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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Seq__id_8hpp_source.html below:

NCBI C++ ToolKit: include/objects/seqloc/Seq_id.hpp Source File

fParse_PartialOK = 0x01,

fParse_RawText = 0x02,

fParse_AnyRaw = fParse_RawText | fParse_RawGI,

fParse_ValidLocal = 0x08,

fParse_AnyLocal = 0x18,

fParse_NoFASTA = 0x20,

fParse_FallbackOK = 0x40,

fParse_Default = fParse_RawText | fParse_ValidLocal

fInvalidChar = 1 << 1,

fExceedsMaxLength = 1 << 2

eFasta_AsTypeAndContent

TParseFlags

= fParse_AnyRaw);

(EFastaAsTypeAndContent, E_Choice the_type,

& Set(E_Choice the_type,

& Set(E_Choice the_type,

& Set(EFastaAsTypeAndContent, E_Choice the_type,

E_Choice WhichInverseSeqId(

& SeqIdCode);

* WhichFastaTag(E_Choice choice);

eSeqId_refseq = eSeqId_other,

eAcc_type_mask = 0xff,

fAcc_nuc = 0x80000000,

fAcc_prot = 0x40000000,

fAcc_predicted = 0x20000000,

fAcc_specials = 0x10000000,

fAcc_master = 0x08000000,

fAcc_ncbo = 0x04000000,

fAcc_fallback = 0x02000000,

fAcc_vdb_only = 0x01000000,

eAcc_flag_mask = 0xff000000,

eAcc_dirsub = 2 << 8,

eAcc_div_patent = 3 << 8,

eAcc_gsdb_ds = 6 << 8,

eAcc_backbone = 8 << 8,

eAcc_segset = 10 << 8,

eAcc_unique = 12 << 8,

eAcc_ambig = 112 << 8,

eAcc_ambig_g = 113 << 8,

eAcc_ambig_e = 114 << 8,

eAcc_ambig_ge = 115 << 8,

eAcc_ambig_d = 116 << 8,

eAcc_ambig_gd = 117 << 8,

eAcc_ambig_ed = 118 << 8,

eAcc_ambig_ged = 119 << 8,

eAcc_unreserved = 127 << 8,

fAcc_genomic = 128 << 8,

eAcc_genome = 128 << 8,

eAcc_htgs = 129 << 8,

eAcc_chromosome = 133 << 8,

eAcc_genomic_rgn = 134 << 8,

eAcc_wgs_intermed = 135 << 8,

eAcc_optical_map = 138 << 8,

eAcc_targeted = 139 << 8,

eAcc_division_mask = 0xff00,

eAcc_wgs_master = eAcc_wgs | fAcc_master,

eAcc_wgs_intermed_master = eAcc_wgs_intermed | fAcc_master,

eAcc_tsa_master = eAcc_tsa | fAcc_master,

eAcc_targeted_master = eAcc_targeted | fAcc_master,

eAcc_wgs_vdb_only = eAcc_wgs | fAcc_vdb_only,

eAcc_wgs_intermed_vdb_only = eAcc_wgs_intermed | fAcc_vdb_only,

eAcc_tsa_vdb_only = eAcc_tsa | fAcc_vdb_only,

eAcc_targeted_vdb_only = eAcc_targeted | fAcc_vdb_only,

eAcc_wgs_vdb_master = eAcc_wgs | fAcc_master | fAcc_vdb_only,

eAcc_wgs_intermed_vdb_master

= eAcc_wgs_intermed | fAcc_master | fAcc_vdb_only,

eAcc_tsa_vdb_master = eAcc_tsa | fAcc_master | fAcc_vdb_only,

eAcc_targeted_vdb_master = eAcc_targeted | fAcc_master | fAcc_vdb_only,

eAcc_gb_patent =

(genbank, div_patent, seq),

eAcc_refseq_unreserved =

(refseq, unreserved, seq),

eAcc_refseq_wgsm_intermed =

(refseq, wgs_intermed_master,

eAcc_refseq_wgsv_intermed =

(refseq, wgs_intermed_vdb_only,

eAcc_refseq_wgsvm_intermed =

(refseq, wgs_intermed_vdb_master,

eAcc_refseq_prot_predicted = eAcc_refseq_prot | fAcc_predicted,

eAcc_refseq_mrna_predicted = eAcc_refseq_mrna | fAcc_predicted,

eAcc_refseq_ncrna_predicted = eAcc_refseq_ncrna | fAcc_predicted,

eAcc_refseq_chromosome_ncbo = eAcc_refseq_chromosome | fAcc_ncbo,

eAcc_refseq_contig_ncbo = eAcc_refseq_contig | fAcc_ncbo,

eAcc_ddbj_targetedv_nuc =

(ddbj, targeted_vdb_only,

),

eAcc_ddbj_targetedvm_nuc =

(ddbj, targeted_vdb_master,

),

eAcc_ddbj_tpa_targetedm_nuc =

(tpd, targeted_master,

),

eAcc_ddbj_tpa_targetedv_nuc =

(tpd, targeted_vdb_only,

),

eAcc_ddbj_tpa_targetedvm_nuc =

(tpd, targeted_vdb_master,

),

eAcc_gpipe_unreserved =

(gpipe, unreserved, seq),

eAcc_named_annot_track =

(named_annot_track, other, seq)

{

(

& eAcc_type_mask); }

EAccessionInfo IdentifyAccession(

& accession,

TParseFlags

= fParse_AnyRaw);

EAccessionInfo IdentifyAccession(TParseFlags

= fParse_AnyRaw | fParse_AnyLocal)

;

LoadAccessionGuide(

& filename);

Match(

& sid2)

;

CompareOrdered(

& sid2)

;

CompareOrdered(sid2) < 0;

AsFastaString(

)

;

fLabel_Version = 0x10,

fLabel_GeneralDbIsContent = 0x20,

fLabel_Trimmed = 0x40,

fLabel_UpperCase = 0x80,

fLabel_Default = fLabel_Version

eFormat_BestWithVersion

IsValidLocalID(

& s);

TErrorFlags CheckLocalID(

& s);

TParseFlags

= fParse_Default);

allow_partial_failure =

);

fRequireAccessions = 1 << 0

AdjustScore (

base_score,

TAdjustScoreFlags

= TAdjustScoreFlags())

{

AdjustScore(base_score, fRequireAccessions); }

BaseTextScore (

)

;

BaseBestRankScore (

)

;

BaseFastaAAScore (

)

;

BaseFastaNAScore (

)

;

BaseBlastScore (

)

;

(

)

{

AdjustScore(BaseTextScore()); }

(

)

{

AdjustScore(BaseBestRankScore()); }

(

)

{

AdjustScore(BaseFastaAAScore()); }

(

)

{

AdjustScore(BaseFastaNAScore()); }

(

)

{

AdjustScore(BaseBlastScore()); }

{

StrictAdjustScore(BaseTextScore()); }

{

StrictAdjustScore(BaseBestRankScore()); }

{

StrictAdjustScore(BaseFastaAAScore()); }

{

StrictAdjustScore(BaseFastaNAScore()); }

{

StrictAdjustScore(BaseBlastScore()); }

{

?

->TextScore() :

; }

{

?

->TextScore() :

; }

{

?

->BestRankScore() :

; }

{

Score(

); }

{

?

->FastaAAScore() :

; }

{

?

->FastaNAScore() :

; }

{

?

->BlastScore() :

; }

{

?

->StrictTextScore() :

; }

{

?

->StrictBestRankScore() :

; }

{

?

->StrictFastaAAScore() :

; }

{

?

->StrictFastaNAScore() :

; }

{

?

->StrictBlastScore() :

; }

PreferAccessionOverGi(

);

AvoidGi(

);

fAllowLocalId = (1 << 0),

fGpipeAddSecondary = (1 << 1)

ComposeOSLT(list<string>* secondary_ids =

,

kMaxLocalIDLength = 50;

kMaxGeneralDBLength = 20;

kMaxGeneralTagLength = 50;

kMaxAccessionLength = 30;

eSNPScaleLimit_Chromosome

* GetSNPScaleLimit_Name(ESNPScaleLimit

);

ESNPScaleLimit GetSNPScaleLimit_Value(

& name);

IsAllowedSNPScaleLimit(ESNPScaleLimit scale_limit)

;

ETypeVariant x_IdentifyTypeVariant(E_Choice

,

E_Choice x_Init(list<CTempString>& fasta_pieces, E_Choice

,

x_WriteContentAsFasta(ostream&

)

;

fAllowUnderscores = 0x1

: m_Range(&range), m_Number(range.start)

: m_Range(&range), m_Number(

)

: m_Range(it.m_Range), m_Number(it.m_Number)

{

m_Accession.empty() ? x_SetAccession() : m_Accession; }

{

m_Accession.empty() ? &x_SetAccession() : &m_Accession; }

{

*(*

+

); }

{ m_Accession.erase(); ++m_Number;

*

; }

{ m_Accession.erase(); --m_Number;

*

; }

{ m_Accession.erase(); m_Number +=

;

*

; }

{ m_Accession.erase(); m_Number -=

;

*

; }

{

m_Number == it.

; }

{

m_Number != it.

; }

{

m_Number < it.

; }

{

m_Number > it.

; }

{

m_Number <= it.

; }

{

m_Number >= it.

; }

{

m_Number - it.

; }

& x_SetAccession(

)

;

{

stop - start + 1; }

* GetErrCodeString(

)

;

<

TId>

<

container>

(

container, iter, ids) {

<

container>

?

->GetGi() :

;

<

container>

(

container, iter, ids) {

@ eBoth

Both preliminary and traceback stages.

*** Sequence identifiers ******************************** *

Base class for all serializable objects.

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

Abstract base class for lightweight line-by-line reading.

string GetSeqIdString(const CSeq_id &id)

bool operator<(const CEquivRange &A, const CEquivRange &B)

std::ofstream out("events_result.xml")

main entry point for tests

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

EErrCode

Error types that an application can generate.

CVect2< NCBI_PROMOTE(int,U) > operator*(int v1, const CVect2< U > &v2)

ESerialRecursionMode

How to assign and compare child sub-objects of serial objects.

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

Set object to copy of another one.

virtual void WriteAsFasta(CNcbiOstream &out) const

@ eRecursive

Recursively.

const_iterator operator--(int)

TGi FindGi(const container &ids)

Return gi from id list if exists, return 0 otherwise.

int WorstRankScore(void) const

int StrictFastaAAScore(void) const

static int StrictBestRank(const CRef< CSeq_id > &id)

const_iterator(const SSeqIdRange &range)

CProxy DumpAsFasta(void) const

const_iterator & operator++(void)

CConstRef< CSeq_id > GetSeq_idByType(const container &ids, CSeq_id::E_Choice choice)

Search the container of CRef<CSeq_id> for the id of given type.

static int StrictScore(const CRef< CSeq_id > &id)

EAccessionInfo

For IdentifyAccession (below)

const_iterator & operator+=(int n)

CConstRef< CSeq_id > Get_ConstRef_Seq_id(TId &id)

Dummy convertor for container search functions.

int BestRankScore(void) const

const SSeqIdRange * m_Range

static E_Choice GetAccType(EAccessionInfo info)

static int StrictBlastRank(const CRef< CSeq_id > &id)

E_SIC

Compare return values.

const_iterator(const SSeqIdRange &range, int number)

EFastaAsTypeAndContent

Tag for method variants that would otherwise be ambiguous.

int BaseWorstRankScore(void) const

int TextScore(void) const

bool operator<=(const const_iterator &it) const

EComposeOSLTFlags

Flags specifying special treatment for certain types of Seq-ids in ComposeOSLT().

const_iterator end(void) const

int BlastScore(void) const

const string * operator->(void) const

int TFlags

binary OR of EFlags

const_iterator operator+(int n) const

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

int operator-(const const_iterator &it) const

static int WorstRank(const CRef< CSeq_id > &id)

const_iterator operator++(int)

static int StrictFastaNARank(const CRef< CSeq_id > &id)

const_iterator(const const_iterator &it)

const_iterator begin(void) const

int StrictBestRankScore(void) const

static int StrictFastaAARank(const CRef< CSeq_id > &id)

EMaxScore

Numerical quality ranking; lower is better.

NCBI_EXCEPTION_DEFAULT(CSeqIdException, CException)

int StrictTextScore(void) const

int StrictBlastScore(void) const

bool operator==(const const_iterator &it) const

const_iterator operator-(int n) const

EStringFormat

Get a string representation of the sequence IDs of a given bioseq.

CSeq_id::EAccessionInfo acc_info

ptrdiff_t difference_type

#define NCBI_ACC(type, div, mol)

static int Score(const CRef< CSeq_id > &id)

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

const_iterator & operator-=(int n)

bool operator>=(const const_iterator &it) const

static int BestRank(const CRef< CSeq_id > &id)

bool operator<(const CSeq_id &sid2) const

random_access_iterator_tag iterator_category

string operator[](int n) const

static int ConstScore(const CConstRef< CSeq_id > &id)

int StrictAdjustScore(int base_score) const

static int BlastRank(const CRef< CSeq_id > &id)

ELabelType

return the label for a given string

const_iterator & operator--(void)

DECLARE_SAFE_FLAGS_TYPE(EAdjustScoreFlags, TAdjustScoreFlags)

string GetLabel(const CSeq_id &id)

static int FastaNARank(const CRef< CSeq_id > &id)

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

int FastaAAScore(void) const

const_iterator & operator=(const const_iterator &it)

set< CSeq_id_Handle > TSeqIdHandles

int StrictFastaNAScore(void) const

bool operator!=(const const_iterator &it) const

CConstRef< CSeq_id > FindTextseq_id(const container &ids)

Return text seq-id from id list if exists, return 0 otherwise.

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

ESNPScaleLimit

SNP annotation scale limits.

int FastaNAScore(void) const

static int FastaAARank(const CRef< CSeq_id > &id)

@ eUnknownType

Unrecognized Seq-id type.

@ e_NO

different SeqId types-can't compare

@ e_YES

SeqIds compared, but are different.

@ eFormat_BestWithoutVersion

@ eFastaContent

Like eFasta, but without any tag.

@ eContent

Untagged human-readable accession or the like.

@ eBoth

Type and content, delimited by a vertical bar.

@ eFasta

Tagged ID in NCBI's traditional FASTA style.

@ eType

FASTA-style type, or database in GeneralDbIsContent mode.

@ eSNPScaleLimit_Supercontig

bool IsValid(const CSeq_point &pt, CScope *scope)

Checks that point >= 0 and point < length of Bioseq.

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

NCBI_NS_STD::string::size_type SIZE_TYPE

#define NCBI_SEQLOC_EXPORT

static const char label[]

CSeq_id_Base & operator=(const CSeq_id_Base &)

E_Choice Which(void) const

Which variant is currently selected.

E_Choice

Choice variants.

@ e_Gibbmt

Geninfo backbone moltype.

@ e_Giim

Geninfo import id.

@ 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_Gibbsq

Geninfo backbone seqid.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_Named_annot_track

Internal named annotation tracking ID.

@ e_not_set

No variant selected.

@ e_Tpg

Third Party Annot/Seq Genbank.

list< CRef< CSeq_id > > TId

unsigned int

A callback function used to compare two keys in a database.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

const string version

version string

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

std::istream & in(std::istream &in_, double &x_)

string GetStringDescr(const CBioseq &bioseq)

static const char * kMaxScore

void Dump(CSplitCacheApp *app, const C &obj, ESerialDataFormat format, const string &key, const string &suffix=kEmptyStr)

bool operator>(const typename tree< T, tree_node_allocator >::iterator_base &one, const typename tree< T, tree_node_allocator >::iterator_base &two)

static bool ambig(char c)

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