GC_AssemblySet_.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.
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 *
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 *  and reliability of the software and data, the NLM and the U.S.
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 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
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/// @file GC_AssemblySet_.hpp
/// Data storage class.
///
/// This file was generated by application DATATOOL
/// using the following specifications:
/// <a href="/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/genomecoll/genome_collection.asn">genome_collection.asn</a>
/// and additional tune-up parameters:
/// <a href="/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/genomecoll/genome_collection.def">genome_collection.def</a>
///
/// ATTENTION:
///   Don't edit or commit this file into CVS as this file will
///   be overridden (by DATATOOL) without warning!
 
#ifndef OBJECTS_GENOMECOLL_GC_ASSEMBLYSET_BASE_HPP
#define OBJECTS_GENOMECOLL_GC_ASSEMBLYSET_BASE_HPP
 
// standard includes
#include <serial/serialbase.hpp>
 
// generated includes
#include <list>
 
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 CGC_Assembly;
class CGC_AssemblyDesc;
class CGC_SequenceStats;
 
 
// generated classes
 
 
/** @addtogroup dataspec_NCBI_GenomeCollection
 *
 * @{
 */
 
/////////////////////////////////////////////////////////////////////////////
///
/// CGC_AssemblySet_Base --
///
 
class NCBI_GENOME_COLLECTION_EXPORT CGC_AssemblySet_Base : public CSerialObject
{
    typedef CSerialObject Tparent;
public:
    // constructor
    CGC_AssemblySet_Base(void);
    // destructor
    virtual ~CGC_AssemblySet_Base(void);
 
    // type info
    DECLARE_INTERNAL_TYPE_INFO();
 
    /// set type: Assembly-Sets can be of 2 categories
    enum ESet_type {
        eSet_type_full_assembly =   0,  ///< full-assembly: set of asm-units
        eSet_type_assembly_set  = 100,  ///<set of full-assemblies  stopper
        eSet_type_other         = 255
    };
    
    /// Access to ESet_type's attributes (values, names) as defined in spec
    static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME(ESet_type)(void);
    
    /// 'class' defines the semantics of how to interpret this item
    enum EClass {
        eClass_full_assembly             =   0,  ///< general type of full-assembly (not expected to be used)
        eClass_haploid                   =   1,  ///< this assembly represents a single haploid assembly in its entirety
        eClass_haploid_with_alt_loci     =   2,  ///< this assembly has exactly one unit and at least one alt-loci
        eClass_diploid                   =   3,  ///< assembly represents a diploid assembly; we expect at least two  haploid-unit assemblies contained herein
        eClass_unresolved_diploid        =   4,  ///< unresolved-diploid: single unit which includes the diploid sequences
        eClass_alternate_haplotype       =   5,  ///< second part of diploid; linked to another haploid full-assembly  this one is alt-loci or second full-haploid
        eClass_alternate_pseudohaplotype =   6,
        eClass_annotation_target_set     = 101,  ///< assembly is a collection for annotation
        eClass_analysis_set              = 102,  ///< analysis set used for sequencing by alignments
        eClass_other                     = 255  ///< stopper
    };
    
    /// Access to EClass's attributes (values, names) as defined in spec
    static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME(EClass)(void);
    
    // types
    typedef list< CRef< CDbtag > > TId;
    typedef int TSet_type;
    typedef int TClass;
    typedef CGC_AssemblyDesc TDesc;
    typedef CGC_Assembly TPrimary_assembly;
    typedef list< CRef< CGC_Assembly > > TMore_assemblies;
    typedef CGC_SequenceStats TStats;
 
    // member index
    enum class E_memberIndex {
        e__allMandatory = 0,
        e_id,
        e_set_type,
        e_class,
        e_desc,
        e_primary_assembly,
        e_more_assemblies,
        e_stats
    };
    typedef Tparent::CMemberIndex<E_memberIndex, 8> TmemberIndex;
 
    // getters
    // setters
 
    /// The identifier of this assembly
    /// examples: GC internal id, Assembly-accession.version
    /// Types of DbTags used:
    /// db "GenColl", tag id <assembly-release-id>
    /// db "GenColl", tag str <assembly-accession.version>
    /// db "AGP", tag id <agp-sumbission-id>
    /// db "GenColl_Chain", tag id <assembly-chain-id>
    /// db "UCSC_name", tag str <UCSC identifier for assembly>
    /// db "Ensembl_name",tag str <Ensembl identifier for assembly>
    /// Check if a value has been assigned to Id data member.
    ///
    /// Data member Id is mandatory;
    /// its type is defined as 'typedef list< CRef< CDbtag > > TId'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetId(void) const;
 
    /// Check if it is safe to call GetId method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetId(void) const;
 
    /// Reset Id data member.
    void ResetId(void);
 
    /// Get the Id member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TId& GetId(void) const;
 
    /// Assign a value to Id data member.
    ///
    /// @return
    ///   Reference to the data value.
    TId& SetId(void);
 
    /// Check if a value has been assigned to Set_type data member.
    ///
    /// Data member Set_type is mandatory;
    /// its type is defined as 'typedef int TSet_type'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetSet_type(void) const;
 
    /// Check if it is safe to call GetSet_type method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetSet_type(void) const;
 
    /// Reset Set_type data member.
    void ResetSet_type(void);
 
    /// Get the Set_type member data.
    ///
    /// @return
    ///   Copy of the member data.
    TSet_type GetSet_type(void) const;
 
    /// Assign a value to Set_type data member.
    ///
    /// @param value
    ///   Value to assign
    void SetSet_type(TSet_type value);
 
    /// Assign a value to Set_type data member.
    ///
    /// @return
    ///   Reference to the data value.
    TSet_type& SetSet_type(void);
 
    /// Check if a value has been assigned to Class data member.
    ///
    /// Data member Class is mandatory;
    /// its type is defined as 'typedef int TClass'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetClass(void) const;
 
    /// Check if it is safe to call GetClass method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetClass(void) const;
 
    /// Reset Class data member.
    void ResetClass(void);
 
    /// Get the Class member data.
    ///
    /// @return
    ///   Copy of the member data.
    TClass GetClass(void) const;
 
    /// Assign a value to Class data member.
    ///
    /// @param value
    ///   Value to assign
    void SetClass(TClass value);
 
    /// Assign a value to Class data member.
    ///
    /// @return
    ///   Reference to the data value.
    TClass& SetClass(void);
 
    /// descriptors live in a shared data block
    /// Check if a value has been assigned to Desc data member.
    ///
    /// Data member Desc is mandatory;
    /// its type is defined as 'typedef CGC_AssemblyDesc TDesc'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetDesc(void) const;
 
    /// Check if it is safe to call GetDesc method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetDesc(void) const;
 
    /// Reset Desc data member.
    void ResetDesc(void);
 
    /// Get the Desc member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TDesc& GetDesc(void) const;
 
    /// Assign a value to Desc data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetDesc(TDesc& value);
 
    /// Assign a value to Desc data member.
    ///
    /// @return
    ///   Reference to the data value.
    TDesc& SetDesc(void);
 
    /// we contain hierarchically a set of assemblies
    /// Check if a value has been assigned to Primary_assembly data member.
    ///
    /// Data member Primary_assembly is mandatory;
    /// its type is defined as 'typedef CGC_Assembly TPrimary_assembly'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetPrimary_assembly(void) const;
 
    /// Check if it is safe to call GetPrimary_assembly method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetPrimary_assembly(void) const;
 
    /// Reset Primary_assembly data member.
    void ResetPrimary_assembly(void);
 
    /// Get the Primary_assembly member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TPrimary_assembly& GetPrimary_assembly(void) const;
 
    /// Assign a value to Primary_assembly data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetPrimary_assembly(TPrimary_assembly& value);
 
    /// Assign a value to Primary_assembly data member.
    ///
    /// @return
    ///   Reference to the data value.
    TPrimary_assembly& SetPrimary_assembly(void);
 
    /// Check if a value has been assigned to More_assemblies data member.
    ///
    /// Data member More_assemblies is optional;
    /// its type is defined as 'typedef list< CRef< CGC_Assembly > > TMore_assemblies'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetMore_assemblies(void) const;
 
    /// Check if it is safe to call GetMore_assemblies method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetMore_assemblies(void) const;
 
    /// Reset More_assemblies data member.
    void ResetMore_assemblies(void);
 
    /// Get the More_assemblies member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TMore_assemblies& GetMore_assemblies(void) const;
 
    /// Assign a value to More_assemblies data member.
    ///
    /// @return
    ///   Reference to the data value.
    TMore_assemblies& SetMore_assemblies(void);
 
    /// statistics
    /// "stats" field holds stats for all chromosomes combined:
    /// Check if a value has been assigned to Stats data member.
    ///
    /// Data member Stats is optional;
    /// its type is defined as 'typedef CGC_SequenceStats TStats'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetStats(void) const;
 
    /// Check if it is safe to call GetStats method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetStats(void) const;
 
    /// Reset Stats data member.
    void ResetStats(void);
 
    /// Get the Stats member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TStats& GetStats(void) const;
 
    /// Assign a value to Stats data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetStats(TStats& value);
 
    /// Assign a value to Stats data member.
    ///
    /// @return
    ///   Reference to the data value.
    TStats& SetStats(void);
 
    /// Reset the whole object
    virtual void Reset(void);
 
 
private:
    // Prohibit copy constructor and assignment operator
    CGC_AssemblySet_Base(const CGC_AssemblySet_Base&);
    CGC_AssemblySet_Base& operator=(const CGC_AssemblySet_Base&);
 
    // data
    Uint4 m_set_State[1];
    list< CRef< CDbtag > > m_Id;
    int m_Set_type;
    int m_Class;
    CRef< TDesc > m_Desc;
    CRef< TPrimary_assembly > m_Primary_assembly;
    list< CRef< CGC_Assembly > > m_More_assemblies;
    CRef< TStats > m_Stats;
};
 
/* @} */
 
 
 
 
 
///////////////////////////////////////////////////////////
///////////////////// inline methods //////////////////////
///////////////////////////////////////////////////////////
inline
bool CGC_AssemblySet_Base::IsSetId(void) const
{
    return ((m_set_State[0] & 0x3) != 0);
}
 
inline
bool CGC_AssemblySet_Base::CanGetId(void) const
{
    return true;
}
 
inline
const CGC_AssemblySet_Base::TId& CGC_AssemblySet_Base::GetId(void) const
{
    return m_Id;
}
 
inline
CGC_AssemblySet_Base::TId& CGC_AssemblySet_Base::SetId(void)
{
    m_set_State[0] |= 0x1;
    return m_Id;
}
 
inline
bool CGC_AssemblySet_Base::IsSetSet_type(void) const
{
    return ((m_set_State[0] & 0xc) != 0);
}
 
inline
bool CGC_AssemblySet_Base::CanGetSet_type(void) const
{
    return IsSetSet_type();
}
 
inline
void CGC_AssemblySet_Base::ResetSet_type(void)
{
    m_Set_type = (ESet_type)(0);
    m_set_State[0] &= ~0xc;
}
 
inline
CGC_AssemblySet_Base::TSet_type CGC_AssemblySet_Base::GetSet_type(void) const
{
    if (!CanGetSet_type()) {
        ThrowUnassigned(1);
    }
    return m_Set_type;
}
 
inline
void CGC_AssemblySet_Base::SetSet_type(CGC_AssemblySet_Base::TSet_type value)
{
    m_Set_type = value;
    m_set_State[0] |= 0xc;
}
 
inline
CGC_AssemblySet_Base::TSet_type& CGC_AssemblySet_Base::SetSet_type(void)
{
#ifdef _DEBUG
    if (!IsSetSet_type()) {
        memset(&m_Set_type,UnassignedByte(),sizeof(m_Set_type));
    }
#endif
    m_set_State[0] |= 0x4;
    return m_Set_type;
}
 
inline
bool CGC_AssemblySet_Base::IsSetClass(void) const
{
    return ((m_set_State[0] & 0x30) != 0);
}
 
inline
bool CGC_AssemblySet_Base::CanGetClass(void) const
{
    return IsSetClass();
}
 
inline
void CGC_AssemblySet_Base::ResetClass(void)
{
    m_Class = (EClass)(0);
    m_set_State[0] &= ~0x30;
}
 
inline
CGC_AssemblySet_Base::TClass CGC_AssemblySet_Base::GetClass(void) const
{
    if (!CanGetClass()) {
        ThrowUnassigned(2);
    }
    return m_Class;
}
 
inline
void CGC_AssemblySet_Base::SetClass(CGC_AssemblySet_Base::TClass value)
{
    m_Class = value;
    m_set_State[0] |= 0x30;
}
 
inline
CGC_AssemblySet_Base::TClass& CGC_AssemblySet_Base::SetClass(void)
{
#ifdef _DEBUG
    if (!IsSetClass()) {
        memset(&m_Class,UnassignedByte(),sizeof(m_Class));
    }
#endif
    m_set_State[0] |= 0x10;
    return m_Class;
}
 
inline
bool CGC_AssemblySet_Base::IsSetDesc(void) const
{
    return m_Desc.NotEmpty();
}
 
inline
bool CGC_AssemblySet_Base::CanGetDesc(void) const
{
    return true;
}
 
inline
const CGC_AssemblySet_Base::TDesc& CGC_AssemblySet_Base::GetDesc(void) const
{
    if ( !m_Desc ) {
        const_cast<CGC_AssemblySet_Base*>(this)->ResetDesc();
    }
    return (*m_Desc);
}
 
inline
CGC_AssemblySet_Base::TDesc& CGC_AssemblySet_Base::SetDesc(void)
{
    if ( !m_Desc ) {
        ResetDesc();
    }
    return (*m_Desc);
}
 
inline
bool CGC_AssemblySet_Base::IsSetPrimary_assembly(void) const
{
    return m_Primary_assembly.NotEmpty();
}
 
inline
bool CGC_AssemblySet_Base::CanGetPrimary_assembly(void) const
{
    return true;
}
 
inline
const CGC_AssemblySet_Base::TPrimary_assembly& CGC_AssemblySet_Base::GetPrimary_assembly(void) const
{
    if ( !m_Primary_assembly ) {
        const_cast<CGC_AssemblySet_Base*>(this)->ResetPrimary_assembly();
    }
    return (*m_Primary_assembly);
}
 
inline
CGC_AssemblySet_Base::TPrimary_assembly& CGC_AssemblySet_Base::SetPrimary_assembly(void)
{
    if ( !m_Primary_assembly ) {
        ResetPrimary_assembly();
    }
    return (*m_Primary_assembly);
}
 
inline
bool CGC_AssemblySet_Base::IsSetMore_assemblies(void) const
{
    return ((m_set_State[0] & 0xc00) != 0);
}
 
inline
bool CGC_AssemblySet_Base::CanGetMore_assemblies(void) const
{
    return true;
}
 
inline
const CGC_AssemblySet_Base::TMore_assemblies& CGC_AssemblySet_Base::GetMore_assemblies(void) const
{
    return m_More_assemblies;
}
 
inline
CGC_AssemblySet_Base::TMore_assemblies& CGC_AssemblySet_Base::SetMore_assemblies(void)
{
    m_set_State[0] |= 0x400;
    return m_More_assemblies;
}
 
inline
bool CGC_AssemblySet_Base::IsSetStats(void) const
{
    return m_Stats.NotEmpty();
}
 
inline
bool CGC_AssemblySet_Base::CanGetStats(void) const
{
    return IsSetStats();
}
 
inline
const CGC_AssemblySet_Base::TStats& CGC_AssemblySet_Base::GetStats(void) const
{
    if (!CanGetStats()) {
        ThrowUnassigned(6);
    }
    return (*m_Stats);
}
 
///////////////////////////////////////////////////////////
////////////////// end of inline methods //////////////////
///////////////////////////////////////////////////////////
 
 
 
 
 
END_objects_SCOPE // namespace ncbi::objects::
 
END_NCBI_SCOPE
 
 
#endif // OBJECTS_GENOMECOLL_GC_ASSEMBLYSET_BASE_HPP