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NCBI C++ ToolKit: src/misc/hgvs/hgvs_writer2.cpp Source File

&& inst.

().front()->IsSetAction()

placement->

(*dinucleotide_loc);

placement->

(*loc);

(!

.GetData().IsInstance() || !

.GetData().GetInstance().IsSetObservation()) {

&& !

.IsSetPlacements()

&&

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

&&

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

&&

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

asserted_seq.

(&

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

& first_var_data = vset.

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

(!first_var_data.IsInstance() ||

s_ParentIsInvDup(

& var)

.FlipStrand(*flipped_variation);

flipped_asserted_seq->

(*asserted_seq);

(asserted_seq->IsSetSeq_data()) {

asserted_seq->GetSeq_data(),

0, asserted_seq->GetLength());

hgvs_data_str =

;

subvariation_count(0);

(

.GetData().IsInstance()

&&

.GetData().GetInstance().IsSetObservation()

hgvs_data_str += delim + subvariation_expr;

++subvariation_count;

}

(

.GetData().IsInstance()) {

}

(

.GetData().IsUnknown()) {

hgvs_data_str =

;

}

(

.GetData().IsNote()) {

hgvs_data_str =

+

.GetData().GetNote();

hgvs_data_str =

;

(hgvs_data_str ==

|| hgvs_data_str ==

) {

hgvs_data_str +=

;

(

.GetFrameshift().IsSetX_length()) {

&& find(

.GetMethod().GetMethod().begin(),

.GetMethod().GetMethod().end(),

hgvs_data_str =

+ hgvs_data_str +

;

is_bracketed =

;

location_within_brackets =

;

is_bracketed =

;

}

(subvariation_count > 1) {

location_within_brackets =

;

hgvs_loc_str =

;

(placement &&

.IsSetPlacements()) {

(location_within_brackets) {

hgvs_data_str =

+ hgvs_loc_str + hgvs_data_str +

;

hgvs_data_str = hgvs_loc_str +

+ hgvs_data_str +

;

hgvs_data_str = hgvs_loc_str + hgvs_data_str;

hgvs_data_str;

* ncbieaa =

;

* iupac3aa =

;

(

= 0;

< prot_str.size();

++) {

aa = prot_str[

];

(

.IsSetSeq_data()) {

.SetId(is_mito ? 2 : 1);

(translate &&

.GetLength() > 0) {

sign = hgvs_pos > 0 ? 1

k = (with_sign && sign == -1) ? -1 : 1;

(fuzz && fuzz->

()) {

=

+ from +

+ to +

;

&& (fuzz_gt || fuzz_lt) ?

: !hgvs_pos && fuzz_gt ?

: !fuzz->

() ?

+

+

: fuzz_gt ?

+

+

: fuzz_lt ?

+

+

sign_str = (!with_sign ?

sign_str +

;

moltype =

;

:

.GetSeqIdString(

);

idstr = idstr.substr(4);

+idstr +

+ moltype;

* offset_pos,

(offset_pos && (anchor_pos == 0 || anchor_pos >= effective_seq_length - 1)) {

resolved_pos = anchor_pos + *offset_pos;

anchor_str =

(anchor_pos, &anchor_ref_pos,

, anchor_fuzz);

anchor_str+offset_str;

vp_ref->

(orig_vp);

.AttachSeq(*vp_ref);

(

.IsGeneral() &&

.GetGeneral().GetDb() ==

) {

(lrg_resolver->CanCreate(

.GetGeneral().GetTag().GetStr())) {

idh = lrg_resolver->Get(

.GetGeneral().GetTag().GetStr());

effective_seq_length =

.GetEffectiveTranscriptLength(bsh);

loc_str =

;

start_offset = 0;

is_cdsstop_relative = cds_last_pos

&& ( pnt.

() > cds_last_pos

is_cdsstop_relative ? cds_last_pos + 1 : first_pos,

effective_seq_length,

(is_cdsstop_relative) {

loc_str =

+ loc_str;

biostart_offset = 0;

is_biostart_cdsstop_relative ? cds_last_pos + 1 : first_pos,

effective_seq_length,

(is_biostart_cdsstop_relative) {

biostart_str =

+ biostart_str;

biostop_offset = 0;

is_biostop_cdsstop_relative ? cds_last_pos + 1 : first_pos,

effective_seq_length,

biostop_str =

(prot_str.substr(prot_str.size() - 1,1)) + biostop_str;

(is_biostop_cdsstop_relative) {

biostop_str =

+ biostop_str;

(biostart_str, biostop_str);

loc_str = biostart_str +

+ biostop_str;

+= d_len * multiplier;

: p->IsSetStart_offset_fuzz() ?

: p->IsSetStop_offset_fuzz() ?

&& placement->IsSetSeq()

&& placement->GetSeq().IsSetSeq_data()

asserted_seq.

(&placement->GetSeq());

(

.AttachSeq(*p2)) {

&& explicit_asserted_seq

asserted_seq = explicit_asserted_seq.

();

s_max_literal_length = 16;

asserted_seq_str =

: asserted_seq->GetLength() < s_max_literal_length ?

(*asserted_seq, is_prot, is_mito)

inst_str =

;

append_delta =

;

inst_str = ( asserted_seq

&& asserted_seq->GetLength() < s_max_literal_length

&& asserted_seq->IsSetSeq_data()

&& !is_prot ? asserted_seq_str :

)

}

(!asserted_seq_str.empty() && s_ParentIsInvDup(

)) {

inst_str =

+ asserted_seq_str;

inst_str = (asserted_seq ? asserted_seq_str :

)+

;

append_delta =

;

placement && placement->GetLoc().IsPnt() &&

placement->GetLoc().GetPnt().GetPoint() == 0)

inst_str =

;

&& placement && placement->GetLoc().IsPnt()

&& placement->GetLoc().GetPnt().GetPoint() == bsh.

() - 1)

inst_str =

;

inst_str =

+ asserted_seq_str +

;

append_delta =

;

(placement && placement->GetLoc().IsWhole()) {

}

(is_prot) {

inst_str =

+ asserted_seq_str;

is_dup =

;

(inst.

().size() == 1) {

(

.GetSeq().IsThis() &&

.IsSetMultiplier() &&

.GetMultiplier() == 2) {

append_delta =

;

append_delta =

;

append_delta =

;

append_delta =

;

append_delta =

;

&&

.GetParent()->GetData().GetSet().GetVariations().front().GetPointer() != &

)

}

(

.GetSeq().IsThis()) {

}

(

.GetSeq().IsLiteral()) {

( inst_str == variant_str +

|| inst_str ==

+ variant_str +

)

inst_str = (!variant_str.empty() &&

(variant_str.at(0)) ?

: variant_str) +

;

inst_str += variant_str;

}

(

.GetSeq().IsLoc()) {

delta_loc_str;

p_tmp->

().Assign(

.GetSeq().GetLoc());

&& placement->GetLoc().GetId()

inst_str += delta_loc_str;

(

.IsSetMultiplier()) {

.GetMultiplier(),

.IsSetMultiplier_fuzz() ? &

.GetMultiplier_fuzz() :

);

multiplier_str =

+ multiplier_str +

;

inst_str += multiplier_str;

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_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.

Resolve LRG seq-ids, e.g. LRG_123, LRG_123t1, LRG_123p1.

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)

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 (non-medifiable version)

Template class for iteration on objects of class C.

Set of related Variations.

const CVariation * GetParent() const

static string s_OffsetPointToString(TSeqPos anchor_pos, const CInt_fuzz *anchor_fuzz, TSeqPos anchor_ref_pos, TSeqPos effective_seq_length, const long *offset_pos, const CInt_fuzz *offset_fuzz)

Construct an HGVS coordinate, which may be an intronic offset-point, e.g. "5+(10_11)".

static TSignedSeqPos s_GetHgvsPos(TSeqPos abs_pos, const TSeqPos *atg_pos)

if no atg_pos, assume that not dealing with coordinate systems (simply return abs-pos) otherwise,...

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....

CRef< CVariantPlacement > x_AdjustPlacementForHgvs(const CVariantPlacement &p, const CVariation_inst &inst)

In some cases the placement needs to be adjusted depending on inst, e.g.

string x_AsHgvsInstExpression(const CVariation &inst_variation, CConstRef< CVariantPlacement > p, CConstRef< CSeq_literal > asserted_seq)

Create "inst" part of HGVS expression.

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

static string s_IntWithFuzzToStr(long pos, const TSeqPos *ref_pos, bool with_sign, const CInt_fuzz *fuzz)

this function may be used to create hgvs-coordinates (if ref_pos is not null), or to create a fuzzy h...

CConstRef< CSeq_literal > x_FindAssertedSequence(const CVariation &v)

If the variation is a package-set, find the subvariation with observation-type "asserted" and return ...

string x_LocToSeqStr(const CSeq_loc &loc)

Get literal seq at location.

TSeqPos x_GetInstLength(const CVariation_inst &inst, const CVariantPlacement &p, bool account_for_multiplier)

Compute length of the delta.

string x_AsHgvsExpression(const CVariation &variation, CConstRef< CSeq_id > id, CConstRef< CSeq_literal > asserted_seq)

Construct HGVS expression for a variation: use first VariantPlacement, or, if id is specified,...

string x_SeqLiteralToStr(const CSeq_literal &literal, bool translate, bool is_mito)

translate=true will translate nucleotide literal to prot as appropriate.

string x_PlacementCoordsToStr(const CVariantPlacement &vp)

static const CVariation::TPlacements * s_GetPlacements(const CVariation &v)

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

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.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_THROW(exception_class, err_code, message)

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

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

Set object to copy of another one.

const TPrim & Get(void) const

#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.

ENa_strand GetStrand(void) const

Get the location's strand.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

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

TSeqPos GetStop(ESeqLocExtremes ext) 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.

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

Merge ranges in the seq-loc.

CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Add two seq-locs.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

const CBioSource * GetBioSource(const CBioseq &bioseq)

Retrieve the BioSource object for a given bioseq handle.

string GetAccessionForGi(TGi gi, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0)

Retrieve the accession for a given GI.

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

@ fIs5PrimePartial

= 0x4 Translate first codon even if not start codon (because sequence is 5' partial)

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

const CSeqFeatData & GetData(void) const

TInst_Length GetInst_Length(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

const CSeq_loc & GetLocation(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

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#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 string LongToString(long value, TNumToStringFlags flags=0, int base=10)

Convert Int to string.

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

Check if a string starts with a specified prefix value.

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

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.

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...

TGenome GetGenome(void) const

Get the Genome member data.

bool IsLim(void) const

Check if variant Lim is selected.

TLim GetLim(void) const

Get the variant data.

TMin GetMin(void) const

Get the Min member data.

bool IsRange(void) const

Check if variant Range is selected.

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

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TFuzz_from & GetFuzz_from(void) const

Get the Fuzz_from member data.

bool IsEmpty(void) const

Check if variant Empty is selected.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

const TFuzz_to & GetFuzz_to(void) const

Get the Fuzz_to member data.

TFrom GetFrom(void) const

Get the From member data.

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.

bool IsSetFuzz_to(void) const

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

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 IsNull(void) const

Check if variant Null is selected.

bool IsSetFuzz_from(void) const

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

bool IsPnt(void) const

Check if variant Pnt is selected.

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.

bool IsNcbi4na(void) const

Check if variant Ncbi4na is selected.

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 IsSetSeq_data(void) const

may have the data Check if a value has been assigned to Seq_data data member.

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_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Iupacna

IUPAC 1 letter nuc acid code.

TMol GetMol(void) const

Get the Mol member data.

bool IsSetStop_offset_fuzz(void) const

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

list< CRef< CVariantPlacement > > TPlacements

list< CRef< CVariation > > TVariations

const TStop_offset_fuzz & GetStop_offset_fuzz(void) const

Get the Stop_offset_fuzz member data.

bool IsInstance(void) const

Check if variant Instance is selected.

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...

const TInstance & GetInstance(void) const

Get the variant data.

bool IsSetStart_offset_fuzz(void) const

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

const TVariations & GetVariations(void) const

Get the Variations member data.

TStop_offset GetStop_offset(void) const

Get the Stop_offset member data.

const TSeq & GetSeq(void) const

Get the Seq member data.

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.

const TStart_offset_fuzz & GetStart_offset_fuzz(void) const

Get the Start_offset_fuzz 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.

TType GetType(void) const

Get the Type member data.

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_alleles

set represents a set of observed alleles

@ 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

@ eMethod_E_computational

TType GetType(void) const

Get the Type member data.

const TLoc & GetLoc(void) const

Get the variant data.

const TDelta & GetDelta(void) const

Get the Delta member data.

const TSeq & GetSeq(void) const

Get the Seq member data.

const TLiteral & GetLiteral(void) const

Get the variant data.

TMultiplier GetMultiplier(void) const

Get the Multiplier member data.

list< CRef< CDelta_item > > TDelta

bool IsLiteral(void) const

Check if variant Literal is selected.

bool IsSetMultiplier(void) const

Multiplier allows representing a tandem, e.g.

bool IsThis(void) const

Check if variant This is selected.

bool IsLoc(void) const

Check if variant Loc is selected.

@ 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_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_prot_neutral

delta=[morph of length 1]

@ eAction_ins_before

insert seq before the location.start

@ eObservation_variant

inst represent the observed variant at a given position

@ eObservation_asserted

inst represents the asserted base at a position

@ eObservation_reference

inst represents the reference base at the position

string Ncbieaa2HgvsAA(const string &prot_str)

bool ContainsAnyFuzz(CConstRef< CVariantPlacement > p)

bool IsMitochondrion(CBioseq_Handle bsh)

Int4 delta(size_t dimension_, const Int4 *score_)

Calculate upstream (first) and downstream(second) flanks for loc.

CRef< CSeq_loc > upstream

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