if a value has been assigned to B data member.

const TBond & GetBond(void) const

Get the variant data.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ 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

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_segset

segmented sequence + parts

EGIBB_method

sequencing methods

const THet & GetHet(void) const

Get the variant data.

const TUser & GetUser(void) const

Get the variant data.

const TDbxref & GetDbxref(void) const

Get the variant data.

const TUpdate_date & GetUpdate_date(void) const

Get the variant data.

const TTitle & GetTitle(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

const TPub & GetPub(void) const

Get the variant data.

const TMaploc & GetMaploc(void) const

Get the variant data.

TMethod GetMethod(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

const TOrg & GetOrg(void) const

Get the variant data.

list< CRef< CSeq_id > > TId

EGIBB_mod

GenInfo Backbone modifiers.

TMol_type GetMol_type(void) const

Get the variant data.

const TModif & GetModif(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TCreate_date & GetCreate_date(void) const

Get the variant data.

EGIBB_mol

type of molecule represented

const TPub & GetPub(void) const

Get the Pub member data.

const TComment & GetComment(void) const

Get the variant data.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

const TName & GetName(void) const

Get the variant data.

const TRegion & GetRegion(void) const

Get the variant data.

@ e_Het

cofactor, etc associated but not bound

@ e_Org

if all from one organism

@ e_User

user defined object

@ e_Update_date

date of last update

@ e_Pub

a reference to the publication

@ e_Mol_type

type of molecule

@ e_Dbxref

xref to other databases

@ e_Comment

a more extensive comment

@ e_Method

sequencing method

@ e_Region

overall region (globin locus)

@ e_Molinfo

info on the molecule and techniques

@ e_Maploc

map location of this sequence

@ e_Create_date

date entry first created/released

@ e_Title

a title for this sequence

@ e_Name

a name for this sequence

@ e_Source

source of materials, includes Org-ref

string GetProductForCDS(const CSeq_feat &cds, CScope &scope)

void GetSeqFeatLabel(const CSeq_feat &seq_feat, string &label)

static bool IsAccession(const CSeq_id &id)

string GetLocusTagForFeature(const CSeq_feat &seq_feat, CScope &scope)

CConstRef< CSeq_id > GetBestId(const CBioseq &bioseq)

string GetProduct(const CProt_ref &prot_ref)

string GetSeqLocDescription(const CSeq_loc &loc, CScope &scope)

void UpgradeSeqLocId(CSeq_point &pnt, CScope &scope)

Generic utility macros and templates for exploring NCBI objects.

#define GET_FIELD_OR_DEFAULT(Var, Fld, Dflt)

GET_FIELD_OR_DEFAULT base macro.

static CS_CONTEXT * context

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