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NCBI C++ ToolKit: src/objtools/variation/variation_utils.cpp Source File

deltas.front()->GetSeq().GetLiteral().GetSeq_data().GetIupacna().Get();

);

|| !

.GetData().GetSet().IsSetVariations())

(isFullyShifted) {

ref_at_location;

asserted_ref = delta_item.

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

delta_item.

().SetLiteral().SetSeq_data().SetIupacna().Set(ref_at_location);

vp.

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

(isFullyShifted) {

annot.

().SetFtable()) {

(isFullyShifted) {

(isFullyShifted) {

asserted_ref = delta_item.

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

delta_item.

().SetLiteral().SetSeq_data().SetIupacna().Set(ref_at_location);

(asserted_ref.empty()

(asserted_ref.empty()) {

(

<<

<< asserted_ref <<

<< ref_at_location

(asserted_ref == ref_at_location)

add_asserted_ref =

;

allele = delta_item.

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

(asserted_ref == allele) {

add_asserted_ref =

;

(ref_at_location == allele) {

delta_item.

().SetLiteral().SetSeq_data().SetIupacna().Set(asserted_ref);

add_asserted_ref =

;

(

<<

<< add_asserted_ref);

(add_asserted_ref) {

inst->SetType(asserted_allele_type);

->SetIupacna().Set(asserted_ref);

item->SetSeq().SetLiteral().Assign(*

);

inst->SetDelta().push_back(item);

->SetData().SetInstance().Assign(*inst);

vr.

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

);

ref_at_location;

(ref_at_location.empty())

(

=0;

<ref_at_location.size();

++)

(ref_at_location[

] !=

&& ref_at_location[

] !=

&& ref_at_location[

] !=

&& ref_at_location[

] !=

)

ref_at_location;

loc.GetLabel(&loc_label);

ref_at_location;

(asserted_ref == ref_at_location)

add_asserted_ref =

;

allele = delta_item.

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

(asserted_ref == allele) {

add_asserted_ref =

;

(ref_at_location == allele) {

delta_item.

().SetLiteral().SetSeq_data().SetIupacna().Set(asserted_ref);

add_asserted_ref =

;

(add_asserted_ref)

inst->SetType(asserted_allele_type);

->SetIupacna().Set(asserted_ref);

item->SetSeq().SetLiteral().Assign(*

);

inst->SetDelta().push_back(item);

->SetData().SetInstance().Assign(*inst);

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

);

asserted_ref.clear();

ref_at_location.clear();

feat = feat_to_shift;

(ref_at_location.empty())

found_allele_from_identity =

;

found_allele_from_identity =

;

(found_allele_from_identity) {

(asserted_ref.empty() ||

asserted_ref == ref_at_location);

(asserted_ref.empty()) {

(asserted_ref == ref_at_location);

identity_present =

;

identity_present =

;

(

.empty()) {

(identity_present)

(

.size() == 1)

*

.begin();

identity_present =

;

set<CVariation_inst::TType>

;

identity_present =

;

(

.empty()) {

(identity_present)

(

.size() == 1)

*

.begin();

(vector<string>, alt_it, alts) {

(crus.

() != 1)

*crus.

();

(vector<string>, alt_it, alts) {

(crus.

() != 1)

*crus.

();

& candidate,

& target)

(target.length() % candidate.length() != 0)

factor = target.length() / candidate.length();

test_candidate;

(

jj=0; jj<factor ; jj++) {

test_candidate += candidate;

(test_candidate == target)

(vector<string>::size_type ii=1; ii <=

.length() / 2 ; ++ii) {

(

.length() % ii != 0 )

;

candidate =

.substr(0,ii);

uo->

().SetStr(

);

var.

().push_back(uo);

uo->

(

,

);

uo->

().SetStr(

);

feat.

().push_back(uo);

uo->

(

,

);

(

<<

<< accession );

( !seqvec_ref || seqvec_ref->

() )

(

<<

<< accession );

(

<<

<< accession );

(

<<

<< accession );

seqvec.

();

(v.rbegin(), v.rbegin() + 1, v.rend());

(

<<

);

|| !

.GetData().GetSet().IsSetVariations())

CSeq_loc& loc = vp.

();

ResetFullyShifted(

, loc, sep,

, deletion_size);

x_ConvertIntervalToPoint(loc,

(loc.IsSetStrand())

strand = loc.GetStrand();

common_repeat_unit_allele =

(

<<

<< common_repeat_unit_allele);

( common_repeat_unit_allele ==

)

rotation_counter=0;

(!ProcessShift(common_repeat_unit_allele, sep,

(

<<

<<

rotation_counter <<

<<

common_repeat_unit_allele);

allele_size = 0;

CVariation::TData::C_Data::e_Instance:

(

ii=0; ii<rotation_counter; ++ii) {

inst.

().front()->SetSeq().SetLiteral().SetSeq_data().SetIupacna().Set(allele);

(

<<

);

CVariation::TData::C_Data::e_Set:

(

ii=0; ii<rotation_counter; ++ii) {

inst.

().front()->SetSeq().SetLiteral().SetSeq_data().SetIupacna().Set(allele);

(

<<

);

(

<<

);

ref_literal =

(&delta_item.

().SetLiteral());

rotation_counter = 0;

found = ProcessShift(ref_allele,

*seqvec, rotation_counter,

);

ref_literal->

().SetIupacna().Set(ref_allele);

(ref_allele.size()));

annot.

().SetFtable()) {

x_Shift(**feat_it, scope);

vector<string> alts;

ResetFullyShifted(feat, featloc, sep,

, deletion_size);

&& featloc.IsInt()) {

x_ConvertIntervalToPoint(featloc,

seqvec = PrefetchSequence(scope,seq_id,strand);

common_repeat_unit_allele =

( common_repeat_unit_allele ==

)

rotation_counter=0;

(!ProcessShift(common_repeat_unit_allele, sep,

(

<<

<<

rotation_counter <<

<<

common_repeat_unit_allele);

allele_size = 0;

(

ii=0; ii<rotation_counter; ++ii) {

(

<<

<< ii <<

<< allele);

inst.

().front()->SetSeq().SetLiteral().SetSeq_data().SetIupacna().Set(allele);

(

<<

);

(

ii=0; ii<rotation_counter; ++ii) {

(

<<

<< ii <<

<< allele);

inst.

().front()->SetSeq().SetLiteral().SetSeq_data().SetIupacna().Set(allele);

(

<<

);

(

<<

);

ref_literal =

(&delta_item.

().SetLiteral());

rotation_counter = 0;

found = ProcessShift(ref_allele,

sep, *seqvec, rotation_counter,

);

ref_literal->

().SetIupacna().Set(ref_allele);

ModifyLocation(featloc, sep,

&seq_id = *loc.GetId();

(loc.IsSetStrand())

strand = loc.GetStrand();

rotation_counter=0;

isShifted =

;

tmp_allele = allele;

isShifted = ProcessShift(tmp_allele,

*seqvec, rotation_counter,

);

isShifted = ProcessShift(compact,

*seqvec, rotation_counter,

);

(loc.GetInt().IsSetStrand())

pnt->

( loc.GetInt().GetStrand() );

pnt->

().Assign(loc.GetInt().GetId());

loc.SetPnt().Assign(*pnt);

pos_left,

pos_right)

interval->

(pos_left);

interval->

(pos_right);

(loc.GetPnt().IsSetStrand())

interval->

( loc.GetPnt().GetStrand() );

interval->

().Assign(loc.GetPnt().GetId());

loc.SetInt().Assign(*interval);

& field_text)

uo->

().SetStr(

);

var.

().push_back(uo);

& field_text)

uo->

().SetStr(

);

feat.

().push_back(uo);

& common_repeat_unit_allele,

& rotation_counter,

(common_repeat_unit_allele.empty())

five_prime_last_nt;

five_prime_last_nt =

(sep.

-1,1,seqvec);

<< five_prime_last_nt <<

<< common_repeat_unit_allele);

did_rotate =

;

( !five_prime_last_nt.empty()

&& (*common_repeat_unit_allele.rbegin() == *five_prime_last_nt.begin()) ) {

*common_repeat_unit_allele.rbegin() <<

<<

*five_prime_last_nt.begin() <<

<<

sep.

-1 <<

);

(common_repeat_unit_allele);

(

<<

<< rotation_counter <<

<< common_repeat_unit_allele);

five_prime_last_nt =

(sep.

-1,1,seqvec);

*common_repeat_unit_allele.rbegin() <<

<<

*five_prime_last_nt.begin() <<

<<

<<

<< common_repeat_unit_allele);

& rotation_counter,

(compact_allele.empty())

three_prime_first_nt;

three_prime_first_nt =

(sep.

,1,seqvec);

three_prime_first_nt =

(sep.

+1,1,seqvec);

<< sep.

<<

<< three_prime_first_nt <<

<< *compact_allele.begin());

did_rotate =

;

( !three_prime_first_nt.empty()

&& (*compact_allele.begin() == *three_prime_first_nt.begin()) ) {

*compact_allele.begin() <<

<<

*three_prime_first_nt.begin() <<

<<

three_prime_first_nt =

(sep.

,1,seqvec);

three_prime_first_nt =

(sep.

+1,1,seqvec);

<<

<< sep.

<<

<< compact_allele);

loc.SetInt().SetFrom(sep.

);

loc.SetInt().SetTo(sep.

);

loc.SetPnt().SetPoint(sep.

);

loc.SetInt().SetFrom(sep.

);

loc.SetInt().SetTo(sep.

);

loc.SetPnt().SetPoint(sep.

);

loc.SetPnt().SetPoint(sep.

);

loc.SetInt().SetFrom(sep.

);

loc.SetInt().SetTo(sep.

);

loc.SetInt().SetFrom(sep.

-1);

loc.SetInt().SetTo(sep.

);

(deletion_size == 1)

loc.SetPnt().SetPoint(sep.

);

loc.SetInt().SetFrom(sep.

);

loc.SetInt().SetTo(sep.

+deletion_size-1);

|| uo->

().

() !=

)

& deletion_size)

sep.

= sep.

+ deletion_size -1;

, deletion_size);

(var.

().size() == 0)

& deletion_size)

sep.

= sep.

+ deletion_size -1;

, deletion_size);

(feat.

().size() == 0)

common_repeat_unit_allele_tmp = common_repeat_unit_allele;

common_repeat_unit_allele, sep_tmp,

seqvec,rotation_counter,

);

ignored_counter=0;

common_repeat_unit_allele_tmp, sep,

seqvec,ignored_counter,

);

found_left | found_right;

orig_common_repeat_unit_allele = common_repeat_unit_allele;

common_repeat_unit_allele,sep,

seqvec,rotation_counter,

);

sep.

= orig_pos_left;

common_repeat_unit_allele = orig_common_repeat_unit_allele;

annot.

().SetFtable()) {

vinst_identity->SetType(

);

vinst_identity->SetDelta().push_back(

);

->SetSeq_data(*seq_data);

vref_identity->SetData().SetInstance(*vinst_identity);

vref_identity;

* seq_id = loc.GetId();

(loc.IsSetStrand()) {

strand = loc.GetStrand();

vector<string> alts;

inserted_seq = alts.front() + ref_seq;

= feat.

().SetVariation().SetData().SetSet().SetVariations();

variation_list.clear();

(ref_seq.length() == 1) {

loc.SetInt().SetTo() = loc.SetInt().SetTo() - 1;

* seq_id = loc.GetId();

(loc.IsSetStrand()) {

strand = loc.GetStrand();

vector<string> alts;

inserted_seq = ref_seq.substr(ref.length());

= feat.

().SetVariation().SetData().SetSet().SetVariations();

variation_list.clear();

(target_ctxt) {

(target_ctxt) {

(target_ctxt) {

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

static CRef< CSeqVector > PrefetchSequence(CScope &scope, const CSeq_id &seq_id, ENa_strand strand)

static TSeqPos GetSeqSize(CSeqVector &seqvec)

static CCache< string, CRef< CSeqVector > > m_cache

static string GetSeq(int pos, int length, CSeqVector &seqvec)

namespace ncbi::objects::

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

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

static void Rotate(string &v)

static void ModifyLocation(CSeq_loc &loc, SEndPosition &sep, const CVariation_inst::TType type, const TSeqPos &deletion_size)

static void ConvertExpandedDeletionToDelIns(CSeq_feat &feat, CScope &scope)

static void ConvertExpandedInsertionToDelIns(CSeq_feat &feat, CScope &scope)

static bool ProcessShift(string &allele, SEndPosition &sep, CSeqVector &seqvec, int &rotation_counter, const CVariation_inst::TType type)

static void ModifyLocation(CSeq_loc &loc, SEndPosition &sep, const CVariation_inst::TType type, const TSeqPos &deletion_size)

static void Rotate(string &v)

static bool ProcessShift(string &allele, SEndPosition &sep, CSeqVector &seqvec, int &rotation_counter, const CVariation_inst::TType type)

static void Rotate(string &v)

static void ModifyLocation(CSeq_loc &loc, SEndPosition &sep, const CVariation_inst::TType type, const TSeqPos &deletion_size)

static bool ProcessShift(string &allele, SEndPosition &sep, CSeqVector &seqvec, int &rotation_counter, const CVariation_inst::TType type)

static void Rotate(string &v)

static bool ProcessShift(string &allele, SEndPosition &sep, CSeqVector &seqvec, int &rotation_counter, const CVariation_inst::TType type)

static void ModifyLocation(CSeq_loc &loc, SEndPosition &sep, const CVariation_inst::TType type, const TSeqPos &deletion_size)

static void RotateRight(string &v)

static bool x_IsShiftable(const CSeq_loc &loc, const string &allele, CScope &scope, CVariation_inst::TType type)

This method determine if a SeqLoc, and associated allele, are shiftable.

static void RotateLeft(string &v)

static void x_Shift(CVariation &var, CScope &scope)

static void x_SetShiftFlag(CVariation &var, const string &field_text)

static void ResetFullyShifted(CVariation &var, CSeq_loc &loc, SEndPosition &sep, const CVariation_inst::TType type, const TSeqPos &deletion_size)

static void x_ConvertIntervalToPoint(CSeq_loc &loc, int pos)

Convert Interval SeqLoc into a Point.

static void x_ConvertPointToInterval(CSeq_loc &loc, int pos_left, int pos_right)

Convert a Point SeqLoc into an Interval.

static void AlterToHGVSVar(CVariation &var, CScope &scope)

static bool IsShiftable(const CSeq_loc &loc, const string &allele, CScope &scope, CVariation_inst::TType type)

static void NormalizeVariation(CVariation &var, ETargetContext target_ctxt, CScope &scope)

static bool isFullyShifted(const CVariation &var)

static void AlterToDelIns(CVariation &var, CScope &scope)

static void AlterToVCFVar(CVariation &var, CScope &scope)

static void AlterToVarLoc(CVariation &var, CScope &scope)

static bool x_isBaseRepeatingUnit(const string &candidate, const string &target)

static bool x_SetReference(CVariation_ref &var, const string &ref_at_location)

static CVariation_inst::TType GetVariationType(const CVariation_ref &vr)

static void x_AddRefAlleleFixFlag(CVariation &var)

static string x_GetRefAlleleFromVP(CVariantPlacement &vp, CScope &scope, TSeqPos length)

static bool IsReferenceCorrect(const CSeq_feat &feat, string &asserted_ref, string &ref_at_location, CScope &scope)

static const unsigned int MAX_LEN

static string RepeatedSubstring(const string &str)

static string x_GetAlleleFromLoc(const CSeq_loc &loc, CScope &scope)

static string GetCommonRepeatUnit(const CVariation_ref &vr)

static void GetVariationRefAlt(const CVariation_ref &vr, string &ref, vector< string > &alt)

static void CorrectRefAllele(CVariation &var, CScope &scope)

static bool x_FixAlleles(CVariation &variation, string asserted_ref, string ref_at_location)

static bool IsIntronicVariation(const CVariation_inst &inst)

iterator_bool insert(const value_type &val)

const_iterator begin() const

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

static const struct type types[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

TValueType Get(const TKeyType &key, TGetFlags get_flags=0, EGetResult *result=NULL)

Get an object from the cache by its key.

TOrder Add(const TKeyType &key, const TValueType &value, TWeight weight=1, TAddFlags add_flags=0, EAddResult *result=NULL)

Add new element to the cache or replace the existing value.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_USER_THROW_FMT(message)

Throw a "user exception" with message processed as output to ostream.

void Error(CExceptionArgs_Base &args)

#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.

void Trace(CExceptionArgs_Base &args)

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

const TPrim & Get(void) const

C * SerialClone(const C &src)

Create on heap a clone of the source object.

#define MSerial_AsnText

I/O stream manipulators –.

const string AsFastaString(void) const

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

ENa_strand GetStrand(void) const

Get the location's strand.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

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

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

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

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

CRef< C > Ref(C *object)

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

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

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

Templatized initialization from a string literal.

bool IsStr(void) const

Check if variant Str is selected.

const TData & GetData(void) const

Get the Data member data.

const TStr & GetStr(void) const

Get the variant data.

void SetType(TType &value)

Assign a value to Type data member.

const TType & GetType(void) const

Get the Type member data.

bool IsBool(void) const

Check if variant Bool is selected.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

const TExts & GetExts(void) const

Get the Exts member data.

void SetLocation(TLocation &value)

Assign a value to Location data member.

TExts & SetExts(void)

Assign a value to Exts data member.

const TLocation & GetLocation(void) const

Get the Location member data.

void ResetExts(void)

Reset Exts data member.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetExts(void) const

set of extensions; will replace 'ext' field Check if a value has been assigned to Exts data member.

bool IsVariation(void) const

Check if variant Variation is selected.

const TVariation & GetVariation(void) const

Get the variant data.

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

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

void SetId(TId &value)

Assign a value to Id data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

void SetFrom(TFrom value)

Assign a value to From data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

void SetData(TData &value)

Assign a value to Data data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

const TIupacna & GetIupacna(void) const

Get the variant data.

bool IsSetData(void) const

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

TIupacna & SetIupacna(void)

Select the variant.

list< CRef< CSeq_feat > > TFtable

bool IsFtable(void) const

Check if variant Ftable is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsSetSeq_data(void) const

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

bool IsIupacna(void) const

Check if variant Iupacna is selected.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

list< CRef< CVariation > > TVariations

TExt & SetExt(void)

Assign a value to Ext data member.

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 SetData(TData &value)

Assign a value to Data data member.

bool IsInstance(void) const

Check if variant Instance is selected.

const TExt & GetExt(void) const

Get the Ext member data.

const TSet & GetSet(void) const

Get the variant data.

const TInstance & GetInstance(void) const

Get the variant data.

bool IsSetVariations(void) const

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

const TVariations & GetVariations(void) const

Get the Variations member data.

TStop_offset GetStop_offset(void) const

Get the Stop_offset member data.

void SetSeq(TSeq &value)

Assign a value to Seq data member.

bool IsSetData(void) const

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

const TPlacements & GetPlacements(void) const

Get the Placements member data.

list< CRef< CUser_object > > TExt

TPlacements & SetPlacements(void)

Assign a value to Placements data member.

const TData & GetData(void) const

Get the Data member data.

bool IsSetExt(void) const

Additional undescribed extensions Check if a value has been assigned to Ext data member.

bool IsSetStop_offset(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

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.

TStart_offset GetStart_offset(void) const

Get the Start_offset member data.

void ResetExt(void)

Reset Ext data member.

@ e_Instance

actual sequence-edit at feat.location

TType GetType(void) const

Get the Type member data.

const TInstance & GetInstance(void) const

Get the variant data.

TAction GetAction(void) const

Get the Action member data.

list< CRef< CVariation_ref > > TVariations

E_Choice Which(void) const

Which variant is currently selected.

const TSet & GetSet(void) const

Get the variant data.

bool IsSetDelta(void) const

Sequence that replaces the location, in biological order.

bool IsSetSeq(void) const

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

bool IsSetAction(void) const

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

void SetObservation(TObservation value)

Assign a value to Observation data member.

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.

bool IsInstance(void) const

Check if variant Instance is selected.

const TLiteral & GetLiteral(void) const

Get the variant data.

bool IsSet(void) const

Check if variant Set is selected.

void SetSeq(TSeq &value)

Assign a value to Seq data member.

list< CRef< CDelta_item > > TDelta

bool IsLiteral(void) const

Check if variant Literal is selected.

bool IsSetVariations(void) const

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

TDelta & SetDelta(void)

Assign a value to Delta data member.

const TVariations & GetVariations(void) const

Get the Variations member data.

bool IsSetData(void) const

Check if a value has been assigned to Data 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_identity

delta=[]

@ e_Instance

actual sequence-edit at feat.location

@ eAction_offset

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

@ eData_set_type_package

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

@ 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

constexpr auto rotate(list< Ts... >) -> decltype((list<>{}+...+rotate_item< Ts >{}))

Int4 delta(size_t dimension_, const Int4 *score_)

A struct to keep track of the start and stop of the range.

static bool s_ContainsOffset(const CVariation_inst &inst)

bool isVarNormType(const CRef< CUser_object > &uo)

static bool s_ContainsSeqDataIupacna(const CDelta_item &delta_item)

static void s_GetAltRefFromInst(const CVariation_inst &inst, string &ref, vector< string > &alt)

static string s_GetFirstSeqDataIupacna(const CVariation_inst_Base::TDelta &deltas)

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