hgvs_protein_parser.cpp

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#include <ncbi_pch.hpp>
#include <boost/spirit/include/phoenix.hpp>
#include <objtools/readers/hgvs/hgvs_protein_parser.hpp>
#include <objtools/readers/hgvs/semantic_actions.hpp>
 
using boost::spirit::qi::_1;
using boost::spirit::qi::_2;
using boost::spirit::qi::_3;
using boost::spirit::qi::_val;
using boost::spirit::qi::_a;
using boost::phoenix::bind;
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
 
void IsMet1(const CRef<CAaSite>& aa_site, boost::spirit::unused_type context, bool& match)
{
    match = false;
    if (aa_site->IsSetAa() &&
        aa_site->IsSetIndex() &&
        (aa_site->GetIndex() == 1 &&
         (NStr::Equal(aa_site->GetAa(), "Met")
          || NStr::Equal(aa_site->GetAa(), "M"))))
       {
           match = true;
       }
}
 
 
SHgvsProteinGrammar::SHgvsProteinGrammar(const SHgvsLexer& tok) :
    SHgvsProteinGrammar::base_type(simple_protein_variant)
{
    simple_protein_variant = protein_confirmed_simple_variation | protein_fuzzy_simple_variation;
 
    protein_fuzzy_simple_variation = ("(" >> protein_confirmed_simple_variation >> ")") ACTION1(AssignFuzzyLocalVariation);
 
    protein_confirmed_simple_variation =
                                         frameshift |
                                         protein_extension |
                                         missense |
                                         nonsense |
                                         unknown_sub |
                                         silent |
                                         aa_dup |
                                         aa_delins |
                                         aa_del |
                                         aa_ins |
                                         aa_ssr;
 
    missense = (aa3_site >> tok.aa3) ACTION2(AssignMissense) |
               (aa1_site >> aa1) ACTION2(AssignMissense);
 
    nonsense = (aa_site >> tok.stop) ACTION1(AssignNonsense);
 
    unknown_sub = (aa_site >> tok.unknown_val) ACTION1(AssignUnknownSub);
 
    silent = (aa_loc >> tok.nochange) ACTION1(AssignSilent);
 
    aa_delins = (aa3_loc >> tok.delins >> aa3_stop_seq) ACTION2(AssignAaDelins) |
                (aa3_loc >> tok.delins >> aa3_seq) ACTION2(AssignAaDelins) |
                (aa1_loc >> tok.delins >> aa1_stop_seq) ACTION2(AssignAaDelins) |
                (aa1_loc >> tok.delins >> aa1_seq) ACTION2(AssignAaDelins) |
                (aa_loc >> tok.delins >> seq_size) ACTION2(AssignAaDelinsSize);
 
    aa1_stop_seq = (aa1_seq >> tok.stop) [_val = _1 + "*"];
 
    aa3_stop_seq = (aa3_seq >> tok.stop) [_val = _1 + "*"];
 
    aa_dup = (aa_loc >> tok.dup) ACTION1(AssignAaDup);
 
    aa_del = (aa_loc >> tok.del) ACTION1(AssignAaDel);
 
    aa_ins =  (aa3_interval >> tok.ins >>  aa3_seq) ACTION2(AssignAaInsertion) |
              (aa1_interval >> tok.ins >> aa1_seq) ACTION2(AssignAaInsertion) |
              (aa_interval >> tok.ins >> seq_size) ACTION2(AssignAaInsertionSize);
              // Need to be able to insert a "remote" sequence
 
    aa_ssr = (aa_loc >> aa_repeat) ACTION2(AssignAaSSR);
 
    aa_repeat = aa_repeat_fuzzy | aa_repeat_precise | aa_repeat_range;
 
    aa_repeat_precise = ("[" >> tok.pos_int >> "]") ACTION1(AssignCount);
 
    aa_repeat_fuzzy = tok.fuzzy_pos_int ACTION1(AssignFuzzyCount);
 
    aa_repeat_range = ("(" >> nn_int >> "_" >> tok.pos_int >> ")") ACTION2(AssignCountRange) |
                      ("(" >> nn_int >> "_" >> tok.unknown_val >> ")") ACTION2(AssignCountRange) |
                      ("(" >> tok.unknown_val >> "_" >> tok.pos_int >> ")") ACTION2(AssignCountRange);
 
    frameshift = frameshift_long_form |
                 frameshift_nonstandard |
                 frameshift_short_form;
 
    frameshift_long_form = (aa1_site >> aa1 >> tok.fs >> tok.stop >> (tok.pos_int | tok.unknown_val )) ACTION1(AssignFrameshift) |
                           (aa3_site >> tok.aa3 >> tok.fs >> tok.stop >> (tok.pos_int | tok.unknown_val)) ACTION1(AssignFrameshift);
 
    frameshift_nonstandard  = (aa1_site >> aa1 >> tok.fs) ACTION1(AssignFrameshift) |
                              (aa3_site >> tok.aa3 >> tok.fs) ACTION1(AssignFrameshift);
 
    frameshift_short_form = (aa_site >> tok.fs) ACTION1(AssignFrameshift);
 
    protein_extension = cterm_extension | nterm_extension;
 
    cterm_extension = (tok.stop >> tok.pos_int >> (aa1 | tok.aa3) >> tok.ext >> tok.stop >> end_codon_shift)
                      ACTION3(AssignCtermExtension);
 
    nterm_extension = (aa_site [IsMet1] >> tok.ext >> "-" >> end_codon_shift)
                      ACTION2(AssignNtermExtension) |
                      (aa3_site [IsMet1] >> tok.aa3 >> tok.ext >> "-" >> end_codon_shift)
                      ACTION3(AssignNtermExtension) |
                      (aa1_site [IsMet1] >> aa1 >> tok.ext >> "-" >> end_codon_shift)
                      ACTION3(AssignNtermExtension);
 
    end_codon_shift = tok.pos_int ACTION1(AssignCount) |
                      tok.fuzzy_pos_int ACTION1(AssignFuzzyCount);
 
    seq_size = tok.pos_int ACTION1(AssignCount);
 
    aa_loc = aa3_loc | aa1_loc;
 
    aa_interval = aa3_interval | aa1_interval;
 
    aa_site = aa3_site | aa1_site;
 
    aa3_loc = aa3_interval ACTION1(AssignAaIntervalLocation) |
              aa3_site ACTION1(AssignAaSiteLocation);
 
    aa3_interval = (aa3_site >> "_" >> aa3_site) ACTION2(AssignAaInterval);
 
    aa3_site = (tok.aa3 >> tok.pos_int) ACTION2(AssignAaSite);
 
    aa3_seq = +(tok.aa3) [_val += _1];
 
    aa1_loc = aa1_interval ACTION1(AssignAaIntervalLocation) |
              aa1_site ACTION1(AssignAaSiteLocation);
 
    aa1_interval = (aa1_site >> "_" >> aa1_site) ACTION2(AssignAaInterval);
 
    aa1_site = (aa1 >> tok.pos_int) ACTION2(AssignAaSite);
 
    aa1_seq = +(aa1) [_val += _1];
 
    aa1 = tok.ACGT | tok.definite_aa1;
 
    nn_int = tok.zero [_val = "0"] |
             tok.pos_int [_val = _1];
}
 
END_NCBI_SCOPE