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NCBI C++ ToolKit: src/misc/hgvs/hgvs_parser2.cpp Source File

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

* iupac_bases =

;

(

= 0;

<

.size();

++) {

(eSemantic,

);

ext_interval = 10000;

(str1.size() >= seq.size()) {

(

= 0u;

< str1.size() - seq.size(); ++

) {

repeat_unit_loc->

(*loc1);

repeat_unit_loc->

().SetTo() -=

;

repeat_unit_loc->

().SetFrom(repeat_unit_loc->

().

() - (seq.size() - 1));

repeat_unit_loc->

().SetFrom() +=

;

repeat_unit_loc->

().SetTo(repeat_unit_loc->

().

() + (seq.size() - 1));

container->

().Set().push_back(repeat_unit_loc);

(CSeq_loc_CI ci(*merged_repeats); ci; ++ci) {

CSeq_loc& loc2 = ci.GetEmbeddingSeq_loc();

->ResetPlacements();

container->SetData().SetSet().SetVariations().push_back(

);

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

);

container->SetData().SetSet().SetVariations().push_back(asserted_vr);

: m_hgvs(other.m_hgvs)

(m_cds.IsNull()) {

(eContext,

);

SetPlacement().SetMol(mol);

SetPlacement().SetLoc().SetWhole().Assign(

);

(eContext,

+

.AsFastaString());

(

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

(m_cds.IsNull()) {

(eContext,

);

(m_cds.IsNull()) {

(eContext,

);

(eLogic,

);

s_rule_names[

.to_long()];

(

->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 ==

) {

<

T>

(

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

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

(eGrammatic,

);

(eContext,

);

(

->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) {

(ofpnt.

->

() >= transcribed_len) {

anchor_pos = transcribed_len - 1;

(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()

(

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

annotated_transcript_feats.

(

(

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

annotated_transcript_aligns.

(

vector<CSeq_id_Handle> v;

set_intersection(annotated_transcript_feats.

(),

annotated_transcript_feats.

(),

annotated_transcript_aligns.

(),

annotated_transcript_aligns.

(),

&

= *it->GetSeqId();

&&

.GetGeneral().GetDb() ==

)

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());

(eSemantic,

+ id_str +

+ idh.

());

already_found =

;

(

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

(eSemantic,

+ idh.

());

already_found =

;

(!already_found) {

(eSemantic,

+ idh.

());

(eSemantic,

);

(eSemantic,

+ idh.

());

(

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

it = (

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

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

flip_strand =

;

(

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

(eSemantic,

);

(eSemantic,

);

(eSemantic,

);

(eSemantic,

);

? p->

().SetSeq_data().SetNcbieaa().Set()

: p->

().SetSeq_data().SetIupacna().Set();

placement->

().SetPnt(*pnt.

);

? placement->

().SetSeq_data().SetNcbieaa().Set()

: placement->

().SetSeq_data().SetIupacna().Set();

exception->SetMessage(

);

.CheckPlacement(*placement);

flip_strand =

;

(

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

flip_strand =

;

p->

().FlipStrand();

(eSemantic,

);

(it ==

->children.end()) {

(eLogic,

+

.GetHgvs());

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

(eSemantic,

);

tmp_out(

);

(

!=

) {

found =

;

(

i_ncbistdaa = 0; i_ncbistdaa < 28; i_ncbistdaa++) {

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

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

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

->SetLength(seq_str.size());

vector<TSeqPos> bad;

(bad.size() > 0) {

:

.GetSeq().IsLiteral() ?

.GetSeq().GetLiteral().GetLength()

:

.GetSeq().IsThis() ? loc_len

(

.IsSetMultiplier()) {

del_len =

(*del_vr->GetData().GetInstance().GetDelta().front(), placement_len);

ins_len =

(*ins_vr->GetData().GetInstance().GetDelta().front(), placement_len);

del_vr->SetData().SetInstance().SetType(

(del_len, ins_len));

del_vr->SetData().SetInstance().SetDelta() = ins_vr->SetData().SetInstance().SetDelta();

del_vr->SetData().SetInstance().SetDelta().front()->ResetAction();

(ins_len == 1 && del_len == 1) {

ex->SetMessage(

);

di->SetSeq().SetThis();

var_inst.

().push_back(di);

ex->SetMessage(

);

(eSemantic,

);

var_inst.

().push_back(delta_ins);

->SetSeq().SetThis();

->SetMultiplier(2);

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

(eSemantic,

);

->SetSeq().SetLiteral().Assign(p.

());

->SetSeq().SetThis();

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

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

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

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

&&

->GetSeq_data().IsIupacna()

->GetSeq_data().GetIupacna(),

p.

().Assign(*ssr_loc);

(; it !=

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

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

->SetSeq().SetThis();

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

);

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

->SetSeq().SetThis();

->SetMultiplier_fuzz(*int_fuzz.

);

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

);

it =

->children.begin();

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

vr->SetSynonyms().push_back(

+ iscn_expr);

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

(eContext,

);

vr->SetData().SetNote(

);

vr->SetFrameshift();

(it !=

->children.end()) {

(it !=

->children.end()) {

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

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

(eContext,

);

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

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

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

(ext_len) + 1);

(ext_type_str ==

) {

(eSemantic,

);

}

(ext_type_str ==

|| ext_type_str ==

|| ext_type_str ==

)

(eSemantic,

);

(eGrammatic,

+ ext_type_str);

(eContext,

);

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

s(

->value.begin(),

->value.end());

vr->SetData().SetNote(s);

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

vr->SetData().SetUnknown();

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

(it->value.id() ==

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

) {

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

(it->value.id() ==

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

) {

vr =

(it, local_context);

}

(it->value.id() ==

->value.id()) {

vr->SetData().SetUnknown();

}

(s ==

|| s ==

) {

di->SetSeq().SetThis();

var_inst.

().push_back(di);

(eGrammatic,

+ s);

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

(it->value.id() ==

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

) {

(; it !=

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

(inst_ref->GetData().IsNote()

&& inst_ref->GetData().GetNote() ==

)

(vr->SetData().SetSet().SetVariations().size() > 0) {

vr->SetData().SetSet().SetVariations().back()->SetFrameshift().Assign(inst_ref->GetFrameshift());

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

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

);

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

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

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

(

it =

->children.begin(); it !=

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

(it !=

->children.begin()) {

}

(set_type != varset.

()) {

(eSemantic,

);

(p.

() != mol) {

ex->SetMessage(

+ asserted_header +

+ expected_header +

);

tree_parse_info<>

= pt_parse(hgvs2.c_str(), *

, +space_p);

tree_to_xml(ostr,

.trees, hgvs2.c_str() , CHgvsParser::SGrammar::s_GetRuleNames());

.CheckAmbiguitiesInLiterals(*vr);

(!

.IsSetPlacements()) {

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.

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:

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

namespace ncbi::objects::

static TIndex GetMapToIndex(CSeq_data::E_Choice from_type, CSeq_data::E_Choice to_type, TIndex from_idx)

static const string & GetCode(CSeq_data::E_Choice code_type, TIndex idx)

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

static const string & GetIupacaa3(TIndex ncbistdaa)

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

Template class for iteration on objects of class C.

Set of related Variations.

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

CContext(CRef< CScope > scope, CSeq_id_Resolver::TResolvers &id_resolvers, const string &hgvs)

const CSeq_id & GetId() const

void SetId(const CSeq_id &id, CVariantPlacement::TMol mol)

CVariantPlacement & SetPlacement()

const CSeq_feat & GetCDS() const

CSeq_id_Resolver::TResolvers m_seq_id_resolvers

CRef< CVariantPlacement > m_placement

static CRef< CVariation > x_string_content(TIterator const &i, const CContext &context)

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

static CVariation::TData::TSet::EData_set_type x_list_delimiter(TIterator const &i, const CContext &context)

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

static void sx_AppendMoltypeExceptions(CVariation &v, CScope &scope)

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

static string s_SeqIdToHgvsStr(const CVariantPlacement &vp, CScope *scope=NULL)

Construct an hgvs "header" consisting of seq-id and mol-type, e.g. "NG_016831.1:g....

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

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

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

static CRef< CVariation > x_unwrap_iff_singleton(CVariation &v)

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 > x_no_change(TIterator const &i, const CContext &context)

TParseTreeMatch::const_tree_iterator TIterator

static CRef< CVariation > x_insertion(TIterator const &i, const CContext &context, bool check_loc)

static void s_SetStopOffset(CVariantPlacement &p, const CHgvsParser::SFuzzyInt &fint)

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

static void s_SetStartOffset(CVariantPlacement &p, const CHgvsParser::SFuzzyInt &fint)

CSeq_id_Resolver::TResolvers m_seq_id_resolvers

string AsHgvsExpression(const CVariation &variation, CConstRef< CSeq_id > seq_id=CConstRef< CSeq_id >(NULL))

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

CVariation_inst::TDelta::value_type TDelta

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

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

static CSafeStatic< SGrammar > s_grammar

void AttachHgvs(CVariation &v)

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

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

static bool s_hgvs_iupacaa2ncbieaa(const string &hgvsaa, string &out)

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

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

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

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

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

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

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

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

static CRef< CVariantPlacement > x_range(TIterator const &i, const CContext &context)

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

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< CVariantPlacement > x_location(TIterator const &i, const CContext &context)

static bool s_hgvsaa2ncbieaa(const string &hgvsaa, string &out)

Convert HGVS amino-acid code to ncbi code.

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

CRef< CVariation > AsVariation(const string &hgvs_expression, TOpFlags=fOpFlags_Default)

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

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

static void s_FactorOutPlacements(CVariation &v)

If at any level in variation-set all variations have all same placements, move them to the parent lev...

static TSeqPos s_GetLength(const CVariantPlacement &p, CScope *scope)

TSeqPos GetEffectiveTranscriptLength(const CBioseq_Handle &bsh)

Length up to last position of the last exon (i.e.

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

main entry point for tests

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

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_REPORT_EXCEPTION(title, ex)

Generate a report on the exception.

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

Set object to copy of another one.

#define MSerial_AsnText

I/O stream manipulators –.

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

Check if both objects contain the same values.

CConstRef< CSeq_id > GetSeqId(void) const

CSeq_id::EAccessionInfo IdentifyAccession(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

string AsString(void) const

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

Override Assign() to incorporate cache invalidation.

const CSeq_id * GetId(void) const

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

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

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...

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

Returns the sequence::ECompare containment relationship between CSeq_locs.

CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)

Merge ranges in the seq-loc.

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eNoOverlap

CSeq_locs do not overlap or abut.

@ eGetId_ForceAcc

return only an accession based seq-id

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

vector< CSeq_id_Handle > TId

bool IsNucleotide(void) const

const CSeqFeatData & GetData(void) const

bool IsSetProduct(void) const

TInst_Length GetInst_Length(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const TId & GetId(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & SetResolveTSE(void)

SetResolveTSE() is equivalent to SetResolveMethod(eResolve_TSE).

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

const CSeq_loc & GetProduct(void) const

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().

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert size_t to string.

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

Convert int to string.

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.

size_type find(const CTempString match, size_type pos=0) const

Find the first instance of the entire matching string within the current string, beginning at an opti...

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.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

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.

void SetMax(TMax value)

Assign a value to Max data member.

TLim & SetLim(void)

Select the variant.

bool IsRange(void) const

Check if variant Range is selected.

@ eLim_other

something else

@ eLim_tl

space to left of position

@ eLim_tr

space to right of position

bool IsSpliced(void) const

Check if variant Spliced is selected.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

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.

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.

const TId & GetId(void) const

Get the Id member data.

TStrand GetStrand(void) const

Get the Strand member data.

TTo GetTo(void) const

Get the To member data.

bool IsWhole(void) const

Check if variant Whole is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsPnt(void) const

Check if variant Pnt is selected.

TLength GetLength(void) const

Get the Length member data.

const TNcbieaa & GetNcbieaa(void) const

Get the variant data.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Ncbistdaa

consecutive codes for std aas

void SetStop_offset_fuzz(TStop_offset_fuzz &value)

Assign a value to Stop_offset_fuzz data member.

TMol GetMol(void) const

Get the Mol member data.

TMethod & SetMethod(void)

Assign a value to Method data member.

list< CRef< CVariantPlacement > > TPlacements

void SetStop_offset(TStop_offset value)

Assign a value to Stop_offset data member.

bool IsSetMol(void) const

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

list< CRef< CVariation > > TVariations

bool IsSetPlacements(void) const

where this beast is seen note that this is a set of locations, and there are no restrictions to the c...

void SetHgvs_name(const THgvs_name &value)

Assign a value to Hgvs_name data member.

void ResetExceptions(void)

Reset Exceptions data member.

void SetData(TData &value)

Assign a value to Data data member.

void ResetStop_offset(void)

Reset Stop_offset data member.

void ResetStart_offset_fuzz(void)

Reset Start_offset_fuzz data member.

const TSet & GetSet(void) const

Get the variant data.

bool IsSetSeq(void) const

for situations in which a raw location isn't sufficient Check if a value has been assigned to Seq dat...

TExceptions & SetExceptions(void)

Assign a value to Exceptions data member.

const TVariations & GetVariations(void) const

Get the Variations member data.

void SetSeq(TSeq &value)

Assign a value to Seq data member.

void ResetStop_offset_fuzz(void)

Reset Stop_offset_fuzz data member.

void ResetStart_offset(void)

Reset Start_offset data member.

void SetType(TType value)

Assign a value to Type data member.

const TSeq & GetSeq(void) const

Get the Seq member data.

TPlacements & SetPlacements(void)

Assign a value to Placements data member.

void SetStart_offset(TStart_offset value)

Assign a value to Start_offset data member.

void ResetSeq(void)

Reset Seq data member.

const TData & GetData(void) const

Get the Data member data.

void SetMol(TMol value)

Assign a value to Mol data member.

bool IsSetStop_offset(void) const

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

TVariations & SetVariations(void)

Assign a value to Variations data member.

const TMethod & GetMethod(void) const

Get the Method member data.

bool IsSetStart_offset(void) const

location refinements, describing offsets into introns from product coordinates.

const TLoc & GetLoc(void) const

Get the Loc member data.

bool IsSet(void) const

Check if variant Set is selected.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

TSynonyms & SetSynonyms(void)

Assign a value to Synonyms data member.

TType GetType(void) const

Get the Type member data.

void SetStart_offset_fuzz(TStart_offset_fuzz &value)

Assign a value to Start_offset_fuzz data member.

TStart_offset GetStart_offset(void) const

Get the Start_offset member data.

@ eData_set_type_genotype

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

@ eData_set_type_chimeric

e.g. c.[1C>T//2G>T]

@ eData_set_type_package

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

@ eData_set_type_compound

complex change at the same location on the same molecule

@ eData_set_type_individual

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

@ eData_set_type_products

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

@ eData_set_type_haplotype

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

@ eData_set_type_mosaic

different genotypes in the same individual

@ eMol_cdna

"c." coordinates in HGVS

@ eMol_mitochondrion

"mt." coordinates in HGVS

@ eMol_rna

"n." coordinates in HGVS

@ eMol_protein

"p." coordinates in HGVS

@ eMol_genomic

"g." coordinates in HGVS

@ eCode_hgvs_exon_boundary

anchor position in an intronic HGVS expression is not at an exon boundary

@ eCode_hgvs_parsing

invalid hgvs expression

@ eCode_inconsistent_asserted_moltype

asserted mol-type is inconsistent with seq-id (e.g. NM_12345.6:g.)

@ eMethod_E_computational

void SetType(TType value)

Assign a value to Type data member.

TDelta & SetDelta(void)

Assign a value to Delta data member.

@ 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_transposon

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

@ eType_prot_other

delta=any

@ 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

@ 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

@ eObservation_asserted

inst represents the asserted base at a position

#define HGVS_ASSERT_RULE(i, rule_id)

#define HGVS_THROW(err_code, message)

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

static void text(MDB_val *v)

CVariation_inst::EType GetDelInsSubtype(int del_len, int ins_len)

void SetComputational(CVariation &variation)

bool IsPureFuzzPoint(const CSeq_point &p)

void RepackageAssertedSequence(CVariation &vr)

bool IsLRG(CBioseq_Handle &bsh)

T AdjustHgvsCoord(T val, TSeqPos offset, bool adjust)

CSeq_id_Handle GetUniquePrimaryTranscriptId(CBioseq_Handle &bsh)

bool SeqsMatch(const string &query, const char *text)

CVariantPlacement & SetFirstPlacement(CVariation &v)

CRef< CSeq_loc > FindSSRLoc(const CSeq_loc &loc, const string &seq, CScope &scope)

int GetDeltaLength(const CDelta_item &delta, int loc_len)

void AdjustMoltype(CVariation &vr, CScope &scope)

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

Int4 delta(size_t dimension_, const Int4 *score_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

int GetLoc(const string &acc, const string &pat, CSeq_loc &loc, CScope &scope)

static bool s_is_list(parser_id id)

static bool s_is_list_a(parser_id id)

static const char * s_rule_names[SGrammar::eNodeIds_SIZE]

static const string s_GetRuleName(parser_id id)

void Assign(const SOffsetPoint &other)

static CS_CONTEXT * context

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