NCBI C++ Toolkit Cross Reference

  C++/include/objects/seqfeat/Variation_ref_.hpp


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/* $Id$ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * */ /// @file Variation_ref_.hpp /// Data storage class. /// /// This file was generated by application DATATOOL /// using the following specifications: /// 'seqfeat.asn'. /// /// ATTENTION: /// Don't edit or commit this file into CVS as this file will /// be overridden (by DATATOOL) without warning! #ifndef OBJECTS_SEQFEAT_VARIATION_REF_BASE_HPP #define OBJECTS_SEQFEAT_VARIATION_REF_BASE_HPP // standard includes #include <serial/serialbase.hpp> // generated includes #include <list> #include <string> BEGIN_NCBI_SCOPE #ifndef BEGIN_objects_SCOPE # define BEGIN_objects_SCOPE BEGIN_SCOPE(objects) # define END_objects_SCOPE END_SCOPE(objects) #endif BEGIN_objects_SCOPE // namespace ncbi::objects:: // forward declarations class CDbtag; class CExt_loc; class CObject_id; class CPhenotype; class CPopulation_data; class CPub; class CSeq_loc; class CSubSource; class CUser_object; class CVariantProperties; class CVariation_inst; class CVariation_ref; // generated classes ///////////////////////////////////////////////////////////////////////////// class NCBI_SEQFEAT_EXPORT CVariation_ref_Base : public CSerialObject { typedef CSerialObject Tparent; public: // constructor CVariation_ref_Base(void); // destructor virtual ~CVariation_ref_Base(void); // type info DECLARE_INTERNAL_TYPE_INFO(); 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 }; /// Access to EMethod_E's attributes (values, names) as defined in spec static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME(EMethod_E)(void); /// 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 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 ///< stopper - 2^31 }; /// Access to EAllele_origin's attributes (values, names) as defined in spec static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME(EAllele_origin)(void); /// observed allele state, if known /// DEPRECATED: new field = VariantProperties.allele-state 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 }; /// Access to EAllele_state's attributes (values, names) as defined in spec static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME(EAllele_state)(void); ///////////////////////////////////////////////////////////////////////////// class NCBI_SEQFEAT_EXPORT C_Data : public CSerialObject { typedef CSerialObject Tparent; public: // constructor C_Data(void); // destructor ~C_Data(void); // type info DECLARE_INTERNAL_TYPE_INFO(); ///////////////////////////////////////////////////////////////////////////// /// Set of related Variations. /// Location of the set equals to the union of member locations class NCBI_SEQFEAT_EXPORT C_Set : public CSerialObject { typedef CSerialObject Tparent; public: // constructor C_Set(void); // destructor ~C_Set(void); // type info DECLARE_INTERNAL_TYPE_INFO(); enum EData_set_type { eData_set_type_unknown = 0, eData_set_type_compound = 1, ///< complex change at the same location on the same molecule eData_set_type_products = 2, ///< different products arising from the same variation in a precursor, e.g. r.[13g>a, 13_88del] eData_set_type_haplotype = 3, ///< changes on the same allele, e.g r.[13g>a;15u>c] eData_set_type_genotype = 4, ///< changes on different alleles in the same genotype, e.g. g.[476C>T]+[476C>T] eData_set_type_mosaic = 5, ///< different genotypes in the same individual eData_set_type_individual = 6, ///< same organism; allele relationship unknown, e.g. g.[476C>T(+)183G>C] eData_set_type_population = 7, ///< population eData_set_type_alleles = 8, ///< set represents a set of observed alleles eData_set_type_package = 9, ///< set represents a package of observations at a given location, generally containing asserted + reference eData_set_type_other = 255 }; /// Access to EData_set_type's attributes (values, names) as defined in spec static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME(EData_set_type)(void); // types typedef int TType; typedef list< CRef< CVariation_ref > > TVariations; typedef string TName; // getters // setters /// mandatory /// typedef int TType /// Check whether the Type data member has been assigned a value. bool IsSetType(void) const; /// Check whether it is safe or not to call GetType method. bool CanGetType(void) const; void ResetType(void); TType GetType(void) const; void SetType(TType value); TType& SetType(void); /// mandatory /// typedef list< CRef< CVariation_ref > > TVariations /// Check whether the Variations data member has been assigned a value. bool IsSetVariations(void) const; /// Check whether it is safe or not to call GetVariations method. bool CanGetVariations(void) const; void ResetVariations(void); const TVariations& GetVariations(void) const; TVariations& SetVariations(void); /// optional /// typedef string TName /// Check whether the Name data member has been assigned a value. bool IsSetName(void) const; /// Check whether it is safe or not to call GetName method. bool CanGetName(void) const; void ResetName(void); const TName& GetName(void) const; void SetName(const TName& value); TName& SetName(void); /// Reset the whole object void Reset(void); private: // Prohibit copy constructor and assignment operator C_Set(const C_Set&); C_Set& operator=(const C_Set&); // data Uint4 m_set_State[1]; int m_Type; list< CRef< CVariation_ref > > m_Variations; string m_Name; }; /// Choice variants. enum E_Choice { e_not_set = 0, ///< No variant selected e_Unknown, e_Note, ///<free-form e_Uniparental_disomy, e_Instance, ///< actual sequence-edit at feat.location e_Set, e_Complex ///< variant is a complex and undescribed change at the location This type of variant is known to occur in dbVar submissions }; /// Maximum+1 value of the choice variant enumerator. enum E_ChoiceStopper { e_MaxChoice = 7 ///< == e_Complex+1 }; /// Reset the whole object void Reset(void); /// Reset the selection (set it to e_not_set). void ResetSelection(void); /// Which variant is currently selected. E_Choice Which(void) const; /// Verify selection, throw exception if it differs from the expected. void CheckSelected(E_Choice index) const; /// Throw 'InvalidSelection' exception. NCBI_NORETURN void ThrowInvalidSelection(E_Choice index) const; /// Retrieve selection name (for diagnostic purposes). static string SelectionName(E_Choice index); /// Select the requested variant if needed. void Select(E_Choice index, EResetVariant reset = eDoResetVariant); /// Select the requested variant if needed, /// allocating CObject variants from memory pool. void Select(E_Choice index, EResetVariant reset, CObjectMemoryPool* pool); // types typedef string TNote; typedef CVariation_inst TInstance; typedef C_Set TSet; // getters // setters bool IsUnknown(void) const; void SetUnknown(void); // typedef string TNote bool IsNote(void) const; const TNote& GetNote(void) const; TNote& SetNote(void); void SetNote(const TNote& value); bool IsUniparental_disomy(void) const; void SetUniparental_disomy(void); // typedef CVariation_inst TInstance bool IsInstance(void) const; const TInstance& GetInstance(void) const; TInstance& SetInstance(void); void SetInstance(TInstance& value); // typedef C_Set TSet bool IsSet(void) const; const TSet& GetSet(void) const; TSet& SetSet(void); void SetSet(TSet& value); bool IsComplex(void) const; void SetComplex(void); private: // copy constructor and assignment operator C_Data(const C_Data& ); C_Data& operator=(const C_Data& ); // choice state E_Choice m_choice; // helper methods void DoSelect(E_Choice index, CObjectMemoryPool* pool = 0); static const char* const sm_SelectionNames[]; // data union { NCBI_NS_NCBI::CUnionBuffer<NCBI_NS_STD::string> m_string; NCBI_NS_NCBI::CSerialObject *m_object; }; }; ///////////////////////////////////////////////////////////////////////////// class NCBI_SEQFEAT_EXPORT C_E_Consequence : public CSerialObject { typedef CSerialObject Tparent; public: // constructor C_E_Consequence(void); // destructor ~C_E_Consequence(void); // type info DECLARE_INTERNAL_TYPE_INFO(); ///////////////////////////////////////////////////////////////////////////// /// see http://www.hgvs.org/mutnomen/recs-prot.html class NCBI_SEQFEAT_EXPORT C_Frameshift : public CSerialObject { typedef CSerialObject Tparent; public: // constructor C_Frameshift(void); // destructor ~C_Frameshift(void); // type info DECLARE_INTERNAL_TYPE_INFO(); // types typedef int TPhase; typedef int TX_length; // getters // setters /// optional /// typedef int TPhase /// Check whether the Phase data member has been assigned a value. bool IsSetPhase(void) const; /// Check whether it is safe or not to call GetPhase method. bool CanGetPhase(void) const; void ResetPhase(void); TPhase GetPhase(void) const; void SetPhase(TPhase value); TPhase& SetPhase(void); /// optional /// typedef int TX_length /// Check whether the X_length data member has been assigned a value. bool IsSetX_length(void) const; /// Check whether it is safe or not to call GetX_length method. bool CanGetX_length(void) const; void ResetX_length(void); TX_length GetX_length(void) const; void SetX_length(TX_length value); TX_length& SetX_length(void); /// Reset the whole object void Reset(void); private: // Prohibit copy constructor and assignment operator C_Frameshift(const C_Frameshift&); C_Frameshift& operator=(const C_Frameshift&); // data Uint4 m_set_State[1]; int m_Phase; int m_X_length; }; ///////////////////////////////////////////////////////////////////////////// class NCBI_SEQFEAT_EXPORT C_Loss_of_heterozygosity : public CSerialObject { typedef CSerialObject Tparent; public: // constructor C_Loss_of_heterozygosity(void); // destructor ~C_Loss_of_heterozygosity(void); // type info DECLARE_INTERNAL_TYPE_INFO(); // types typedef string TReference; typedef string TTest; // getters // setters /// In germline comparison, it will be reference genome assembly /// (default) or reference/normal population. In somatic mutation, /// it will be a name of the normal tissue. /// optional /// typedef string TReference /// Check whether the Reference data member has been assigned a value. bool IsSetReference(void) const; /// Check whether it is safe or not to call GetReference method. bool CanGetReference(void) const; void ResetReference(void); const TReference& GetReference(void) const; void SetReference(const TReference& value); TReference& SetReference(void); /// Name of the testing subject type or the testing tissue. /// optional /// typedef string TTest /// Check whether the Test data member has been assigned a value. bool IsSetTest(void) const; /// Check whether it is safe or not to call GetTest method. bool CanGetTest(void) const; void ResetTest(void); const TTest& GetTest(void) const; void SetTest(const TTest& value); TTest& SetTest(void); /// Reset the whole object void Reset(void); private: // Prohibit copy constructor and assignment operator C_Loss_of_heterozygosity(const C_Loss_of_heterozygosity&); C_Loss_of_heterozygosity& operator=(const C_Loss_of_heterozygosity&); // data Uint4 m_set_State[1]; string m_Reference; string m_Test; }; /// Choice variants. enum E_Choice { e_not_set = 0, ///< No variant selected e_Unknown, e_Splicing, ///<some effect on splicing e_Note, ///<freeform e_Variation, ///< Describe resulting variation in the product, e.g. missense, nonsense, silent, neutral, etc in a protein, that arises from THIS variation. e_Frameshift, e_Loss_of_heterozygosity }; /// Maximum+1 value of the choice variant enumerator. enum E_ChoiceStopper { e_MaxChoice = 7 ///< == e_Loss_of_heterozygosity+1 }; /// Reset the whole object void Reset(void); /// Reset the selection (set it to e_not_set). void ResetSelection(void); /// Which variant is currently selected. E_Choice Which(void) const; /// Verify selection, throw exception if it differs from the expected. void CheckSelected(E_Choice index) const; /// Throw 'InvalidSelection' exception. NCBI_NORETURN void ThrowInvalidSelection(E_Choice index) const; /// Retrieve selection name (for diagnostic purposes). static string SelectionName(E_Choice index); /// Select the requested variant if needed. void Select(E_Choice index, EResetVariant reset = eDoResetVariant); /// Select the requested variant if needed, /// allocating CObject variants from memory pool. void Select(E_Choice index, EResetVariant reset, CObjectMemoryPool* pool); // types typedef string TNote; typedef CVariation_ref TVariation; typedef C_Frameshift TFrameshift; typedef C_Loss_of_heterozygosity TLoss_of_heterozygosity; // getters // setters bool IsUnknown(void) const; void SetUnknown(void); bool IsSplicing(void) const; void SetSplicing(void); // typedef string TNote bool IsNote(void) const; const TNote& GetNote(void) const; TNote& SetNote(void); void SetNote(const TNote& value); // typedef CVariation_ref TVariation bool IsVariation(void) const; const TVariation& GetVariation(void) const; TVariation& SetVariation(void); void SetVariation(TVariation& value); // typedef C_Frameshift TFrameshift bool IsFrameshift(void) const; const TFrameshift& GetFrameshift(void) const; TFrameshift& SetFrameshift(void); void SetFrameshift(TFrameshift& value); // typedef C_Loss_of_heterozygosity TLoss_of_heterozygosity bool IsLoss_of_heterozygosity(void) const; const TLoss_of_heterozygosity& GetLoss_of_heterozygosity(void) const; TLoss_of_heterozygosity& SetLoss_of_heterozygosity(void); void SetLoss_of_heterozygosity(TLoss_of_heterozygosity& value); private: // copy constructor and assignment operator C_E_Consequence(const C_E_Consequence& ); C_E_Consequence& operator=(const C_E_Consequence& ); // choice state E_Choice m_choice; // helper methods void DoSelect(E_Choice index, CObjectMemoryPool* pool = 0); static const char* const sm_SelectionNames[]; // data union { NCBI_NS_NCBI::CUnionBuffer<NCBI_NS_STD::string> m_string; NCBI_NS_NCBI::CSerialObject *m_object; }; }; ///////////////////////////////////////////////////////////////////////////// class NCBI_SEQFEAT_EXPORT C_E_Somatic_origin : public CSerialObject { typedef CSerialObject Tparent; public: // constructor C_E_Somatic_origin(void); // destructor ~C_E_Somatic_origin(void); // type info DECLARE_INTERNAL_TYPE_INFO(); ///////////////////////////////////////////////////////////////////////////// /// condition related to this origin's type class NCBI_SEQFEAT_EXPORT C_Condition : public CSerialObject { typedef CSerialObject Tparent; public: // constructor C_Condition(void); // destructor ~C_Condition(void); // type info DECLARE_INTERNAL_TYPE_INFO(); // types typedef string TDescription; typedef list< CRef< CDbtag > > TObject_id; // getters // setters /// optional /// typedef string TDescription /// Check whether the Description data member has been assigned a value. bool IsSetDescription(void) const; /// Check whether it is safe or not to call GetDescription method. bool CanGetDescription(void) const; void ResetDescription(void); const TDescription& GetDescription(void) const; void SetDescription(const TDescription& value); TDescription& SetDescription(void); /// reference to BioTerm / other descriptive database /// optional /// typedef list< CRef< CDbtag > > TObject_id /// Check whether the Object_id data member has been assigned a value. bool IsSetObject_id(void) const; /// Check whether it is safe or not to call GetObject_id method. bool CanGetObject_id(void) const; void ResetObject_id(void); const TObject_id& GetObject_id(void) const; TObject_id& SetObject_id(void); /// Reset the whole object void Reset(void); private: // Prohibit copy constructor and assignment operator C_Condition(const C_Condition&); C_Condition& operator=(const C_Condition&); // data Uint4 m_set_State[1]; string m_Description; list< CRef< CDbtag > > m_Object_id; }; // types typedef CSubSource TSource; typedef C_Condition TCondition; // getters // setters /// description of the somatic origin itself /// optional /// typedef CSubSource TSource /// Check whether the Source data member has been assigned a value. bool IsSetSource(void) const; /// Check whether it is safe or not to call GetSource method. bool CanGetSource(void) const; void ResetSource(void); const TSource& GetSource(void) const; void SetSource(TSource& value); TSource& SetSource(void); /// optional /// typedef C_Condition TCondition /// Check whether the Condition data member has been assigned a value. bool IsSetCondition(void) const; /// Check whether it is safe or not to call GetCondition method. bool CanGetCondition(void) const; void ResetCondition(void); const TCondition& GetCondition(void) const; void SetCondition(TCondition& value); TCondition& SetCondition(void); /// Reset the whole object void Reset(void); private: // Prohibit copy constructor and assignment operator C_E_Somatic_origin(const C_E_Somatic_origin&); C_E_Somatic_origin& operator=(const C_E_Somatic_origin&); // data Uint4 m_set_State[1]; CRef< TSource > m_Source; CRef< TCondition > m_Condition; }; // types 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; // getters // setters /// ids (i.e., SNP rsid / ssid, dbVar nsv/nssv) /// expected values include 'dbSNP|rs12334', 'dbSNP|ss12345', 'dbVar|nsv1' /// /// we relate three kinds of IDs here: /// - our current object's id /// - the id of this object's parent, if it exists /// - the sample ID that this item originates from /// optional /// typedef CDbtag TId /// Check whether the Id data member has been assigned a value. bool IsSetId(void) const; /// Check whether it is safe or not to call GetId method. bool CanGetId(void) const; void ResetId(void); const TId& GetId(void) const; void SetId(TId& value); TId& SetId(void); /// optional /// typedef CDbtag TParent_id /// Check whether the Parent_id data member has been assigned a value. bool IsSetParent_id(void) const; /// Check whether it is safe or not to call GetParent_id method. bool CanGetParent_id(void) const; void ResetParent_id(void); const TParent_id& GetParent_id(void) const; void SetParent_id(TParent_id& value); TParent_id& SetParent_id(void); /// optional /// typedef CObject_id TSample_id /// Check whether the Sample_id data member has been assigned a value. bool IsSetSample_id(void) const; /// Check whether it is safe or not to call GetSample_id method. bool CanGetSample_id(void) const; void ResetSample_id(void); const TSample_id& GetSample_id(void) const; void SetSample_id(TSample_id& value); TSample_id& SetSample_id(void); /// optional /// typedef list< CRef< CDbtag > > TOther_ids /// Check whether the Other_ids data member has been assigned a value. bool IsSetOther_ids(void) const; /// Check whether it is safe or not to call GetOther_ids method. bool CanGetOther_ids(void) const; void ResetOther_ids(void); const TOther_ids& GetOther_ids(void) const; TOther_ids& SetOther_ids(void); /// names and synonyms /// some variants have well-known canonical names and possible accepted /// synonyms /// optional /// typedef string TName /// Check whether the Name data member has been assigned a value. bool IsSetName(void) const; /// Check whether it is safe or not to call GetName method. bool CanGetName(void) const; void ResetName(void); const TName& GetName(void) const; void SetName(const TName& value); TName& SetName(void); /// optional /// typedef list< string > TSynonyms /// Check whether the Synonyms data member has been assigned a value. bool IsSetSynonyms(void) const; /// Check whether it is safe or not to call GetSynonyms method. bool CanGetSynonyms(void) const; void ResetSynonyms(void); const TSynonyms& GetSynonyms(void) const; TSynonyms& SetSynonyms(void); /// tag for comment and descriptions /// optional /// typedef string TDescription /// Check whether the Description data member has been assigned a value. bool IsSetDescription(void) const; /// Check whether it is safe or not to call GetDescription method. bool CanGetDescription(void) const; void ResetDescription(void); const TDescription& GetDescription(void) const; void SetDescription(const TDescription& value); TDescription& SetDescription(void); /// phenotype /// optional /// typedef list< CRef< CPhenotype > > TPhenotype /// Check whether the Phenotype data member has been assigned a value. bool IsSetPhenotype(void) const; /// Check whether it is safe or not to call GetPhenotype method. bool CanGetPhenotype(void) const; void ResetPhenotype(void); const TPhenotype& GetPhenotype(void) const; TPhenotype& SetPhenotype(void); /// optional /// typedef list< int > TMethod /// Check whether the Method data member has been assigned a value. bool IsSetMethod(void) const; /// Check whether it is safe or not to call GetMethod method. bool CanGetMethod(void) const; void ResetMethod(void); const TMethod& GetMethod(void) const; TMethod& SetMethod(void); /// 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. /// population data /// DEPRECATED - do not use /// optional /// typedef list< CRef< CPopulation_data > > TPopulation_data /// Check whether the Population_data data member has been assigned a value. bool IsSetPopulation_data(void) const; /// Check whether it is safe or not to call GetPopulation_data method. bool CanGetPopulation_data(void) const; void ResetPopulation_data(void); const TPopulation_data& GetPopulation_data(void) const; TPopulation_data& SetPopulation_data(void); /// variant properties bit fields /// optional /// typedef CVariantProperties TVariant_prop /// Check whether the Variant_prop data member has been assigned a value. bool IsSetVariant_prop(void) const; /// Check whether it is safe or not to call GetVariant_prop method. bool CanGetVariant_prop(void) const; void ResetVariant_prop(void); const TVariant_prop& GetVariant_prop(void) const; void SetVariant_prop(TVariant_prop& value); TVariant_prop& SetVariant_prop(void); /// has this variant been validated? /// DEPRECATED: new field = VariantProperties.other-validation /// optional /// typedef bool TValidated /// Check whether the Validated data member has been assigned a value. bool IsSetValidated(void) const; /// Check whether it is safe or not to call GetValidated method. bool CanGetValidated(void) const; void ResetValidated(void); TValidated GetValidated(void) const; void SetValidated(TValidated value); TValidated& SetValidated(void); /// link-outs to GeneTests database /// DEPRECATED - do not use /// optional /// typedef list< CRef< CDbtag > > TClinical_test /// Check whether the Clinical_test data member has been assigned a value. bool IsSetClinical_test(void) const; /// Check whether it is safe or not to call GetClinical_test method. bool CanGetClinical_test(void) const; void ResetClinical_test(void); const TClinical_test& GetClinical_test(void) const; TClinical_test& SetClinical_test(void); /// optional /// typedef int TAllele_origin /// Check whether the Allele_origin data member has been assigned a value. bool IsSetAllele_origin(void) const; /// Check whether it is safe or not to call GetAllele_origin method. 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); /// optional /// typedef int TAllele_state /// Check whether the Allele_state data member has been assigned a value. bool IsSetAllele_state(void) const; /// Check whether it is safe or not to call GetAllele_state method. 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); /// NOTE: /// 'allele-frequency' here refers to the minor allele frequency of the /// default population /// DEPRECATED: new field = VariantProperties.allele-frequency /// optional /// typedef double TAllele_frequency /// Check whether the Allele_frequency data member has been assigned a value. bool IsSetAllele_frequency(void) const; /// Check whether it is safe or not to call GetAllele_frequency method. 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); /// is this variant the ancestral allele? /// DEPRECATED: new field = VariantProperties.is-ancestral-allele /// optional /// typedef bool TIs_ancestral_allele /// Check whether the Is_ancestral_allele data member has been assigned a value. bool IsSetIs_ancestral_allele(void) const; /// Check whether it is safe or not to call GetIs_ancestral_allele method. 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); /// publication support. /// Note: made this pub instead of pub-equiv, since /// Pub can be pub-equiv and pub-equiv is a set of pubs, but it looks like /// Pub is more often used as top-level container /// DEPRECATED - do not use; use Seq-feat.dbxref instead /// optional /// typedef CPub TPub /// Check whether the Pub data member has been assigned a value. bool IsSetPub(void) const; /// Check whether it is safe or not to call GetPub method. bool CanGetPub(void) const; void ResetPub(void); const TPub& GetPub(void) const; void SetPub(TPub& value); TPub& SetPub(void); /// mandatory /// typedef C_Data TData /// Check whether the Data data member has been assigned a value. bool IsSetData(void) const; /// Check whether it is safe or not to call GetData method. bool CanGetData(void) const; void ResetData(void); const TData& GetData(void) const; void SetData(TData& value); TData& SetData(void); /// optional /// typedef list< CRef< C_E_Consequence > > TConsequence /// Check whether the Consequence data member has been assigned a value. bool IsSetConsequence(void) const; /// Check whether it is safe or not to call GetConsequence method. bool CanGetConsequence(void) const; void ResetConsequence(void); const TConsequence& GetConsequence(void) const; TConsequence& SetConsequence(void); /// Observed location, if different from the parent set or feature.location. /// DEPRECATED - do not use /// optional /// typedef CSeq_loc TLocation /// Check whether the Location data member has been assigned a value. bool IsSetLocation(void) const; /// Check whether it is safe or not to call GetLocation method. bool CanGetLocation(void) const; void ResetLocation(void); const TLocation& GetLocation(void) const; void SetLocation(TLocation& value); TLocation& SetLocation(void); /// reference other locs, e.g. mapped source /// DEPRECATED - do not use /// optional /// typedef list< CRef< CExt_loc > > TExt_locs /// Check whether the Ext_locs data member has been assigned a value. bool IsSetExt_locs(void) const; /// Check whether it is safe or not to call GetExt_locs method. bool CanGetExt_locs(void) const; void ResetExt_locs(void); const TExt_locs& GetExt_locs(void) const; TExt_locs& SetExt_locs(void); /// DEPRECATED - do not use; use Seq-feat.exts instead /// optional /// typedef CUser_object TExt /// Check whether the Ext data member has been assigned a value. bool IsSetExt(void) const; /// Check whether it is safe or not to call GetExt method. bool CanGetExt(void) const; void ResetExt(void); const TExt& GetExt(void) const; void SetExt(TExt& value); TExt& SetExt(void); /// optional /// typedef list< CRef< C_E_Somatic_origin > > TSomatic_origin /// Check whether the Somatic_origin data member has been assigned a value. bool IsSetSomatic_origin(void) const; /// Check whether it is safe or not to call GetSomatic_origin method. bool CanGetSomatic_origin(void) const; void ResetSomatic_origin(void); const TSomatic_origin& GetSomatic_origin(void) const; TSomatic_origin& SetSomatic_origin(void); /// Reset the whole object virtual void Reset(void); private: // Prohibit copy constructor and assignment operator CVariation_ref_Base(const CVariation_ref_Base&); CVariation_ref_Base& operator=(const CVariation_ref_Base&); // data Uint4 m_set_State[2]; CRef< TId > m_Id; CRef< TParent_id > m_Parent_id; CRef< TSample_id > m_Sample_id; list< CRef< CDbtag > > m_Other_ids; string m_Name; list< string > m_Synonyms; string m_Description; list< CRef< CPhenotype > > m_Phenotype; list< int > m_Method; list< CRef< CPopulation_data > > m_Population_data; CRef< TVariant_prop > m_Variant_prop; bool m_Validated; list< CRef< CDbtag > > m_Clinical_test; int m_Allele_origin; int m_Allele_state; double m_Allele_frequency; bool m_Is_ancestral_allele; CRef< TPub > m_Pub; CRef< TData > m_Data; list< CRef< C_E_Consequence > > m_Consequence; CRef< TLocation > m_Location; list< CRef< CExt_loc > > m_Ext_locs; CRef< TExt > m_Ext; list< CRef< C_E_Somatic_origin > > m_Somatic_origin; }; /////////////////////////////////////////////////////////// ///////////////////// inline methods ////////////////////// /////////////////////////////////////////////////////////// inline bool CVariation_ref_Base::C_Data::C_Set::IsSetType(void) const { return ((m_set_State[0] & 0x3) != 0); } inline bool CVariation_ref_Base::C_Data::C_Set::CanGetType(void) const { return IsSetType(); } inline void CVariation_ref_Base::C_Data::C_Set::ResetType(void) { m_Type = (EData_set_type)(0); m_set_State[0] &= ~0x3; } inline CVariation_ref_Base::C_Data::C_Set::TType CVariation_ref_Base::C_Data::C_Set::GetType(void) const { if (!CanGetType()) { ThrowUnassigned(0); } return m_Type; } inline void CVariation_ref_Base::C_Data::C_Set::SetType(CVariation_ref_Base::C_Data::C_Set::TType value) { m_Type = value; m_set_State[0] |= 0x3; } inline CVariation_ref_Base::C_Data::C_Set::TType& CVariation_ref_Base::C_Data::C_Set::SetType(void) { #ifdef _DEBUG if (!IsSetType()) { memset(&m_Type,UnassignedByte(),sizeof(m_Type)); } #endif m_set_State[0] |= 0x1; return m_Type; } inline bool CVariation_ref_Base::C_Data::C_Set::IsSetVariations(void) const { return ((m_set_State[0] & 0xc) != 0); } inline bool CVariation_ref_Base::C_Data::C_Set::CanGetVariations(void) const { return true; } inline const CVariation_ref_Base::C_Data::C_Set::TVariations& CVariation_ref_Base::C_Data::C_Set::GetVariations(void) const { return m_Variations; } inline CVariation_ref_Base::C_Data::C_Set::TVariations& CVariation_ref_Base::C_Data::C_Set::SetVariations(void) { m_set_State[0] |= 0x4; return m_Variations; } inline bool CVariation_ref_Base::C_Data::C_Set::IsSetName(void) const { return ((m_set_State[0] & 0x30) != 0); } inline bool CVariation_ref_Base::C_Data::C_Set::CanGetName(void) const { return IsSetName(); } inline const CVariation_ref_Base::C_Data::C_Set::TName& CVariation_ref_Base::C_Data::C_Set::GetName(void) const { if (!CanGetName()) { ThrowUnassigned(2); } return m_Name; } inline void CVariation_ref_Base::C_Data::C_Set::SetName(const CVariation_ref_Base::C_Data::C_Set::TName& value) { m_Name = value; m_set_State[0] |= 0x30; } inline CVariation_ref_Base::C_Data::C_Set::TName& CVariation_ref_Base::C_Data::C_Set::SetName(void) { #ifdef _DEBUG if (!IsSetName()) { m_Name = UnassignedString(); } #endif m_set_State[0] |= 0x10; return m_Name; } inline CVariation_ref_Base::C_Data::E_Choice CVariation_ref_Base::C_Data::Which(void) const { return m_choice; } inline void CVariation_ref_Base::C_Data::CheckSelected(E_Choice index) const { if ( m_choice != index ) ThrowInvalidSelection(index); } inline void CVariation_ref_Base::C_Data::Select(E_Choice index, NCBI_NS_NCBI::EResetVariant reset, NCBI_NS_NCBI::CObjectMemoryPool* pool) { if ( reset == NCBI_NS_NCBI::eDoResetVariant || m_choice != index ) { if ( m_choice != e_not_set ) ResetSelection(); DoSelect(index, pool); } } inline void CVariation_ref_Base::C_Data::Select(E_Choice index, NCBI_NS_NCBI::EResetVariant reset) { Select(index, reset, 0); } inline bool CVariation_ref_Base::C_Data::IsUnknown(void) const { return m_choice == e_Unknown; } inline void CVariation_ref_Base::C_Data::SetUnknown(void) { Select(e_Unknown, NCBI_NS_NCBI::eDoNotResetVariant); } inline bool CVariation_ref_Base::C_Data::IsNote(void) const { return m_choice == e_Note; } inline const CVariation_ref_Base::C_Data::TNote& CVariation_ref_Base::C_Data::GetNote(void) const { CheckSelected(e_Note); return *m_string; } inline CVariation_ref_Base::C_Data::TNote& CVariation_ref_Base::C_Data::SetNote(void) { Select(e_Note, NCBI_NS_NCBI::eDoNotResetVariant); return *m_string; } inline bool CVariation_ref_Base::C_Data::IsUniparental_disomy(void) const { return m_choice == e_Uniparental_disomy; } inline void CVariation_ref_Base::C_Data::SetUniparental_disomy(void) { Select(e_Uniparental_disomy, NCBI_NS_NCBI::eDoNotResetVariant); } inline bool CVariation_ref_Base::C_Data::IsInstance(void) const { return m_choice == e_Instance; } inline bool CVariation_ref_Base::C_Data::IsSet(void) const { return m_choice == e_Set; } inline bool CVariation_ref_Base::C_Data::IsComplex(void) const { return m_choice == e_Complex; } inline void CVariation_ref_Base::C_Data::SetComplex(void) { Select(e_Complex, NCBI_NS_NCBI::eDoNotResetVariant); } inline bool CVariation_ref_Base::C_E_Consequence::C_Frameshift::IsSetPhase(void) const { return ((m_set_State[0] & 0x3) != 0); } inline bool CVariation_ref_Base::C_E_Consequence::C_Frameshift::CanGetPhase(void) const { return IsSetPhase(); } inline void CVariation_ref_Base::C_E_Consequence::C_Frameshift::ResetPhase(void) { m_Phase = 0; m_set_State[0] &= ~0x3; } inline CVariation_ref_Base::C_E_Consequence::C_Frameshift::TPhase CVariation_ref_Base::C_E_Consequence::C_Frameshift::GetPhase(void) const { if (!CanGetPhase()) { ThrowUnassigned(0); } return m_Phase; } inline void CVariation_ref_Base::C_E_Consequence::C_Frameshift::SetPhase(CVariation_ref_Base::C_E_Consequence::C_Frameshift::TPhase value) { m_Phase = value; m_set_State[0] |= 0x3; } inline CVariation_ref_Base::C_E_Consequence::C_Frameshift::TPhase& CVariation_ref_Base::C_E_Consequence::C_Frameshift::SetPhase(void) { #ifdef _DEBUG if (!IsSetPhase()) { memset(&m_Phase,UnassignedByte(),sizeof(m_Phase)); } #endif m_set_State[0] |= 0x1; return m_Phase; } inline bool CVariation_ref_Base::C_E_Consequence::C_Frameshift::IsSetX_length(void) const { return ((m_set_State[0] & 0xc) != 0); } inline bool CVariation_ref_Base::C_E_Consequence::C_Frameshift::CanGetX_length(void) const { return IsSetX_length(); } inline void CVariation_ref_Base::C_E_Consequence::C_Frameshift::ResetX_length(void) { m_X_length = 0; m_set_State[0] &= ~0xc; } inline CVariation_ref_Base::C_E_Consequence::C_Frameshift::TX_length CVariation_ref_Base::C_E_Consequence::C_Frameshift::GetX_length(void) const { if (!CanGetX_length()) { ThrowUnassigned(1); } return m_X_length; } inline void CVariation_ref_Base::C_E_Consequence::C_Frameshift::SetX_length(CVariation_ref_Base::C_E_Consequence::C_Frameshift::TX_length value) { m_X_length = value; m_set_State[0] |= 0xc; } inline CVariation_ref_Base::C_E_Consequence::C_Frameshift::TX_length& CVariation_ref_Base::C_E_Consequence::C_Frameshift::SetX_length(void) { #ifdef _DEBUG if (!IsSetX_length()) { memset(&m_X_length,UnassignedByte(),sizeof(m_X_length)); } #endif m_set_State[0] |= 0x4; return m_X_length; } inline bool CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::IsSetReference(void) const { return ((m_set_State[0] & 0x3) != 0); } inline bool CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::CanGetReference(void) const { return IsSetReference(); } inline const CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::TReference& CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::GetReference(void) const { if (!CanGetReference()) { ThrowUnassigned(0); } return m_Reference; } inline void CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::SetReference(const CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::TReference& value) { m_Reference = value; m_set_State[0] |= 0x3; } inline CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::TReference& CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::SetReference(void) { #ifdef _DEBUG if (!IsSetReference()) { m_Reference = UnassignedString(); } #endif m_set_State[0] |= 0x1; return m_Reference; } inline bool CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::IsSetTest(void) const { return ((m_set_State[0] & 0xc) != 0); } inline bool CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::CanGetTest(void) const { return IsSetTest(); } inline const CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::TTest& CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::GetTest(void) const { if (!CanGetTest()) { ThrowUnassigned(1); } return m_Test; } inline void CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::SetTest(const CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::TTest& value) { m_Test = value; m_set_State[0] |= 0xc; } inline CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::TTest& CVariation_ref_Base::C_E_Consequence::C_Loss_of_heterozygosity::SetTest(void) { #ifdef _DEBUG if (!IsSetTest()) { m_Test = UnassignedString(); } #endif m_set_State[0] |= 0x4; return m_Test; } inline CVariation_ref_Base::C_E_Consequence::E_Choice CVariation_ref_Base::C_E_Consequence::Which(void) const { return m_choice; } inline void CVariation_ref_Base::C_E_Consequence::CheckSelected(E_Choice index) const { if ( m_choice != index ) ThrowInvalidSelection(index); } inline void CVariation_ref_Base::C_E_Consequence::Select(E_Choice index, NCBI_NS_NCBI::EResetVariant reset, NCBI_NS_NCBI::CObjectMemoryPool* pool) { if ( reset == NCBI_NS_NCBI::eDoResetVariant || m_choice != index ) { if ( m_choice != e_not_set ) ResetSelection(); DoSelect(index, pool); } } inline void CVariation_ref_Base::C_E_Consequence::Select(E_Choice index, NCBI_NS_NCBI::EResetVariant reset) { Select(index, reset, 0); } inline bool CVariation_ref_Base::C_E_Consequence::IsUnknown(void) const { return m_choice == e_Unknown; } inline void CVariation_ref_Base::C_E_Consequence::SetUnknown(void) { Select(e_Unknown, NCBI_NS_NCBI::eDoNotResetVariant); } inline bool CVariation_ref_Base::C_E_Consequence::IsSplicing(void) const { return m_choice == e_Splicing; } inline void CVariation_ref_Base::C_E_Consequence::SetSplicing(void) { Select(e_Splicing, NCBI_NS_NCBI::eDoNotResetVariant); } inline bool CVariation_ref_Base::C_E_Consequence::IsNote(void) const { return m_choice == e_Note; } inline const CVariation_ref_Base::C_E_Consequence::TNote& CVariation_ref_Base::C_E_Consequence::GetNote(void) const { CheckSelected(e_Note); return *m_string; } inline CVariation_ref_Base::C_E_Consequence::TNote& CVariation_ref_Base::C_E_Consequence::SetNote(void) { Select(e_Note, NCBI_NS_NCBI::eDoNotResetVariant); return *m_string; } inline bool CVariation_ref_Base::C_E_Consequence::IsVariation(void) const { return m_choice == e_Variation; } inline bool CVariation_ref_Base::C_E_Consequence::IsFrameshift(void) const { return m_choice == e_Frameshift; } inline bool CVariation_ref_Base::C_E_Consequence::IsLoss_of_heterozygosity(void) const { return m_choice == e_Loss_of_heterozygosity; } inline bool CVariation_ref_Base::C_E_Somatic_origin::C_Condition::IsSetDescription(void) const { return ((m_set_State[0] & 0x3) != 0); } inline bool CVariation_ref_Base::C_E_Somatic_origin::C_Condition::CanGetDescription(void) const { return IsSetDescription(); } inline const CVariation_ref_Base::C_E_Somatic_origin::C_Condition::TDescription& CVariation_ref_Base::C_E_Somatic_origin::C_Condition::GetDescription(void) const { if (!CanGetDescription()) { ThrowUnassigned(0); } return m_Description; } inline void CVariation_ref_Base::C_E_Somatic_origin::C_Condition::SetDescription(const CVariation_ref_Base::C_E_Somatic_origin::C_Condition::TDescription& value) { m_Description = value; m_set_State[0] |= 0x3; } inline CVariation_ref_Base::C_E_Somatic_origin::C_Condition::TDescription& CVariation_ref_Base::C_E_Somatic_origin::C_Condition::SetDescription(void) { #ifdef _DEBUG if (!IsSetDescription()) { m_Description = UnassignedString(); } #endif m_set_State[0] |= 0x1; return m_Description; } inline bool CVariation_ref_Base::C_E_Somatic_origin::C_Condition::IsSetObject_id(void) const { return ((m_set_State[0] & 0xc) != 0); } inline bool CVariation_ref_Base::C_E_Somatic_origin::C_Condition::CanGetObject_id(void) const { return true; } inline const CVariation_ref_Base::C_E_Somatic_origin::C_Condition::TObject_id& CVariation_ref_Base::C_E_Somatic_origin::C_Condition::GetObject_id(void) const { return m_Object_id; } inline CVariation_ref_Base::C_E_Somatic_origin::C_Condition::TObject_id& CVariation_ref_Base::C_E_Somatic_origin::C_Condition::SetObject_id(void) { m_set_State[0] |= 0x4; return m_Object_id; } inline bool CVariation_ref_Base::C_E_Somatic_origin::IsSetSource(void) const { return m_Source.NotEmpty(); } inline bool CVariation_ref_Base::C_E_Somatic_origin::CanGetSource(void) const { return IsSetSource(); } inline const CVariation_ref_Base::C_E_Somatic_origin::TSource& CVariation_ref_Base::C_E_Somatic_origin::GetSource(void) const { if (!CanGetSource()) { ThrowUnassigned(0); } return (*m_Source); } inline bool CVariation_ref_Base::C_E_Somatic_origin::IsSetCondition(void) const { return m_Condition.NotEmpty(); } inline bool CVariation_ref_Base::C_E_Somatic_origin::CanGetCondition(void) const { return IsSetCondition(); } inline const CVariation_ref_Base::C_E_Somatic_origin::TCondition& CVariation_ref_Base::C_E_Somatic_origin::GetCondition(void) const { if (!CanGetCondition()) { ThrowUnassigned(1); } return (*m_Condition); } inline bool CVariation_ref_Base::IsSetId(void) const { return m_Id.NotEmpty(); } inline bool CVariation_ref_Base::CanGetId(void) const { return IsSetId(); } inline const CVariation_ref_Base::TId& CVariation_ref_Base::GetId(void) const { if (!CanGetId()) { ThrowUnassigned(0); } return (*m_Id); } inline bool CVariation_ref_Base::IsSetParent_id(void) const { return m_Parent_id.NotEmpty(); } inline bool CVariation_ref_Base::CanGetParent_id(void) const { return IsSetParent_id(); } inline const CVariation_ref_Base::TParent_id& CVariation_ref_Base::GetParent_id(void) const { if (!CanGetParent_id()) { ThrowUnassigned(1); } return (*m_Parent_id); } inline bool CVariation_ref_Base::IsSetSample_id(void) const { return m_Sample_id.NotEmpty(); } inline bool CVariation_ref_Base::CanGetSample_id(void) const { return IsSetSample_id(); } inline const CVariation_ref_Base::TSample_id& CVariation_ref_Base::GetSample_id(void) const { if (!CanGetSample_id()) { ThrowUnassigned(2); } return (*m_Sample_id); } inline bool CVariation_ref_Base::IsSetOther_ids(void) const { return ((m_set_State[0] & 0xc0) != 0); } inline bool CVariation_ref_Base::CanGetOther_ids(void) const { return true; } inline const CVariation_ref_Base::TOther_ids& CVariation_ref_Base::GetOther_ids(void) const { return m_Other_ids; } inline CVariation_ref_Base::TOther_ids& CVariation_ref_Base::SetOther_ids(void) { m_set_State[0] |= 0x40; return m_Other_ids; } inline bool CVariation_ref_Base::IsSetName(void) const { return ((m_set_State[0] & 0x300) != 0); } inline bool CVariation_ref_Base::CanGetName(void) const { return IsSetName(); } inline const CVariation_ref_Base::TName& CVariation_ref_Base::GetName(void) const { if (!CanGetName()) { ThrowUnassigned(4); } return m_Name; } inline void CVariation_ref_Base::SetName(const CVariation_ref_Base::TName& value) { m_Name = value; m_set_State[0] |= 0x300; } inline CVariation_ref_Base::TName& CVariation_ref_Base::SetName(void) { #ifdef _DEBUG if (!IsSetName()) { m_Name = UnassignedString(); } #endif m_set_State[0] |= 0x100; return m_Name; } inline bool CVariation_ref_Base::IsSetSynonyms(void) const { return ((m_set_State[0] & 0xc00) != 0); } inline bool CVariation_ref_Base::CanGetSynonyms(void) const { return true; } inline const CVariation_ref_Base::TSynonyms& CVariation_ref_Base::GetSynonyms(void) const { return m_Synonyms; } inline CVariation_ref_Base::TSynonyms& CVariation_ref_Base::SetSynonyms(void) { m_set_State[0] |= 0x400; return m_Synonyms; } inline bool CVariation_ref_Base::IsSetDescription(void) const { return ((m_set_State[0] & 0x3000) != 0); } inline bool CVariation_ref_Base::CanGetDescription(void) const { return IsSetDescription(); } inline const CVariation_ref_Base::TDescription& CVariation_ref_Base::GetDescription(void) const { if (!CanGetDescription()) { ThrowUnassigned(6); } return m_Description; } inline void CVariation_ref_Base::SetDescription(const CVariation_ref_Base::TDescription& value) { m_Description = value; m_set_State[0] |= 0x3000; } inline CVariation_ref_Base::TDescription& CVariation_ref_Base::SetDescription(void) { #ifdef _DEBUG if (!IsSetDescription()) { m_Description = UnassignedString(); } #endif m_set_State[0] |= 0x1000; return m_Description; } inline bool CVariation_ref_Base::IsSetPhenotype(void) const { return ((m_set_State[0] & 0xc000) != 0); } inline bool CVariation_ref_Base::CanGetPhenotype(void) const { return true; } inline const CVariation_ref_Base::TPhenotype& CVariation_ref_Base::GetPhenotype(void) const { return m_Phenotype; } inline CVariation_ref_Base::TPhenotype& CVariation_ref_Base::SetPhenotype(void) { m_set_State[0] |= 0x4000; return m_Phenotype; } inline bool CVariation_ref_Base::IsSetMethod(void) const { return ((m_set_State[0] & 0x30000) != 0); } inline bool CVariation_ref_Base::CanGetMethod(void) const { return true; } inline const CVariation_ref_Base::TMethod& CVariation_ref_Base::GetMethod(void) const { return m_Method; } inline CVariation_ref_Base::TMethod& CVariation_ref_Base::SetMethod(void) { m_set_State[0] |= 0x10000; return m_Method; } inline bool CVariation_ref_Base::IsSetPopulation_data(void) const { return ((m_set_State[0] & 0xc0000) != 0); } inline bool CVariation_ref_Base::CanGetPopulation_data(void) const { return true; } inline const CVariation_ref_Base::TPopulation_data& CVariation_ref_Base::GetPopulation_data(void) const { return m_Population_data; } inline CVariation_ref_Base::TPopulation_data& CVariation_ref_Base::SetPopulation_data(void) { m_set_State[0] |= 0x40000; return m_Population_data; } inline bool CVariation_ref_Base::IsSetVariant_prop(void) const { return m_Variant_prop.NotEmpty(); } inline bool CVariation_ref_Base::CanGetVariant_prop(void) const { return IsSetVariant_prop(); } inline const CVariation_ref_Base::TVariant_prop& CVariation_ref_Base::GetVariant_prop(void) const { if (!CanGetVariant_prop()) { ThrowUnassigned(10); } return (*m_Variant_prop); } inline bool CVariation_ref_Base::IsSetValidated(void) const { return ((m_set_State[0] & 0xc00000) != 0); } inline bool CVariation_ref_Base::CanGetValidated(void) const { return IsSetValidated(); } inline void CVariation_ref_Base::ResetValidated(void) { m_Validated = 0; m_set_State[0] &= ~0xc00000; } inline CVariation_ref_Base::TValidated CVariation_ref_Base::GetValidated(void) const { if (!CanGetValidated()) { ThrowUnassigned(11); } return m_Validated; } inline void CVariation_ref_Base::SetValidated(CVariation_ref_Base::TValidated value) { m_Validated = value; m_set_State[0] |= 0xc00000; } inline CVariation_ref_Base::TValidated& CVariation_ref_Base::SetValidated(void) { #ifdef _DEBUG if (!IsSetValidated()) { memset(&m_Validated,UnassignedByte(),sizeof(m_Validated)); } #endif m_set_State[0] |= 0x400000; return m_Validated; } inline bool CVariation_ref_Base::IsSetClinical_test(void) const { return ((m_set_State[0] & 0x3000000) != 0); } inline bool CVariation_ref_Base::CanGetClinical_test(void) const { return true; } inline const CVariation_ref_Base::TClinical_test& CVariation_ref_Base::GetClinical_test(void) const { return m_Clinical_test; } inline CVariation_ref_Base::TClinical_test& CVariation_ref_Base::SetClinical_test(void) { m_set_State[0] |= 0x1000000; return m_Clinical_test; } inline bool CVariation_ref_Base::IsSetAllele_origin(void) const { return ((m_set_State[0] & 0xc000000) != 0); } inline bool CVariation_ref_Base::CanGetAllele_origin(void) const { return IsSetAllele_origin(); } inline void CVariation_ref_Base::ResetAllele_origin(void) { m_Allele_origin = (EAllele_origin)(0); m_set_State[0] &= ~0xc000000; } inline CVariation_ref_Base::TAllele_origin CVariation_ref_Base::GetAllele_origin(void) const { if (!CanGetAllele_origin()) { ThrowUnassigned(13); } return m_Allele_origin; } inline void CVariation_ref_Base::SetAllele_origin(CVariation_ref_Base::TAllele_origin value) { m_Allele_origin = value; m_set_State[0] |= 0xc000000; } inline CVariation_ref_Base::TAllele_origin& CVariation_ref_Base::SetAllele_origin(void) { #ifdef _DEBUG if (!IsSetAllele_origin()) { memset(&m_Allele_origin,UnassignedByte(),sizeof(m_Allele_origin)); } #endif m_set_State[0] |= 0x4000000; return m_Allele_origin; } inline bool CVariation_ref_Base::IsSetAllele_state(void) const { return ((m_set_State[0] & 0x30000000) != 0); } inline bool CVariation_ref_Base::CanGetAllele_state(void) const { return IsSetAllele_state(); } inline void CVariation_ref_Base::ResetAllele_state(void) { m_Allele_state = (EAllele_state)(0); m_set_State[0] &= ~0x30000000; } inline CVariation_ref_Base::TAllele_state CVariation_ref_Base::GetAllele_state(void) const { if (!CanGetAllele_state()) { ThrowUnassigned(14); } return m_Allele_state; } inline void CVariation_ref_Base::SetAllele_state(CVariation_ref_Base::TAllele_state value) { m_Allele_state = value; m_set_State[0] |= 0x30000000; } inline CVariation_ref_Base::TAllele_state& CVariation_ref_Base::SetAllele_state(void) { #ifdef _DEBUG if (!IsSetAllele_state()) { memset(&m_Allele_state,UnassignedByte(),sizeof(m_Allele_state)); } #endif m_set_State[0] |= 0x10000000; return m_Allele_state; } inline bool CVariation_ref_Base::IsSetAllele_frequency(void) const { return ((m_set_State[0] & 0xc0000000) != 0); } inline bool CVariation_ref_Base::CanGetAllele_frequency(void) const { return IsSetAllele_frequency(); } inline void CVariation_ref_Base::ResetAllele_frequency(void) { m_Allele_frequency = 0; m_set_State[0] &= ~0xc0000000; } inline CVariation_ref_Base::TAllele_frequency CVariation_ref_Base::GetAllele_frequency(void) const { if (!CanGetAllele_frequency()) { ThrowUnassigned(15); } return m_Allele_frequency; } inline void CVariation_ref_Base::SetAllele_frequency(CVariation_ref_Base::TAllele_frequency value) { m_Allele_frequency = value; m_set_State[0] |= 0xc0000000; } inline CVariation_ref_Base::TAllele_frequency& CVariation_ref_Base::SetAllele_frequency(void) { #ifdef _DEBUG if (!IsSetAllele_frequency()) { memset(&m_Allele_frequency,UnassignedByte(),sizeof(m_Allele_frequency)); } #endif m_set_State[0] |= 0x40000000; return m_Allele_frequency; } inline bool CVariation_ref_Base::IsSetIs_ancestral_allele(void) const { return ((m_set_State[1] & 0x3) != 0); } inline bool CVariation_ref_Base::CanGetIs_ancestral_allele(void) const { return IsSetIs_ancestral_allele(); } inline void CVariation_ref_Base::ResetIs_ancestral_allele(void) { m_Is_ancestral_allele = 0; m_set_State[1] &= ~0x3; } inline CVariation_ref_Base::TIs_ancestral_allele CVariation_ref_Base::GetIs_ancestral_allele(void) const { if (!CanGetIs_ancestral_allele()) { ThrowUnassigned(16); } return m_Is_ancestral_allele; } inline void CVariation_ref_Base::SetIs_ancestral_allele(CVariation_ref_Base::TIs_ancestral_allele value) { m_Is_ancestral_allele = value; m_set_State[1] |= 0x3; } inline CVariation_ref_Base::TIs_ancestral_allele& CVariation_ref_Base::SetIs_ancestral_allele(void) { #ifdef _DEBUG if (!IsSetIs_ancestral_allele()) { memset(&m_Is_ancestral_allele,UnassignedByte(),sizeof(m_Is_ancestral_allele)); } #endif m_set_State[1] |= 0x1; return m_Is_ancestral_allele; } inline bool CVariation_ref_Base::IsSetPub(void) const { return m_Pub.NotEmpty(); } inline bool CVariation_ref_Base::CanGetPub(void) const { return IsSetPub(); } inline const CVariation_ref_Base::TPub& CVariation_ref_Base::GetPub(void) const { if (!CanGetPub()) { ThrowUnassigned(17); } return (*m_Pub); } inline bool CVariation_ref_Base::IsSetData(void) const { return m_Data.NotEmpty(); } inline bool CVariation_ref_Base::CanGetData(void) const { return true; } inline const CVariation_ref_Base::TData& CVariation_ref_Base::GetData(void) const { if ( !m_Data ) { const_cast<CVariation_ref_Base*>(this)->ResetData(); } return (*m_Data); } inline CVariation_ref_Base::TData& CVariation_ref_Base::SetData(void) { if ( !m_Data ) { ResetData(); } return (*m_Data); } inline bool CVariation_ref_Base::IsSetConsequence(void) const { return ((m_set_State[1] & 0xc0) != 0); } inline bool CVariation_ref_Base::CanGetConsequence(void) const { return true; } inline const CVariation_ref_Base::TConsequence& CVariation_ref_Base::GetConsequence(void) const { return m_Consequence; } inline CVariation_ref_Base::TConsequence& CVariation_ref_Base::SetConsequence(void) { m_set_State[1] |= 0x40; return m_Consequence; } inline bool CVariation_ref_Base::IsSetLocation(void) const { return m_Location.NotEmpty(); } inline bool CVariation_ref_Base::CanGetLocation(void) const { return IsSetLocation(); } inline const CVariation_ref_Base::TLocation& CVariation_ref_Base::GetLocation(void) const { if (!CanGetLocation()) { ThrowUnassigned(20); } return (*m_Location); } inline bool CVariation_ref_Base::IsSetExt_locs(void) const { return ((m_set_State[1] & 0xc00) != 0); } inline bool CVariation_ref_Base::CanGetExt_locs(void) const { return true; } inline const CVariation_ref_Base::TExt_locs& CVariation_ref_Base::GetExt_locs(void) const { return m_Ext_locs; } inline CVariation_ref_Base::TExt_locs& CVariation_ref_Base::SetExt_locs(void) { m_set_State[1] |= 0x400; return m_Ext_locs; } inline bool CVariation_ref_Base::IsSetExt(void) const { return m_Ext.NotEmpty(); } inline bool CVariation_ref_Base::CanGetExt(void) const { return IsSetExt(); } inline const CVariation_ref_Base::TExt& CVariation_ref_Base::GetExt(void) const { if (!CanGetExt()) { ThrowUnassigned(22); } return (*m_Ext); } inline bool CVariation_ref_Base::IsSetSomatic_origin(void) const { return ((m_set_State[1] & 0xc000) != 0); } inline bool CVariation_ref_Base::CanGetSomatic_origin(void) const { return true; } inline const CVariation_ref_Base::TSomatic_origin& CVariation_ref_Base::GetSomatic_origin(void) const { return m_Somatic_origin; } inline CVariation_ref_Base::TSomatic_origin& CVariation_ref_Base::SetSomatic_origin(void) { m_set_State[1] |= 0x4000; return m_Somatic_origin; } /////////////////////////////////////////////////////////// ////////////////// end of inline methods ////////////////// /////////////////////////////////////////////////////////// END_objects_SCOPE // namespace ncbi::objects:: END_NCBI_SCOPE #endif // OBJECTS_SEQFEAT_VARIATION_REF_BASE_HPP

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