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NCBI C++ ToolKit: src/misc/hgvs/hgvs_parser.cpp Source File

+ CHgvsParser::SGrammar::s_GetRuleName(i->value.id()) ); }

uo->

().SetStr(

);

(

.GetSeq_data().IsIupacna()) {

}

(

.GetSeq_data().IsNcbieaa()) {

(eLogic,

);

->ResetLocation();

vr.

().SetSet().SetVariations().push_back(

);

(

->IsSetExt() &&

->GetExt().GetType().GetStr() ==

) {

vr.

().SetSet().SetVariations().push_back(asserted_vr);

->SetSeq().SetLiteral().SetLength(

->GetExt().GetField(

).GetData().GetInt());

(

->GetExt().HasField(

)) {

->SetSeq().SetLiteral().SetSeq_data().SetIupacna().Set(

->GetExt().GetField(

).GetData().GetStr());

->SetSeq().SetLiteral().SetSeq_data().SetNcbieaa().Set(

->GetExt().GetField(

).GetData().GetStr());

(

->GetData().GetInstance().GetDelta().size() > 0

&&

->GetData().GetInstance().GetDelta().front()->IsSetAction()

offset_di->Assign(*

->GetData().GetInstance().GetDelta().front());

asserted_vr->SetData().SetInstance().SetDelta().push_back(offset_di);

asserted_vr->SetData().SetInstance().SetDelta().push_back(

);

(

->GetData().GetInstance().GetDelta().size() > 0

&&

->GetData().GetInstance().GetDelta().back() !=

->GetData().GetInstance().GetDelta().front()

&&

->GetData().GetInstance().GetDelta().back()->IsSetAction()

offset_di->Assign(*

->GetData().GetInstance().GetDelta().back());

asserted_vr->SetData().SetInstance().SetDelta().push_back(offset_di);

(m_loc.loc.IsNull()) {

(eContext,

);

(m_seq_id.IsNull()) {

(eContext,

);

(m_cds.IsNull()) {

(eContext,

);

(

&& m_mol_type == eMol_not_set) {

(eContext,

);

m_mol_type = mol_type;

(m_seq_id.IsNull()) {

m_seq_id->Assign(

);

(eContext,

+

.AsFastaString());

(mol_type == eMol_c) {

(

ci(m_bsh); ci; ++ci) {

(m_cds.IsNull()) {

(eContext,

);

(m_cds.IsNull()) {

(eContext,

);

(!

.IsSetSeq_data()) {

(

.GetLength() != loc.GetTotalRange().GetLength()) {

(eSemantic,

);

(

.GetSeq_data().IsIupacna()) {

seq1 =

.GetSeq_data().GetIupacna();

}

(

.GetSeq_data().IsNcbieaa()) {

seq1 =

.GetSeq_data().GetNcbieaa();

(eLogic,

);

(seq1 != seq2 && seq2 !=

) {

(eSemantic,

+ seq1 +

+ seq2 +

);

TRuleNames::const_iterator it = s_GetRuleNames().find(

);

(it == s_GetRuleNames().end()) {

(eLogic,

);

(

->children.size() == 1) {

s(it->value.begin(), it->value.end());

}

(

->children.size() == 3) {

s(it->value.begin(), it->value.end());

}

(

->children.size() == 5) {

s1(it->value.begin(), it->value.end());

s2(it->value.begin(), it->value.end());

(s1 ==

&& s2 ==

) {

}

(s1 !=

&& s2 !=

) {

}

(s2 ==

) {

}

(s1 ==

) {

fuzzy_int.

= fuzz;

is_relative_to_stop_codon =

;

(

->children.size() == 2) {

is_relative_to_stop_codon =

;

s(it->value.begin(), it->value.end());

(eGrammatic,

);

(eContext,

);

(int_fuzz.

> 0 && !is_relative_to_stop_codon) {

(

->children.size() == 1) {

s_sign(it->value.begin(), it->value.end());

sign1 = s_sign ==

? -1 : 1;

s_ivs(it->value.begin(), it->value.end());

s_ivs_num(it->value.begin(), it->value.end());

target_exon_num = sign1 < 0 ? ivs_num + 1 : ivs_num;

(

ci(bsh, sel); ci; ++ci) {

(exon_num == target_exon_num) {

(eSemantic,

);

(eSemantic,

);

(eSemantic,

);

pnt.

.Assign(*pnt1.

);

(!pnt1->IsSetFuzz() && !pnt2->IsSetFuzz()) {

pnt->SetFuzz().SetRange().SetMin(min_pos);

pnt->SetFuzz().SetRange().SetMax(max_pos);

}

(pnt1->IsSetFuzz() && pnt2->IsSetFuzz()) {

pnt->SetFuzz().SetRange().SetMin(min_pos);

pnt->SetFuzz().SetRange().SetMax(max_pos);

pnt->

(pnt1->IsSetFuzz() ? *pnt2 : *pnt1);

pnt->SetFuzz().

(pnt1->IsSetFuzz() ? pnt1->GetFuzz()

it =

->children.rbegin()->children.begin();

mol(it->value.begin(), it->value.end());

it = (

->children.rbegin() + 1)->children.begin();

id_str(it->value.begin(), it->value.end());

.SetId(*

, mol_type);

(

->children.size() == 3) {

it = (

->children.rbegin() + 2)->children.begin();

tag_str(it->value.begin(), it->value.end());

flip_strand =

;

(

->children.size() == 3) {

(eSemantic,

);

(eSemantic,

);

.Validate(*prot_literal, *tmp_loc);

(eSemantic,

);

(eSemantic,

);

flip_strand =

;

(

->children.size() == 3) {

(eSemantic,

);

->SetSeq().SetLoc(*loc);

(eSemantic,

);

->SetSeq().SetLoc().Assign(*ofloc.

);

->SetSeq().SetLiteral(*raw_seq);

->SetSeq().SetLiteral().SetLength(int_fuzz.

);

->SetSeq().SetLiteral().SetFuzz(*int_fuzz.

);

ncbieaa = hgvsaa;

seq_str(it->value.begin(), it->value.end());

->SetSeq_data().SetNcbieaa().Set(seq_str);

->SetSeq_data().SetIupacna().Set(seq_str);

->SetLength(seq_str.size());

(bad.size() > 0) {

vr->SetLocation().Assign(

.GetLoc());

di_del->SetSeq().SetThis();

var_inst.

().push_back(di_del);

var_inst.

().push_back(di_ins);

vr->SetLocation().Assign(

.GetLoc());

di->SetSeq().SetThis();

var_inst.

().push_back(di);

(eSemantic,

);

pnt_loc->

().SetId().Assign(*

.GetLoc().GetId());

pnt_loc->

().SetStrand(

.GetLoc().GetStrand());

vr->SetLocation(*pnt_loc);

var_inst.

().push_back(delta_ins);

vr->SetLocation().Assign(

.GetLoc());

->SetSeq().SetThis();

->SetMultiplier(2);

(!dup_seq->GetSeq().IsLiteral()) {

(eSemantic,

);

}

(dup_seq->GetSeq().GetLiteral().GetLength() !=

.GetOffsetLoc().GetLength()) {

(eSemantic,

);

}

(dup_seq->GetSeq().GetLiteral().IsSetSeq_data()) {

vr->SetLocation().Assign(

.GetLoc());

(eSemantic,

);

(eSemantic,

);

->SetSeq().SetLiteral(*seq_to);

vr->SetLocation(*loc);

->SetSeq().SetLoc().Assign(*loc);

->SetSeq().SetLoc().FlipStrand();

(it !=

->children.end()) {

len_str(it->value.begin(), it->value.end());

(eSemantic,

);

(

.GetLoc().IsPnt()) {

loc->

().SetId().Assign(*

.GetLoc().GetId());

loc->

().SetFrom(

.GetLoc().GetPnt().GetPoint() - d);

loc->

().SetTo(

.GetLoc().GetPnt().GetPoint());

loc->

().SetFrom(

.GetLoc().GetPnt().GetPoint());

loc->

().SetTo(

.GetLoc().GetPnt().GetPoint() + d);

vr->SetLocation().Assign(*loc);

(; it !=

->children.end(); ++it) {

s1(it->value.begin(), it->value.end());

->SetSeq().SetLoc().Assign(*loc);

vr2->SetData().SetInstance().SetDelta().push_back(

);

vr2->SetLocation().Assign(*loc);

vr->SetData().SetSet().SetVariations().push_back(vr2);

->SetSeq().SetLoc().Assign(*loc);

->SetMultiplier_fuzz(*int_fuzz.

);

vr->SetData().SetInstance().SetDelta().push_back(

);

vr->SetLocation(*loc);

->SetSeq().SetLoc().SetNull();

vr->SetLocation().Assign(

.GetLoc());

->SetSeq().SetLoc().SetEquiv().Set().push_back(loc_this);

->SetSeq().SetLoc().SetEquiv().Set().push_back(loc_other);

(eContext,

);

vr->SetData().SetNote(

);

vr->SetLocation().Assign(

.GetLoc());

CVariation_ref::TConsequence::value_type::TObjectType TConsequence;

cons->SetFrameshift();

vr->SetConsequence().push_back(cons);

(it !=

->children.end()) {

s(it->value.begin(), it->value.end());

cons->SetFrameshift().SetX_length(x_length);

(eContext,

);

ext_type_str(it->value.begin(), it->value.end());

ext_len_str(it->value.begin(), it->value.end());

vr->SetLocation().SetPnt().SetId().Assign(

.GetId());

->SetSeq().SetLiteral().SetLength(

(ext_len));

delta_this(

TDelta::TObjectType);

delta_this->SetSeq().SetThis();

(ext_type_str ==

) {

(eSemantic,

);

vr->SetLocation().SetPnt().SetPoint(0);

var_inst.

().push_back(delta_this);

}

(ext_type_str ==

) {

(eSemantic,

);

vr->SetLocation().SetPnt().SetPoint(

.GetLength() - 1);

var_inst.

().push_back(delta_this);

(eGrammatic,

+ ext_type_str);

seq_str(it2->value.begin(), it2->value.end());

(eContext,

);

vr->SetLocation().Assign(

.GetLoc());

->SetSeq().SetLiteral().SetSeq_data().SetNcbieaa().Set(seq_str);

->SetSeq().SetLiteral().SetLength(1);

vr->SetLocation(*loc);

->SetSeq().SetThis();

s(it->value.begin(), it->value.end());

}

(s ==

) {

(eGrammatic,

+ s);

s(it->value.begin(), it->value.end());

(it->value.id() ==

->value.id() && s ==

) {

vr->SetValidated(

);

s(it->value.begin(), it->value.end());

(it->value.id() ==

->value.id() && s ==

) {

vr->SetValidated(

);

local_context.

(ofloc);

vr =

(it, local_context);

di1->SetMultiplier(-1);

di2->SetMultiplier(-1);

di2->SetSeq().SetLiteral().SetFuzz().Assign(*ofloc.

.

);

}

(it->value.id() ==

->value.id()) {

vr->SetData().SetUnknown();

vr->SetLocation().SetEmpty().Assign(

.GetId());

}

(s ==

|| s ==

) {

vr->SetData().SetUnknown();

CVariation_ref::TConsequence::value_type::TObjectType TConsequence;

cons->SetNote(

);

vr->SetConsequence().push_back(cons);

vr->SetLocation().SetEmpty().Assign(

.GetId());

vr->SetValidated(

);

}

(s ==

) {

(eGrammatic,

+ s);

s(it->value.begin(), it->value.end());

(it->value.id() ==

->value.id() && s ==

) {

vr->SetValidated(

);

(; it !=

->children.end(); ++it) {

vr->SetData().SetSet().SetVariations().push_back(inst_ref);

(

it =

->children.begin(); it !=

->children.end(); ++it) {

(it !=

->children.begin()) {

delim(it->value.begin(), it->value.end());

(it->value.id() !=

->value.id()) {

(eGrammatic,

);

(eSemantic,

);

vr->ResetLocation();

feat->

().SetVariation(*vr);

*v.

().SetSet().SetVariations().begin();

tree_parse_info<>

= pt_parse(hgvs_expression.c_str(), *

, +space_p);

feat->

().SetVariation().SetName(hgvs_expression);

CSeq_loc& parent_loc,

(

.IsSetLocation() || is_top_level) {

outs = loc_str + outs;

append_delta =

;

flipped_strand =

;

flipped_strand =

;

append_delta =

;

append_delta =

;

}

(

< 10) {

is_dup =

;

(inst.

().size() == 1) {

(

.GetSeq().IsThis() &&

.IsSetMultiplier() &&

.GetMultiplier() == 2) {

append_delta =

;

(inst.

().size() != 2) {

ins_after =

;

(inst.

().begin()->GetObject().GetSeq().IsThis()) {

}

(inst.

().rbegin()->GetObject().GetSeq().IsThis()) {

ins_after = !ins_after;

hgvs_loc.

(

CSeq_loc);

append_delta =

;

append_delta =

;

loc.Assign(*hgvs_loc);

(

.GetSeq().IsThis()) {

}

(

.GetSeq().IsLiteral()) {

}

(

.GetSeq().IsLoc()) {

(flipped_strand) {

delta_loc_str;

+= delta_loc_str;

(

.IsSetMultiplier()) {

.GetMultiplier(),

.IsSetMultiplier_fuzz() ? &

.GetMultiplier_fuzz() :

);

multiplier_str =

+ multiplier_str +

;

+= multiplier_str;

loc.Assign(*hgvs_loc);

(

.IsSetSeq_data()) {

+= multiplier_str;

(

ci(bsh); ci; ++ci) {

loc_str =

;

(loc.IsInt() && loc.GetInt().IsSetFuzz_from()) {

p_start->

().Assign(loc.GetInt().GetFuzz_from());

(loc.IsInt() && loc.GetInt().IsSetFuzz_to()) {

p_stop->

().Assign(loc.GetInt().GetFuzz_to());

loc_str = s_start +

+ s_stop;

= (with_header ? header :

) + loc_str;

mapped_pnt->

(pnt);

point_pos = mapped_pnt->

() + 1;

point_pos -= first_pos;

(point_pos <= 0) {

moltype =

;

accver +

+ moltype;

=

+ from +

+ to +

;

}

(fuzz->

()) {

=

+

+

;

=

+

+

;

+= d_len * multiplier;

(

= 0;

< multiplier;

++) {

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.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

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.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

namespace ncbi::objects::

static TSeqPos Convert(const CSeq_data &in_seq, CSeq_data *out_seq, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx=0, TSeqPos uLength=0, bool bAmbig=false, Uint4 seed=17734276)

static TSeqPos ReverseComplement(CSeq_data *in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

static void Validate(const CSeq_data &in_seq, vector< TSeqPos > *badIdx, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

Template class for iteration on objects of class C.

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

CUser_field & SetField(const string &str, const string &delim=".", const string &obj_subtype=kEmptyStr, NStr::ECase use_case=NStr::eCase)

Access a named field in this user object.

Set of related Variations.

void Validate(const CSeq_literal &literal) const

void SetLoc(const SOffsetLoc &loc)

const CSeq_loc & GetLoc() const

const CSeq_feat & GetCDS() const

void SetId(const CSeq_id &id, EMolType mol_type)

const SOffsetLoc & GetOffsetLoc() const

EMolType GetMolType(bool check=true) const

const CSeq_id & GetId() const

CVariation_inst::TDelta::value_type TDelta

static SOffsetPoint x_general_pos(TIterator const &i, const CContext &context)

static CRef< CVariation_ref > x_ssr(TIterator const &i, const CContext &context)

static CRef< CVariation_ref > x_expr2(TIterator const &i, const CContext &context)

static string s_hgvsaa2ncbieaa(const string &hgvsaa)

Convert HGVS amino-acid code to ncbieaa.

CRef< CSeq_feat > AsVariationFeat(const string &hgvs_expression, TOpFlags=fOpFlags_Default)

static CRef< CVariation_ref > x_prot_missense(TIterator const &i, const CContext &context)

string x_SeqIdToHgvsHeader(const CSeq_id &id)

Convert seq-id to HGVS seq-id header, e.g. "NM_123456.7:c." or "NG_123456.7:p".

string x_GetInstData(const CVariation_inst &inst, const CSeq_loc &this_loc)

static CRef< CVariation_ref > x_nuc_subst(TIterator const &i, const CContext &context)

static SOffsetLoc x_range(TIterator const &i, const CContext &context)

TSeqPos x_GetInstLength(const CVariation_inst &inst, const CSeq_loc &this_loc)

static CRef< CVariation_ref > x_duplication(TIterator const &i, const CContext &context)

static CRef< CVariation_ref > x_prot_ext(TIterator const &i, const CContext &context)

string x_AsHgvsExpression(const CVariation_ref &variation, const CSeq_loc &parent_loc, bool is_top_level)

variatino must have seq-loc specified

string AsHgvsExpression(const CSeq_feat &feat)

static CRef< CVariation_ref > x_mut_inst(TIterator const &i, const CContext &context)

string x_SeqPntToStr(const CSeq_point &pnt, TSeqPos first_pos)

static SFuzzyInt x_int_fuzz(TIterator const &i, const CContext &context)

static CRef< CSeq_loc > x_seq_loc(TIterator const &i, const CContext &context)

static CRef< CVariation_ref > x_list(TIterator const &i, const CContext &context)

string x_IntWithFuzzToStr(int value, const CInt_fuzz *fuzz=NULL)

static CContext x_header(TIterator const &i, const CContext &context)

static CRef< CVariation_ref > x_identity(const CContext &context)

static CRef< CVariation_ref > x_delins(TIterator const &i, const CContext &context)

static CRef< CSeq_literal > x_raw_seq(TIterator const &i, const CContext &context)

string x_InstToString(const CVariation_inst &inst, CSeq_loc &loc)

Only subset of insts can be expressed as HGVS, this will throw otherwise.

static CRef< CVariation_ref > x_insertion(TIterator const &i, const CContext &context)

static CRef< CVariation_ref > x_unwrap_iff_singleton(CVariation_ref &v)

static CSafeStatic< SGrammar > s_grammar

static SOffsetPoint x_prot_pos(TIterator const &i, const CContext &context)

static SOffsetPoint x_pos_spec(TIterator const &i, const CContext &context)

static CRef< CVariation_ref > x_translocation(TIterator const &i, const CContext &context)

string x_LocToSeqStr(const CSeq_loc &loc)

static CRef< CVariation_ref > x_deletion(TIterator const &i, const CContext &context)

static string s_hgvsUCaa2hgvsUL(const string &hgvsaa)

Convert non-HGVS compliant all-uppercase AAs to UpLow, e.g. ILECYS ->IleCys.

static TDelta x_seq_ref(TIterator const &i, const CContext &context)

static SOffsetLoc x_location(TIterator const &i, const CContext &context)

string x_SeqLocToStr(const CSeq_loc &loc, bool with_header)

static CRef< CVariation_ref > x_expr1(TIterator const &i, const CContext &context)

TParseTreeMatch::const_tree_iterator TIterator

string x_SeqLiteralToStr(const CSeq_literal &literal, bool flip_strand)

static CRef< CSeq_point > x_abs_pos(TIterator const &i, const CContext &context)

static SOffsetPoint x_fuzzy_pos(TIterator const &i, const CContext &context)

static CRef< CVariation_ref > x_expr3(TIterator const &i, const CContext &context)

static CRef< CVariation_ref > x_nuc_inv(TIterator const &i, const CContext &context)

@ fOpFlags_RelaxedAA

try assumbing all-uppercase three-letter AA representation

static CRef< CVariation_ref > x_conversion(TIterator const &i, const CContext &context)

static CRef< CVariation_ref > x_prot_fs(TIterator const &i, const CContext &context)

static CRef< CSeq_feat > x_root(TIterator const &i, const CContext &context)

static void s_FactorOutLocsInPlace(CVariation_ref &v)

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

main entry point for tests

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#define NCBI_RETHROW_SAME(prev_exception, message)

Generic macro to re-throw the same exception.

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

Set object to copy of another one.

const TPrim & Get(void) const

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

Check if both objects contain the same values.

void FlipStrand(void)

Flip the strand (e.g. plus to minus)

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

Override Assign() to incorporate cache invalidation.

TRange GetTotalRange(void) const

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

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.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

string GetAccessionForId(const objects::CSeq_id &id, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0)

Retrieve the accession string for a Seq-id.

@ eWithAccessionVersion

accession.version (when possible)

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

const TDescr & GetDescr(void) const

const CSeqFeatData & GetData(void) const

TInst_Mol GetInst_Mol(void) const

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

const_iterator begin(void) const

const_iterator end(void) const

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CTempString literal(const char(&str)[Size])

Templatized initialization from a string literal.

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

Convert string to int.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

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

Check if a string starts with a specified prefix value.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

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.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

@ fWithSign

Prefix the output value with a sign ('+'/'-')

TGenome GetGenome(void) const

Get the Genome member data.

bool IsSetGenome(void) const

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

void SetMin(TMin value)

Assign a value to Min data member.

bool IsLim(void) const

Check if variant Lim is selected.

TRange & SetRange(void)

Select the variant.

TLim GetLim(void) const

Get the variant data.

TMin GetMin(void) const

Get the Min member data.

void SetMax(TMax value)

Assign a value to Max data member.

TLim & SetLim(void)

Select the variant.

void SetType(TType &value)

Assign a value to Type data member.

bool IsRange(void) const

Check if variant Range is selected.

void SetData(TData &value)

Assign a value to Data data member.

TMax GetMax(void) const

Get the Max member data.

const TRange & GetRange(void) const

Get the variant data.

@ eLim_tl

space to left of position

@ eLim_tr

space to right of position

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TVariation & GetVariation(void) const

Get the variant data.

void SetPoint(TPoint value)

Assign a value to Point data member.

void SetId(TId &value)

Assign a value to Id data member.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

void SetStrand(TStrand value)

Assign a value to Strand data member.

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.

const TId & GetId(void) const

Get the Id member data.

TStrand GetStrand(void) const

Get the Strand member data.

bool IsPnt(void) const

Check if variant Pnt is selected.

const TIupacaa & GetIupacaa(void) const

Get the variant data.

void SetLength(TLength value)

Assign a value to Length data member.

list< CRef< CSeqdesc > > Tdata

bool IsNcbipna(void) const

Check if variant Ncbipna is selected.

bool IsNcbieaa(void) const

Check if variant Ncbieaa is selected.

bool IsNcbi8aa(void) const

Check if variant Ncbi8aa is selected.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

bool IsIupacaa(void) const

Check if variant Iupacaa is selected.

const TIupacna & GetIupacna(void) const

Get the variant data.

bool IsNcbistdaa(void) const

Check if variant Ncbistdaa is selected.

const TSource & GetSource(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

bool IsNcbi4na(void) const

Check if variant Ncbi4na is selected.

const Tdata & Get(void) const

Get the member data.

bool IsNcbi8na(void) const

Check if variant Ncbi8na is selected.

TLength GetLength(void) const

Get the Length member data.

const TNcbieaa & GetNcbieaa(void) const

Get the variant data.

bool IsNcbipaa(void) const

Check if variant Ncbipaa is selected.

bool IsNcbi2na(void) const

Check if variant Ncbi2na is selected.

bool IsIupacna(void) const

Check if variant Iupacna is selected.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

@ e_Iupacna

IUPAC 1 letter nuc acid code.

@ e_Iupacaa

IUPAC 1 letter amino acid code.

TType GetType(void) const

Get the Type member data.

list< CRef< CVariation_ref > > TVariations

const TSet & GetSet(void) const

Get the variant data.

TType GetType(void) const

Get the Type member data.

void SetType(TType value)

Assign a value to Type data member.

const TLoc & GetLoc(void) const

Get the variant data.

const TDelta & GetDelta(void) const

Get the Delta member data.

void SetData(TData &value)

Assign a value to Data data member.

const TData & GetData(void) const

Get the Data member data.

const TSeq & GetSeq(void) const

Get the Seq member data.

const TLiteral & GetLiteral(void) const

Get the variant data.

bool IsSet(void) const

Check if variant Set is selected.

void SetType(TType value)

Assign a value to Type data member.

TMultiplier GetMultiplier(void) const

Get the Multiplier member data.

list< CRef< CDelta_item > > TDelta

TVariations & SetVariations(void)

Assign a value to Variations data member.

bool IsLiteral(void) const

Check if variant Literal is selected.

bool IsSetMultiplier(void) const

Multiplier allows representing a tandem, e.g.

TDelta & SetDelta(void)

Assign a value to Delta data member.

bool IsThis(void) const

Check if variant This is selected.

bool IsLoc(void) const

Check if variant Loc is selected.

const TVariations & GetVariations(void) const

Get the Variations member data.

@ eType_snv

delta=[morph of length 1] NOTE: this is snV not snP; the latter requires frequency-based validation t...

@ eType_inv

delta=[del, ins.seq= RevComp(variation-location)]

@ eType_mnp

delta=[morph of length >1]

@ eType_microsatellite

delta=[del, ins.seq= repeat-unit with fuzzy multiplier] variation-location is the microsat expansion ...

@ eType_delins

delta=[del, ins]

@ eType_prot_nonsense

delta=[del]; variation-location is the tail of the protein being truncated

@ eType_transposon

delta=[del, ins.seq= known donor or 'this'] variation-location is equiv of transposon locs.

@ eType_prot_silent

delta=[morph of length 1, same AA as at variation-location]

@ eType_identity

delta=[]

@ eType_prot_missense

delta=[morph of length 1]

@ eType_translocation

delta=like delins

@ eType_prot_neutral

delta=[morph of length 1]

@ eAction_offset

go downstream by distance specified by multiplier (upstream if < 0), in genomic context.

@ eAction_del_at

excise sequence at location if multiplier is specified, delete len(location)*multiplier positions dow...

@ eAction_ins_before

insert seq before the location.start

@ eData_set_type_haplotype

changes on the same allele, e.g r.[13g>a;15u>c]

@ eData_set_type_compound

complex change at the same location on the same molecule

@ eData_set_type_genotype

changes on different alleles in the same genotype, e.g. g.[476C>T]+[476C>T]

@ eData_set_type_package

set represents a package of observations at a given location, generally containing asserted + referen...

@ eData_set_type_individual

same organism; allele relationship unknown, e.g. g.[476C>T(+)183G>C]

@ eData_set_type_mosaic

different genotypes in the same individual

@ eData_set_type_alleles

set represents a set of observed alleles

@ eData_set_type_products

different products arising from the same variation in a precursor, e.g. r.[13g>a, 13_88del]

@ eObservation_asserted

inst represents the asserted base at a position

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

#define HGVS_ASSERT_RULE(i, rule_id)

#define HGVS_THROW(err_code, message)

const GenericPointer< typename T::ValueType > T2 value

void AttachAssertedSequence(CVariation_ref &vr, const CSeq_literal &literal)

void RepackageAssertedSequence(CVariation_ref &vr)

Int4 delta(size_t dimension_, const Int4 *score_)

static const char delimiter[]

static CSafeStatic< TRuleNames > s_rule_names

static const string & s_GetRuleName(parser_id id)

static TRuleNames & s_GetRuleNames()

static bool s_is_list(parser_id id)

TSeqPos GetLength() const

void Assign(const SOffsetPoint &other)

static CS_CONTEXT * context

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