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CVariation_ref Class Reference

Represents ASN.1 type Variation-ref defined in file seqfeat.asn

Search Toolkit Book for CVariation_ref

#include <objects/seqfeat/Variation_ref.hpp>

+ Inheritance diagram for CVariation_ref:
+ Collaboration diagram for CVariation_ref:

Public Types

enum  ESeqType { eSeqType_na, eSeqType_aa }
 Enum governing sequence types for supplied sequence strings. More...
 
- Public Types inherited from CVariation_ref_Base
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  E_memberIndex {
  E_memberIndex::e__allMandatory = 0, E_memberIndex::e_id, E_memberIndex::e_parent_id, E_memberIndex::e_sample_id,
  E_memberIndex::e_other_ids, E_memberIndex::e_name, E_memberIndex::e_synonyms, E_memberIndex::e_description,
  E_memberIndex::e_phenotype, E_memberIndex::e_method, E_memberIndex::e_population_data, E_memberIndex::e_variant_prop,
  E_memberIndex::e_validated, E_memberIndex::e_clinical_test, E_memberIndex::e_allele_origin, E_memberIndex::e_allele_state,
  E_memberIndex::e_allele_frequency, E_memberIndex::e_is_ancestral_allele, E_memberIndex::e_pub, E_memberIndex::e_data,
  E_memberIndex::e_consequence, E_memberIndex::e_location, E_memberIndex::e_ext_locs, E_memberIndex::e_ext,
  E_memberIndex::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< stringTSynonyms
 
typedef string TDescription
 
typedef list< CRef< CPhenotype > > TPhenotype
 
typedef list< intTMethod
 
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
 
- 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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 

Public Member Functions

 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...
 
Deprecated Methods
bool IsSetLocation (void) const
 NOTE: THESE ARE GOING AWAY SOON!! More...
 
bool CanGetLocation (void) const
 
void ResetLocation (void)
 
const TLocationGetLocation (void) const
 
void SetLocation (TLocation &value)
 
TLocationSetLocation (void)
 
bool IsSetExt_locs (void) const
 
bool CanGetExt_locs (void) const
 
void ResetExt_locs (void)
 
const TExt_locsGetExt_locs (void) const
 
TExt_locsSetExt_locs (void)
 
bool IsSetExt (void) const
 
bool CanGetExt (void) const
 
void ResetExt (void)
 
const TExtGetExt (void) const
 
void SetExt (TExt &value)
 
TExtSetExt (void)
 
bool IsSetValidated (void) const
 
bool CanGetValidated (void) const
 
void ResetValidated (void)
 
TValidated GetValidated (void) const
 
void SetValidated (TValidated value)
 
TValidatedSetValidated (void)
 
bool IsSetClinical_test (void) const
 
bool CanGetClinical_test (void) const
 
void ResetClinical_test (void)
 
const TClinical_testGetClinical_test (void) const
 
TClinical_testSetClinical_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_originSetAllele_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_stateSetAllele_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_frequencySetAllele_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_alleleSetIs_ancestral_allele (void)
 
- Public Member Functions inherited from CVariation_ref_Base
 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 TIdGetId (void) const
 Get the Id member data. More...
 
void SetId (TId &value)
 Assign a value to Id data member. More...
 
TIdSetId (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_idGetParent_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_idSetParent_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_idGetSample_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_idSetSample_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_idsGetOther_ids (void) const
 Get the Other_ids member data. More...
 
TOther_idsSetOther_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 TNameGetName (void) const
 Get the Name member data. More...
 
void SetName (const TName &value)
 Assign a value to Name data member. More...
 
TNameSetName (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 TSynonymsGetSynonyms (void) const
 Get the Synonyms member data. More...
 
TSynonymsSetSynonyms (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 TDescriptionGetDescription (void) const
 Get the Description member data. More...
 
void SetDescription (const TDescription &value)
 Assign a value to Description data member. More...
 
TDescriptionSetDescription (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 TPhenotypeGetPhenotype (void) const
 Get the Phenotype member data. More...
 
TPhenotypeSetPhenotype (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 TMethodGetMethod (void) const
 Get the Method member data. More...
 
TMethodSetMethod (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_dataGetPopulation_data (void) const
 Get the Population_data member data. More...
 
TPopulation_dataSetPopulation_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_propGetVariant_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_propSetVariant_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...
 
TValidatedSetValidated (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_testGetClinical_test (void) const
 Get the Clinical_test member data. More...
 
TClinical_testSetClinical_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_originSetAllele_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_stateSetAllele_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_frequencySetAllele_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_alleleSetIs_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 TPubGetPub (void) const
 Get the Pub member data. More...
 
void SetPub (TPub &value)
 Assign a value to Pub data member. More...
 
TPubSetPub (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 TDataGetData (void) const
 Get the Data member data. More...
 
void SetData (TData &value)
 Assign a value to Data data member. More...
 
TDataSetData (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 TConsequenceGetConsequence (void) const
 Get the Consequence member data. More...
 
TConsequenceSetConsequence (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 TLocationGetLocation (void) const
 Get the Location member data. More...
 
void SetLocation (TLocation &value)
 Assign a value to Location data member. More...
 
TLocationSetLocation (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_locsGetExt_locs (void) const
 Get the Ext_locs member data. More...
 
TExt_locsSetExt_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 TExtGetExt (void) const
 Get the Ext member data. More...
 
void SetExt (TExt &value)
 Assign a value to Ext data member. More...
 
TExtSetExt (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_originGetSomatic_origin (void) const
 Get the Somatic_origin member data. More...
 
TSomatic_originSetSomatic_origin (void)
 Assign a value to Somatic_origin data member. More...
 
virtual void Reset (void)
 Reset the whole object. More...
 
- Public Member Functions inherited from CSerialObject
 CSerialObject (void)
 
virtual ~CSerialObject (void)
 
virtual const CTypeInfoGetThisTypeInfo (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 stringGetNamespaceName (void) const
 Get namespace name. More...
 
bool HasNamespacePrefix (void) const
 Check if data type has namespace prefix. More...
 
const stringGetNamespacePrefix (void) const
 Get namespace prefix. More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (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...
 
- 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
 

Private Types

typedef CVariation_ref_Base Tparent
 

Private Member Functions

 CVariation_ref (const CVariation_ref &value)
 
CVariation_refoperator= (const CVariation_ref &value)
 
bool IsSetPopulation_data (void) const
 Prohibited deprecated functions Due to limitations in ASN spec-land, we cannot officially remove these data elements from the spec. More...
 
bool CanGetPopulation_data (void) const
 
void ResetPopulation_data (void)
 
const TPopulation_dataGetPopulation_data (void) const
 
TPopulation_dataSetPopulation_data (void)
 
bool IsSetPub (void) const
 
bool CanGetPub (void) const
 
void ResetPub (void)
 
const TPubGetPub (void) const
 
void SetPub (TPub &value)
 
TPubSetPub (void)
 

Additional Inherited Members

- Static Public Member Functions inherited from CVariation_ref_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EMethod_E (void)
 Access to EMethod_E's attributes (values, names) as defined in spec. More...
 
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EAllele_origin (void)
 Access to EAllele_origin's attributes (values, names) as defined in spec. More...
 
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EAllele_state (void)
 Access to EAllele_state's attributes (values, names) as defined in spec. More...
 
- Static Public Member Functions inherited from CSerialObject
static void SetVerifyDataThread (ESerialVerifyData verify)
 
static void SetVerifyDataGlobal (ESerialVerifyData verify)
 
static string UnassignedString (void)
 
static CStringUTF8 UnassignedStringUTF8 (void)
 
static char UnassignedByte (void)
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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 CSerialObject
static const char * ms_UnassignedStr = "<*unassigned*>"
 
static const char ms_UnassignedByte = char(0xcd)
 
- 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 56 of file Variation_ref.hpp.

Member Typedef Documentation

Definition at line 58 of file Variation_ref.hpp.

Member Enumeration Documentation

Enum governing sequence types for supplied sequence strings.

Enumerator
eSeqType_na 
eSeqType_aa 

Definition at line 66 of file Variation_ref.hpp.

Constructor & Destructor Documentation

CVariation_ref::CVariation_ref ( void  )
inline

Definition at line 288 of file Variation_ref.hpp.

CVariation_ref::~CVariation_ref ( void  )

Definition at line 51 of file Variation_ref.cpp.

CVariation_ref::CVariation_ref ( const CVariation_ref value)
private

Member Function Documentation

bool CVariation_ref::CanGetAllele_frequency ( void  ) const
bool CVariation_ref::CanGetAllele_origin ( void  ) const
bool CVariation_ref::CanGetAllele_state ( void  ) const
bool CVariation_ref::CanGetClinical_test ( void  ) const

Definition at line 304 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

bool CVariation_ref::CanGetExt ( void  ) const

Definition at line 822 of file Variation_ref.cpp.

References CVariation_ref_Base::CanGetExt().

bool CVariation_ref::CanGetExt_locs ( void  ) const

Definition at line 791 of file Variation_ref.cpp.

References CVariation_ref_Base::CanGetExt_locs().

bool CVariation_ref::CanGetIs_ancestral_allele ( void  ) const
bool CVariation_ref::CanGetLocation ( void  ) const

Definition at line 753 of file Variation_ref.cpp.

References CVariation_ref_Base::CanGetLocation().

bool CVariation_ref::CanGetPopulation_data ( void  ) const
private

Definition at line 196 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

bool CVariation_ref::CanGetPub ( void  ) const
private

Definition at line 608 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

bool CVariation_ref::CanGetValidated ( void  ) const
CVariation_ref::TAllele_frequency CVariation_ref::GetAllele_frequency ( void  ) const
CVariation_ref::TAllele_origin CVariation_ref::GetAllele_origin ( void  ) const
CVariation_ref::TAllele_state CVariation_ref::GetAllele_state ( void  ) const
const CVariation_ref::TClinical_test & CVariation_ref::GetClinical_test ( void  ) const

Definition at line 320 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

const CVariation_ref::TExt & CVariation_ref::GetExt ( void  ) const
const CVariation_ref::TExt_locs & CVariation_ref::GetExt_locs ( void  ) const

Definition at line 803 of file Variation_ref.cpp.

References CVariation_ref_Base::GetExt_locs().

CVariation_ref::TIs_ancestral_allele CVariation_ref::GetIs_ancestral_allele ( void  ) const
const CVariation_ref::TLocation & CVariation_ref::GetLocation ( void  ) const
const CVariation_ref::TPopulation_data & CVariation_ref::GetPopulation_data ( void  ) const
private

Definition at line 212 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

const CVariation_ref::TPub & CVariation_ref::GetPub ( void  ) const
private

Definition at line 624 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

CVariation_ref::TValidated CVariation_ref::GetValidated ( void  ) const
bool CVariation_ref::IsCNV ( ) const
bool CVariation_ref::IsComplex ( ) const
bool CVariation_ref::IsDeletion ( ) const
bool CVariation_ref::IsDeletionInsertion ( ) const
bool CVariation_ref::IsEversion ( ) const
bool CVariation_ref::IsGain ( ) const
bool CVariation_ref::IsInsertion ( ) const
bool CVariation_ref::IsInversion ( ) const
bool CVariation_ref::IsLoss ( ) const
bool CVariation_ref::IsMicrosatellite ( ) const
bool CVariation_ref::IsMNP ( ) const
bool CVariation_ref::IsOther ( void  ) const
bool CVariation_ref::IsSetAllele_frequency ( void  ) const
bool CVariation_ref::IsSetAllele_origin ( void  ) const
bool CVariation_ref::IsSetAllele_state ( void  ) const
bool CVariation_ref::IsSetClinical_test ( void  ) const

Definition at line 296 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

bool CVariation_ref::IsSetExt ( void  ) const
bool CVariation_ref::IsSetExt_locs ( void  ) const

Definition at line 785 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetExt_locs().

bool CVariation_ref::IsSetIs_ancestral_allele ( void  ) const
bool CVariation_ref::IsSetLocation ( void  ) const
bool CVariation_ref::IsSetPopulation_data ( void  ) const
private

Prohibited deprecated functions Due to limitations in ASN spec-land, we cannot officially remove these data elements from the spec.

We can, however, hide them from client access.

Definition at line 188 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

bool CVariation_ref::IsSetPub ( void  ) const
private

Definition at line 600 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

bool CVariation_ref::IsSetValidated ( void  ) const
bool CVariation_ref::IsSNV ( ) const
bool CVariation_ref::IsTranslocation ( ) const
bool CVariation_ref::IsUniparentalDisomy ( ) const
bool CVariation_ref::IsUnknown ( ) const
CVariation_ref& CVariation_ref::operator= ( const CVariation_ref value)
private
void CVariation_ref::PostRead ( void  )
void CVariation_ref::ResetAllele_frequency ( void  )
void CVariation_ref::ResetAllele_origin ( void  )
void CVariation_ref::ResetAllele_state ( void  )
void CVariation_ref::ResetClinical_test ( void  )

Definition at line 312 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

void CVariation_ref::ResetExt ( void  )
void CVariation_ref::ResetExt_locs ( void  )

Definition at line 797 of file Variation_ref.cpp.

References CVariation_ref_Base::ResetExt_locs().

void CVariation_ref::ResetIs_ancestral_allele ( void  )
void CVariation_ref::ResetLocation ( void  )
void CVariation_ref::ResetPopulation_data ( void  )
private

Definition at line 204 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

void CVariation_ref::ResetPub ( void  )
private

Definition at line 616 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

void CVariation_ref::ResetValidated ( void  )
void CVariation_ref::SetAllele_frequency ( TAllele_frequency  value)
CVariation_ref::TAllele_frequency & CVariation_ref::SetAllele_frequency ( void  )
void CVariation_ref::SetAllele_origin ( TAllele_origin  value)
CVariation_ref::TAllele_origin & CVariation_ref::SetAllele_origin ( void  )
void CVariation_ref::SetAllele_state ( TAllele_state  value)
CVariation_ref::TAllele_state & CVariation_ref::SetAllele_state ( void  )
CVariation_ref::TClinical_test & CVariation_ref::SetClinical_test ( void  )

Definition at line 328 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

void CVariation_ref::SetCNV ( )
void CVariation_ref::SetCNV ( TSeqPos  min_copy,
TSeqPos  max_copy 
)

Make this variant a copy number variant.

NOTE: This API variant establishes a CNV with a range of possible copies

Definition at line 1201 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_cnv, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), CDelta_item_Base::SetMultiplier_fuzz(), CDelta_item_Base::SetSeq(), and CVariation_inst_Base::SetType().

void CVariation_ref::SetCNV ( const vector< TSeqPos > &  observed_copies)

Make this variant a copy number variant.

NOTE: This API variant establishes a CNV with a fixed set of possible copies

Definition at line 1216 of file Variation_ref.cpp.

References copy(), CVariation_inst_Base::eType_cnv, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), CDelta_item_Base::SetMultiplier_fuzz(), CDelta_item_Base::SetSeq(), and CVariation_inst_Base::SetType().

void CVariation_ref::SetComplex ( )

Create a complex undescribed variant.

Establish a complex undescribed variant.

Definition at line 1314 of file Variation_ref.cpp.

References CVariation_ref_Base::C_Data::SetComplex(), and CVariation_ref_Base::SetData().

Referenced by CGvfReader::xVariationMakeComplex().

void CVariation_ref::SetDeletion ( void  )
void CVariation_ref::SetDeletionInsertion ( const string sequence,
ESeqType  seq_type 
)
void CVariation_ref::SetDuplication ( CRef< CDelta_item start_offset = null,
CRef< CDelta_item stop_offset = null 
)
void CVariation_ref::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.

Definition at line 1250 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_everted_copy, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), CDelta_item_Base::SetSeq(), and CVariation_inst_Base::SetType().

Referenced by CGvfReader::xVariationMakeEversions().

void CVariation_ref::SetExt ( TExt value)
CVariation_ref::TExt & CVariation_ref::SetExt ( void  )

Definition at line 846 of file Variation_ref.cpp.

References CVariation_ref_Base::SetExt().

CVariation_ref::TExt_locs & CVariation_ref::SetExt_locs ( void  )
void CVariation_ref::SetGain ( )
void CVariation_ref::SetIdentity ( CRef< CSeq_literal seq_literal,
CRef< CDelta_item start_offset = null,
CRef< CDelta_item stop_offset = null 
)
void CVariation_ref::SetInsertion ( const string sequence,
ESeqType  seq_type 
)
void CVariation_ref::SetInsertion ( )
void CVariation_ref::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.

Definition at line 1230 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_inverted_copy, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), CDelta_item_Base::SetSeq(), and CVariation_inst_Base::SetType().

Referenced by CGvfReader::xVariationMakeInversions().

void CVariation_ref::SetIs_ancestral_allele ( TIs_ancestral_allele  value)
CVariation_ref::TIs_ancestral_allele & CVariation_ref::SetIs_ancestral_allele ( void  )
void CVariation_ref::SetLocation ( TLocation value)
CVariation_ref::TLocation & CVariation_ref::SetLocation ( void  )

Definition at line 777 of file Variation_ref.cpp.

References CVariation_ref_Base::SetLocation().

void CVariation_ref::SetLoss ( )
void CVariation_ref::SetMicrosatellite ( const string nucleotide_seq,
TSeqPos  min_repeats,
TSeqPos  max_repeats 
)

Set the standard fields for a microsatellite.

This API establishes a microsatellite with a range of possible observed repeats.

Definition at line 1075 of file Variation_ref.cpp.

References eSeqType_na, CVariation_inst_Base::eType_microsatellite, s_SetReplaces(), CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), and CVariation_ref_Base::C_Data::SetInstance().

void CVariation_ref::SetMicrosatellite ( const string nucleotide_seq,
const vector< TSeqPos > &  observed_repeats 
)

Set the standard fields for a microsatellite.

This API establishes a microsatellite with a fixed set of possible observed repeats

Definition at line 1103 of file Variation_ref.cpp.

References copy(), eSeqType_na, CVariation_inst_Base::eType_microsatellite, s_SetReplaces(), CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), and CVariation_ref_Base::C_Data::SetInstance().

void CVariation_ref::SetMissense ( const CSeq_data amino_acid)
void CVariation_ref::SetMNP ( const CSeq_data nucleotide,
TSeqPos  length,
CRef< CDelta_item offset = null 
)
void CVariation_ref::SetMNP ( const vector< string > &  replaces,
ESeqType  seq_type 
)

Set a standard multinucleotide variant.

The replaces set can include empty strings and/or '-' as a character to indicate a deletion.

Definition at line 974 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_mnp, s_SetReplaces(), CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), and CVariation_ref_Base::C_Data::SetInstance().

void CVariation_ref::SetOther ( void  )
CVariation_ref::TPopulation_data & CVariation_ref::SetPopulation_data ( void  )
private

Definition at line 220 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

void CVariation_ref::SetPub ( TPub value)
private

Definition at line 632 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

CVariation_ref::TPub & CVariation_ref::SetPub ( void  )
private

Definition at line 640 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

void CVariation_ref::SetSNV ( const CSeq_data nucleotide,
CRef< CDelta_item offset = null 
)
void CVariation_ref::SetSNV ( const vector< string > &  replaces,
ESeqType  seq_type 
)

Set a standard single nucleotide variant.

The replaces set can include empty strings and/or '-' as a character to indicate a deletion.

Definition at line 941 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_snv, s_SetReplaces(), CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), and CVariation_ref_Base::C_Data::SetInstance().

void CVariation_ref::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.

The feature represents an eversion at the specified location 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.

Definition at line 1274 of file Variation_ref.cpp.

References CDelta_item_Base::eAction_del_at, CVariation_inst_Base::eType_translocation, CRef< C, Locker >::Reset(), CDelta_item_Base::SetAction(), CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), CDelta_item_Base::SetSeq(), and CVariation_inst_Base::SetType().

Referenced by CGvfReader::xVariationMakeTranslocations().

void CVariation_ref::SetUniparentalDisomy ( )

Establish a uniparental disomy mark-up.

Definition at line 1301 of file Variation_ref.cpp.

References CVariation_ref_Base::SetData(), and CVariation_ref_Base::C_Data::SetUniparental_disomy().

void CVariation_ref::SetUnknown ( )

Create a variant of unknown type.

Definition at line 1325 of file Variation_ref.cpp.

References CVariation_ref_Base::SetData(), and CVariation_ref_Base::C_Data::SetUnknown().

Referenced by g_CreateSpecialSeqfeat(), and CGvfReader::xVariationMakeUnknown().

void CVariation_ref::SetValidated ( TValidated  value)
CVariation_ref::TValidated & CVariation_ref::SetValidated ( void  )
void CVariation_ref::Validate ( void  )

Validate that all semantic fields are correct.

perform necessary validation

Definition at line 1356 of file Variation_ref.cpp.


The documentation for this class was generated from the following files:
Modified on Wed Nov 22 17:11:36 2017 by modify_doxy.py rev. 546573