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NCBI C++ ToolKit: src/objtools/readers/hgvs/semantic_actions.cpp Source File

(

());

->SetReference_id(identifier.substr(0,identifier.size()-1));

& sub =

->SetType().SetProt_sub();

sub.SetInitial(*initial);

sub.SetFinal(

);

->SetType().SetProt_silent(*loc);

->SetType().SetProt_sub().SetInitial(*initial);

->SetType().SetProt_sub().SetInitial(*initial);

->SetType().SetDup().SetLoc().SetAaloc(*aa_loc);

->SetType().SetDel().SetLoc().SetAaloc(*aa_loc);

->SetType().SetProt_ext().SetNterm_ext().SetNewStart(*new_start_site);

->SetType().SetProt_ext().SetNterm_ext().SetNewAa(new_aa);

index = NStr::StringToNumeric<TSeqPos>(reference_stop);

& cterm_ext =

->SetType().SetProt_ext().SetCterm_ext();

cterm_ext.SetRefStop(index);

cterm_ext.SetNewAa(aa);

cterm_ext.SetLength(*length);

->SetInt(*aa_interval);

->SetSite(*aa_site);

->SetStart(*start);

index = NStr::StringToNumeric<CAaSite::TIndex>(pos);

(

==

) {

= NStr::StringToNumeric<CCount::TVal>(

);

c = NStr::StringToNumeric<CCount::TVal>(

.substr(1,

-2));

( start ==

) {

->SetRange().SetStart().SetUnknown();

start_val = NStr::StringToNumeric<CCount::TVal>(start);

->SetRange().SetStart().SetVal(start_val);

->SetRange().SetStop().SetUnknown();

stop_val = NStr::StringToNumeric<CCount::TVal>(stop);

->SetRange().SetStop().SetVal(stop_val);

& ssr =

->SetType().SetRepeat();

ssr.SetLoc().SetAaloc(*aa_loc);

ssr.SetCount(*

);

->SetType().SetIns().SetInt().SetAaint(*aa_interval);

->SetType().SetIns().SetSeqinfo().SetRaw_seq(raw_seq);

& insertion =

->SetType().SetIns();

insertion.SetInt().SetAaint(*aa_interval);

insertion.SetSeqinfo().SetCount(*seq_size);

->SetType().SetFrameshift().SetAasite(*aa_site);

& delins =

->SetType().SetDelins();

delins.SetLoc().SetAaloc(*aa_loc);

delins.SetInserted_seq_info().SetRaw_seq(raw_seq);

& delins =

->SetType().SetDelins();

delins.SetLoc().SetAaloc(*aa_loc);

delins.SetInserted_seq_info().SetCount(*seq_size);

<

T>

->SetSimple(*simple_var);

->SetSpecial() = special_variant;

->SetSubvariants().push_back(variant);

(site_index ==

) {

->SetBase().SetUnknown();

base_val = NStr::StringToNumeric<CNtSite::TBase::TVal>(site_index);

->SetBase().SetVal(base_val);

center_site = site_index;

->SetBase().SetUnknown();

base_val = NStr::StringToNumeric<CNtSite::TBase::TVal>(base);

->SetBase().SetVal(base_val);

->SetOffset().SetPlus_unknown();

->SetOffset().SetMinus_unknown();

(base.front() ==

&&

.back() ==

) {

(

.size() >= 2 &&

&&

.back() ==

) {

->SetFuzzy_offset();

offset_value =

;

->SetOffset().SetVal(NStr::StringToNumeric<CNtSite::TOffset::TVal>(offset_value));

->SetUtr().SetFive_prime();

->SetUtr().SetThree_prime();

->SetRange().SetStart(*start);

->SetRange().SetStop(*stop);

->SetSite(*nt_site);

is_minus_strand = (identifier[0] ==

);

seq_id = is_minus_strand ? identifier.substr(1) : identifier;

(nt_loc->

()) {

(nt_loc->

()) {

stop_loc->SetRange(nt_loc->

().

().SetRange());

seq_id = identifier.substr(0,identifier.size()-1);

->SetType().SetRepeat().SetLoc().SetNtloc(*nt_loc);

->SetType().SetRepeat().SetLoc().SetNtloc(*nt_loc);

(raw_seq.empty()) {

->SetType().SetRepeat().SetRaw_seq(raw_seq);

->SetType().SetInv().SetNtint(nt_loc->

());

(raw_seq.empty()) {

->SetType().SetInv().SetRaw_seq(raw_seq);

->SetType().SetInv().SetNtint(nt_loc->

());

->SetType().SetInv().SetSize(NStr::StringToNumeric<CInversion::TSize>(

));

->SetType().SetConv().SetOrigin(

.GetNCObject());

->SetType().SetIns().SetInt().SetNtint(nt_loc->

());

(raw_seq.empty()) {

->SetType().SetIns().SetSeqinfo().SetRaw_seq(raw_seq);

->SetType().SetDel().SetLoc().SetNtloc(*nt_loc);

->SetType().SetDel().SetLoc().SetNtloc(*nt_loc);

(raw_seq.empty()) {

->SetType().SetDel().SetRaw_seq(raw_seq);

->SetType().SetDelins().SetLoc().SetNtloc(*nt_loc);

(inserted_seq.empty()) {

->SetType().SetDelins().SetInserted_seq_info().SetRaw_seq(inserted_seq);

(deleted_seq.empty()) {

->SetType().SetDelins().SetDeleted_raw_seq(deleted_seq);

->SetType().SetDup().SetLoc().SetNtloc(*nt_loc);

->SetType().SetDup().SetLoc().SetNtloc(*nt_loc);

(raw_seq.empty()) {

->SetType().SetDup().SetRaw_seq(raw_seq);

->SetType().SetNa_sub().SetLoc(*nt_loc);

->SetType().SetNa_sub().SetInitial(initial_nt);

->SetType().SetNa_sub().SetFinal(final_nt);

->SetType().SetNa_identity().SetLoc(*nt_loc);

->SetType().SetNa_identity().SetNucleotide(nucleotide);

->SetType().SetNa_identity().SetLoc(*nt_loc);

->SetSeqtype(seq_type);

CRef< C > Ref(C *object)

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

TObjectType & GetNCObject(void) const

Get object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static 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.

ESpecialVariant

Access to ESpecialVariant's attributes (values, names) as defined in spec.

EVariantSeqType

Access to EVariantSeqType's attributes (values, names) as defined in spec.

const TStart & GetStart(void) const

Get the Start member data.

void SetStrand_minus(TStrand_minus value)

Assign a value to Strand_minus data member.

TInt & SetInt(void)

Select the variant.

void SetSeqtype(TSeqtype value)

Assign a value to Seqtype data member.

bool IsSite(void) const

Check if variant Site is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsInt(void) const

Check if variant Int is selected.

void SetStart(TStart &value)

Assign a value to Start data member.

bool IsRange(void) const

Check if variant Range is selected.

void SetComplex(TComplex value)

Assign a value to Complex data member.

TRange & SetRange(void)

Select the variant.

void SetStop(TStop &value)

Assign a value to Stop data member.

bool IsSite(void) const

Check if variant Site is selected.

TSite & SetSite(void)

Select the variant.

void SetStop(TStop &value)

Assign a value to Stop data member.

void SetStart(TStart &value)

Assign a value to Start data member.

const TStop & GetStop(void) const

Get the Stop member data.

void SetSeqid(const TSeqid &value)

Assign a value to Seqid data member.

@ eVariantSeqType_n

non-coding rna

@ eVariantSeqType_p

protein

@ eVariantSeqType_g

genomic

@ eVariantSeqType_m

mitochondrial

@ eVariantSeqType_c

coding

@ eVariantSeqType_u

unknown

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

static const GLdouble origin[]

void AssignAaIntervalLocation(CRef< CAaInterval > aa_interval, CRef< CAaLocation > &result)

void AssignNtInterval(CRef< CNtLocation > start, CRef< CNtLocation > stop, CRef< CNtLocation > &result)

void TagAsMosaic(CRef< CSequenceVariant > seq_var)

void AssignFuzzyCount(const string &count, CRef< CCount > &result)

void AssignUnknownSub(CRef< CAaSite > initial, CRef< CSimpleVariant > &result)

CRef< T > MakeResult(CRef< T > result)

void AssignSequenceVariant(CRef< CSequenceVariant > variant, CRef< CVariantExpression > &result)

void AssignFuzzySimpleNtSite(const string &site_index, CRef< CNtSite > &result)

void AssignFrameshift(CRef< CAaSite > aa_site, CRef< CSimpleVariant > &result)

void AssignSingleVariation(CRef< CVariant > variant, CRef< CSequenceVariant > &result)

void AssignMissense(CRef< CAaSite > initial, const CProteinSub::TFinal &final, CRef< CSimpleVariant > &result)

void AssignNtDeletion(CRef< CNtLocation > nt_loc, CRef< CSimpleVariant > &result)

void AssignAaInsertion(CRef< CAaInterval > aa_interval, const CInsertion::TSeqinfo::TRaw_seq &raw_seq, CRef< CSimpleVariant > &result)

void AssignAaSiteLocation(CRef< CAaSite > aa_site, CRef< CAaLocation > &result)

void AssignNtSSR(CRef< CNtLocation > nt_loc, CRef< CCount > count, CRef< CSimpleVariant > &result)

void AssignNtInv(CRef< CNtLocation > nt_loc, const CInversion::TRaw_seq &raw_seq, CRef< CSimpleVariant > &result)

void AssignNtermExtension(CRef< CAaSite > initial_start_site, CRef< CCount > new_start_site, CRef< CSimpleVariant > &result)

void AssignCountRange(const string &start, const string &stop, CRef< CCount > &result)

void AssignIntronSite(const string &base, const string &offset, CRef< CNtSite > &result)

void AssignCount(const string &count, CRef< CCount > &result)

void AssignAaDup(CRef< CAaLocation > aa_loc, CRef< CSimpleVariant > &result)

void AssignSimpleVariant(CRef< CSimpleVariant > simple_var, CRef< CVariant > &result)

void AssignRefSeqIdentifier(const string &identifier, CRef< CVariantExpression > &result)

void AssignNtDelins(CRef< CNtLocation > nt_loc, const CInsertion::TSeqinfo::TRaw_seq &inserted_seq, CRef< CSimpleVariant > &result)

void AssignAaInterval(CRef< CAaSite > start, CRef< CAaSite > &stop, CRef< CAaInterval > &result)

void AssignFuzzyNtSite(CRef< CNtSite > center_site, CRef< CNtSite > &result)

void Assign3primeUTRSite(CRef< CNtSite > nt_site, CRef< CNtSite > &result)

void AssignNtInsertion(CRef< CNtLocation > nt_loc, const CInsertion::TSeqinfo::TRaw_seq &raw_seq, CRef< CSimpleVariant > &result)

void AssignNtRemoteLocation(const string &identifier, const string &type_string, CRef< CNtLocation > &nt_loc, CRef< CNtLocation > &result)

void AssignSilent(CRef< CAaLocation > loc, CRef< CSimpleVariant > &result)

void AssignSpecialVariant(ESpecialVariant special_variant, CRef< CVariant > &result)

void AssignAaDel(CRef< CAaLocation > aa_loc, CRef< CSimpleVariant > &result)

EVariantSeqType s_GetSeqType(const string &type_string)

void AssignNtSite(CRef< CNtSite > nt_site, CRef< CNtLocation > &result)

void AssignAaInsertionSize(CRef< CAaInterval > aa_interval, CRef< CCount > seq_size, CRef< CSimpleVariant > &result)

void AssignNtDup(CRef< CNtLocation > nt_loc, CRef< CSimpleVariant > &result)

void AssignNtConversion(CRef< CNtLocation > nt_loc, CRef< CNtLocation > origin, CRef< CSimpleVariant > &result)

void AssignNtSub(CRef< CNtLocation > nt_loc, const CNaSub::TInitial &initial_nt, const CNaSub::TFinal &final_nt, CRef< CSimpleVariant > &result)

void AssignNtIdentity(CRef< CNtLocation > nt_loc, const CNaIdentity::TNucleotide &nucleotide, CRef< CSimpleVariant > &result)

void AssignNtSiteRange(CRef< CNtSite > start, CRef< CNtSite > stop, CRef< CNtLocation > &result)

void AssignAaDelinsSize(CRef< CAaLocation > aa_loc, CRef< CCount > seq_size, CRef< CSimpleVariant > &result)

void Assign5primeUTRSite(CRef< CNtSite > nt_site, CRef< CNtSite > &result)

void AssignAaDelins(CRef< CAaLocation > aa_loc, const CInsertion::TSeqinfo::TRaw_seq &raw_seq, CRef< CSimpleVariant > &result)

void AssignAaSite(const string &aa, const string &pos, CRef< CAaSite > &result)

CRef< T > CreateResultIfNull(CRef< T > result)

void TagAsChimera(CRef< CSequenceVariant > seq_var)

void AssignFuzzy(CRef< T > input, CRef< T > &result)

void AssignSequenceType(CRef< CSequenceVariant > &result)

void AssignCtermExtension(const string &reference_stop, const string &aa, CRef< CCount > length, CRef< CSimpleVariant > &result)

void AssignAaSSR(CRef< CAaLocation > aa_loc, CRef< CCount > count, CRef< CSimpleVariant > &result)

void s_SetSequenceInfo(CRef< CNtLocation > &nt_loc, const string &identifier, const EVariantSeqType &seq_type)

void AssignNonsense(CRef< CAaSite > initial, CRef< CSimpleVariant > &result)

void AssignFuzzyLocalVariation(CRef< CSimpleVariant > input, CRef< CSimpleVariant > &result)

void AssignSimpleNtSite(const string &site_index, CRef< CNtSite > &result)

void AssignNtInvSize(CRef< CNtLocation > nt_loc, string size, CRef< CSimpleVariant > &result)

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