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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/locus__item_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/format/locus_item.cpp Source File

m_Length(0), m_Biomol(

::eBiomol_unknown), m_Date("01-JAN-1900")

((

.IsSegmented() && !

.HasParts()) ||

(

.IsDelta() && !

.IsDeltaLitOnly()));

(

.length() + suffix_len < 16) {

((

==

) && (!

((

) next_to_last))) {

numsegs =

.GetMaster().GetNumParts();

locus << setfill(

) << setw(suffix_len) <<

.GetPartNumber();

(! desc.

())

;

(! oi.

())

;

(

.Config().IsFormatLite())

;

& sid = **id_itr;

(sid.

()) {

& db = dbtag.

();

(

.IsPart()) {

MAX_LOCUS_ACCN_LEN = 38;

* tsip =

.GetSeqId()->GetTextseq_Id();

=

.GetSeqId()->GetSeqIdString();

(

.length() > MAX_LOCUS_ACCN_LEN ) {

.resize(MAX_LOCUS_ACCN_LEN);

*

.rbegin() =

;

(

, iter, name) {

current_char = (

char)(*iter);

( !

(current_char) && current_char !=

) {

( !

.Config().IsFormatGBSeq() && !

.Config().IsFormatINSDSeq() ) {

( (! is_nucleic_acid || is_in_set_1 || is_in_set_2) &&

(

.IsProt() ) {

( loc.

()) {

(! idx)

division;

(! bsx)

division;

}

( is_prot ) {

is_transgenic =

;

is_env_sample =

;

is_transgenic =

;

is_env_sample =

;

}

(is_env_sample) {

(*iter && iter->GetSeqId()->IsPatent()) {

cds_loc_piece_id = cds_loc_iter.GetSeq_id_Handle();

( cds_loc_piece_id ) {

cds_loc_piece_id, bsh );

(*iter && iter->GetSeqId()->IsPatent()) {

& gb = gb_desc->GetGenbank();

(division.

() ||

gb.

() ==

) {

( division.

() ) {

}

( is_prot ) {

is_transgenic =

;

is_env_sample =

;

is_transgenic =

;

is_env_sample =

;

}

(is_env_sample) {

(*iter && iter->GetSeqId()->IsPatent()) {

cds_loc_piece_id = cds_loc_iter.GetSeq_id_Handle();

( cds_loc_piece_id ) {

cds_loc_piece_id, bsh );

(*iter && iter->GetSeqId()->IsPatent()) {

& gb = gb_desc->GetGenbank();

(division.

() ||

gb.

() ==

) {

( division.

() ) {

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

desc_choices.reserve(1);

(

desc_it(bsh, desc_choices); desc_it; ++desc_it) {

tech = desc_it->GetMolinfo().GetTech();

(

&&

->UsingSeqEntryIndex()) {

(

.DoContigStyle() ) {

(

.UsingSeqEntryIndex() ) {

(

.Config().IsFormatEMBL() ) {

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.

CRef< CFeatureIndex > GetFeatureForProduct(void)

CConstRef< CBioSource > GetBioSource(void)

ECompare Compare(const CDate &date) const

@ eCompare_after

*this comes second.

CRef< CFeatureIndex > GetOverlappingSource(void)

const CMappedFeat GetMappedFeat(void) const

void x_SetObject(const CSerialObject &obj)

const CSerialObject * GetObject(void) const

void x_SetDivision(CBioseqContext &ctx)

void x_SetBiomol(CBioseqContext &ctx)

void x_SetStrand(CBioseqContext &ctx)

void x_SetDate(CBioseqContext &ctx)

const CDate * x_GetLaterDate(const CDate *d1, const CDate *d2) const

EItem GetItemType() const override

void x_GatherInfo(CBioseqContext &ctx) override

const string & GetDivision(void) const

bool x_NameHasBadChars(const string &name) const

const CDate * x_GetDateForBioseq(const CBioseq_Handle &bsh) const

void x_SetTopology(CBioseqContext &ctx)

void Format(IFormatter &formatter, IFlatTextOStream &text_os) const override

void x_SetLength(CBioseqContext &ctx)

void x_SetName(CBioseqContext &ctx)

CRef< CBioseqIndex > GetBioseqIndex(void)

namespace ncbi::objects::

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

virtual void FormatLocus(const CLocusItem &locus, IFlatTextOStream &text_os)=0

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

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

Utility macros and typedefs for exploring NCBI objects from general.asn.

#define FOR_EACH_USERFIELD_ON_USEROBJECT(Itr, Var)

FOR_EACH_USERFIELD_ON_USEROBJECT EDIT_EACH_USERFIELD_ON_USEROBJECT.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

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

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,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

@ 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.

const CBioseq * GetNucleotideParent(const CBioseq &product, CScope *scope)

Get the encoding nucleotide sequnce of a protein.

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id &id, const CTSE_Handle &tse)

Get bioseq handle for sequence withing one TSE.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

vector< CSeq_id_Handle > TId

bool IsSetInst_Strand(void) const

bool IsSetInst_Mol(void) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

const TInst_Ext & GetInst_Ext(void) const

bool IsSetInst_Ext(void) const

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

TInst_Mol GetInst_Mol(void) const

TInst_Strand GetInst_Strand(void) const

bool IsSetInst_Length(void) const

TInst_Topology GetInst_Topology(void) const

bool IsSetInst_Repr(void) const

TInst_Repr GetInst_Repr(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const TId & GetId(void) const

vector< CSeqdesc::E_Choice > TDescChoices

#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).

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

const TCreation_date & GetCreation_date(void) const

Get the Creation_date member data.

bool CanGetUpdate_date(void) const

Check if it is safe to call GetUpdate_date method.

const TUpdate_date & GetUpdate_date(void) const

Get the Update_date member data.

bool CanGetCreation_date(void) const

Check if it is safe to call GetCreation_date method.

TDiv GetDiv(void) const

Get the Div member data.

bool CanGetDiv(void) const

Check if it is safe to call GetDiv method.

const TEntry_date & GetEntry_date(void) const

Get the Entry_date member data.

const TDiv & GetDiv(void) const

Get the Div member data.

bool CanGetEntry_date(void) const

Check if it is safe to call GetEntry_date method.

bool CanGetDiv(void) const

Check if it is safe to call GetDiv method.

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

TOrigin GetOrigin(void) const

Get the Origin member data.

bool CanGetOrg(void) const

Check if it is safe to call GetOrg method.

list< CRef< CSubSource > > TSubtype

const TOrg & GetOrg(void) const

Get the Org member data.

@ eSubtype_environmental_sample

@ eOrigin_synthetic

purely synthetic

@ eOrigin_mut

artificially mutagenized

@ eOrigin_artificial

artificially engineered

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetDb(void) const

name of database or system Check if a value has been assigned to Db data member.

bool IsSetType(void) const

type of object within class Check if a value has been assigned to Type data member.

bool IsStd(void) const

Check if variant Std is selected.

const TData & GetData(void) const

Get the Data member data.

const TDb & GetDb(void) const

Get the Db member data.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

bool IsSetData(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

@ e_Str

for those unparsed dates

bool CanGetDiv(void) const

Check if it is safe to call GetDiv method.

const TDiv & GetDiv(void) const

Get the Div member data.

bool CanGetOrgname(void) const

Check if it is safe to call GetOrgname method.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

bool IsSetAccession(void) const

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

const TName & GetName(void) const

Get the Name member data.

bool CanGetStrand(void) const

Check if it is safe to call GetStrand method.

TFrom GetFrom(void) const

Get the From member data.

E_Choice Which(void) const

Which variant is currently selected.

TStrand GetStrand(void) const

Get the Strand member data.

const TGeneral & GetGeneral(void) const

Get the variant data.

TTo GetTo(void) const

Get the To member data.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsSetName(void) const

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

const TAccession & GetAccession(void) const

Get the Accession member data.

@ e_General

for other databases

const TUser & GetUser(void) const

Get the variant data.

const TUpdate_date & GetUpdate_date(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

const TPdb & GetPdb(void) const

Get the variant data.

const TGenbank & GetGenbank(void) const

Get the variant data.

const TSp & GetSp(void) const

Get the variant data.

bool IsDelta(void) const

Check if variant Delta is selected.

const TEmbl & GetEmbl(void) const

Get the variant data.

TBiomol GetBiomol(void) const

Get the Biomol member data.

EMol

molecule class in living organism

const TDelta & GetDelta(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TCreate_date & GetCreate_date(void) const

Get the variant data.

list< CRef< CDelta_seq > > Tdata

const TMolinfo & GetMolinfo(void) const

Get the variant data.

bool IsUser(void) const

Check if variant User is selected.

@ eRepr_delta

sequence made by changes (delta) to others

@ eTech_htgs_2

ordered High Throughput sequence contig

@ eTech_other

use Source.techexp

@ eTech_htc

high throughput cDNA

@ eTech_both

concept transl. w/ partial pept. seq.

@ eTech_seq_pept_homol

sequenced peptide, ordered by homology

@ eTech_sts

Sequence Tagged Site.

@ eTech_htgs_3

finished High Throughput sequence

@ eTech_seq_pept_overlap

sequenced peptide, ordered by overlap

@ eTech_htgs_1

unordered High Throughput sequence contig

@ eTech_concept_trans

conceptual translation

@ eTech_tsa

transcriptome shotgun assembly

@ eTech_standard

standard sequencing

@ eTech_wgs

whole genome shotgun sequencing

@ eTech_seq_pept

peptide was sequenced

@ eTech_survey

one-pass genomic sequence

@ eTech_htgs_0

single genomic reads for coordination

@ eTech_est

Expressed Sequence Tag.

@ eTech_concept_trans_a

conceptual transl. supplied by author

@ eBiomol_pre_RNA

precursor RNA of any sort really

@ eBiomol_cRNA

viral RNA genome copy intermediate

@ eBiomol_other_genetic

other genetic material

@ e_Embl

EMBL specific information.

@ e_Update_date

date of last update

@ e_Genbank

GenBank specific info.

@ e_Sp

SWISSPROT specific info.

@ e_Molinfo

info on the molecule and techniques

@ e_Create_date

date entry first created/released

@ e_Pdb

PDB specific information.

@ e_Source

source of materials, includes Org-ref

@ eMol_not_set

> cdna = rna

@ eMol_na

just a nucleic acid

@ eStrand_other

default ds for DNA, ss for RNA, pept

@ eStrand_ds

double strand

@ eStrand_ss

single strand

const TDate & GetDate(void) const

Get the Date member data.

bool CanGetDeposition(void) const

Check if it is safe to call GetDeposition method.

const TReplace & GetReplace(void) const

Get the Replace member data.

bool CanGetDate(void) const

Check if it is safe to call GetDate method.

bool CanGetReplace(void) const

Check if it is safe to call GetReplace method.

const TDeposition & GetDeposition(void) const

Get the Deposition member data.

bool CanGetCreated(void) const

Check if it is safe to call GetCreated method.

const TCreated & GetCreated(void) const

Get the Created member data.

bool CanGetAnnotupd(void) const

Check if it is safe to call GetAnnotupd method.

const TAnnotupd & GetAnnotupd(void) const

Get the Annotupd member data.

const TSequpd & GetSequpd(void) const

Get the Sequpd member data.

bool CanGetSequpd(void) const

Check if it is safe to call GetSequpd method.

static CTempString x_GetDivisionProc(const CBioseq_Handle &bsh, bool is_prot, CMolInfo::TTech tech)

static void s_AddLocusSuffix(string &basename, CBioseqContext &ctx)

static bool s_IsSeperatorNeeded(const string &basename, size_t suffix_len)

static bool s_ShouldUseOriginalID(CBioseqContext &ctx)

static string s_FastaGetOriginalID(CBioseqContext &ctx)

static CTempString x_GetDivisionProcIdx(const CBioseqContext &ctx, const CBioseq_Handle &bsh, bool is_prot, CMolInfo::TTech tech)

static bool s_IsGenomeView(const CBioseqContext &ctx)

void DateToString(const CDate &date, string &str, EDateToString format_choice=eDateToString_regular)

static const GLdouble origin[]

Utility macros and typedefs for exploring NCBI objects from seq.asn.

#define FOR_EACH_SEQDESC_ON_BIOSEQ(Itr, Var)

FOR_EACH_SEQDESC_ON_BIOSEQ EDIT_EACH_SEQDESC_ON_BIOSEQ.

#define FOR_EACH_SEQID_ON_BIOSEQ(Itr, Var)

FOR_EACH_SEQID_ON_BIOSEQ EDIT_EACH_SEQID_ON_BIOSEQ.

#define FIELD_IS_SET_AND_IS(Var, Fld, Chs)

FIELD_IS_SET_AND_IS base macro.

#define GET_FIELD(Var, Fld)

GET_FIELD base macro.

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