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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCVariation__ref.html below:

NCBI C++ ToolKit: CVariation_ref Class Reference

enum ESeqType { eSeqType_na , eSeqType_aa } Enum governing sequence types for supplied sequence strings. More...
enum EMethod_E {
  eMethod_E_unknown = 0 , eMethod_E_bac_acgh = 1 , eMethod_E_computational = 2 , eMethod_E_curated = 3 ,
  eMethod_E_digital_array = 4 , eMethod_E_expression_array = 5 , eMethod_E_fish = 6 , eMethod_E_flanking_sequence = 7 ,
  eMethod_E_maph = 8 , eMethod_E_mcd_analysis = 9 , eMethod_E_mlpa = 10 , eMethod_E_oea_assembly = 11 ,
  eMethod_E_oligo_acgh = 12 , eMethod_E_paired_end = 13 , eMethod_E_pcr = 14 , eMethod_E_qpcr = 15 ,
  eMethod_E_read_depth = 16 , eMethod_E_roma = 17 , eMethod_E_rt_pcr = 18 , eMethod_E_sage = 19 ,
  eMethod_E_sequence_alignment = 20 , eMethod_E_sequencing = 21 , eMethod_E_snp_array = 22 , eMethod_E_snp_genoytyping = 23 ,
  eMethod_E_southern = 24 , eMethod_E_western = 25 , eMethod_E_optical_mapping = 26 , eMethod_E_other = 255
} enum EAllele_origin {
  eAllele_origin_unknown = 0 , eAllele_origin_germline = 1 , eAllele_origin_somatic = 2 , eAllele_origin_inherited = 4 ,
  eAllele_origin_paternal = 8 , eAllele_origin_maternal = 16 , eAllele_origin_de_novo = 32 , eAllele_origin_biparental = 64 ,
  eAllele_origin_uniparental = 128 , eAllele_origin_not_tested = 256 , eAllele_origin_tested_inconclusive = 512 , eAllele_origin_other = 1073741824
} origin of this allele, if known note that these are powers-of-two, and represent bits; thus, we can represent more than one state simultaneously through a bitwise OR DEPRECATED: new field = VariantProperties.allele-origin More...
enum EAllele_state {
  eAllele_state_unknown = 0 , eAllele_state_homozygous = 1 , eAllele_state_heterozygous = 2 , eAllele_state_hemizygous = 3 ,
  eAllele_state_nullizygous = 4 , eAllele_state_other = 255
} observed allele state, if known DEPRECATED: new field = VariantProperties.allele-state More...
enum class E_memberIndex {
  e__allMandatory = 0 , e_id , e_parent_id , e_sample_id ,
  e_other_ids , e_name , e_synonyms , e_description ,
  e_phenotype , e_method , e_population_data , e_variant_prop ,
  e_validated , e_clinical_test , e_allele_origin , e_allele_state ,
  e_allele_frequency , e_is_ancestral_allele , e_pub , e_data ,
  e_consequence , e_location , e_ext_locs , e_ext ,
  e_somatic_origin
} typedef CDbtag TId typedef CDbtag TParent_id typedef CObject_id TSample_id typedef list< CRef< CDbtag > > TOther_ids typedef string TName typedef list< string > TSynonyms typedef string TDescription typedef list< CRef< CPhenotype > > TPhenotype typedef list< int > TMethod typedef list< CRef< CPopulation_data > > TPopulation_data typedef CVariantProperties TVariant_prop typedef bool TValidated typedef list< CRef< CDbtag > > TClinical_test typedef int TAllele_origin typedef int TAllele_state typedef double TAllele_frequency typedef bool TIs_ancestral_allele typedef CPub TPub typedef C_Data TData typedef C_E_Consequence C_E typedef list< CRef< C_E_Consequence > > TConsequence typedef CSeq_loc TLocation typedef list< CRef< CExt_loc > > TExt_locs typedef CUser_object TExt typedef list< CRef< C_E_Somatic_origin > > TSomatic_origin typedef Tparent::CMemberIndex< E_memberIndex, 25 > TmemberIndex 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...
CVariation_ref (void) ~CVariation_ref (void) void PostRead () PostRead() hooks to establish correct, non-deprecated data layout. More...
void SetSNV (const CSeq_data &nucleotide, CRef< CDelta_item > offset=null) void SetMNP (const CSeq_data &nucleotide, TSeqPos length, CRef< CDelta_item > offset=null) void SetMissense (const CSeq_data &amino_acid) void SetDuplication (CRef< CDelta_item > start_offset=null, CRef< CDelta_item > stop_offset=null) void SetIdentity (CRef< CSeq_literal > seq_literal, CRef< CDelta_item > start_offset=null, CRef< CDelta_item > stop_offset=null) void SetSNV (const vector< string > &replaces, ESeqType seq_type) Set a standard single nucleotide variant. More...
bool IsSNV () const void SetMNP (const vector< string > &replaces, ESeqType seq_type) Set a standard multinucleotide variant. More...
bool IsMNP () const void SetDeletion () Make this variant a deletion. More...
bool IsDeletion () const void SetInsertion (const string &sequence, ESeqType seq_type) Make this variant an insertion. More...
bool IsInsertion () const void SetInsertion () Make this variant an insertion of unknown sequence. More...
void SetDeletionInsertion (const string &sequence, ESeqType seq_type) Make this variant an insertion. More...
bool IsDeletionInsertion () const void SetMicrosatellite (const string &nucleotide_seq, TSeqPos min_repeats, TSeqPos max_repeats) Set the standard fields for a microsatellite. More...
bool IsMicrosatellite () const void SetMicrosatellite (const string &nucleotide_seq, const vector< TSeqPos > &observed_repeats) Set the standard fields for a microsatellite. More...
void SetCNV () Make this variant a copy number variant. More...
bool IsCNV () const void SetGain () Special subtype of CNV: 'gain' - an unspecified increase in copy number. More...
bool IsGain () const void SetLoss () Special subtype of CNV: 'loss' - an unspecified decrease in copy number. More...
bool IsLoss () const void SetCNV (TSeqPos min_copy, TSeqPos max_copy) Make this variant a copy number variant. More...
void SetCNV (const vector< TSeqPos > &observed_copies) Make this variant a copy number variant. More...
void SetInversion (const CSeq_loc &other_loc) The feature represents an inversion at the specified location The provided location should be upstream and on the opposite strand. More...
bool IsInversion () const void SetEversion (const CSeq_loc &other_loc) The feature represents an eversion at the specified location The provided location should be downstream and on the opposite strand. More...
bool IsEversion () const void SetTranslocation (const CSeq_loc &other_loc) The feature represents a translocation event The provided location can be anywhere; a special case exists when the provided location is on a different chromosome, in which case the feature is considered a transchromosomal rearrangement. More...
bool IsTranslocation () const void SetUniparentalDisomy () Establish a uniparental disomy mark-up. More...
bool IsUniparentalDisomy () const void SetComplex () Create a complex undescribed variant. More...
bool IsComplex () const void SetUnknown () Create a variant of unknown type. More...
bool IsUnknown () const void SetOther () Create a variant of type 'other'. More...
bool IsOther () const void Validate () Validate that all semantic fields are correct. More...
bool IsSetLocation (void) const NOTE: THESE ARE GOING AWAY SOON!! More...
bool CanGetLocation (void) const void ResetLocation (void) const TLocation & GetLocation (void) const void SetLocation (TLocation &value) TLocation & SetLocation (void) bool IsSetExt_locs (void) const bool CanGetExt_locs (void) const void ResetExt_locs (void) const TExt_locs & GetExt_locs (void) const TExt_locs & SetExt_locs (void) bool IsSetExt (void) const bool CanGetExt (void) const void ResetExt (void) const TExt & GetExt (void) const void SetExt (TExt &value) TExt & SetExt (void) bool IsSetValidated (void) const bool CanGetValidated (void) const void ResetValidated (void) TValidated GetValidated (void) const void SetValidated (TValidated value) TValidated & SetValidated (void) bool IsSetClinical_test (void) const bool CanGetClinical_test (void) const void ResetClinical_test (void) const TClinical_test & GetClinical_test (void) const TClinical_test & SetClinical_test (void) bool IsSetAllele_origin (void) const bool CanGetAllele_origin (void) const void ResetAllele_origin (void) TAllele_origin GetAllele_origin (void) const void SetAllele_origin (TAllele_origin value) TAllele_origin & SetAllele_origin (void) bool IsSetAllele_state (void) const bool CanGetAllele_state (void) const void ResetAllele_state (void) TAllele_state GetAllele_state (void) const void SetAllele_state (TAllele_state value) TAllele_state & SetAllele_state (void) bool IsSetAllele_frequency (void) const bool CanGetAllele_frequency (void) const void ResetAllele_frequency (void) TAllele_frequency GetAllele_frequency (void) const void SetAllele_frequency (TAllele_frequency value) TAllele_frequency & SetAllele_frequency (void) bool IsSetIs_ancestral_allele (void) const bool CanGetIs_ancestral_allele (void) const void ResetIs_ancestral_allele (void) TIs_ancestral_allele GetIs_ancestral_allele (void) const void SetIs_ancestral_allele (TIs_ancestral_allele value) TIs_ancestral_allele & SetIs_ancestral_allele (void) CVariation_ref_Base (void) virtual ~CVariation_ref_Base (void) DECLARE_INTERNAL_TYPE_INFO () bool IsSetId (void) const ids (i.e., SNP rsid / ssid, dbVar nsv/nssv) expected values include 'dbSNP|rs12334', 'dbSNP|ss12345', 'dbVar|nsv1' More...
bool CanGetId (void) const Check if it is safe to call GetId method. More...
void ResetId (void) Reset Id data member. More...
const TId & GetId (void) const Get the Id member data. More...
void SetId (TId &value) Assign a value to Id data member. More...
TId & SetId (void) Assign a value to Id data member. More...
bool IsSetParent_id (void) const Check if a value has been assigned to Parent_id data member. More...
bool CanGetParent_id (void) const Check if it is safe to call GetParent_id method. More...
void ResetParent_id (void) Reset Parent_id data member. More...
const TParent_id & GetParent_id (void) const Get the Parent_id member data. More...
void SetParent_id (TParent_id &value) Assign a value to Parent_id data member. More...
TParent_id & SetParent_id (void) Assign a value to Parent_id data member. More...
bool IsSetSample_id (void) const Check if a value has been assigned to Sample_id data member. More...
bool CanGetSample_id (void) const Check if it is safe to call GetSample_id method. More...
void ResetSample_id (void) Reset Sample_id data member. More...
const TSample_id & GetSample_id (void) const Get the Sample_id member data. More...
void SetSample_id (TSample_id &value) Assign a value to Sample_id data member. More...
TSample_id & SetSample_id (void) Assign a value to Sample_id data member. More...
bool IsSetOther_ids (void) const Check if a value has been assigned to Other_ids data member. More...
bool CanGetOther_ids (void) const Check if it is safe to call GetOther_ids method. More...
void ResetOther_ids (void) Reset Other_ids data member. More...
const TOther_ids & GetOther_ids (void) const Get the Other_ids member data. More...
TOther_ids & SetOther_ids (void) Assign a value to Other_ids data member. More...
bool IsSetName (void) const names and synonyms some variants have well-known canonical names and possible accepted synonyms Check if a value has been assigned to Name data member. More...
bool CanGetName (void) const Check if it is safe to call GetName method. More...
void ResetName (void) Reset Name data member. More...
const TName & GetName (void) const Get the Name member data. More...
void SetName (const TName &value) Assign a value to Name data member. More...
void SetName (TName &&value) TName & SetName (void) Assign a value to Name data member. More...
bool IsSetSynonyms (void) const Check if a value has been assigned to Synonyms data member. More...
bool CanGetSynonyms (void) const Check if it is safe to call GetSynonyms method. More...
void ResetSynonyms (void) Reset Synonyms data member. More...
const TSynonyms & GetSynonyms (void) const Get the Synonyms member data. More...
TSynonyms & SetSynonyms (void) Assign a value to Synonyms data member. More...
bool IsSetDescription (void) const tag for comment and descriptions Check if a value has been assigned to Description data member. More...
bool CanGetDescription (void) const Check if it is safe to call GetDescription method. More...
void ResetDescription (void) Reset Description data member. More...
const TDescription & GetDescription (void) const Get the Description member data. More...
void SetDescription (const TDescription &value) Assign a value to Description data member. More...
void SetDescription (TDescription &&value) TDescription & SetDescription (void) Assign a value to Description data member. More...
bool IsSetPhenotype (void) const phenotype Check if a value has been assigned to Phenotype data member. More...
bool CanGetPhenotype (void) const Check if it is safe to call GetPhenotype method. More...
void ResetPhenotype (void) Reset Phenotype data member. More...
const TPhenotype & GetPhenotype (void) const Get the Phenotype member data. More...
TPhenotype & SetPhenotype (void) Assign a value to Phenotype data member. More...
bool IsSetMethod (void) const Check if a value has been assigned to Method data member. More...
bool CanGetMethod (void) const Check if it is safe to call GetMethod method. More...
void ResetMethod (void) Reset Method data member. More...
const TMethod & GetMethod (void) const Get the Method member data. More...
TMethod & SetMethod (void) Assign a value to Method data member. More...
bool IsSetPopulation_data (void) const Note about SNP representation and pretinent fields: allele-frequency, population, quality-codes: The case of multiple alleles for a SNP would be described by parent-feature of type Variation-set.diff-alleles, where the child features of type Variation-inst, all at the same location, would describe individual alleles. More...
bool CanGetPopulation_data (void) const Check if it is safe to call GetPopulation_data method. More...
void ResetPopulation_data (void) Reset Population_data data member. More...
const TPopulation_data & GetPopulation_data (void) const Get the Population_data member data. More...
TPopulation_data & SetPopulation_data (void) Assign a value to Population_data data member. More...
bool IsSetVariant_prop (void) const variant properties bit fields Check if a value has been assigned to Variant_prop data member. More...
bool CanGetVariant_prop (void) const Check if it is safe to call GetVariant_prop method. More...
void ResetVariant_prop (void) Reset Variant_prop data member. More...
const TVariant_prop & GetVariant_prop (void) const Get the Variant_prop member data. More...
void SetVariant_prop (TVariant_prop &value) Assign a value to Variant_prop data member. More...
TVariant_prop & SetVariant_prop (void) Assign a value to Variant_prop data member. More...
bool IsSetValidated (void) const has this variant been validated? DEPRECATED: new field = VariantProperties.other-validation Check if a value has been assigned to Validated data member. More...
bool CanGetValidated (void) const Check if it is safe to call GetValidated method. More...
void ResetValidated (void) Reset Validated data member. More...
TValidated GetValidated (void) const Get the Validated member data. More...
void SetValidated (TValidated value) Assign a value to Validated data member. More...
TValidated & SetValidated (void) Assign a value to Validated data member. More...
bool IsSetClinical_test (void) const link-outs to GeneTests database DEPRECATED - do not use Check if a value has been assigned to Clinical_test data member. More...
bool CanGetClinical_test (void) const Check if it is safe to call GetClinical_test method. More...
void ResetClinical_test (void) Reset Clinical_test data member. More...
const TClinical_test & GetClinical_test (void) const Get the Clinical_test member data. More...
TClinical_test & SetClinical_test (void) Assign a value to Clinical_test data member. More...
bool IsSetAllele_origin (void) const Check if a value has been assigned to Allele_origin data member. More...
bool CanGetAllele_origin (void) const Check if it is safe to call GetAllele_origin method. More...
void ResetAllele_origin (void) Reset Allele_origin data member. More...
TAllele_origin GetAllele_origin (void) const Get the Allele_origin member data. More...
void SetAllele_origin (TAllele_origin value) Assign a value to Allele_origin data member. More...
TAllele_origin & SetAllele_origin (void) Assign a value to Allele_origin data member. More...
bool IsSetAllele_state (void) const Check if a value has been assigned to Allele_state data member. More...
bool CanGetAllele_state (void) const Check if it is safe to call GetAllele_state method. More...
void ResetAllele_state (void) Reset Allele_state data member. More...
TAllele_state GetAllele_state (void) const Get the Allele_state member data. More...
void SetAllele_state (TAllele_state value) Assign a value to Allele_state data member. More...
TAllele_state & SetAllele_state (void) Assign a value to Allele_state data member. More...
bool IsSetAllele_frequency (void) const NOTE: 'allele-frequency' here refers to the minor allele frequency of the default population DEPRECATED: new field = VariantProperties.allele-frequency Check if a value has been assigned to Allele_frequency data member. More...
bool CanGetAllele_frequency (void) const Check if it is safe to call GetAllele_frequency method. More...
void ResetAllele_frequency (void) Reset Allele_frequency data member. More...
TAllele_frequency GetAllele_frequency (void) const Get the Allele_frequency member data. More...
void SetAllele_frequency (TAllele_frequency value) Assign a value to Allele_frequency data member. More...
TAllele_frequency & SetAllele_frequency (void) Assign a value to Allele_frequency data member. More...
bool IsSetIs_ancestral_allele (void) const is this variant the ancestral allele? DEPRECATED: new field = VariantProperties.is-ancestral-allele Check if a value has been assigned to Is_ancestral_allele data member. More...
bool CanGetIs_ancestral_allele (void) const Check if it is safe to call GetIs_ancestral_allele method. More...
void ResetIs_ancestral_allele (void) Reset Is_ancestral_allele data member. More...
TIs_ancestral_allele GetIs_ancestral_allele (void) const Get the Is_ancestral_allele member data. More...
void SetIs_ancestral_allele (TIs_ancestral_allele value) Assign a value to Is_ancestral_allele data member. More...
TIs_ancestral_allele & SetIs_ancestral_allele (void) Assign a value to Is_ancestral_allele data member. More...
bool IsSetPub (void) const publication support. More...
bool CanGetPub (void) const Check if it is safe to call GetPub method. More...
void ResetPub (void) Reset Pub data member. More...
const TPub & GetPub (void) const Get the Pub member data. More...
void SetPub (TPub &value) Assign a value to Pub data member. More...
TPub & SetPub (void) Assign a value to Pub data member. More...
bool IsSetData (void) const Check if a value has been assigned to Data data member. More...
bool CanGetData (void) const Check if it is safe to call GetData method. More...
void ResetData (void) Reset Data data member. More...
const TData & GetData (void) const Get the Data member data. More...
void SetData (TData &value) Assign a value to Data data member. More...
TData & SetData (void) Assign a value to Data data member. More...
bool IsSetConsequence (void) const Check if a value has been assigned to Consequence data member. More...
bool CanGetConsequence (void) const Check if it is safe to call GetConsequence method. More...
void ResetConsequence (void) Reset Consequence data member. More...
const TConsequence & GetConsequence (void) const Get the Consequence member data. More...
TConsequence & SetConsequence (void) Assign a value to Consequence data member. More...
bool IsSetLocation (void) const Observed location, if different from the parent set or feature.location. More...
bool CanGetLocation (void) const Check if it is safe to call GetLocation method. More...
void ResetLocation (void) Reset Location data member. More...
const TLocation & GetLocation (void) const Get the Location member data. More...
void SetLocation (TLocation &value) Assign a value to Location data member. More...
TLocation & SetLocation (void) Assign a value to Location data member. More...
bool IsSetExt_locs (void) const reference other locs, e.g. More...
bool CanGetExt_locs (void) const Check if it is safe to call GetExt_locs method. More...
void ResetExt_locs (void) Reset Ext_locs data member. More...
const TExt_locs & GetExt_locs (void) const Get the Ext_locs member data. More...
TExt_locs & SetExt_locs (void) Assign a value to Ext_locs data member. More...
bool IsSetExt (void) const DEPRECATED - do not use; use Seq-feat.exts instead Check if a value has been assigned to Ext data member. More...
bool CanGetExt (void) const Check if it is safe to call GetExt method. More...
void ResetExt (void) Reset Ext data member. More...
const TExt & GetExt (void) const Get the Ext member data. More...
void SetExt (TExt &value) Assign a value to Ext data member. More...
TExt & SetExt (void) Assign a value to Ext data member. More...
bool IsSetSomatic_origin (void) const Check if a value has been assigned to Somatic_origin data member. More...
bool CanGetSomatic_origin (void) const Check if it is safe to call GetSomatic_origin method. More...
void ResetSomatic_origin (void) Reset Somatic_origin data member. More...
const TSomatic_origin & GetSomatic_origin (void) const Get the Somatic_origin member data. More...
TSomatic_origin & SetSomatic_origin (void) Assign a value to Somatic_origin data member. More...
virtual void Reset (void) Reset the whole object. More...
CSerialObject (void) virtual ~CSerialObject (void) virtual const CTypeInfo * GetThisTypeInfo (void) const =0 virtual void Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) Set object to copy of another one. More...
virtual bool Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const Check if both objects contain the same values. More...
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const Define method for dumping debug information. More...
void ThrowUnassigned (TMemberIndex index) const void ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const bool HasNamespaceName (void) const Check if object data type has namespace name. More...
const string & GetNamespaceName (void) const Get namespace name. More...
bool HasNamespacePrefix (void) const Check if data type has namespace prefix. More...
const string & GetNamespacePrefix (void) const Get namespace prefix. More...
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...
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

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