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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/misc_2hgvs_2hgvs__parser_8hpp_source.html below:

NCBI C++ ToolKit: include/misc/hgvs/hgvs_parser.hpp Source File

34 #ifndef HGVSPARSER_HPP_ 35 #define HGVSPARSER_HPP_ 40 #include <boost/version.hpp> 41 #if BOOST_VERSION >= 103800 42 #include <boost/spirit/include/classic.hpp> 43 #include <boost/spirit/include/classic_core.hpp> 44 #include <boost/spirit/include/classic_ast.hpp> 45 #include <boost/spirit/include/classic_parse_tree.hpp> 46 #include <boost/spirit/include/classic_tree_to_xml.hpp> 48 using namespace

BOOST_SPIRIT_CLASSIC_NS;

51 #include <boost/spirit.hpp> 52 #include <boost/spirit/core.hpp> 53 #include <boost/spirit/tree/ast.hpp> 54 #include <boost/spirit/tree/parse_tree.hpp> 55 #include <boost/spirit/tree/tree_to_xml.hpp> 56 using namespace

boost::spirit;

78 #define HGVS_THROW(err_code, message) NCBI_THROW(CHgvsParser::CHgvsParserException, err_code, message) 91

fOpFlags_RelaxedAA = 1 << 0,

92

fOpFlags_Default = fOpFlags_RelaxedAA

98 string

AsHgvsExpression(

const CSeq_feat

& feat);

120 switch

(GetErrCode()) {

121 case

eLogic:

return "eLogic"

;

122 case

eGrammatic:

return "eGrammatic"

;

123 case

eSemantic:

return "eSemantic"

;

124 case

eContext:

return "eContext"

;

125 case

eAlignment:

return "eAlignment"

;

126 case

ePrecondition:

return "ePrecondition"

;

127 case eOther

return "eOther"

;

152

fuzz->Assign(*other.

fuzz

);

192

pnt->Assign(*other.

pnt

);

211

start_offset.Reset();

223

loc.Reset(

new

CSeq_loc);

225

loc->Assign(*other.

loc

);

231 return

start_offset.value || start_offset.value || stop_offset.fuzz || stop_offset.fuzz;

273

m_mol_type = eMol_not_set;

281 return

m_bsh.GetBioseqLength();

289 void

SetId(

const CSeq_id

id

, EMolType mol_type);

293 if

(!m_loc.IsOffset()) {

311 return

!m_loc.loc.IsNull();

319 const

CSeq_loc&

GetLoc

()

const

;

327

EMolType GetMolType(

bool check

true

)

const

;

419 if

(s_rule_names->size() == 0) {

420

m_[eID_NONE] =

"NONE"

;

421

m_[eID_root] =

"root"

;

422

m_[eID_list1a] =

"list1a"

;

423

m_[eID_list2a] =

"list2a"

;

424

m_[eID_list3a] =

"list3a"

;

425

m_[eID_list1b] =

"list1b"

;

426

m_[eID_list2b] =

"list2b"

;

427

m_[eID_list3b] =

"list3b"

;

428

m_[eID_expr1] =

"expr1"

;

429

m_[eID_expr2] =

"expr2"

;

430

m_[eID_expr3] =

"expr3"

;

431

m_[eID_translocation] =

"translocation"

;

432

m_[eID_header] =

"header"

;

433

m_[eID_location] =

"location"

;

434

m_[eID_mol] =

"mol"

;

435

m_[eID_seq_id] =

"seq_id"

;

436

m_[eID_mut_list] =

"mut_list"

;

437

m_[eID_mut_ref] =

"mut_ref"

;

438

m_[eID_nuc_range] =

"nuc_range"

;

439

m_[eID_prot_range] =

"prot_range"

;

440

m_[eID_mut_inst] =

"mut_inst"

;

441

m_[eID_int_fuzz] =

"int_fuzz"

;

442

m_[eID_abs_pos] =

"abs_pos"

;

443

m_[eID_general_pos] =

"general_pos"

;

444

m_[eID_fuzzy_pos] =

"fuzzy_pos"

;

445

m_[eID_pos_spec] =

"pos_spec"

;

446

m_[eID_raw_seq] =

"raw_seq"

;

447

m_[eID_aminoacid] =

"aminoacid"

;

448

m_[eID_nuc_subst] =

"nuc_subst"

;

449

m_[eID_deletion] =

"deletion"

;

450

m_[eID_insertion] =

"insertion"

;

451

m_[eID_delins] =

"delins"

;

452

m_[eID_duplication] =

"duplication"

;

453

m_[eID_nuc_inv] =

"nuc_inv"

;

454

m_[eID_ssr] =

"ssr"

;

455

m_[eID_conversion] =

"conversion"

;

456

m_[eID_seq_loc] =

"seq_loc"

;

457

m_[eID_seq_ref] =

"seq_ref"

;

458

m_[eID_prot_pos] =

"prot_pos"

;

459

m_[eID_prot_fs] =

"prot_fs"

;

460

m_[eID_prot_missense] =

"prot_missense"

;

461

m_[eID_prot_ext] =

"prot_ext"

;

463 return

s_rule_names.

Get

();

466 static const string

& s_GetRuleName(parser_id

id

);

468 template

typename

ScannerT>

471

rule<ScannerT, parser_context<>, parser_tag<eID_root> >

root

;

472

rule<ScannerT, parser_context<>, parser_tag<eID_list1a> >

list1a

;

473

rule<ScannerT, parser_context<>, parser_tag<eID_list2a> >

list2a

;

474

rule<ScannerT, parser_context<>, parser_tag<eID_list3a> >

list3a

;

475

rule<ScannerT, parser_context<>, parser_tag<eID_list1b> >

list1b

;

476

rule<ScannerT, parser_context<>, parser_tag<eID_list2b> >

list2b

;

477

rule<ScannerT, parser_context<>, parser_tag<eID_list3b> >

list3b

;

478

rule<ScannerT, parser_context<>, parser_tag<eID_expr1> >

expr1

;

479

rule<ScannerT, parser_context<>, parser_tag<eID_expr2> >

expr2

;

480

rule<ScannerT, parser_context<>, parser_tag<eID_expr3> >

expr3

;

481

rule<ScannerT, parser_context<>, parser_tag<eID_translocation> >

translocation

;

482

rule<ScannerT, parser_context<>, parser_tag<eID_header> >

header

;

483

rule<ScannerT, parser_context<>, parser_tag<eID_seq_id> >

seq_id

;

484

rule<ScannerT, parser_context<>, parser_tag<eID_mol> >

mol

;

485

rule<ScannerT, parser_context<>, parser_tag<eID_mut_list > >

mut_list

;

486

rule<ScannerT, parser_context<>, parser_tag<eID_mut_ref> >

mut_ref

;

487

rule<ScannerT, parser_context<>, parser_tag<eID_mut_inst> >

mut_inst

;

488

rule<ScannerT, parser_context<>, parser_tag<eID_int_fuzz> >

int_fuzz

;

489

rule<ScannerT, parser_context<>, parser_tag<eID_abs_pos> >

abs_pos

;

490

rule<ScannerT, parser_context<>, parser_tag<eID_general_pos> >

general_pos

;

491

rule<ScannerT, parser_context<>, parser_tag<eID_fuzzy_pos> >

fuzzy_pos

;

492

rule<ScannerT, parser_context<>, parser_tag<eID_pos_spec> >

pos_spec

;

493

rule<ScannerT, parser_context<>, parser_tag<eID_location> >

location

;

494

rule<ScannerT, parser_context<>, parser_tag<eID_nuc_range> >

nuc_range

;

495

rule<ScannerT, parser_context<>, parser_tag<eID_prot_range> >

prot_range

;

496

rule<ScannerT, parser_context<>, parser_tag<eID_raw_seq> >

raw_seq

;

497

rule<ScannerT, parser_context<>, parser_tag<eID_aminoacid> >

aminoacid

;

498

rule<ScannerT, parser_context<>, parser_tag<eID_nuc_subst> >

nuc_subst

;

499

rule<ScannerT, parser_context<>, parser_tag<eID_deletion> >

deletion

;

500

rule<ScannerT, parser_context<>, parser_tag<eID_insertion> >

insertion

;

501

rule<ScannerT, parser_context<>, parser_tag<eID_delins> >

delins

;

502

rule<ScannerT, parser_context<>, parser_tag<eID_duplication> >

duplication

;

503

rule<ScannerT, parser_context<>, parser_tag<eID_nuc_inv> >

nuc_inv

;

504

rule<ScannerT, parser_context<>, parser_tag<eID_ssr> >

ssr

;

505

rule<ScannerT, parser_context<>, parser_tag<eID_conversion> >

conversion

;

506

rule<ScannerT, parser_context<>, parser_tag<eID_seq_loc> >

seq_loc

;

507

rule<ScannerT, parser_context<>, parser_tag<eID_seq_ref> >

seq_ref

;

508

rule<ScannerT, parser_context<>, parser_tag<eID_prot_pos> >

prot_pos

;

509

rule<ScannerT, parser_context<>, parser_tag<eID_prot_missense> >

prot_missense

;

510

rule<ScannerT, parser_context<>, parser_tag<eID_prot_ext> >

prot_ext

;

511

rule<ScannerT, parser_context<>, parser_tag<eID_prot_fs> >

prot_fs

;

515

aminoacid = str_p(

"Ala"

)

537

| chset<>(

"XARNDCEQGHILKMFPSTWYV"

)

540

raw_seq = leaf_node_d[+aminoacid | +chset<>(

"ACGTN"

) | +chset<>(

"acgun"

)];

556

int_fuzz = ch_p(

'('

) >> (ch_p(

'?'

)|int_p) >> ch_p(

'_'

) >> (ch_p(

'?'

)|int_p) >> ch_p(

')'

)

557

| ch_p(

'('

) >> int_p >> ch_p(

')'

)

558

| (ch_p(

'?'

)|int_p);

560

abs_pos = !ch_p(

'*'

) >> int_fuzz;

564

general_pos = (str_p(

"IVS"

) >> int_p | abs_pos) >> sign_p >> int_fuzz

570

fuzzy_pos = discard_node_d[ch_p(

'('

)]

572

>> discard_node_d[ch_p(

'_'

)]

574

>> discard_node_d[ch_p(

')'

)];

576

pos_spec = general_pos

578

| !ch_p(

'o'

) >> header >> pos_spec;

581

prot_pos = raw_seq >> pos_spec;

583

prot_range = prot_pos >> discard_node_d[ch_p(

'_'

)] >> prot_pos;

585

nuc_range = pos_spec >> discard_node_d[ch_p(

'_'

)] >> pos_spec;

587 location

= nuc_range | pos_spec | prot_range | prot_pos;

593

seq_id = leaf_node_d[alpha_p >> +(alnum_p | chset<>(

"._-|"

))];

595

mol = str_p(

"mt"

) | chset<>(

"gcrpm"

);

598

>> !(discard_node_d[ch_p(

'{'

)]

600

>> discard_node_d[ch_p(

'}'

)])

601

>> discard_node_d[ch_p(

':'

)]

603

>> discard_node_d[ch_p(

'.'

)];

612

seq_loc = !ch_p(

'o'

) >> header >>

location

;

615

| (nuc_range|prot_range)

623

nuc_subst = raw_seq >> ch_p(

'>'

) >> raw_seq;

625

deletion = str_p(

"del"

) >> !(raw_seq | int_p);

627

duplication = str_p(

"dup"

) >> !seq_ref;

629

insertion = str_p(

"ins"

) >> seq_ref;

631

conversion = str_p(

"con"

) >> seq_loc;

633

delins = str_p(

"del"

) >> !raw_seq >> str_p(

"ins"

) >> seq_ref;

635

nuc_inv = str_p(

"inv"

) >> !int_p;

637

ssr = !raw_seq >> ( int_fuzz - (ch_p(

'?'

)|int_p)

638

| list_p(discard_node_d[ch_p(

'['

)]

640

>> discard_node_d[ch_p(

']'

)],

641

discard_node_d[ch_p(

'+'

)]));

655

prot_fs = str_p(

"fs"

) >> !(ch_p(

'X'

) >> int_p);

657

prot_ext = (str_p(

"extMet"

) | str_p(

"extX"

)) >> int_p;

659

prot_missense = aminoacid;

662

translocation = str_p(

"t("

)

663

>> leaf_node_d[*(print_p - ch_p(

'('

) - ch_p(

')'

))]

665

>> leaf_node_d[*(print_p - ch_p(

'('

) - ch_p(

')'

))]

669

mut_inst = ch_p(

'?'

)

688

root = list_p(expr1, ch_p(

'+'

));

694

expr1 = ch_p(

'('

) >> expr1 >> ch_p(

')'

)

698

list1a = list_p(discard_node_d[ch_p(

'['

)] >> list1b >> discard_node_d[ch_p(

']'

)], ch_p(

'+'

));

699

list1b = list_p(expr1, chset<>(

",;"

) | str_p(

"(+)"

));

702

expr2 = ch_p(

'('

) >> expr2 >> ch_p(

')'

)

710

list2a = list_p(discard_node_d[ch_p(

'['

)] >> list2b >> discard_node_d[ch_p(

']'

)], ch_p(

'+'

));

711

list2b = list_p(expr2, chset<>(

",;"

) | str_p(

"(+)"

));

714

expr3 = ch_p(

'('

) >> expr3 >> ch_p(

')'

)

724

list3a = list_p(discard_node_d[ch_p(

'['

)] >> list3b >> discard_node_d[ch_p(

']'

)], ch_p(

'+'

));

725

list3b = list_p(expr3, chset<>(

",;"

) | str_p(

"(+)"

));

730

rule<ScannerT, parser_context<>, parser_tag<eID_root> >

const

start

()

const 738 return id

== SGrammar::eID_list1a

739

id

== SGrammar::eID_list2a

740

id

== SGrammar::eID_list3a

741

id

== SGrammar::eID_list1b

742

id

== SGrammar::eID_list2b

743

id

== SGrammar::eID_list3b

744

id

== SGrammar::eID_root;

752 typedef

TParseTreeMatch::const_tree_iterator

TIterator

;

796 static string

s_hgvsaa2ncbieaa(

const string

& hgvsaa);

799 static string

s_hgvsUCaa2hgvsUL(

const string

& hgvsaa);

806 const

CSeq_loc& parent_loc,

813 string

x_GetInstData(

const CVariation_inst

& inst,

const

CSeq_loc& this_loc);

824 string

x_LocToSeqStr(

const

CSeq_loc& loc);

833 string

x_SeqLocToStr(

const

CSeq_loc& loc,

bool

with_header);

839 string

x_SeqIdToHgvsHeader(

const CSeq_id

id

);

User-defined methods of the data storage class.

T & Get(void)

Create the variable if not created yet, return the reference.

namespace ncbi::objects::

Set of related Variations.

void Validate(const CSeq_literal &literal) const

void SetLoc(const SOffsetLoc &loc)

CContext(CRef< CScope > scope)

TSeqPos GetLength() const

CContext(const CContext &other)

CScope & GetScope() const

NCBI_EXCEPTION_DEFAULT(CHgvsParserException, CException)

@ eGrammatic

Expression is not a valid language.

@ eAlignment

Some problem with getting alignment.

@ ePrecondition

Precondition is not met.

@ eLogic

Problem with the code.

@ eSemantic

Expression is invalid in some way.

@ eContext

Some problem with context.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

tree_match< char const * > TParseTreeMatch

CVariation_inst::TDelta::value_type TDelta

static CSafeStatic< SGrammar > s_grammar

CVariation_ref::TData::TSet TVariationSet

static CRef< CVariation_ref > s_ProtToCdna(const CVariation_ref &vr, CScope &scope)

TParseTreeMatch::const_tree_iterator TIterator

CHgvsParser(CScope &scope)

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

EErrCode

Error types that an application can generate.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

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.

#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.

double value_type

The numeric datatype used by the parser.

const GenericPointer< typename T::ValueType > T2 value

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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

void Assign(const SFuzzyInt &other)

rule< ScannerT, parser_context<>, parser_tag< eID_insertion > > insertion

rule< ScannerT, parser_context<>, parser_tag< eID_seq_loc > > seq_loc

rule< ScannerT, parser_context<>, parser_tag< eID_seq_ref > > seq_ref

rule< ScannerT, parser_context<>, parser_tag< eID_prot_fs > > prot_fs

rule< ScannerT, parser_context<>, parser_tag< eID_prot_pos > > prot_pos

rule< ScannerT, parser_context<>, parser_tag< eID_prot_range > > prot_range

rule< ScannerT, parser_context<>, parser_tag< eID_list3b > > list3b

rule< ScannerT, parser_context<>, parser_tag< eID_expr1 > > expr1

rule< ScannerT, parser_context<>, parser_tag< eID_nuc_subst > > nuc_subst

rule< ScannerT, parser_context<>, parser_tag< eID_location > > location

rule< ScannerT, parser_context<>, parser_tag< eID_list3a > > list3a

rule< ScannerT, parser_context<>, parser_tag< eID_delins > > delins

rule< ScannerT, parser_context<>, parser_tag< eID_abs_pos > > abs_pos

rule< ScannerT, parser_context<>, parser_tag< eID_prot_ext > > prot_ext

rule< ScannerT, parser_context<>, parser_tag< eID_nuc_inv > > nuc_inv

rule< ScannerT, parser_context<>, parser_tag< eID_ssr > > ssr

rule< ScannerT, parser_context<>, parser_tag< eID_general_pos > > general_pos

rule< ScannerT, parser_context<>, parser_tag< eID_pos_spec > > pos_spec

rule< ScannerT, parser_context<>, parser_tag< eID_header > > header

rule< ScannerT, parser_context<>, parser_tag< eID_mut_ref > > mut_ref

rule< ScannerT, parser_context<>, parser_tag< eID_list2b > > list2b

rule< ScannerT, parser_context<>, parser_tag< eID_root > > const & start() const

rule< ScannerT, parser_context<>, parser_tag< eID_list1b > > list1b

rule< ScannerT, parser_context<>, parser_tag< eID_int_fuzz > > int_fuzz

rule< ScannerT, parser_context<>, parser_tag< eID_expr2 > > expr2

rule< ScannerT, parser_context<>, parser_tag< eID_translocation > > translocation

rule< ScannerT, parser_context<>, parser_tag< eID_fuzzy_pos > > fuzzy_pos

rule< ScannerT, parser_context<>, parser_tag< eID_list1a > > list1a

rule< ScannerT, parser_context<>, parser_tag< eID_prot_missense > > prot_missense

rule< ScannerT, parser_context<>, parser_tag< eID_duplication > > duplication

definition(SGrammar const &)

rule< ScannerT, parser_context<>, parser_tag< eID_mut_list > > mut_list

rule< ScannerT, parser_context<>, parser_tag< eID_deletion > > deletion

rule< ScannerT, parser_context<>, parser_tag< eID_aminoacid > > aminoacid

rule< ScannerT, parser_context<>, parser_tag< eID_seq_id > > seq_id

rule< ScannerT, parser_context<>, parser_tag< eID_list2a > > list2a

rule< ScannerT, parser_context<>, parser_tag< eID_root > > root

rule< ScannerT, parser_context<>, parser_tag< eID_mut_inst > > mut_inst

rule< ScannerT, parser_context<>, parser_tag< eID_expr3 > > expr3

rule< ScannerT, parser_context<>, parser_tag< eID_nuc_range > > nuc_range

rule< ScannerT, parser_context<>, parser_tag< eID_conversion > > conversion

rule< ScannerT, parser_context<>, parser_tag< eID_mol > > mol

rule< ScannerT, parser_context<>, parser_tag< eID_raw_seq > > raw_seq

static CSafeStatic< TRuleNames > s_rule_names

std::map< parser_id, std::string > TRuleNames

static TRuleNames & s_GetRuleNames()

static bool s_is_list(parser_id id)

void Assign(const SOffsetLoc &other)

void Assign(const SOffsetPoint &other)

static CS_CONTEXT * context

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