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Definition at line 382 of file semantic_actions.cpp.
References CRef< C, Locker >::GetPointer(), Ref(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
Definition at line 375 of file semantic_actions.cpp.
References CRef< C, Locker >::GetPointer(), Ref(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignAaDel | ( | CRef< CAaLocation > | aa_loc, |
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 89 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignAaDelins | ( | CRef< CAaLocation > | aa_loc, |
const string & | raw_seq, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 239 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignAaDelinsSize | ( | CRef< CAaLocation > | aa_loc, |
CRef< CCount > | seq_size, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 252 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignAaDup | ( | CRef< CAaLocation > | aa_loc, |
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 82 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignAaInsertion | ( | CRef< CAaInterval > | aa_interval, |
const CInsertion::TSeqinfo::TRaw_seq & | raw_seq, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 211 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignAaInsertionSize | ( | CRef< CAaInterval > | aa_interval, |
CRef< CCount > | seq_size, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 221 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignAaInterval | ( | CRef< CAaSite > | start, |
CRef< CAaSite > & | stop, | ||
CRef< CAaInterval > & | result | ||
) |
Definition at line 137 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignAaIntervalLocation | ( | CRef< CAaInterval > | aa_interval, |
CRef< CAaLocation > & | result | ||
) |
Definition at line 123 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
Definition at line 145 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignAaSiteLocation | ( | CRef< CAaSite > | aa_site, |
CRef< CAaLocation > & | result | ||
) |
Definition at line 130 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignAaSSR | ( | CRef< CAaLocation > | aa_loc, |
CRef< CCount > | count, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 200 of file semantic_actions.cpp.
References count, CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
Definition at line 156 of file semantic_actions.cpp.
References count, CreateResultIfNull(), result, and val.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar(), and SHgvsProteinGrammar::SHgvsProteinGrammar().
Definition at line 179 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar(), and SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignCtermExtension | ( | const string & | initial_stop_site, |
const string & | aa, | ||
CRef< CCount > | new_stop_site, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 110 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignFrameshift | ( | CRef< CAaSite > | aa_site, |
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 232 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
Definition at line 170 of file semantic_actions.cpp.
References count, CreateResultIfNull(), len, and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar(), and SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignFuzzyLocalVariation | ( | CRef< CSimpleVariant > | input, |
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 270 of file semantic_actions.cpp.
References AssignFuzzy(), input(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar(), and SHgvsProteinGrammar::SHgvsProteinGrammar().
Definition at line 317 of file semantic_actions.cpp.
References result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
Definition at line 324 of file semantic_actions.cpp.
References AssignSimpleNtSite(), NStr::ReplaceInPlace(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
Definition at line 336 of file semantic_actions.cpp.
References CreateResultIfNull(), offset, NStr::ReplaceInPlace(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignMissense | ( | CRef< CAaSite > | initial, |
const CProteinSub::TFinal & | final, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 43 of file semantic_actions.cpp.
References CreateResultIfNull(), CProteinSub_Base::eType_missense, and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignNonsense | ( | CRef< CAaSite > | initial, |
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 64 of file semantic_actions.cpp.
References CreateResultIfNull(), CProteinSub_Base::eType_nonsense, and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignNtConversion | ( | CRef< CNtLocation > | src_int, |
CRef< CNtLocation > | dest_int, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 548 of file semantic_actions.cpp.
References CreateResultIfNull(), CRef< C, Locker >::GetNCObject(), origin, and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtDeletion | ( | CRef< CNtLocation > | nt_loc, |
const CDeletion::TRaw_seq & | raw_seq, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 576 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
void AssignNtDeletion | ( | CRef< CNtLocation > | nt_loc, |
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 569 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtDelins | ( | CRef< CNtLocation > | nt_loc, |
const CDeletion::TRaw_seq & | deleted_seq, | ||
const CInsertion::TSeqinfo::TRaw_seq & | inserted_seq, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 598 of file semantic_actions.cpp.
References AssignNtDelins(), and result.
void AssignNtDelins | ( | CRef< CNtLocation > | nt_loc, |
const CInsertion::TSeqinfo::TRaw_seq & | inserted_seq, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 587 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by AssignNtDelins(), and SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtDup | ( | CRef< CNtLocation > | nt_loc, |
const CDuplication::TRaw_seq & | raw_seq, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 619 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
void AssignNtDup | ( | CRef< CNtLocation > | nt_loc, |
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 612 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtermExtension | ( | CRef< CAaSite > | initial_start_site, |
const string & | new_aa, | ||
CRef< CCount > | new_start_site, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 103 of file semantic_actions.cpp.
References AssignNtermExtension(), and result.
void AssignNtermExtension | ( | CRef< CAaSite > | initial_start_site, |
CRef< CCount > | new_start_site, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 96 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by AssignNtermExtension(), and SHgvsProteinGrammar::SHgvsProteinGrammar().
void AssignNtIdentity | ( | CRef< CNtLocation > | nt_loc, |
const CNaIdentity::TNucleotide & | nucleotide, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 642 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtIdentity | ( | CRef< CNtLocation > | nt_loc, |
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 652 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
void AssignNtInsertion | ( | CRef< CNtLocation > | nt_int, |
const CInsertion::TSeqinfo::TRaw_seq & | raw_seq, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 557 of file semantic_actions.cpp.
References CreateResultIfNull(), result, and CNtLocation_Base::SetInt().
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtInterval | ( | CRef< CNtLocation > | start, |
CRef< CNtLocation > | stop, | ||
CRef< CNtLocation > & | result | ||
) |
Definition at line 402 of file semantic_actions.cpp.
References CreateResultIfNull(), CNtLocation_Base::IsRange(), CNtLocation_Base::IsSite(), result, CNtLocation_Base::SetRange(), and CNtLocation_Base::SetSite().
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtInv | ( | CRef< CNtLocation > | nt_int, |
const CInversion::TRaw_seq & | raw_seq, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 522 of file semantic_actions.cpp.
References CreateResultIfNull(), result, and CNtLocation_Base::SetInt().
Referenced by AssignNtInvSize().
void AssignNtInv | ( | CRef< CNtLocation > | nt_int, |
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 534 of file semantic_actions.cpp.
References CreateResultIfNull(), result, and CNtLocation_Base::SetInt().
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtInvSize | ( | CRef< CNtLocation > | nt_int, |
string | size, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 541 of file semantic_actions.cpp.
References AssignNtInv(), result, and ncbi::grid::netcache::search::fields::size.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtRemoteLocation | ( | const string & | seq_id, |
const string & | seq_type, | ||
CRef< CNtLocation > & | nt_loc, | ||
CRef< CNtLocation > & | result | ||
) |
Definition at line 492 of file semantic_actions.cpp.
References CRef< C, Locker >::GetPointer(), Ref(), result, s_GetSeqType(), s_SetSequenceInfo(), and xslt::type_string.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtSite | ( | CRef< CNtSite > | local_site, |
CRef< CNtLocation > & | result | ||
) |
Definition at line 396 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtSiteRange | ( | CRef< CNtSite > | start, |
CRef< CNtSite > | stop, | ||
CRef< CNtLocation > & | result | ||
) |
Definition at line 389 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtSSR | ( | CRef< CNtLocation > | nt_loc, |
const CRepeat::TRaw_seq & | raw_seq, | ||
CRef< CCount > | count, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 510 of file semantic_actions.cpp.
References count, CreateResultIfNull(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignNtSSR | ( | CRef< CNtLocation > | nt_loc, |
CRef< CCount > | count, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 502 of file semantic_actions.cpp.
References count, CreateResultIfNull(), and result.
void AssignNtSub | ( | CRef< CNtLocation > | nt_loc, |
const CNaSub::TInitial & | initial_nt, | ||
const CNaSub::TFinal & | final_nt, | ||
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 630 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignRefSeqIdentifier | ( | const string & | identifier, |
CRef< CVariantExpression > & | result | ||
) |
Definition at line 29 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsVariantGrammar::SHgvsVariantGrammar().
void AssignSequenceType | ( | const string & | type, |
CRef< CSequenceVariant > & | result | ||
) |
Definition at line 660 of file semantic_actions.cpp.
References CreateResultIfNull(), result, s_GetSeqType(), and xslt::type_string.
void AssignSequenceType | ( | CRef< CSequenceVariant > & | result | ) |
Definition at line 297 of file semantic_actions.cpp.
References CreateResultIfNull(), eVariantSeqType_p, and result.
Referenced by SHgvsVariantGrammar::SHgvsVariantGrammar().
void AssignSequenceVariant | ( | CRef< CSequenceVariant > | variant, |
CRef< CVariantExpression > & | result | ||
) |
Definition at line 36 of file semantic_actions.cpp.
References CreateResultIfNull(), CRef< C, Locker >::GetNCObject(), and result.
Referenced by SHgvsVariantGrammar::SHgvsVariantGrammar().
void AssignSilent | ( | CRef< CAaLocation > | loc, |
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 56 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
Definition at line 305 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by AssignFuzzySimpleNtSite(), and SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().
void AssignSimpleVariant | ( | CRef< CSimpleVariant > | simple_variant, |
CRef< CVariant > & | result | ||
) |
Definition at line 276 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsVariantGrammar::SHgvsVariantGrammar().
void AssignSingleVariation | ( | CRef< CVariant > | variant, |
CRef< CSequenceVariant > & | result | ||
) |
Definition at line 290 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsVariantGrammar::SHgvsVariantGrammar().
void AssignSpecialVariant | ( | ESpecialVariant | special_variant, |
CRef< CVariant > & | result | ||
) |
Definition at line 283 of file semantic_actions.cpp.
References CreateResultIfNull(), and result.
Referenced by SHgvsVariantGrammar::SHgvsVariantGrammar().
void AssignUnknownSub | ( | CRef< CAaSite > | initial, |
CRef< CSimpleVariant > & | result | ||
) |
Definition at line 73 of file semantic_actions.cpp.
References CreateResultIfNull(), CProteinSub_Base::eType_unknown, and result.
Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().
void TagAsChimera | ( | CRef< CSequenceVariant > | seq_var | ) |
Definition at line 19 of file semantic_actions.cpp.
References CSequenceVariant_Base::eComplex_chimera, and CSequenceVariant_Base::SetComplex().
Referenced by SHgvsVariantGrammar::SHgvsVariantGrammar().
void TagAsMosaic | ( | CRef< CSequenceVariant > | seq_var | ) |
Definition at line 24 of file semantic_actions.cpp.
References CSequenceVariant_Base::eComplex_mosaic, and CSequenceVariant_Base::SetComplex().
Referenced by SHgvsVariantGrammar::SHgvsVariantGrammar().