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

boost::spirit::qi::_1;

boost::spirit::qi::_2;

boost::spirit::qi::_3;

boost::spirit::qi::_val;

boost::spirit::qi::_a;

boost::phoenix::bind;

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

bool IsSetIndex(void) const

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

TIndex GetIndex(void) const

Get the Index member data.

const TAa & GetAa(void) const

Get the Aa member data.

bool IsSetAa(void) const

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

void IsMet1(const CRef< CAaSite > &aa_site, boost::spirit::unused_type context, bool &match)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

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

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

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

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

void AssignMissense(CRef< CAaSite > initial, const CProteinSub::TFinal &final, 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 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 AssignCount(const string &count, CRef< CCount > &result)

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

void AssignAaDelins(CRef< CAaLocation > aa_loc, const string &raw_seq, CRef< CSimpleVariant > &result)

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

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

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

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

void AssignCtermExtension(const string &initial_stop_site, const string &aa, CRef< CCount > new_stop_site, CRef< CSimpleVariant > &result)

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

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

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

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

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

TAttributedToken unknown_val

TAttributedToken definite_aa1

TAttributedToken fuzzy_pos_int

TRule< CSimpleVariant > frameshift_nonstandard

TRule< CSimpleVariant > aa_ins

TRule< CSimpleVariant > nterm_extension

TRule< CCount > aa_repeat

TRule< CSimpleVariant > silent

TRule< CCount > aa_repeat_precise

TRule< CSimpleVariant > simple_protein_variant

TRule< CSimpleVariant > aa_ssr

TRule< CAaInterval > aa3_interval

TRule< CAaLocation > aa_loc

TRule< CAaLocation > aa3_loc

TRule< CCount > aa_repeat_range

TRule< CSimpleVariant > missense

TRule< CAaSite > aa3_site

TRule< CSimpleVariant > protein_extension

TRule< CSimpleVariant > cterm_extension

TRule< CSimpleVariant > aa_delins

TRule< CSimpleVariant > unknown_sub

TRule< CSimpleVariant > frameshift

TRule< CCount > aa_repeat_fuzzy

TRule< CCount > end_codon_shift

SHgvsProteinGrammar(const SHgvsLexer &tok)

TRule< CSimpleVariant > frameshift_short_form

TRule< CSimpleVariant > nonsense

TRule< CAaInterval > aa1_interval

TRule< CSimpleVariant > aa_del

TRule< CSimpleVariant > frameshift_long_form

TRule< CSimpleVariant > protein_confirmed_simple_variation

TRule< CAaSite > aa1_site

TRule< CSimpleVariant > aa_dup

TRule< CAaInterval > aa_interval

TRule< CSimpleVariant > protein_fuzzy_simple_variation

TRule< CAaLocation > aa1_loc

static CS_CONTEXT * context

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