NCBI C++ ToolKit
Functions
semantic_actions.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <objects/varrep/varrep__.hpp>
+ Include dependency graph for semantic_actions.hpp:
+ This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Go to the SVN repository for this file.

Functions

void AssignRefSeqIdentifier (const string &identifier, CRef< CVariantExpression > &result)
 
void TagAsChimera (CRef< CSequenceVariant > seq_var)
 
void TagAsMosaic (CRef< CSequenceVariant > seq_var)
 
void AssignSequenceVariant (CRef< CSequenceVariant > variant, CRef< CVariantExpression > &result)
 
void AssignMissense (CRef< CAaSite > initial, const CProteinSub::TFinal &final, CRef< CSimpleVariant > &result)
 
void AssignSilent (CRef< CAaLocation > loc, CRef< CSimpleVariant > &result)
 
void AssignNonsense (CRef< CAaSite > initial, CRef< CSimpleVariant > &result)
 
void AssignUnknownSub (CRef< CAaSite > initial, CRef< CSimpleVariant > &result)
 
void AssignAaDup (CRef< CAaLocation > aa_loc, CRef< CSimpleVariant > &result)
 
void AssignAaDel (CRef< CAaLocation > aa_loc, CRef< CSimpleVariant > &result)
 
void AssignNtermExtension (CRef< CAaSite > initial_start_site, CRef< CCount > new_start_site, CRef< CSimpleVariant > &result)
 
void AssignNtermExtension (CRef< CAaSite > initial_start_site, const string &new_aa, CRef< CCount > new_start_site, CRef< CSimpleVariant > &result)
 
void AssignCtermExtension (const string &initial_stop_site, const string &aa, CRef< CCount > new_stop_site, CRef< CSimpleVariant > &result)
 
void AssignAaIntervalLocation (CRef< CAaInterval > aa_interval, CRef< CAaLocation > &result)
 
void AssignAaSiteLocation (CRef< CAaSite > aa_site, CRef< CAaLocation > &result)
 
void AssignAaInterval (CRef< CAaSite > start, CRef< CAaSite > &stop, CRef< CAaInterval > &result)
 
void AssignAaSite (const string &aa, const string &pos, CRef< CAaSite > &result)
 
void AssignCount (const string &count, CRef< CCount > &result)
 
void AssignFuzzyCount (const string &count, CRef< CCount > &result)
 
void AssignCountRange (const string &start, const string &stop, CRef< CCount > &result)
 
void AssignMinCount (const string &min_count, CRef< CCount > &result)
 
void AssignMaxCount (const string &max_count, CRef< CCount > &result)
 
void AssignAaSSR (CRef< CAaLocation > aa_loc, CRef< CCount > count, CRef< CSimpleVariant > &result)
 
void AssignAaInsertion (CRef< CAaInterval > aa_interval, const CInsertion::TSeqinfo::TRaw_seq &raw_seq, CRef< CSimpleVariant > &result)
 
void AssignAaInsertionSize (CRef< CAaInterval > aa_interval, CRef< CCount > seq_size, CRef< CSimpleVariant > &result)
 
void AssignFrameshift (CRef< CAaSite > aa_site, CRef< CSimpleVariant > &result)
 
void AssignAaDelins (CRef< CAaLocation > aa_loc, const string &raw_seq, CRef< CSimpleVariant > &result)
 
void AssignAaDelinsSize (CRef< CAaLocation > aa_loc, CRef< CCount > seq_size, CRef< CSimpleVariant > &result)
 
void AssignFuzzyLocalVariation (CRef< CSimpleVariant > input, CRef< CSimpleVariant > &result)
 
void AssignSimpleVariant (CRef< CSimpleVariant > simple_variant, CRef< CVariant > &result)
 
void AssignSpecialVariant (ESpecialVariant special_variant, CRef< CVariant > &result)
 
void AssignSingleVariation (CRef< CVariant > variant, CRef< CSequenceVariant > &result)
 
void AssignSequenceType (CRef< CSequenceVariant > &result)
 
void AssignFuzzyNtSite (CRef< CNtSite > center_site, CRef< CNtSite > &result)
 
void AssignFuzzySimpleNtSite (const string &site_index, CRef< CNtSite > &result)
 
void AssignSimpleNtSite (const string &site_index, CRef< CNtSite > &result)
 
void Assign3primeUTRSite (CRef< CNtSite > nt_site, CRef< CNtSite > &result)
 
void Assign5primeUTRSite (CRef< CNtSite > nt_site, CRef< CNtSite > &result)
 
void AssignIntronSite (const string &base, const string &offset, CRef< CNtSite > &result)
 
void AssignNtSiteRange (CRef< CNtSite > start, CRef< CNtSite > stop, CRef< CNtLocation > &result)
 
void AssignNtSite (CRef< CNtSite > local_site, CRef< CNtLocation > &result)
 
void AssignNtInterval (CRef< CNtLocation > start, CRef< CNtLocation > stop, CRef< CNtLocation > &result)
 
void AssignNtRemoteLocation (const string &seq_id, const string &seq_type, CRef< CNtLocation > &nt_loc, CRef< CNtLocation > &result)
 
void AssignNtSSR (CRef< CNtLocation > nt_loc, const CRepeat::TRaw_seq &raw_seq, CRef< CCount > count, CRef< CSimpleVariant > &result)
 
void AssignNtSSR (CRef< CNtLocation > nt_loc, CRef< CCount > count, CRef< CSimpleVariant > &result)
 
void AssignNtInv (CRef< CNtLocation > nt_int, CRef< CSimpleVariant > &result)
 
void AssignNtInv (CRef< CNtLocation > nt_int, const CInversion::TRaw_seq &raw_seq, CRef< CSimpleVariant > &result)
 
void AssignNtInvSize (CRef< CNtLocation > nt_int, string size, CRef< CSimpleVariant > &result)
 
void AssignNtConversion (CRef< CNtLocation > src_int, CRef< CNtLocation > dest_int, CRef< CSimpleVariant > &result)
 
void AssignNtInsertion (CRef< CNtLocation > nt_int, const CInsertion::TSeqinfo::TRaw_seq &raw_seq, CRef< CSimpleVariant > &result)
 
void AssignNtDeletion (CRef< CNtLocation > nt_loc, CRef< CSimpleVariant > &result)
 
void AssignNtDeletion (CRef< CNtLocation > nt_loc, const CDeletion::TRaw_seq &raw_seq, CRef< CSimpleVariant > &result)
 
void AssignNtDelins (CRef< CNtLocation > nt_loc, const CInsertion::TSeqinfo::TRaw_seq &inserted_seq, CRef< CSimpleVariant > &result)
 
void AssignNtDelins (CRef< CNtLocation > nt_loc, const CDeletion::TRaw_seq &deleted_seq, const CInsertion::TSeqinfo::TRaw_seq &inserted_seq, CRef< CSimpleVariant > &result)
 
void AssignNtDup (CRef< CNtLocation > nt_loc, CRef< CSimpleVariant > &result)
 
void AssignNtDup (CRef< CNtLocation > nt_loc, const CDuplication::TRaw_seq &raw_seq, 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 AssignNtIdentity (CRef< CNtLocation > nt_loc, CRef< CSimpleVariant > &result)
 
void AssignSequenceType (const string &type, CRef< CSequenceVariant > &result)
 

Function Documentation

◆ Assign3primeUTRSite()

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

◆ Assign5primeUTRSite()

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

◆ AssignAaDel()

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().

◆ AssignAaDelins()

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().

◆ AssignAaDelinsSize()

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().

◆ AssignAaDup()

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().

◆ AssignAaInsertion()

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().

◆ AssignAaInsertionSize()

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().

◆ AssignAaInterval()

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().

◆ AssignAaIntervalLocation()

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().

◆ AssignAaSite()

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

Definition at line 145 of file semantic_actions.cpp.

References CreateResultIfNull(), and result.

Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().

◆ AssignAaSiteLocation()

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().

◆ AssignAaSSR()

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

Definition at line 200 of file semantic_actions.cpp.

References CreateResultIfNull(), and result.

Referenced by SHgvsProteinGrammar::SHgvsProteinGrammar().

◆ AssignCount()

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

◆ AssignCountRange()

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

◆ AssignCtermExtension()

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().

◆ AssignFrameshift()

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().

◆ AssignFuzzyCount()

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

◆ AssignFuzzyLocalVariation()

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

◆ AssignFuzzyNtSite()

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

Definition at line 317 of file semantic_actions.cpp.

References result.

Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().

◆ AssignFuzzySimpleNtSite()

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

◆ AssignIntronSite()

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

◆ AssignMaxCount()

void AssignMaxCount ( const string max_count,
CRef< CCount > &  result 
)

◆ AssignMinCount()

void AssignMinCount ( const string min_count,
CRef< CCount > &  result 
)

◆ AssignMissense()

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

◆ AssignNonsense()

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

◆ AssignNtConversion()

void AssignNtConversion ( CRef< CNtLocation src_int,
CRef< CNtLocation dest_int,
CRef< CSimpleVariant > &  result 
)

◆ AssignNtDeletion() [1/2]

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.

◆ AssignNtDeletion() [2/2]

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().

◆ AssignNtDelins() [1/2]

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.

◆ AssignNtDelins() [2/2]

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

◆ AssignNtDup() [1/2]

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.

◆ AssignNtDup() [2/2]

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().

◆ AssignNtermExtension() [1/2]

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.

◆ AssignNtermExtension() [2/2]

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

◆ AssignNtIdentity() [1/2]

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().

◆ AssignNtIdentity() [2/2]

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

Definition at line 652 of file semantic_actions.cpp.

References CreateResultIfNull(), and result.

◆ AssignNtInsertion()

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

◆ AssignNtInterval()

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

◆ AssignNtInv() [1/2]

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().

◆ AssignNtInv() [2/2]

void AssignNtInv ( CRef< CNtLocation nt_int,
CRef< CSimpleVariant > &  result 
)

◆ AssignNtInvSize()

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

◆ AssignNtRemoteLocation()

void AssignNtRemoteLocation ( const string seq_id,
const string seq_type,
CRef< CNtLocation > &  nt_loc,
CRef< CNtLocation > &  result 
)

◆ AssignNtSite()

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().

◆ AssignNtSiteRange()

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().

◆ AssignNtSSR() [1/2]

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 CreateResultIfNull(), and result.

Referenced by SHgvsNucleicAcidGrammar::SHgvsNucleicAcidGrammar().

◆ AssignNtSSR() [2/2]

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

Definition at line 502 of file semantic_actions.cpp.

References CreateResultIfNull(), and result.

◆ AssignNtSub()

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().

◆ AssignRefSeqIdentifier()

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().

◆ AssignSequenceType() [1/2]

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.

◆ AssignSequenceType() [2/2]

void AssignSequenceType ( CRef< CSequenceVariant > &  result)

◆ AssignSequenceVariant()

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

◆ AssignSilent()

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().

◆ AssignSimpleNtSite()

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

◆ AssignSimpleVariant()

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().

◆ AssignSingleVariation()

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().

◆ AssignSpecialVariant()

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().

◆ AssignUnknownSub()

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

◆ TagAsChimera()

void TagAsChimera ( CRef< CSequenceVariant seq_var)

◆ TagAsMosaic()

void TagAsMosaic ( CRef< CSequenceVariant seq_var)
Modified on Wed Jul 17 13:20:31 2024 by modify_doxy.py rev. 669887