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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/snp__annot__info_8cpp_source.html below:

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

,

,

,

,

,

,

,

,

,

,

,

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,

,

,

,

,

alleles_count = 0;

qual_allele =

;

qual_replace =

;

weight_qual =

;

weight_ext =

;

& qual_id = gb_qual.

();

& qual_val = gb_qual.

();

qual_replace =

;

( qual_val ==

) {

( exception& ) {

( qual_replace && qual_allele ) {

( qual_replace ) {

have_snp_id =

;

& dbtag = **it;

(

.Which() ) {

( exception& ) {

( !have_snp_id ) {

& ext_id_str = ext_id.

();

( snp_data.empty() ) {

( !user_data.

() ) {

( user_data.

() ) {

( loc.

() ) {

= &point.

();

= &interval.

();

dbxref[0].Reset(

);

& dbtag = *dbxref[0];

( !ref || !ref->ReferencedOnlyOnce() ) {

alleles_count = 0;

& qual_str =

qual_index = 0;

(

= 0;

< alleles_count; ++

) {

( qual_index < qual.size() ) {

( qual_index < qual.size() ) {

qual.resize(qual_index);

CSeq_feat::TExt::TData::iterator it =

.begin();

( it ==

.end() ) {

CSeq_feat::TExt::TData::iterator it =

.begin();

( it ==

.end() ) {

( it ==

.end() ) {

( position_delta == 0 ) {

interval.

(to_position-position_delta);

interval.

(to_position);

( position_delta == 0 ) {

interval.

(to_position-position_delta);

interval.

(to_position);

& allele = annot.

(allele_index);

( !allele.empty() ) {

<<

<< allele;

: m_Seq_annot(&annot)

: m_Seq_id(

.m_Seq_id),

m_SNP_Set(

.m_SNP_Set),

m_Comments(

.m_Comments),

m_Alleles(

.m_Alleles),

m_QualityCodesStr(

.m_QualityCodesStr),

m_QualityCodesOs(

.m_QualityCodesOs),

m_Extra(

.m_Extra),

m_Seq_annot(

.m_Seq_annot)

: m_Strings(ss.m_Strings)

( it !=

->end() && it->first == s ) {

( index <= max_index ) {

: m_ElementSize(ss.m_ElementSize), m_Strings(ss.m_Strings)

= os.size();

( it !=

->end() && it->first == s ) {

( pos > max_index*

) {

index = pos/

;

pos = index*

;

(

* c =

; *c; ++c ) {

(

* c1 =

; *c1; ++c1 ) {

(

* c2 =

; *c2; ++c2 ) {

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

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

size_t GetIndex(const TOctetString &s, size_t max_index)

vector< char > TOctetString

unique_ptr< TIndices > m_Indices

void GetString(size_t index, TOctetString &) const

void SetTotalString(size_t element_size, TOctetString &s)

CIndexedOctetStrings(void)

size_t GetIndex(const string &s, size_t max_index)

unique_ptr< TIndices > m_Indices

void Resize(size_t new_size)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

static bool Assign(string &s, const string &src)

const CSeq_entry_Info & GetParentSeq_entry_Info(void) const

void x_ParentDetach(CSeq_annot_Info &parent)

void x_DropAnnotObjects(CTSE_Info &tse)

SSNP_Info::TAlleleIndex x_GetAlleleIndex(const string &allele)

void OffsetGi(TIntId gi_offset)

SSNP_Info::TQualityCodesIndex x_GetQualityCodesIndex(const string &str)

const CSeq_id & GetSeq_id(void) const

void x_DoUpdate(TNeedUpdateFlags flags)

const CSeq_entry_Info & GetParentSeq_entry_Info(void) const

CIndexedStrings m_Alleles

void SetSeq_id(const CSeq_id &id)

const string & x_GetExtra(SSNP_Info::TExtraIndex index) const

const CSeq_annot_Info & GetParentSeq_annot_Info(void) const

SSNP_Info::TExtraIndex x_GetExtraIndex(const string &str)

CIndexedStrings m_Comments

void x_UpdateAnnotIndexContents(CTSE_Info &tse)

CRef< CSeq_annot > m_Seq_annot

void x_ParentAttach(CSeq_annot_Info &parent)

void x_FinishParsing(void)

SSNP_Info::TCommentIndex x_GetCommentIndex(const string &comment)

CIndexedStrings m_QualityCodesStr

const string & x_GetComment(SSNP_Info::TCommentIndex index) const

bool x_CheckId(const CSeq_id &id)

CSeq_annot_SNP_Info(void)

~CSeq_annot_SNP_Info(void)

const string & x_GetAllele(SSNP_Info::TAlleleIndex index) const

void x_GetQualityCodesOs(SSNP_Info::TQualityCodesIndex index, TOctetString &os) const

const string & x_GetQualityCodesStr(SSNP_Info::TQualityCodesIndex index) const

CIndexedOctetStrings m_QualityCodesOs

void x_UnmapAnnotObjects(CTSE_Info &tse)

namespace ncbi::objects::

void x_SetDirtyAnnotIndex(void)

virtual void x_DoUpdate(TNeedUpdateFlags flags)

void x_BaseParentAttach(CTSE_Info_Object &parent)

void x_BaseParentDetach(CTSE_Info_Object &parent)

const CTSE_Info_Object & GetBaseParent_Info(void) const

virtual void x_UpdateAnnotIndexContents(CTSE_Info &tse)

void x_UnmapSNP_Table(const CAnnotName &name, const CSeq_id_Handle &key, const CSeq_annot_SNP_Info &snp_info)

bool x_MapSNP_Table(const CAnnotName &name, const CSeq_id_Handle &key, const CSeq_annot_SNP_Info &snp_info)

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

container_type::iterator iterator

container_type::value_type value_type

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

#define GI_FROM(T, value)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

C * SerialClone(const C &src)

Create on heap a clone of the source object.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

ENa_strand GetStrand(void) const

Get the location's strand.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

bool ReferencedOnlyOnce(void) const THROWS_NONE

Check if object is referenced only once.

#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 int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

const TStr & GetStr(void) const

Get the variant data.

E_Choice

Choice variants.

bool IsLim(void) const

Check if variant Lim is selected.

const TTag & GetTag(void) const

Get the Tag member data.

void SetTag(TTag &value)

Assign a value to Tag data member.

const TData & GetData(void) const

Get the Data member data.

const TDb & GetDb(void) const

Get the Db member data.

E_Choice Which(void) const

Which variant is currently selected.

TLim GetLim(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

TData & SetData(void)

Assign a value to Data data member.

const TStr & GetStr(void) const

Get the variant data.

bool IsSetNum(void) const

required for strs, ints, reals, oss Check if a value has been assigned to Num data member.

void SetLabel(TLabel &value)

Assign a value to Label data member.

TInt GetInt(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

void SetDb(const TDb &value)

Assign a value to Db data member.

vector< CRef< CUser_field > > TData

const TOs & GetOs(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

@ e_not_set

No variant selected.

@ eLim_tr

space to right of position

bool IsSetTitle(void) const

for user defined label Check if a value has been assigned to Title data member.

const TVal & GetVal(void) const

Get the Val member data.

void SetQual(const TQual &value)

Assign a value to Qual data member.

const TKey & GetKey(void) const

Get the Key member data.

bool IsSetLoc(void) const

original location string Check if a value has been assigned to Loc data member.

bool IsSetComment(void) const

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

vector< CRef< CDbtag > > TDbxref

TDbxref & SetDbxref(void)

Assign a value to Dbxref data member.

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

bool IsSetExt(void) const

user defined structure extension Check if a value has been assigned to Ext data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetComment(const TComment &value)

Assign a value to Comment data member.

bool IsSetDescr(void) const

text description Check if a value has been assigned to Descr data member.

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetPartial(void) const

incomplete in some way? Check if a value has been assigned to Partial data member.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

const TLocation & GetLocation(void) const

Get the Location member data.

void SetExt(TExt &value)

Assign a value to Ext data member.

const TData & GetData(void) const

Get the Data member data.

bool IsSetExcept(void) const

something funny about this? Check if a value has been assigned to Except data member.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

const TDbxref & GetDbxref(void) const

Get the Dbxref member data.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetExp_ev(void) const

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

void ResetComment(void)

Reset Comment data member.

bool IsSetId(void) const

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

bool IsSetPseudo(void) const

annotated on pseudogene? Check if a value has been assigned to Pseudo data member.

const TComment & GetComment(void) const

Get the Comment member data.

void ResetExt(void)

Reset Ext data member.

void SetVal(const TVal &value)

Assign a value to Val data member.

bool IsSetCit(void) const

citations for this feature Check if a value has been assigned to Cit data member.

vector< CRef< CGb_qual > > TQual

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

TQual & SetQual(void)

Assign a value to Qual data member.

bool IsSetProduct(void) const

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

const TExt & GetExt(void) const

Get the Ext member data.

void SetTo(TTo value)

Assign a value to To data member.

void SetPoint(TPoint value)

Assign a value to Point data member.

void SetId(TId &value)

Assign a value to Id data member.

ENa_strand

strand of nucleic acid

const TId & GetId(void) const

Get the Id member data.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

void SetId(TId &value)

Assign a value to Id data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

TFrom GetFrom(void) const

Get the From member data.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

bool IsSetFuzz(void) const

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

const TFuzz & GetFuzz(void) const

Get the Fuzz member data.

void ResetFuzz(void)

Reset Fuzz data member.

E_Choice Which(void) const

Which variant is currently selected.

const TId & GetId(void) const

Get the Id member data.

void SetFrom(TFrom value)

Assign a value to From data member.

TGi GetGi(void) const

Get the variant data.

TGi & SetGi(void)

Select the variant.

void ResetStrand(void)

Reset Strand data member.

bool IsSetStrand(void) const

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

bool IsSetFuzz_to(void) const

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

bool IsSetStrand(void) const

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

TStrand GetStrand(void) const

Get the Strand member data.

bool IsGi(void) const

Check if variant Gi is selected.

TTo GetTo(void) const

Get the To member data.

const TInt & GetInt(void) const

Get the variant data.

bool IsSetFuzz_from(void) const

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

void SetStrand(TStrand value)

Assign a value to Strand data member.

void ResetStrand(void)

Reset Strand data member.

unsigned int

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

constexpr auto sort(_Init &&init)

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

Int4 delta(size_t dimension_, const Int4 *score_)

static const char * kId_Extra

static const char * kId_variation

static const char * kId_replace

static const size_t kMax_AlleleLength

static const char * kId_allele

static const char * kId_weight

C * sx_GetUnreferenced(CRef< C > &ref)

static const char * kId_dbSnpSynonymyData

static const size_t kMax_CommentLength

static const char * kVal_1

static const char * kId_dbSnpQAdata

static const char * kId_QualityCodes

static const char * kId_dbSNP

static const char *const s_SNP_Type_Label[eSNP_Type_last]

void x_UpdateSeq_featData(CSeq_feat &feat, const CSeq_annot_SNP_Info &annot_info) const

ESNP_Type ParseSeq_feat(const CSeq_feat &feat, CSeq_annot_SNP_Info &annot_info)

CRef< CSeq_feat > CreateSeq_feat(const CSeq_annot_SNP_Info &annot_info) const

string GetLabel(const CSeq_annot_SNP_Info &info) const

void x_UpdateSeq_feat(CSeq_feat &feat, const CSeq_annot_SNP_Info &annot_info) const

CUser_field::TData::E_Choice GetQualityCodesWhich(void) const

TAlleleIndex m_AllelesIndices[kMax_AllelesCount]

TQualityCodesIndex m_QualityCodesIndex

void UpdateSeq_feat(CRef< CSeq_feat > &seq_feat, const CSeq_annot_SNP_Info &annot_info) const

@ eSNP_Complex_LocationGiIsBad

@ eSNP_Complex_LocationIsNotPoint

@ eSNP_Complex_IdCountIsNotOne

@ eSNP_Complex_CommentIndexOverflow

@ eSNP_Bad_WrongMemberSet

@ eSNP_Complex_AlleleCountTooLarge

@ eSNP_Complex_WeightBadValue

@ eSNP_Complex_QAdataIndexOverflow

@ eSNP_Complex_WeightCountIsNotOne

@ eSNP_Complex_LocationStrandIsBad

@ eSNP_Complex_AlleleTooBig

@ eSNP_Complex_NoPlaceForQAdata

@ eSNP_Complex_IdCountTooLarge

@ eSNP_Complex_AlleleIndexOverflow

@ eSNP_Complex_CommentTooBig

TPositionDelta m_PositionDelta

CRef< CSeq_feat > x_CreateSeq_feat(void) const

bool MinusStrand(void) const

size_t GetAllelesCount(void) const

bool PlusStrand(void) const

TCommentIndex m_CommentIndex

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