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variation::CHgvsParser Class Reference

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#include <misc/hgvs/hgvs_parser2.hpp>

+ Inheritance diagram for variation::CHgvsParser:
+ Collaboration diagram for variation::CHgvsParser:

Classes

class  CContext
 
class  CHgvsParserException
 
struct  SFuzzyInt
 
struct  SGrammar
 
struct  SOffsetPoint
 

Public Types

enum  EOpFlags { fOpFlags_Default = 0 }
 
typedef int TOpFlags
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8 > TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CHgvsParser (CScope &scope, int tax_id=9606)
 
CRef< CVariation > AsVariation (const string &hgvs_expression, TOpFlags=fOpFlags_Default)
 
string AsHgvsExpression (const CVariation &variation, CConstRef< CSeq_id > seq_id=CConstRef< CSeq_id >(NULL))
 
string AsHgvsExpression (const CVariantPlacement &p)
 
void AttachHgvs (CVariation &v)
 
CScope & SetScope ()
 
CSeq_id_Resolver::TResolvers & SetSeq_id_Resolvers ()
 In order of decreasing priority. More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObject & operator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Static Protected Attributes

static CSafeStatic< SGrammar > s_grammar
 

Private Types

typedef tree_match< char const * > TParseTreeMatch
 
typedef TParseTreeMatch::const_tree_iterator TIterator
 
typedef CVariation_inst::TDelta::value_type TDelta
 
typedef CVariation::TData::TSet TVariationSet
 

Private Member Functions

CRef< CVariantPlacement > x_AdjustPlacementForHgvs (const CVariantPlacement &p, const CVariation_inst &inst)
 In some cases the placement needs to be adjusted depending on inst, e.g. More...
 
CConstRef< CSeq_literal > x_FindAssertedSequence (const CVariation &v)
 If the variation is a package-set, find the subvariation with observation-type "asserted" and return its literal. More...
 
TSeqPos x_GetInstLength (const CVariation_inst &inst, const CVariantPlacement &p, bool account_for_multiplier)
 Compute length of the delta. More...
 
string x_PlacementCoordsToStr (const CVariantPlacement &vp)
 
string x_AsHgvsInstExpression (const CVariation &inst_variation, CConstRef< CVariantPlacement > p, CConstRef< CSeq_literal > asserted_seq)
 Create "inst" part of HGVS expression. More...
 
string x_AsHgvsExpression (const CVariation &variation, CConstRef< CSeq_id > id, CConstRef< CSeq_literal > asserted_seq)
 Construct HGVS expression for a variation: use first VariantPlacement, or, if id is specified, irst placement with matching id; If an asserted sequence is given explicitly, it will be used in construction of HGVS expression; otherwise one will be created based on placement's literal. More...
 
string x_LocToSeqStr (const CSeq_loc &loc)
 Get literal seq at location. More...
 
string x_SeqLiteralToStr (const CSeq_literal &literal, bool translate, bool is_mito)
 translate=true will translate nucleotide literal to prot as appropriate. More...
 

Static Private Member Functions

static SFuzzyInt x_int_fuzz (TIterator const &i, const CContext &context)
 
static CRef< CSeq_point > x_abs_pos (TIterator const &i, const CContext &context)
 
static SOffsetPoint x_general_pos (TIterator const &i, const CContext &context)
 
static SOffsetPoint x_fuzzy_pos (TIterator const &i, const CContext &context)
 
static SOffsetPoint x_pos_spec (TIterator const &i, const CContext &context)
 
static SOffsetPoint x_prot_pos (TIterator const &i, const CContext &context)
 
static CRef< CVariantPlacement > x_range (TIterator const &i, const CContext &context)
 
static CRef< CVariantPlacement > x_location (TIterator const &i, const CContext &context)
 
static CRef< CSeq_loc > x_seq_loc (TIterator const &i, const CContext &context)
 
static CRef< CSeq_literal > x_raw_seq (TIterator const &i, const CContext &context)
 
static TDelta x_seq_ref (TIterator const &i, const CContext &context)
 
static CRef< CSeq_literal > x_raw_seq_or_len (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_delins (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_deletion (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_insertion (TIterator const &i, const CContext &context, bool check_loc)
 
static CRef< CVariation > x_duplication (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_nuc_subst (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_no_change (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_nuc_inv (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_ssr (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_conversion (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_prot_ext (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_prot_missense (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_translocation (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_mut_inst (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_expr1 (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_expr2 (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_expr3 (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_prot_fs (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_list (TIterator const &i, const CContext &context)
 
static CContext x_header (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_root (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_string_content (TIterator const &i, const CContext &context)
 
static CVariation::TData::TSet::EData_set_type x_list_delimiter (TIterator const &i, const CContext &context)
 
static CRef< CVariation > x_unwrap_iff_singleton (CVariation &v)
 
static bool s_hgvsaa2ncbieaa (const string &hgvsaa, string &out)
 Convert HGVS amino-acid code to ncbi code. More...
 
static bool s_hgvs_iupacaa2ncbieaa (const string &hgvsaa, string &out)
 
static bool s_hgvsaa2ncbieaa (const string &hgvsaa, bool uplow, string &out)
 
static string s_hgvsUCaa2hgvsUL (const string &hgvsaa)
 Convert non-HGVS compliant all-uppercase AAs to UpLow, e.g. ILECYS ->IleCys. More...
 
static void s_SetStartOffset (CVariantPlacement &p, const CHgvsParser::SFuzzyInt &fint)
 
static void s_SetStopOffset (CVariantPlacement &p, const CHgvsParser::SFuzzyInt &fint)
 
static TSignedSeqPos s_GetHgvsPos (TSeqPos abs_pos, const TSeqPos *atg_pos)
 if no atg_pos, assume that not dealing with coordinate systems (simply return abs-pos) otherwise, convert to hgvs coordinates: More...
 
static string s_IntWithFuzzToStr (long pos, const TSeqPos *ref_pos, bool with_sign, const CInt_fuzz *fuzz)
 this function may be used to create hgvs-coordinates (if ref_pos is not null), or to create a fuzzy hgvs-number specification (e.g. More...
 
static string s_OffsetPointToString (TSeqPos anchor_pos, const CInt_fuzz *anchor_fuzz, TSeqPos anchor_ref_pos, TSeqPos effective_seq_length, const long *offset_pos, const CInt_fuzz *offset_fuzz)
 Construct an HGVS coordinate, which may be an intronic offset-point, e.g. "5+(10_11)". More...
 
static string s_SeqIdToHgvsStr (const CVariantPlacement &vp, CScope *scope=NULL)
 Construct an hgvs "header" consisting of seq-id and mol-type, e.g. "NG_016831.1:g.". More...
 
static void sx_AppendMoltypeExceptions (CVariation &v, CScope &scope)
 

Private Attributes

CRef< CScope > m_scope
 
CSeq_id_Resolver::TResolvers m_seq_id_resolvers
 

Additional Inherited Members

- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 86 of file hgvs_parser2.hpp.

Member Typedef Documentation

◆ TDelta

typedef CVariation_inst::TDelta::value_type variation::CHgvsParser::TDelta
private

Definition at line 809 of file hgvs_parser2.hpp.

◆ TIterator

typedef TParseTreeMatch::const_tree_iterator variation::CHgvsParser::TIterator
private

Definition at line 808 of file hgvs_parser2.hpp.

◆ TOpFlags

typedef int variation::CHgvsParser::TOpFlags

Definition at line 104 of file hgvs_parser2.hpp.

◆ TParseTreeMatch

typedef tree_match<char const*> variation::CHgvsParser::TParseTreeMatch
private

Definition at line 807 of file hgvs_parser2.hpp.

◆ TVariationSet

typedef CVariation::TData::TSet variation::CHgvsParser::TVariationSet
private

Definition at line 810 of file hgvs_parser2.hpp.

Member Enumeration Documentation

◆ EOpFlags

enum variation::CHgvsParser::EOpFlags
Enumerator
fOpFlags_Default 

Definition at line 100 of file hgvs_parser2.hpp.

Constructor & Destructor Documentation

◆ CHgvsParser()

variation::CHgvsParser::CHgvsParser ( CScope &  scope,
int  tax_id = 9606 
)
inline

Definition at line 89 of file hgvs_parser2.hpp.

Member Function Documentation

◆ AsHgvsExpression() [1/2]

string CHgvsParser::AsHgvsExpression ( const CVariantPlacement &  p)

Definition at line 627 of file hgvs_writer2.cpp.

References m_scope, s_SeqIdToHgvsStr(), and x_PlacementCoordsToStr().

◆ AsHgvsExpression() [2/2]

string CHgvsParser::AsHgvsExpression ( const CVariation &  variation,
CConstRef< CSeq_id >  seq_id = CConstRef<CSeq_id>(NULL) 
)

Definition at line 200 of file hgvs_writer2.cpp.

References Begin(), CVariantPlacement_Base::IsSetSeq(), m_scope, NULL, and x_AsHgvsExpression().

Referenced by AttachHgvs(), x_AsHgvsExpression(), and x_AsHgvsInstExpression().

◆ AsVariation()

CRef< CVariation > CHgvsParser::AsVariation ( const string &  hgvs_expression,
TOpFlags  flags = fOpFlags_Default 
)

Definition at line 2069 of file hgvs_parser2.cpp.

References variation::CHgvsParser::CContext::GetScope(), HGVS_THROW, info, m_scope, m_seq_id_resolvers, s_grammar, NStr::SizetToString(), sx_AppendMoltypeExceptions(), NStr::TruncateSpaces(), and x_root().

Referenced by CHgvsReader::ReadSeqAnnot().

◆ AttachHgvs()

void CHgvsParser::AttachHgvs ( CVariation &  v)

Definition at line 2096 of file hgvs_parser2.cpp.

References AsHgvsExpression(), Begin(), CVariantPlacement_Base::eMol_protein, CSeq_loc::GetId(), CVariantPlacement_Base::GetLoc(), CVariantPlacement_Base::GetMol(), CVariation::Index(), CVariation_Base::IsSetPlacements(), MSerial_AsnText, NCBI_REPORT_EXCEPTION, NON_CONST_ITERATE, CVariantPlacement_Base::SetHgvs_name(), CVariation_Base::SetSynonyms(), and v2.

◆ s_GetHgvsPos()

TSignedSeqPos CHgvsParser::s_GetHgvsPos ( TSeqPos  abs_pos,
const TSeqPos *  atg_pos 
)
staticprivate

if no atg_pos, assume that not dealing with coordinate systems (simply return abs-pos) otherwise, convert to hgvs coordinates:

Definition at line 491 of file hgvs_writer2.cpp.

Referenced by s_IntWithFuzzToStr().

◆ s_hgvs_iupacaa2ncbieaa()

bool CHgvsParser::s_hgvs_iupacaa2ncbieaa ( const string &  hgvsaa,
string &  out 
)
staticprivate

Definition at line 1189 of file hgvs_parser2.cpp.

References out(), and NStr::ReplaceInPlace().

Referenced by s_hgvsaa2ncbieaa().

◆ s_hgvsaa2ncbieaa() [1/2]

bool CHgvsParser::s_hgvsaa2ncbieaa ( const string &  hgvsaa,
bool  uplow,
string &  out 
)
staticprivate

Definition at line 1201 of file hgvs_parser2.cpp.

References CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CSeqportUtil::GetCode(), CSeqportUtil::GetIupacaa3(), CSeqportUtil::GetMapToIndex(), in(), out(), NStr::StartsWith(), and NStr::ToUpper().

◆ s_hgvsaa2ncbieaa() [2/2]

bool CHgvsParser::s_hgvsaa2ncbieaa ( const string &  hgvsaa,
string &  out 
)
staticprivate

Convert HGVS amino-acid code to ncbi code.

Return true iff success; otherwise false and out = in.

Definition at line 1173 of file hgvs_parser2.cpp.

References out(), and s_hgvs_iupacaa2ncbieaa().

Referenced by x_raw_seq().

◆ s_hgvsUCaa2hgvsUL()

static string variation::CHgvsParser::s_hgvsUCaa2hgvsUL ( const string &  hgvsaa)
staticprivate

Convert non-HGVS compliant all-uppercase AAs to UpLow, e.g. ILECYS ->IleCys.

◆ s_IntWithFuzzToStr()

string CHgvsParser::s_IntWithFuzzToStr ( long  pos,
const TSeqPos *  ref_pos,
bool  with_sign,
const CInt_fuzz *  fuzz 
)
staticprivate

this function may be used to create hgvs-coordinates (if ref_pos is not null), or to create a fuzzy hgvs-number specification (e.g.

for multipliers, or fuzzy offset values), where pos is not adjusted (Note that pos may be negative, e.g. for offset value)

Definition at line 505 of file hgvs_writer2.cpp.

References CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, CInt_fuzz_Base::GetLim(), CInt_fuzz_Base::C_Range::GetMax(), CInt_fuzz_Base::C_Range::GetMin(), CInt_fuzz_Base::GetRange(), CInt_fuzz_Base::IsLim(), CInt_fuzz_Base::IsRange(), NStr::LongToString(), s_GetHgvsPos(), and val.

Referenced by s_OffsetPointToString(), x_AsHgvsInstExpression(), and x_SeqLiteralToStr().

◆ s_OffsetPointToString()

string CHgvsParser::s_OffsetPointToString ( TSeqPos  anchor_pos,
const CInt_fuzz *  anchor_fuzz,
TSeqPos  anchor_ref_pos,
TSeqPos  effective_seq_length,
const long *  offset_pos,
const CInt_fuzz *  offset_fuzz 
)
staticprivate

Construct an HGVS coordinate, which may be an intronic offset-point, e.g. "5+(10_11)".

Definition at line 602 of file hgvs_writer2.cpp.

References NULL, and s_IntWithFuzzToStr().

Referenced by x_PlacementCoordsToStr().

◆ s_SeqIdToHgvsStr()

string CHgvsParser::s_SeqIdToHgvsStr ( const CVariantPlacement &  vp,
CScope *  scope = NULL 
)
staticprivate

Construct an hgvs "header" consisting of seq-id and mol-type, e.g. "NG_016831.1:g.".

Definition at line 569 of file hgvs_writer2.cpp.

References CVariantPlacement_Base::eMol_cdna, CVariantPlacement_Base::eMol_genomic, CVariantPlacement_Base::eMol_mitochondrion, CVariantPlacement_Base::eMol_protein, CVariantPlacement_Base::eMol_rna, eNa_strand_minus, GetAccessionForGi(), GetId(), CVariantPlacement_Base::GetLoc(), CVariantPlacement_Base::GetMol(), CSeq_loc::GetStrand(), NULL, and NStr::StartsWith().

Referenced by AsHgvsExpression(), and sx_AppendMoltypeExceptions().

◆ s_SetStartOffset()

void CHgvsParser::s_SetStartOffset ( CVariantPlacement &  p,
const CHgvsParser::SFuzzyInt &  fint 
)
staticprivate

Definition at line 241 of file hgvs_parser2.cpp.

References CInt_fuzz_Base::eLim_lt, CInt_fuzz_Base::eLim_tl, variation::CHgvsParser::SFuzzyInt::fuzz, CInt_fuzz_Base::GetLim(), CInt_fuzz_Base::IsLim(), CVariantPlacement_Base::ResetStart_offset(), CVariantPlacement_Base::ResetStart_offset_fuzz(), CVariantPlacement_Base::SetStart_offset(), CVariantPlacement_Base::SetStart_offset_fuzz(), and variation::CHgvsParser::SFuzzyInt::value.

Referenced by x_location(), and x_range().

◆ s_SetStopOffset()

void CHgvsParser::s_SetStopOffset ( CVariantPlacement &  p,
const CHgvsParser::SFuzzyInt &  fint 
)
staticprivate

Definition at line 268 of file hgvs_parser2.cpp.

References CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_tr, variation::CHgvsParser::SFuzzyInt::fuzz, CInt_fuzz_Base::GetLim(), CInt_fuzz_Base::IsLim(), CVariantPlacement_Base::ResetStop_offset(), CVariantPlacement_Base::ResetStop_offset_fuzz(), CVariantPlacement_Base::SetStop_offset(), CVariantPlacement_Base::SetStop_offset_fuzz(), and variation::CHgvsParser::SFuzzyInt::value.

Referenced by x_range().

◆ SetScope()

CScope& variation::CHgvsParser::SetScope ( void  )
inline

Definition at line 116 of file hgvs_parser2.hpp.

◆ SetSeq_id_Resolvers()

CSeq_id_Resolver::TResolvers& variation::CHgvsParser::SetSeq_id_Resolvers ( )
inline

In order of decreasing priority.

Last resolver is default catch-all, so when adding a custom one don't push_back.

Definition at line 123 of file hgvs_parser2.hpp.

Referenced by CHgvsReader::ReadSeqAnnot().

◆ sx_AppendMoltypeExceptions()

void CHgvsParser::sx_AppendMoltypeExceptions ( CVariation &  v,
CScope &  scope 
)
staticprivate

Definition at line 2047 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), Begin(), CVariationException_Base::eCode_inconsistent_asserted_moltype, GetId(), CVariantPlacement_Base::GetLoc(), CVariantPlacement_Base::GetMol(), NULL, s_SeqIdToHgvsStr(), CVariantPlacement_Base::SetExceptions(), and CVariantPlacement_Base::SetMol().

Referenced by AsVariation().

◆ x_abs_pos()

CRef< CSeq_point > CHgvsParser::x_abs_pos ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 512 of file hgvs_parser2.cpp.

References variation::AdjustHgvsCoord(), eExtreme_Biological, CVariantPlacement_Base::eMol_cdna, eNa_strand_plus, variation::CHgvsParser::SFuzzyInt::fuzz, variation::CHgvsParser::CContext::GetCDS(), CSeq_point_Base::GetFuzz(), variation::CHgvsParser::CContext::GetId(), CSeq_feat_Base::GetLocation(), CVariantPlacement_Base::GetMol(), variation::CHgvsParser::CContext::GetPlacement(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), HGVS_ASSERT_RULE, HGVS_THROW, i, CRef< C, Locker >::IsNull(), variation::CHgvsParser::SFuzzyInt::IsPureFuzz(), CInt_fuzz_Base::IsRange(), kInvalidSeqPos, offset, r(), CSeq_point_Base::SetFuzz(), CSeq_point_Base::SetId(), CSeq_point_Base::SetPoint(), CSeq_point_Base::SetStrand(), variation::CHgvsParser::SFuzzyInt::value, and x_int_fuzz().

Referenced by x_general_pos().

◆ x_AdjustPlacementForHgvs()

CRef< CVariantPlacement > CHgvsParser::x_AdjustPlacementForHgvs ( const CVariantPlacement &  p,
const CVariation_inst &  inst 
)
private

In some cases the placement needs to be adjusted depending on inst, e.g.

if we have a point-relative insertion, it needs to be converted to "between-dinucleotide" representation; or, in case of microsatellites, the location must point to the first repeat unit rather than whole tandem repeat

Definition at line 80 of file hgvs_writer2.cpp.

References CSerialObject::Assign(), CDelta_item_Base::eAction_ins_before, eNa_strand_minus, CVariation_inst_Base::eType_ins, CVariation_inst_Base::eType_microsatellite, CSeq_loc::fMerge_SingleRange, CSeq_loc::fSortAndMerge_All, CVariation_inst_Base::GetDelta(), CSeq_interval_Base::GetFrom(), CSeq_loc_Base::GetInt(), CVariantPlacement_Base::GetLoc(), CSeq_loc::GetStrand(), CSeq_interval_Base::GetTo(), CVariation_inst_Base::GetType(), CSeq_loc_Base::IsPnt(), CVariantPlacement_Base::IsSetStart_offset(), CVariantPlacement_Base::IsSetStop_offset(), m_scope, NULL, Seq_loc_Add(), Seq_loc_Merge(), CSeq_loc::SetInt(), CVariantPlacement_Base::SetLoc(), variation::CVariationUtil::SFlankLocs::upstream, and x_GetInstLength().

Referenced by x_AsHgvsExpression().

◆ x_AsHgvsExpression()

string CHgvsParser::x_AsHgvsExpression ( const CVariation &  variation,
CConstRef< CSeq_id >  id,
CConstRef< CSeq_literal >  asserted_seq 
)
private

Construct HGVS expression for a variation: use first VariantPlacement, or, if id is specified, irst placement with matching id; If an asserted sequence is given explicitly, it will be used in construction of HGVS expression; otherwise one will be created based on placement's literal.

Definition at line 224 of file hgvs_writer2.cpp.

References AsHgvsExpression(), CSerialObject::Assign(), CVariation_Base::C_Data::C_Set::eData_set_type_alleles, CVariation_Base::C_Data::C_Set::eData_set_type_chimeric, CVariation_Base::C_Data::C_Set::eData_set_type_compound, CVariation_Base::C_Data::C_Set::eData_set_type_genotype, CVariation_Base::C_Data::C_Set::eData_set_type_haplotype, CVariation_Base::C_Data::C_Set::eData_set_type_individual, CVariation_Base::C_Data::C_Set::eData_set_type_mosaic, CVariation_Base::C_Data::C_Set::eData_set_type_package, CVariation_Base::C_Data::C_Set::eData_set_type_products, CVariationMethod_Base::eMethod_E_computational, eNa_strand_minus, CVariation_inst_Base::eObservation_variant, CVariation_inst_Base::eType_microsatellite, eUnknown, CSeq_loc::GetId(), CVariantPlacement_Base::GetLoc(), CSeq_loc::GetStrand(), CVariation_Base::C_Data::C_Set::GetType(), CVariation_Base::C_Data::C_Set::GetVariations(), IsSameBioseq(), ITERATE, m_scope, NCBI_THROW, NStr::NumericToString(), CRef< C, Locker >::Reset(), CSeqportUtil::ReverseComplement(), variation::CVariationUtil::s_GetPlacements(), CSeq_literal_Base::SetSeq_data(), v2, x_AdjustPlacementForHgvs(), x_AsHgvsInstExpression(), and x_FindAssertedSequence().

Referenced by AsHgvsExpression().

◆ x_AsHgvsInstExpression()

string CHgvsParser::x_AsHgvsInstExpression ( const CVariation &  inst_variation,
CConstRef< CVariantPlacement >  p,
CConstRef< CSeq_literal >  asserted_seq 
)
private

Create "inst" part of HGVS expression.

Definition at line 834 of file hgvs_writer2.cpp.

References AsHgvsExpression(), CSerialObject::Assign(), Begin(), variation::ContainsAnyFuzz(), delta(), CVariantPlacement_Base::eMol_protein, CSerialObject::Equals(), CVariation_inst_Base::eType_del, CVariation_inst_Base::eType_delins, CVariation_inst_Base::eType_identity, CVariation_inst_Base::eType_ins, CVariation_inst_Base::eType_inv, CVariation_inst_Base::eType_microsatellite, CVariation_inst_Base::eType_mnp, CVariation_inst_Base::eType_prot_missense, CVariation_inst_Base::eType_prot_neutral, CVariation_inst_Base::eType_prot_nonsense, CVariation_inst_Base::eType_prot_other, CVariation_inst_Base::eType_prot_silent, CVariation_inst_Base::eType_snv, CVariation_inst_Base::eType_transposon, eUnknown, CScope::GetBioseqHandle(), CVariation_inst_Base::GetDelta(), GetId(), CSeq_loc::GetId(), CBioseq_Handle::GetInst_Length(), CVariantPlacement_Base::GetLoc(), CConstRef< C, Locker >::GetPointer(), CVariantPlacement_Base::GetSeq(), CVariation_inst_Base::GetType(), isdigit(), variation::IsMitochondrion(), ITERATE, literal(), m_scope, NCBI_THROW, NULL, NStr::NumericToString(), CConstRef< C, Locker >::Reset(), s_IntWithFuzzToStr(), CVariantPlacement_Base::SetLoc(), CVariantPlacement_Base::SetMol(), NStr::StartsWith(), x_LocToSeqStr(), x_PlacementCoordsToStr(), and x_SeqLiteralToStr().

Referenced by x_AsHgvsExpression().

◆ x_conversion()

CRef< CVariation > CHgvsParser::x_conversion ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1634 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), delta(), CVariation_inst_Base::eType_transposon, variation::CHgvsParser::CContext::GetPlacement(), HGVS_ASSERT_RULE, i, CVariation_inst_Base::SetDelta(), variation::SetFirstPlacement(), CVariation_inst_Base::SetType(), and x_seq_loc().

Referenced by x_mut_inst().

◆ x_deletion()

CRef< CVariation > CHgvsParser::x_deletion ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1317 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), CDelta_item_Base::eAction_del_at, CVariationException_Base::eCode_hgvs_parsing, variation::CHgvsParser::SGrammar::eID_raw_seq_or_len, CVariation_inst_Base::eType_del, variation::CHgvsParser::CContext::GetPlacement(), HGVS_ASSERT_RULE, i, literal(), NULL, variation::CVariationUtil::s_GetLength(), CVariation_inst_Base::SetDelta(), CVariantPlacement_Base::SetExceptions(), variation::SetFirstPlacement(), CVariantPlacement_Base::SetSeq(), CVariation_inst_Base::SetType(), and x_raw_seq_or_len().

Referenced by x_delins(), and x_mut_inst().

◆ x_delins()

CRef< CVariation > CHgvsParser::x_delins ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1286 of file hgvs_parser2.cpp.

References CVariationException_Base::eCode_hgvs_parsing, variation::GetDelInsSubtype(), variation::GetDeltaLength(), HGVS_ASSERT_RULE, i, NULL, variation::CVariationUtil::s_GetLength(), CVariantPlacement_Base::SetExceptions(), variation::SetFirstPlacement(), x_deletion(), and x_insertion().

Referenced by x_mut_inst().

◆ x_duplication()

CRef< CVariation > CHgvsParser::x_duplication ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1381 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), delta(), variation::CHgvsParser::SGrammar::eID_seq_ref, CVariation_inst_Base::eType_ins, variation::CHgvsParser::CContext::GetPlacement(), HGVS_ASSERT_RULE, HGVS_THROW, i, NULL, variation::CVariationUtil::s_GetLength(), CVariation_inst_Base::SetDelta(), variation::SetFirstPlacement(), CVariantPlacement_Base::SetSeq(), CVariation_inst_Base::SetType(), and x_seq_ref().

Referenced by x_mut_inst().

◆ x_expr1()

CRef< CVariation > CHgvsParser::x_expr1 ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1814 of file hgvs_parser2.cpp.

References variation::CHgvsParser::SGrammar::eID_header, variation::CHgvsParser::SGrammar::eID_list1a, variation::CHgvsParser::SGrammar::eID_translocation, HGVS_ASSERT_RULE, i, variation::SetComputational(), x_expr2(), x_header(), x_list(), and x_translocation().

Referenced by x_list().

◆ x_expr2()

CRef< CVariation > CHgvsParser::x_expr2 ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1840 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), CDelta_item_Base::eAction_del_at, variation::CHgvsParser::SGrammar::eID_list2a, variation::CHgvsParser::SGrammar::eID_location, variation::CHgvsParser::SGrammar::eID_no_change, variation::CHgvsParser::SGrammar::eID_prot_ext, CVariation_inst_Base::eType_del, variation::CHgvsParser::CContext::GetId(), variation::CHgvsParser::CContext::GetPlacement(), HGVS_ASSERT_RULE, HGVS_THROW, i, CRef< C, Locker >::Reset(), variation::SetComputational(), CVariation_inst_Base::SetDelta(), variation::SetFirstPlacement(), CVariantPlacement_Base::SetLoc(), variation::CHgvsParser::CContext::SetPlacement(), CVariation_inst_Base::SetType(), x_expr3(), x_list(), x_location(), x_no_change(), and x_prot_ext().

Referenced by x_expr1(), and x_list().

◆ x_expr3()

CRef< CVariation > CHgvsParser::x_expr3 ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1894 of file hgvs_parser2.cpp.

References delta(), CVariation_Base::C_Data::C_Set::eData_set_type_compound, variation::CHgvsParser::SGrammar::eID_list3a, variation::CHgvsParser::SGrammar::eID_mut_inst, CVariation_inst_Base::eType_prot_other, HGVS_ASSERT_RULE, i, CRef< C, Locker >::Reset(), variation::SetComputational(), CVariation_inst_Base::SetDelta(), CVariation_inst_Base::SetType(), x_list(), x_mut_inst(), and x_unwrap_iff_singleton().

Referenced by x_expr2(), and x_list().

◆ x_FindAssertedSequence()

CConstRef< CSeq_literal > CHgvsParser::x_FindAssertedSequence ( const CVariation &  v)
private

If the variation is a package-set, find the subvariation with observation-type "asserted" and return its literal.

Definition at line 126 of file hgvs_writer2.cpp.

References CVariation_Base::C_Data::C_Set::eData_set_type_package, CVariation_inst_Base::eObservation_asserted, CVariation_inst_Base::eObservation_reference, CVariation_Base::GetData(), CVariation_Base::C_Data::GetSet(), CVariation_Base::C_Data::C_Set::GetType(), CVariation_Base::C_Data::C_Set::GetVariations(), CVariation_Base::C_Data::IsSet(), ITERATE, CConstRef< C, Locker >::Reset(), and v2.

Referenced by x_AsHgvsExpression().

◆ x_fuzzy_pos()

CHgvsParser::SOffsetPoint CHgvsParser::x_fuzzy_pos ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 680 of file hgvs_parser2.cpp.

References variation::CHgvsParser::SOffsetPoint::Assign(), CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, CInt_fuzz_Base::eLim_unk, eNa_strand_minus, CSerialObject::Equals(), variation::CHgvsParser::SFuzzyInt::fuzz, CSeq_point_Base::GetId(), CSeq_point_Base::GetPoint(), CSeq_point_Base::GetStrand(), HGVS_ASSERT_RULE, HGVS_THROW, i, variation::IsPureFuzzPoint(), kInvalidSeqPos, max(), min(), variation::CHgvsParser::SOffsetPoint::offset, variation::CHgvsParser::SOffsetPoint::pnt, CRef< C, Locker >::Reset(), CSeq_point_Base::SetFuzz(), CInt_fuzz_Base::C_Range::SetMax(), CInt_fuzz_Base::C_Range::SetMin(), CInt_fuzz_Base::SetRange(), variation::CHgvsParser::SFuzzyInt::value, and x_general_pos().

Referenced by x_pos_spec().

◆ x_general_pos()

CHgvsParser::SOffsetPoint CHgvsParser::x_general_pos ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 584 of file hgvs_parser2.cpp.

References eExtreme_Biological, variation::CHgvsParser::SGrammar::eID_abs_pos, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CVariantPlacement_Base::eMol_cdna, CVariantPlacement_Base::eMol_rna, eNa_strand_plus, CSeqFeatData::eSubtype_exon, variation::CHgvsParser::SFuzzyInt::fuzz, variation::CHgvsParser::CContext::GetBioseqHandle(), CScope::GetBioseqHandle(), variation::CVariationUtil::GetEffectiveTranscriptLength(), variation::CHgvsParser::CContext::GetId(), CMappedFeat::GetLocation(), CVariantPlacement_Base::GetMol(), variation::CHgvsParser::CContext::GetPlacement(), CSeq_point_Base::GetPoint(), variation::CHgvsParser::CContext::GetScope(), HGVS_ASSERT_RULE, i, SAnnotSelector::IncludeFeatSubtype(), variation::CHgvsParser::SFuzzyInt::IsPureFuzz(), variation::IsPureFuzzPoint(), CInt_fuzz_Base::IsRange(), variation::CHgvsParser::SOffsetPoint::offset, variation::CHgvsParser::SOffsetPoint::pnt, CRef< C, Locker >::Reset(), CSeq_point_Base::SetId(), CInt_fuzz_Base::SetLim(), CInt_fuzz_Base::C_Range::SetMax(), CInt_fuzz_Base::C_Range::SetMin(), CSeq_point_Base::SetPoint(), CInt_fuzz_Base::SetRange(), CSeq_point_Base::SetStrand(), NStr::StringToInt(), variation::CHgvsParser::SFuzzyInt::value, x_abs_pos(), and x_int_fuzz().

Referenced by x_fuzzy_pos(), and x_pos_spec().

◆ x_GetInstLength()

TSeqPos CHgvsParser::x_GetInstLength ( const CVariation_inst &  inst,
const CVariantPlacement &  p,
bool  account_for_multiplier 
)
private

Compute length of the delta.

Definition at line 794 of file hgvs_writer2.cpp.

References eUnknown, CVariation_inst_Base::GetDelta(), GetLength(), CSeq_literal_Base::GetLength(), CDelta_item_Base::C_Seq::GetLiteral(), CDelta_item_Base::C_Seq::GetLoc(), CDelta_item_Base::GetMultiplier(), CDelta_item_Base::GetSeq(), CDelta_item_Base::C_Seq::IsLiteral(), CDelta_item_Base::C_Seq::IsLoc(), CDelta_item_Base::IsSetMultiplier(), CDelta_item_Base::C_Seq::IsThis(), ITERATE, len, m_scope, NCBI_THROW, and variation::CVariationUtil::s_GetLength().

Referenced by x_AdjustPlacementForHgvs().

◆ x_header()

CHgvsParser::CContext CHgvsParser::x_header ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 844 of file hgvs_parser2.cpp.

References CSeq_id_Handle::AsString(), ctx, CSeqFeatData_Base::e_Cdregion, CSeq_id::eAcc_refseq_genomic, eGetId_ForceAcc, CVariantPlacement_Base::eMol_cdna, CVariantPlacement_Base::eMol_genomic, CVariantPlacement_Base::eMol_mitochondrion, CVariantPlacement_Base::eMol_protein, CVariantPlacement_Base::eMol_rna, CVariantPlacement_Base::eMol_unknown, NStr::Find(), CScope::GetBioseqHandle(), GetId(), CMappedFeat::GetProduct(), variation::CHgvsParser::CContext::GetScope(), CSeq_id_Handle::GetSeqId(), variation::GetUniquePrimaryTranscriptId(), HGVS_ASSERT_RULE, HGVS_THROW, i, CSeq_id_Handle::IdentifyAccession(), SAnnotSelector::IncludeFeatType(), variation::IsLRG(), CBioseq_Handle::IsNucleotide(), CSeq_feat_Handle::IsSetProduct(), variation::CHgvsParser::CContext::ResolevSeqId(), and SAnnotSelector::SetResolveTSE().

Referenced by x_expr1(), x_pos_spec(), and x_seq_loc().

◆ x_insertion()

CRef< CVariation > CHgvsParser::x_insertion ( TIterator const &  i,
const CContext &  context,
bool  check_loc 
)
staticprivate

Definition at line 1353 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), CDelta_item_Base::eAction_ins_before, CVariation_inst_Base::eType_ins, variation::CHgvsParser::CContext::GetPlacement(), HGVS_ASSERT_RULE, HGVS_THROW, i, NULL, variation::CVariationUtil::s_GetLength(), CVariation_inst_Base::SetDelta(), variation::SetFirstPlacement(), CVariation_inst_Base::SetType(), and x_seq_ref().

Referenced by x_delins(), and x_mut_inst().

◆ x_int_fuzz()

CHgvsParser::SFuzzyInt CHgvsParser::x_int_fuzz ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 438 of file hgvs_parser2.cpp.

References CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CInt_fuzz_Base::eLim_unk, variation::CHgvsParser::SFuzzyInt::fuzz, HGVS_ASSERT_RULE, HGVS_THROW, i, CRef< C, Locker >::Reset(), CInt_fuzz_Base::SetLim(), CInt_fuzz_Base::C_Range::SetMax(), CInt_fuzz_Base::C_Range::SetMin(), variation::CHgvsParser::SFuzzyInt::SetPureFuzz(), CInt_fuzz_Base::SetRange(), NStr::StringToInt(), and variation::CHgvsParser::SFuzzyInt::value.

Referenced by x_abs_pos(), x_general_pos(), x_raw_seq_or_len(), and x_ssr().

◆ x_list()

CRef< CVariation > CHgvsParser::x_list ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1963 of file hgvs_parser2.cpp.

References CVariation_Base::C_Data::C_Set::eData_set_type_genotype, CVariation_Base::C_Data::C_Set::eData_set_type_unknown, variation::CHgvsParser::SGrammar::eID_expr1, variation::CHgvsParser::SGrammar::eID_expr2, variation::CHgvsParser::SGrammar::eID_expr3, CVariation_Base::C_Data::C_Set::GetType(), HGVS_ASSERT_RULE, HGVS_THROW, i, variation::CHgvsParser::SGrammar::s_is_list(), variation::CHgvsParser::SGrammar::s_is_list_a(), CVariation_Base::C_Data::C_Set::SetType(), CVariation_Base::C_Data::C_Set::SetVariations(), x_expr1(), x_expr2(), x_expr3(), x_list_delimiter(), and x_unwrap_iff_singleton().

Referenced by x_expr1(), x_expr2(), x_expr3(), and x_root().

◆ x_list_delimiter()

CVariation::TData::TSet::EData_set_type CHgvsParser::x_list_delimiter ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1947 of file hgvs_parser2.cpp.

References CVariation_Base::C_Data::C_Set::eData_set_type_chimeric, CVariation_Base::C_Data::C_Set::eData_set_type_genotype, CVariation_Base::C_Data::C_Set::eData_set_type_haplotype, CVariation_Base::C_Data::C_Set::eData_set_type_individual, CVariation_Base::C_Data::C_Set::eData_set_type_mosaic, CVariation_Base::C_Data::C_Set::eData_set_type_products, CVariation_Base::C_Data::C_Set::eData_set_type_unknown, HGVS_ASSERT_RULE, and i.

Referenced by x_list().

◆ x_location()

CRef< CVariantPlacement > CHgvsParser::x_location ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1039 of file hgvs_parser2.cpp.

References variation::CHgvsParser::SOffsetPoint::asserted_sequence, CSerialObject::Assign(), CVariationException_Base::eCode_hgvs_exon_boundary, variation::CVariationUtil::eFail, variation::CHgvsParser::SGrammar::eID_nuc_range, variation::CHgvsParser::SGrammar::eID_pos_spec, variation::CHgvsParser::SGrammar::eID_prot_pos, variation::CHgvsParser::SGrammar::eID_prot_range, CVariantPlacement_Base::eMol_protein, variation::CHgvsParser::CContext::GetId(), CVariantPlacement_Base::GetLoc(), CVariantPlacement_Base::GetMol(), variation::CHgvsParser::CContext::GetPlacement(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), variation::CHgvsParser::CContext::GetScope(), HGVS_ASSERT_RULE, i, CSeq_loc_Base::IsPnt(), kInvalidSeqPos, NULL, variation::CHgvsParser::SOffsetPoint::offset, variation::CHgvsParser::SOffsetPoint::pnt, variation::CVariationUtil::s_GetLength(), s_SetStartOffset(), CVariantPlacement_Base::SetExceptions(), CVariantPlacement_Base::SetLoc(), CVariantPlacement_Base::SetSeq(), x_pos_spec(), x_prot_pos(), and x_range().

Referenced by x_expr2(), and x_seq_loc().

◆ x_LocToSeqStr()

string CHgvsParser::x_LocToSeqStr ( const CSeq_loc &  loc)
private

Get literal seq at location.

Definition at line 482 of file hgvs_writer2.cpp.

References CSeqVector::begin(), CBioseq_Handle::eCoding_Iupac, CSeqVector::end(), CSeqVector::GetSeqData(), and m_scope.

Referenced by x_AsHgvsInstExpression().

◆ x_mut_inst()

CRef< CVariation > CHgvsParser::x_mut_inst ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1774 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), variation::CHgvsParser::SGrammar::eID_conversion, variation::CHgvsParser::SGrammar::eID_deletion, variation::CHgvsParser::SGrammar::eID_delins, variation::CHgvsParser::SGrammar::eID_duplication, variation::CHgvsParser::SGrammar::eID_insertion, variation::CHgvsParser::SGrammar::eID_mut_inst, variation::CHgvsParser::SGrammar::eID_no_change, variation::CHgvsParser::SGrammar::eID_nuc_inv, variation::CHgvsParser::SGrammar::eID_nuc_subst, variation::CHgvsParser::SGrammar::eID_prot_ext, variation::CHgvsParser::SGrammar::eID_prot_fs, variation::CHgvsParser::SGrammar::eID_prot_missense, variation::CHgvsParser::SGrammar::eID_ssr, variation::CHgvsParser::SGrammar::eID_translocation, variation::CHgvsParser::CContext::GetPlacement(), HGVS_ASSERT_RULE, i, CRef< C, Locker >::IsNull(), NULL, variation::SetFirstPlacement(), x_conversion(), x_deletion(), x_delins(), x_duplication(), x_insertion(), x_no_change(), x_nuc_inv(), x_nuc_subst(), x_prot_ext(), x_prot_fs(), x_prot_missense(), x_ssr(), x_string_content(), and x_translocation().

Referenced by x_expr3().

◆ x_no_change()

CRef< CVariation > CHgvsParser::x_no_change ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1414 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), delta(), variation::CHgvsParser::SGrammar::eID_raw_seq, CVariantPlacement_Base::eMol_protein, CVariation_inst_Base::eType_identity, CVariation_inst_Base::eType_mnp, CVariation_inst_Base::eType_prot_silent, CVariation_inst_Base::eType_snv, CSeq_literal_Base::GetLength(), CVariantPlacement_Base::GetLoc(), CVariantPlacement_Base::GetMol(), variation::CHgvsParser::CContext::GetPlacement(), variation::CHgvsParser::CContext::GetScope(), CVariantPlacement_Base::GetSeq(), HGVS_ASSERT_RULE, i, CVariantPlacement_Base::IsSetSeq(), CSeq_loc_Base::IsWhole(), CVariantPlacement_Base::ResetExceptions(), CVariation_inst_Base::SetDelta(), variation::SetFirstPlacement(), CVariantPlacement_Base::SetSeq(), CVariation_inst_Base::SetType(), and x_raw_seq().

Referenced by x_expr2(), and x_mut_inst().

◆ x_nuc_inv()

CRef< CVariation > CHgvsParser::x_nuc_inv ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1490 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), delta(), variation::CHgvsParser::SGrammar::eID_seq_ref, CVariation_inst_Base::eType_inv, variation::CHgvsParser::CContext::GetPlacement(), HGVS_ASSERT_RULE, i, CVariation_inst_Base::SetDelta(), variation::SetFirstPlacement(), CVariantPlacement_Base::SetSeq(), CVariation_inst_Base::SetType(), and x_seq_ref().

Referenced by x_mut_inst().

◆ x_nuc_subst()

CRef< CVariation > CHgvsParser::x_nuc_subst ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1459 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), delta(), variation::CHgvsParser::SGrammar::eID_raw_seq, variation::GetDelInsSubtype(), CSeq_literal_Base::GetLength(), variation::CHgvsParser::CContext::GetPlacement(), HGVS_ASSERT_RULE, i, NULL, variation::CVariationUtil::s_GetLength(), CVariation_inst_Base::SetDelta(), variation::SetFirstPlacement(), CVariantPlacement_Base::SetSeq(), CVariation_inst_Base::SetType(), and x_raw_seq().

Referenced by x_mut_inst().

◆ x_PlacementCoordsToStr()

string CHgvsParser::x_PlacementCoordsToStr ( const CVariantPlacement &  vp)
private

Definition at line 632 of file hgvs_writer2.cpp.

References CSerialObject::Assign(), CSeqFeatData_Base::e_Cdregion, eExtreme_Biological, CVariantPlacement_Base::eMol_cdna, CVariantPlacement_Base::eMol_protein, eNa_strand_minus, CSeq_loc::fMerge_SingleRange, CAliasBase< TPrim >::Get(), CScope::GetBioseqHandle(), CSeq_feat_Handle::GetData(), CSeq_point_Base::GetFuzz(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), GetId(), CSeq_loc_Base::GetInt(), CVariantPlacement_Base::GetLoc(), CMappedFeat::GetLocation(), CVariantPlacement_Base::GetMol(), CSeq_data_Base::GetNcbieaa(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CVariantPlacement_Base::GetSeq(), CSeq_literal_Base::GetSeq_data(), GetStart(), CSeq_loc::GetStart(), CVariantPlacement_Base::GetStart_offset(), CVariantPlacement_Base::GetStart_offset_fuzz(), GetStop(), CSeq_loc::GetStop(), CVariantPlacement_Base::GetStop_offset(), CVariantPlacement_Base::GetStop_offset_fuzz(), GetStrand(), CSeqFeatData_Base::IsCdregion(), CSeq_loc_Base::IsEmpty(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsNull(), CSeq_loc_Base::IsPnt(), CSeq_point_Base::IsSetFuzz(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CVariantPlacement_Base::IsSetSeq(), CSeq_literal_Base::IsSetSeq_data(), CVariantPlacement_Base::IsSetStart_offset(), CVariantPlacement_Base::IsSetStart_offset_fuzz(), CVariantPlacement_Base::IsSetStop_offset(), CVariantPlacement_Base::IsSetStop_offset_fuzz(), CSeq_loc_Base::IsWhole(), m_scope, variation::Ncbieaa2HgvsAA(), NULL, CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), variation::CVariationUtil::s_GetLength(), s_OffsetPointToString(), Seq_loc_Merge(), and swap().

Referenced by AsHgvsExpression(), and x_AsHgvsInstExpression().

◆ x_pos_spec()

CHgvsParser::SOffsetPoint CHgvsParser::x_pos_spec ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 933 of file hgvs_parser2.cpp.

References variation::CHgvsParser::SGrammar::eID_fuzzy_pos, variation::CHgvsParser::SGrammar::eID_general_pos, CSeq_point::FlipStrand(), HGVS_ASSERT_RULE, i, variation::CHgvsParser::SOffsetPoint::pnt, x_fuzzy_pos(), x_general_pos(), and x_header().

Referenced by x_location(), x_prot_pos(), and x_range().

◆ x_prot_ext()

CRef< CVariation > CHgvsParser::x_prot_ext ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1685 of file hgvs_parser2.cpp.

References abs, CSerialObject::Assign(), delta(), CVariantPlacement_Base::eMol_protein, eNa_strand_plus, CVariation_inst_Base::eType_prot_other, variation::CHgvsParser::CContext::GetBioseqHandle(), variation::CHgvsParser::CContext::GetId(), CBioseq_Handle::GetInst_Length(), CVariantPlacement_Base::GetMol(), variation::CHgvsParser::CContext::GetPlacement(), HGVS_ASSERT_RULE, HGVS_THROW, i, CVariation_inst_Base::SetDelta(), variation::SetFirstPlacement(), CVariantPlacement_Base::SetLoc(), CVariation_inst_Base::SetType(), and NStr::StringToInt().

Referenced by x_expr2(), and x_mut_inst().

◆ x_prot_fs()

CRef< CVariation > CHgvsParser::x_prot_fs ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1655 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), CVariantPlacement_Base::eMol_protein, CVariantPlacement_Base::GetMol(), variation::CHgvsParser::CContext::GetPlacement(), HGVS_ASSERT_RULE, HGVS_THROW, i, variation::SetFirstPlacement(), and NStr::StringToInt().

Referenced by x_mut_inst().

◆ x_prot_missense()

CRef< CVariation > CHgvsParser::x_prot_missense ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1736 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), delta(), CVariantPlacement_Base::eMol_protein, CVariation_inst_Base::eType_prot_missense, CVariation_inst_Base::eType_prot_other, CSeq_literal_Base::GetLength(), CVariantPlacement_Base::GetMol(), variation::CHgvsParser::CContext::GetPlacement(), HGVS_ASSERT_RULE, HGVS_THROW, i, CVariation_inst_Base::SetDelta(), variation::SetFirstPlacement(), CVariation_inst_Base::SetType(), and x_raw_seq().

Referenced by x_mut_inst().

◆ x_prot_pos()

CHgvsParser::SOffsetPoint CHgvsParser::x_prot_pos ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 964 of file hgvs_parser2.cpp.

References variation::CHgvsParser::SOffsetPoint::asserted_sequence, CVariantPlacement_Base::eMol_protein, CSeq_literal_Base::GetLength(), CVariantPlacement_Base::GetMol(), CSeq_data_Base::GetNcbieaa(), variation::CHgvsParser::CContext::GetPlacement(), CSeq_literal_Base::GetSeq_data(), HGVS_ASSERT_RULE, HGVS_THROW, i, x_pos_spec(), and x_raw_seq().

Referenced by x_location(), and x_range().

◆ x_range()

CRef< CVariantPlacement > CHgvsParser::x_range ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 988 of file hgvs_parser2.cpp.

References variation::CHgvsParser::SOffsetPoint::asserted_sequence, CSerialObject::Assign(), variation::CHgvsParser::SGrammar::eID_nuc_range, variation::CHgvsParser::SGrammar::eID_prot_range, CVariantPlacement_Base::eMol_protein, CSerialObject::Equals(), CSeq_point_Base::GetId(), CVariantPlacement_Base::GetMol(), variation::CHgvsParser::CContext::GetPlacement(), CSeq_point_Base::GetPoint(), CSeq_point_Base::GetStrand(), HGVS_ASSERT_RULE, HGVS_THROW, i, CSeq_point_Base::IsSetFuzz(), NULL, variation::CHgvsParser::SOffsetPoint::offset, variation::CHgvsParser::SOffsetPoint::pnt, variation::CVariationUtil::s_GetLength(), s_SetStartOffset(), s_SetStopOffset(), CSeq_point_Base::SetFuzz(), CSeq_point_Base::SetId(), CVariantPlacement_Base::SetLoc(), CVariantPlacement_Base::SetSeq(), x_pos_spec(), and x_prot_pos().

Referenced by x_location(), and x_seq_ref().

◆ x_raw_seq()

CRef< CSeq_literal > CHgvsParser::x_raw_seq ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1234 of file hgvs_parser2.cpp.

References CVariantPlacement_Base::eMol_protein, CVariantPlacement_Base::GetMol(), variation::CHgvsParser::CContext::GetPlacement(), HGVS_ASSERT_RULE, HGVS_THROW, i, NStr::IntToString(), literal(), NStr::ReplaceInPlace(), s_hgvsaa2ncbieaa(), NStr::ToUpper(), and CSeqportUtil::Validate().

Referenced by x_no_change(), x_nuc_subst(), x_prot_missense(), x_prot_pos(), x_raw_seq_or_len(), and x_ssr().

◆ x_raw_seq_or_len()

CRef< CSeq_literal > CHgvsParser::x_raw_seq_or_len ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1116 of file hgvs_parser2.cpp.

References variation::CHgvsParser::SGrammar::eID_int_fuzz, variation::CHgvsParser::SGrammar::eID_raw_seq, CInt_fuzz_Base::eLim_gt, variation::CHgvsParser::SFuzzyInt::fuzz, variation::CHgvsParser::CContext::GetHgvs(), HGVS_ASSERT_RULE, HGVS_THROW, i, CRef< C, Locker >::IsNull(), variation::CHgvsParser::SFuzzyInt::IsPureFuzz(), literal(), variation::CHgvsParser::SFuzzyInt::value, x_int_fuzz(), and x_raw_seq().

Referenced by x_deletion(), and x_seq_ref().

◆ x_root()

CRef< CVariation > CHgvsParser::x_root ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 2019 of file hgvs_parser2.cpp.

References variation::AdjustMoltype(), variation::CHgvsParser::CContext::GetScope(), HGVS_ASSERT_RULE, i, variation::RepackageAssertedSequence(), variation::CVariationUtil::s_FactorOutPlacements(), and x_list().

Referenced by AsVariation().

◆ x_seq_loc()

CRef< CSeq_loc > CHgvsParser::x_seq_loc ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1087 of file hgvs_parser2.cpp.

References CSeq_loc::Assign(), CVariantPlacement_Base::GetLoc(), HGVS_ASSERT_RULE, HGVS_THROW, i, CVariantPlacement_Base::IsSetStart_offset(), CVariantPlacement_Base::IsSetStop_offset(), CVariantPlacement_Base::SetLoc(), x_header(), and x_location().

Referenced by x_conversion(), x_seq_ref(), and x_translocation().

◆ x_seq_ref()

CHgvsParser::TDelta CHgvsParser::x_seq_ref ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1147 of file hgvs_parser2.cpp.

References delta(), variation::CHgvsParser::SGrammar::eID_nuc_range, variation::CHgvsParser::SGrammar::eID_prot_range, variation::CHgvsParser::SGrammar::eID_raw_seq_or_len, variation::CHgvsParser::SGrammar::eID_seq_loc, CVariantPlacement_Base::GetLoc(), HGVS_ASSERT_RULE, HGVS_THROW, i, CVariantPlacement_Base::IsSetStart_offset(), CVariantPlacement_Base::IsSetStop_offset(), literal(), x_range(), x_raw_seq_or_len(), and x_seq_loc().

Referenced by x_duplication(), x_insertion(), and x_nuc_inv().

◆ x_SeqLiteralToStr()

string CHgvsParser::x_SeqLiteralToStr ( const CSeq_literal &  literal,
bool  translate,
bool  is_mito 
)
private

translate=true will translate nucleotide literal to prot as appropriate.

It is intended for cases where delta literal in a protein variation is specified as codons rather than AAs; For HGVS purposes we can't use NAs in a protein context.

Definition at line 427 of file hgvs_writer2.cpp.

References CSerialObject::Assign(), CSeqportUtil::Convert(), CSeq_data_Base::e_Iupacna, CSeq_data_Base::e_Ncbieaa, eUnknown, CSeqTranslator::fIs5PrimePartial, CAliasBase< TPrim >::Get(), CSeq_data_Base::GetIupacna(), CSeq_data_Base::GetNcbieaa(), CSeq_data_Base::IsIupacaa(), CSeq_data_Base::IsIupacna(), CSeq_data_Base::IsNcbi2na(), CSeq_data_Base::IsNcbi4na(), CSeq_data_Base::IsNcbi8aa(), CSeq_data_Base::IsNcbi8na(), CSeq_data_Base::IsNcbieaa(), CSeq_data_Base::IsNcbipaa(), CSeq_data_Base::IsNcbipna(), CSeq_data_Base::IsNcbistdaa(), literal(), MSerial_AsnText, NCBI_THROW, NcbiCerr, variation::Ncbieaa2HgvsAA(), NULL, out(), s_IntWithFuzzToStr(), and CSeqTranslator::Translate().

Referenced by x_AsHgvsInstExpression().

◆ x_ssr()

CRef< CVariation > CHgvsParser::x_ssr ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1525 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), delta(), CVariation_Base::C_Data::C_Set::eData_set_type_genotype, variation::CHgvsParser::SGrammar::eID_raw_seq, variation::CHgvsParser::SGrammar::eID_ssr, CVariation_inst_Base::eType_microsatellite, variation::FindSSRLoc(), variation::CHgvsParser::SFuzzyInt::fuzz, CVariantPlacement_Base::GetLoc(), variation::CHgvsParser::CContext::GetPlacement(), variation::CHgvsParser::CContext::GetScope(), CVariantPlacement_Base::GetStart_offset(), HGVS_ASSERT_RULE, i, CRef< C, Locker >::IsNull(), CSeq_loc_Base::IsPnt(), CVariantPlacement_Base::IsSetStart_offset(), CVariantPlacement_Base::IsSetStop_offset(), literal(), variation::SetFirstPlacement(), CVariantPlacement_Base::SetLoc(), CVariantPlacement_Base::SetStop_offset(), NStr::StringToInt(), variation::CHgvsParser::SFuzzyInt::value, x_int_fuzz(), x_raw_seq(), and x_unwrap_iff_singleton().

Referenced by x_mut_inst().

◆ x_string_content()

CRef< CVariation > CHgvsParser::x_string_content ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1763 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), variation::CHgvsParser::CContext::GetPlacement(), i, and variation::SetFirstPlacement().

Referenced by x_mut_inst().

◆ x_translocation()

CRef< CVariation > CHgvsParser::x_translocation ( TIterator const &  i,
const CContext &  context 
)
staticprivate

Definition at line 1612 of file hgvs_parser2.cpp.

References CVariation_inst_Base::eType_translocation, GetId(), variation::CHgvsParser::CContext::GetScope(), HGVS_ASSERT_RULE, i, NULL, CVariation_inst_Base::SetDelta(), variation::SetFirstPlacement(), CVariantPlacement_Base::SetLoc(), CVariantPlacement_Base::SetMol(), CVariation_inst_Base::SetType(), and x_seq_loc().

Referenced by x_expr1(), and x_mut_inst().

◆ x_unwrap_iff_singleton()

CRef< CVariation > CHgvsParser::x_unwrap_iff_singleton ( CVariation &  v)
staticprivate

Definition at line 2033 of file hgvs_parser2.cpp.

References first(), CVariation_Base::GetData(), CVariation_Base::C_Data::GetSet(), CVariation_Base::C_Data::C_Set::GetVariations(), CVariation_Base::C_Data::IsSet(), CVariation_Base::IsSetPlacements(), CVariation_Base::SetData(), and CVariation_Base::SetPlacements().

Referenced by x_expr3(), x_list(), and x_ssr().

Member Data Documentation

◆ m_scope

CRef<CScope> variation::CHgvsParser::m_scope
private

Definition at line 930 of file hgvs_parser2.hpp.

Referenced by AsHgvsExpression(), AsVariation(), variation::CHgvsParser::CContext::SetId(), x_AdjustPlacementForHgvs(), x_AsHgvsExpression(), x_AsHgvsInstExpression(), x_GetInstLength(), x_LocToSeqStr(), and x_PlacementCoordsToStr().

◆ m_seq_id_resolvers

CSeq_id_Resolver::TResolvers variation::CHgvsParser::m_seq_id_resolvers
private

Definition at line 931 of file hgvs_parser2.hpp.

Referenced by AsVariation().

◆ s_grammar

CSafeStatic< CHgvsParser::SGrammar > CHgvsParser::s_grammar
staticprotected

Definition at line 804 of file hgvs_parser2.hpp.

Referenced by AsVariation().

The documentation for this class was generated from the following files:
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Modified on Sat Dec 09 04:45:32 2023 by modify_doxy.py rev. 669887