Cdd_.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
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 *  and reliability of the software and data, the NLM and the U.S.
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/// @file Cdd_.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/cdd/cdd.asn">cdd.asn</a>
/// and additional tune-up parameters:
/// <a href="/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/cdd/cdd.def">cdd.def</a>
///
/// ATTENTION:
///   Don't edit or commit this file into CVS as this file will
///   be overridden (by DATATOOL) without warning!
 
#ifndef OBJECTS_CDD_CDD_BASE_HPP
#define OBJECTS_CDD_CDD_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 CAlign_annot_set;
class CBioseq;
class CBiostruc_annot_set;
class CCdd_descr_set;
class CCdd_id;
class CCdd_id_set;
class CCn3d_style_dictionary;
class CCn3d_user_annotations;
class CDomain_parent;
class CMatrix;
class CPssmWithParameters;
class CReject_id;
class CSeq_annot;
class CSeq_entry;
class CSeq_id;
class CSeq_interval;
class CSequence_tree;
class CTriangle;
class CUpdate_align;
 
 
// generated classes
 
 
/** @addtogroup dataspec_NCBI_Cdd
 *
 * @{
 */
 
/////////////////////////////////////////////////////////////////////////////
/// the Cdd is the basic ASN.1 object storing an annotated and curated set of
/// alignments (formulated as a set of pairwise master-slave alignments). 
/// The alignment data are contained in Seq-annots, and a special type of
/// object, the Update-align, contains additional alignment data from unfinished
/// editing sessions and update processes. The Biostruc-annot-set holds 
/// structure superposition information for multiple structure-derived rows in
/// the alignment.
/// Version numbers in Global-ids are meant to be updated every time the Cdd is
/// changed in a way that does not require Global-ids to be changed (sequences
/// added in update cycle, annotation changed, alignment errors fixed)
///
/// CCdd_Base --
///
 
class NCBI_CDD_EXPORT CCdd_Base : public CSerialObject
{
    typedef CSerialObject Tparent;
public:
    // constructor
    CCdd_Base(void);
    // destructor
    virtual ~CCdd_Base(void);
 
    // type info
    DECLARE_INTERNAL_TYPE_INFO();
 
    // types
    typedef string TName;
    typedef CCdd_id_set TId;
    typedef CCdd_descr_set TDescription;
    typedef list< CRef< CSeq_annot > > TSeqannot;
    typedef CBiostruc_annot_set TFeatures;
    typedef CSeq_entry TSequences;
    typedef CSeq_interval TProfile_range;
    typedef CBioseq TTrunc_master;
    typedef CMatrix TPosfreq;
    typedef CMatrix TScoremat;
    typedef CTriangle TDistance;
    typedef CCdd_id TParent;
    typedef CCdd_id_set TChildren;
    typedef CCdd_id_set TSiblings;
    typedef CCdd_id_set TNeighbors;
    typedef list< CRef< CUpdate_align > > TPending;
    typedef list< CRef< CReject_id > > TRejects;
    typedef list< CRef< CSeq_id > > TMaster3d;
    typedef CAlign_annot_set TAlignannot;
    typedef CCn3d_style_dictionary TStyle_dictionary;
    typedef CCn3d_user_annotations TUser_annotations;
    typedef list< CRef< CDomain_parent > > TAncestors;
    typedef CPssmWithParameters TScoreparams;
    typedef CSequence_tree TSeqtree;
 
    // member index
    enum class E_memberIndex {
        e__allMandatory = 0,
        e_name,
        e_id,
        e_description,
        e_seqannot,
        e_features,
        e_sequences,
        e_profile_range,
        e_trunc_master,
        e_posfreq,
        e_scoremat,
        e_distance,
        e_parent,
        e_children,
        e_siblings,
        e_neighbors,
        e_pending,
        e_rejects,
        e_master3d,
        e_alignannot,
        e_style_dictionary,
        e_user_annotations,
        e_ancestors,
        e_scoreparams,
        e_seqtree
    };
    typedef Tparent::CMemberIndex<E_memberIndex, 25> TmemberIndex;
 
    // getters
    // setters
 
    /// a short name (can be the accession..)
    /// Check if a value has been assigned to Name data member.
    ///
    /// Data member Name is mandatory;
    /// its type is defined as 'typedef string TName'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetName(void) const;
 
    /// Check if it is safe to call GetName method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetName(void) const;
 
    /// Reset Name data member.
    void ResetName(void);
 
    /// Get the Name member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TName& GetName(void) const;
 
    /// Assign a value to Name data member.
    ///
    /// @param value
    ///   Value to assign
    void SetName(const TName& value);
    void SetName(TName&& value);
 
    /// Assign a value to Name data member.
    ///
    /// @return
    ///   Reference to the data value.
    TName& SetName(void);
 
    /// this CD's Ids
    /// Check if a value has been assigned to Id data member.
    ///
    /// Data member Id is mandatory;
    /// its type is defined as 'typedef CCdd_id_set 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.
    ///
    /// @param value
    ///   Reference to value.
    void SetId(TId& value);
 
    /// Assign a value to Id data member.
    ///
    /// @return
    ///   Reference to the data value.
    TId& SetId(void);
 
    /// status, references, etc.
    /// Check if a value has been assigned to Description data member.
    ///
    /// Data member Description is optional;
    /// its type is defined as 'typedef CCdd_descr_set TDescription'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetDescription(void) const;
 
    /// Check if it is safe to call GetDescription method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetDescription(void) const;
 
    /// Reset Description data member.
    void ResetDescription(void);
 
    /// Get the Description member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TDescription& GetDescription(void) const;
 
    /// Assign a value to Description data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetDescription(TDescription& value);
 
    /// Assign a value to Description data member.
    ///
    /// @return
    ///   Reference to the data value.
    TDescription& SetDescription(void);
 
    /// contains the CD alignment
    /// Check if a value has been assigned to Seqannot data member.
    ///
    /// Data member Seqannot is optional;
    /// its type is defined as 'typedef list< CRef< CSeq_annot > > TSeqannot'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetSeqannot(void) const;
 
    /// Check if it is safe to call GetSeqannot method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetSeqannot(void) const;
 
    /// Reset Seqannot data member.
    void ResetSeqannot(void);
 
    /// Get the Seqannot member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TSeqannot& GetSeqannot(void) const;
 
    /// Assign a value to Seqannot data member.
    ///
    /// @return
    ///   Reference to the data value.
    TSeqannot& SetSeqannot(void);
 
    /// contains structure
    /// alignment data
    /// or "core" definitions
    /// Check if a value has been assigned to Features data member.
    ///
    /// Data member Features is optional;
    /// its type is defined as 'typedef CBiostruc_annot_set TFeatures'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetFeatures(void) const;
 
    /// Check if it is safe to call GetFeatures method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetFeatures(void) const;
 
    /// Reset Features data member.
    void ResetFeatures(void);
 
    /// Get the Features member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TFeatures& GetFeatures(void) const;
 
    /// Assign a value to Features data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetFeatures(TFeatures& value);
 
    /// Assign a value to Features data member.
    ///
    /// @return
    ///   Reference to the data value.
    TFeatures& SetFeatures(void);
 
    /// store as bioseq-set inside seq-entry
    /// Check if a value has been assigned to Sequences data member.
    ///
    /// Data member Sequences is optional;
    /// its type is defined as 'typedef CSeq_entry TSequences'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetSequences(void) const;
 
    /// Check if it is safe to call GetSequences method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetSequences(void) const;
 
    /// Reset Sequences data member.
    void ResetSequences(void);
 
    /// Get the Sequences member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TSequences& GetSequences(void) const;
 
    /// Assign a value to Sequences data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetSequences(TSequences& value);
 
    /// Assign a value to Sequences data member.
    ///
    /// @return
    ///   Reference to the data value.
    TSequences& SetSequences(void);
 
    /// profile for this region only
    /// also stores the Seq-id of the master
    /// Check if a value has been assigned to Profile_range data member.
    ///
    /// Data member Profile_range is optional;
    /// its type is defined as 'typedef CSeq_interval TProfile_range'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetProfile_range(void) const;
 
    /// Check if it is safe to call GetProfile_range method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetProfile_range(void) const;
 
    /// Reset Profile_range data member.
    void ResetProfile_range(void);
 
    /// Get the Profile_range member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TProfile_range& GetProfile_range(void) const;
 
    /// Assign a value to Profile_range data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetProfile_range(TProfile_range& value);
 
    /// Assign a value to Profile_range data member.
    ///
    /// @return
    ///   Reference to the data value.
    TProfile_range& SetProfile_range(void);
 
    /// holds the truncated master, which
    /// may be something like a consensus,
    /// uses the same sequence coordinate
    /// frame as the profile-range
    /// Check if a value has been assigned to Trunc_master data member.
    ///
    /// Data member Trunc_master is optional;
    /// its type is defined as 'typedef CBioseq TTrunc_master'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetTrunc_master(void) const;
 
    /// Check if it is safe to call GetTrunc_master method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetTrunc_master(void) const;
 
    /// Reset Trunc_master data member.
    void ResetTrunc_master(void);
 
    /// Get the Trunc_master member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TTrunc_master& GetTrunc_master(void) const;
 
    /// Assign a value to Trunc_master data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetTrunc_master(TTrunc_master& value);
 
    /// Assign a value to Trunc_master data member.
    ///
    /// @return
    ///   Reference to the data value.
    TTrunc_master& SetTrunc_master(void);
 
    /// relative residue frequencies
    /// Check if a value has been assigned to Posfreq data member.
    ///
    /// Data member Posfreq is optional;
    /// its type is defined as 'typedef CMatrix TPosfreq'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetPosfreq(void) const;
 
    /// Check if it is safe to call GetPosfreq method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetPosfreq(void) const;
 
    /// Reset Posfreq data member.
    void ResetPosfreq(void);
 
    /// Get the Posfreq member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TPosfreq& GetPosfreq(void) const;
 
    /// Assign a value to Posfreq data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetPosfreq(TPosfreq& value);
 
    /// Assign a value to Posfreq data member.
    ///
    /// @return
    ///   Reference to the data value.
    TPosfreq& SetPosfreq(void);
 
    /// Position dependent score matrix
    /// Check if a value has been assigned to Scoremat data member.
    ///
    /// Data member Scoremat is optional;
    /// its type is defined as 'typedef CMatrix TScoremat'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetScoremat(void) const;
 
    /// Check if it is safe to call GetScoremat method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetScoremat(void) const;
 
    /// Reset Scoremat data member.
    void ResetScoremat(void);
 
    /// Get the Scoremat member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TScoremat& GetScoremat(void) const;
 
    /// Assign a value to Scoremat data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetScoremat(TScoremat& value);
 
    /// Assign a value to Scoremat data member.
    ///
    /// @return
    ///   Reference to the data value.
    TScoremat& SetScoremat(void);
 
    /// pairwise distances for all seqs.
    /// Check if a value has been assigned to Distance data member.
    ///
    /// Data member Distance is optional;
    /// its type is defined as 'typedef CTriangle TDistance'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetDistance(void) const;
 
    /// Check if it is safe to call GetDistance method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetDistance(void) const;
 
    /// Reset Distance data member.
    void ResetDistance(void);
 
    /// Get the Distance member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TDistance& GetDistance(void) const;
 
    /// Assign a value to Distance data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetDistance(TDistance& value);
 
    /// Assign a value to Distance data member.
    ///
    /// @return
    ///   Reference to the data value.
    TDistance& SetDistance(void);
 
    /// this CD is the result of a split
    /// Check if a value has been assigned to Parent data member.
    ///
    /// Data member Parent is optional;
    /// its type is defined as 'typedef CCdd_id TParent'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetParent(void) const;
 
    /// Check if it is safe to call GetParent method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetParent(void) const;
 
    /// Reset Parent data member.
    void ResetParent(void);
 
    /// Get the Parent member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TParent& GetParent(void) const;
 
    /// Assign a value to Parent data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetParent(TParent& value);
 
    /// Assign a value to Parent data member.
    ///
    /// @return
    ///   Reference to the data value.
    TParent& SetParent(void);
 
    /// this CD has been split, not used
    /// Check if a value has been assigned to Children data member.
    ///
    /// Data member Children is optional;
    /// its type is defined as 'typedef CCdd_id_set TChildren'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetChildren(void) const;
 
    /// Check if it is safe to call GetChildren method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetChildren(void) const;
 
    /// Reset Children data member.
    void ResetChildren(void);
 
    /// Get the Children member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TChildren& GetChildren(void) const;
 
    /// Assign a value to Children data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetChildren(TChildren& value);
 
    /// Assign a value to Children data member.
    ///
    /// @return
    ///   Reference to the data value.
    TChildren& SetChildren(void);
 
    /// related CDs (common hits), clusters
    /// Check if a value has been assigned to Siblings data member.
    ///
    /// Data member Siblings is optional;
    /// its type is defined as 'typedef CCdd_id_set TSiblings'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetSiblings(void) const;
 
    /// Check if it is safe to call GetSiblings method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetSiblings(void) const;
 
    /// Reset Siblings data member.
    void ResetSiblings(void);
 
    /// Get the Siblings member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TSiblings& GetSiblings(void) const;
 
    /// Assign a value to Siblings data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetSiblings(TSiblings& value);
 
    /// Assign a value to Siblings data member.
    ///
    /// @return
    ///   Reference to the data value.
    TSiblings& SetSiblings(void);
 
    /// co-occurring CDs, not used
    /// Check if a value has been assigned to Neighbors data member.
    ///
    /// Data member Neighbors is optional;
    /// its type is defined as 'typedef CCdd_id_set TNeighbors'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetNeighbors(void) const;
 
    /// Check if it is safe to call GetNeighbors method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetNeighbors(void) const;
 
    /// Reset Neighbors data member.
    void ResetNeighbors(void);
 
    /// Get the Neighbors member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TNeighbors& GetNeighbors(void) const;
 
    /// Assign a value to Neighbors data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetNeighbors(TNeighbors& value);
 
    /// Assign a value to Neighbors data member.
    ///
    /// @return
    ///   Reference to the data value.
    TNeighbors& SetNeighbors(void);
 
    /// contains alignments from
    /// update or "lower panel"
    /// Check if a value has been assigned to Pending data member.
    ///
    /// Data member Pending is optional;
    /// its type is defined as 'typedef list< CRef< CUpdate_align > > TPending'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetPending(void) const;
 
    /// Check if it is safe to call GetPending method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetPending(void) const;
 
    /// Reset Pending data member.
    void ResetPending(void);
 
    /// Get the Pending member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TPending& GetPending(void) const;
 
    /// Assign a value to Pending data member.
    ///
    /// @return
    ///   Reference to the data value.
    TPending& SetPending(void);
 
    /// SeqIds of rejected CD-
    /// members, ignore in update
    /// Check if a value has been assigned to Rejects data member.
    ///
    /// Data member Rejects is optional;
    /// its type is defined as 'typedef list< CRef< CReject_id > > TRejects'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetRejects(void) const;
 
    /// Check if it is safe to call GetRejects method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetRejects(void) const;
 
    /// Reset Rejects data member.
    void ResetRejects(void);
 
    /// Get the Rejects member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TRejects& GetRejects(void) const;
 
    /// Assign a value to Rejects data member.
    ///
    /// @return
    ///   Reference to the data value.
    TRejects& SetRejects(void);
 
    /// record if CD has a 3D representative
    /// Check if a value has been assigned to Master3d data member.
    ///
    /// Data member Master3d is optional;
    /// its type is defined as 'typedef list< CRef< CSeq_id > > TMaster3d'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetMaster3d(void) const;
 
    /// Check if it is safe to call GetMaster3d method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetMaster3d(void) const;
 
    /// Reset Master3d data member.
    void ResetMaster3d(void);
 
    /// Get the Master3d member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TMaster3d& GetMaster3d(void) const;
 
    /// Assign a value to Master3d data member.
    ///
    /// @return
    ///   Reference to the data value.
    TMaster3d& SetMaster3d(void);
 
    /// alignment annotation
    /// Check if a value has been assigned to Alignannot data member.
    ///
    /// Data member Alignannot is optional;
    /// its type is defined as 'typedef CAlign_annot_set TAlignannot'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetAlignannot(void) const;
 
    /// Check if it is safe to call GetAlignannot method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetAlignannot(void) const;
 
    /// Reset Alignannot data member.
    void ResetAlignannot(void);
 
    /// Get the Alignannot member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TAlignannot& GetAlignannot(void) const;
 
    /// Assign a value to Alignannot data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetAlignannot(TAlignannot& value);
 
    /// Assign a value to Alignannot data member.
    ///
    /// @return
    ///   Reference to the data value.
    TAlignannot& SetAlignannot(void);
 
    /// record rendering styles
    /// Check if a value has been assigned to Style_dictionary data member.
    ///
    /// Data member Style_dictionary is optional;
    /// its type is defined as 'typedef CCn3d_style_dictionary TStyle_dictionary'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetStyle_dictionary(void) const;
 
    /// Check if it is safe to call GetStyle_dictionary method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetStyle_dictionary(void) const;
 
    /// Reset Style_dictionary data member.
    void ResetStyle_dictionary(void);
 
    /// Get the Style_dictionary member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TStyle_dictionary& GetStyle_dictionary(void) const;
 
    /// Assign a value to Style_dictionary data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetStyle_dictionary(TStyle_dictionary& value);
 
    /// Assign a value to Style_dictionary data member.
    ///
    /// @return
    ///   Reference to the data value.
    TStyle_dictionary& SetStyle_dictionary(void);
 
    /// user annotations in Cn3D
    /// Check if a value has been assigned to User_annotations data member.
    ///
    /// Data member User_annotations is optional;
    /// its type is defined as 'typedef CCn3d_user_annotations TUser_annotations'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetUser_annotations(void) const;
 
    /// Check if it is safe to call GetUser_annotations method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetUser_annotations(void) const;
 
    /// Reset User_annotations data member.
    void ResetUser_annotations(void);
 
    /// Get the User_annotations member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TUser_annotations& GetUser_annotations(void) const;
 
    /// Assign a value to User_annotations data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetUser_annotations(TUser_annotations& value);
 
    /// Assign a value to User_annotations data member.
    ///
    /// @return
    ///   Reference to the data value.
    TUser_annotations& SetUser_annotations(void);
 
    /// list of parents
    /// Check if a value has been assigned to Ancestors data member.
    ///
    /// Data member Ancestors is optional;
    /// its type is defined as 'typedef list< CRef< CDomain_parent > > TAncestors'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetAncestors(void) const;
 
    /// Check if it is safe to call GetAncestors method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetAncestors(void) const;
 
    /// Reset Ancestors data member.
    void ResetAncestors(void);
 
    /// Get the Ancestors member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TAncestors& GetAncestors(void) const;
 
    /// Assign a value to Ancestors data member.
    ///
    /// @return
    ///   Reference to the data value.
    TAncestors& SetAncestors(void);
 
    /// Check if a value has been assigned to Scoreparams data member.
    ///
    /// Data member Scoreparams is optional;
    /// its type is defined as 'typedef CPssmWithParameters TScoreparams'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetScoreparams(void) const;
 
    /// Check if it is safe to call GetScoreparams method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetScoreparams(void) const;
 
    /// Reset Scoreparams data member.
    void ResetScoreparams(void);
 
    /// Get the Scoreparams member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TScoreparams& GetScoreparams(void) const;
 
    /// Assign a value to Scoreparams data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetScoreparams(TScoreparams& value);
 
    /// Assign a value to Scoreparams data member.
    ///
    /// @return
    ///   Reference to the data value.
    TScoreparams& SetScoreparams(void);
 
    /// Check if a value has been assigned to Seqtree data member.
    ///
    /// Data member Seqtree is optional;
    /// its type is defined as 'typedef CSequence_tree TSeqtree'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetSeqtree(void) const;
 
    /// Check if it is safe to call GetSeqtree method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetSeqtree(void) const;
 
    /// Reset Seqtree data member.
    void ResetSeqtree(void);
 
    /// Get the Seqtree member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TSeqtree& GetSeqtree(void) const;
 
    /// Assign a value to Seqtree data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetSeqtree(TSeqtree& value);
 
    /// Assign a value to Seqtree data member.
    ///
    /// @return
    ///   Reference to the data value.
    TSeqtree& SetSeqtree(void);
 
    /// Reset the whole object
    virtual void Reset(void);
 
 
private:
    // Prohibit copy constructor and assignment operator
    CCdd_Base(const CCdd_Base&);
    CCdd_Base& operator=(const CCdd_Base&);
 
    // data
    Uint4 m_set_State[2];
    string m_Name;
    CRef< TId > m_Id;
    CRef< TDescription > m_Description;
    list< CRef< CSeq_annot > > m_Seqannot;
    CRef< TFeatures > m_Features;
    CRef< TSequences > m_Sequences;
    CRef< TProfile_range > m_Profile_range;
    CRef< TTrunc_master > m_Trunc_master;
    CRef< TPosfreq > m_Posfreq;
    CRef< TScoremat > m_Scoremat;
    CRef< TDistance > m_Distance;
    CRef< TParent > m_Parent;
    CRef< TChildren > m_Children;
    CRef< TSiblings > m_Siblings;
    CRef< TNeighbors > m_Neighbors;
    list< CRef< CUpdate_align > > m_Pending;
    list< CRef< CReject_id > > m_Rejects;
    list< CRef< CSeq_id > > m_Master3d;
    CRef< TAlignannot > m_Alignannot;
    CRef< TStyle_dictionary > m_Style_dictionary;
    CRef< TUser_annotations > m_User_annotations;
    list< CRef< CDomain_parent > > m_Ancestors;
    CRef< TScoreparams > m_Scoreparams;
    CRef< TSeqtree > m_Seqtree;
};
 
/* @} */
 
 
 
 
 
///////////////////////////////////////////////////////////
///////////////////// inline methods //////////////////////
///////////////////////////////////////////////////////////
inline
bool CCdd_Base::IsSetName(void) const
{
    return ((m_set_State[0] & 0x3) != 0);
}
 
inline
bool CCdd_Base::CanGetName(void) const
{
    return IsSetName();
}
 
inline
const CCdd_Base::TName& CCdd_Base::GetName(void) const
{
    if (!CanGetName()) {
        ThrowUnassigned(0);
    }
    return m_Name;
}
 
inline
void CCdd_Base::SetName(const CCdd_Base::TName& value)
{
    m_Name = value;
    m_set_State[0] |= 0x3;
}
 
inline
void CCdd_Base::SetName(CCdd_Base::TName&& value)
{
    m_Name = std::forward<CCdd_Base::TName>(value);
    m_set_State[0] |= 0x3;
}
 
inline
CCdd_Base::TName& CCdd_Base::SetName(void)
{
#ifdef _DEBUG
    if (!IsSetName()) {
        m_Name = UnassignedString();
    }
#endif
    m_set_State[0] |= 0x1;
    return m_Name;
}
 
inline
bool CCdd_Base::IsSetId(void) const
{
    return m_Id.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetId(void) const
{
    return true;
}
 
inline
const CCdd_Base::TId& CCdd_Base::GetId(void) const
{
    if ( !m_Id ) {
        const_cast<CCdd_Base*>(this)->ResetId();
    }
    return (*m_Id);
}
 
inline
CCdd_Base::TId& CCdd_Base::SetId(void)
{
    if ( !m_Id ) {
        ResetId();
    }
    return (*m_Id);
}
 
inline
bool CCdd_Base::IsSetDescription(void) const
{
    return m_Description.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetDescription(void) const
{
    return IsSetDescription();
}
 
inline
const CCdd_Base::TDescription& CCdd_Base::GetDescription(void) const
{
    if (!CanGetDescription()) {
        ThrowUnassigned(2);
    }
    return (*m_Description);
}
 
inline
bool CCdd_Base::IsSetSeqannot(void) const
{
    return ((m_set_State[0] & 0xc0) != 0);
}
 
inline
bool CCdd_Base::CanGetSeqannot(void) const
{
    return true;
}
 
inline
const CCdd_Base::TSeqannot& CCdd_Base::GetSeqannot(void) const
{
    return m_Seqannot;
}
 
inline
CCdd_Base::TSeqannot& CCdd_Base::SetSeqannot(void)
{
    m_set_State[0] |= 0x40;
    return m_Seqannot;
}
 
inline
bool CCdd_Base::IsSetFeatures(void) const
{
    return m_Features.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetFeatures(void) const
{
    return IsSetFeatures();
}
 
inline
const CCdd_Base::TFeatures& CCdd_Base::GetFeatures(void) const
{
    if (!CanGetFeatures()) {
        ThrowUnassigned(4);
    }
    return (*m_Features);
}
 
inline
bool CCdd_Base::IsSetSequences(void) const
{
    return m_Sequences.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetSequences(void) const
{
    return IsSetSequences();
}
 
inline
const CCdd_Base::TSequences& CCdd_Base::GetSequences(void) const
{
    if (!CanGetSequences()) {
        ThrowUnassigned(5);
    }
    return (*m_Sequences);
}
 
inline
bool CCdd_Base::IsSetProfile_range(void) const
{
    return m_Profile_range.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetProfile_range(void) const
{
    return IsSetProfile_range();
}
 
inline
const CCdd_Base::TProfile_range& CCdd_Base::GetProfile_range(void) const
{
    if (!CanGetProfile_range()) {
        ThrowUnassigned(6);
    }
    return (*m_Profile_range);
}
 
inline
bool CCdd_Base::IsSetTrunc_master(void) const
{
    return m_Trunc_master.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetTrunc_master(void) const
{
    return IsSetTrunc_master();
}
 
inline
const CCdd_Base::TTrunc_master& CCdd_Base::GetTrunc_master(void) const
{
    if (!CanGetTrunc_master()) {
        ThrowUnassigned(7);
    }
    return (*m_Trunc_master);
}
 
inline
bool CCdd_Base::IsSetPosfreq(void) const
{
    return m_Posfreq.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetPosfreq(void) const
{
    return IsSetPosfreq();
}
 
inline
const CCdd_Base::TPosfreq& CCdd_Base::GetPosfreq(void) const
{
    if (!CanGetPosfreq()) {
        ThrowUnassigned(8);
    }
    return (*m_Posfreq);
}
 
inline
bool CCdd_Base::IsSetScoremat(void) const
{
    return m_Scoremat.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetScoremat(void) const
{
    return IsSetScoremat();
}
 
inline
const CCdd_Base::TScoremat& CCdd_Base::GetScoremat(void) const
{
    if (!CanGetScoremat()) {
        ThrowUnassigned(9);
    }
    return (*m_Scoremat);
}
 
inline
bool CCdd_Base::IsSetDistance(void) const
{
    return m_Distance.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetDistance(void) const
{
    return IsSetDistance();
}
 
inline
const CCdd_Base::TDistance& CCdd_Base::GetDistance(void) const
{
    if (!CanGetDistance()) {
        ThrowUnassigned(10);
    }
    return (*m_Distance);
}
 
inline
bool CCdd_Base::IsSetParent(void) const
{
    return m_Parent.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetParent(void) const
{
    return IsSetParent();
}
 
inline
const CCdd_Base::TParent& CCdd_Base::GetParent(void) const
{
    if (!CanGetParent()) {
        ThrowUnassigned(11);
    }
    return (*m_Parent);
}
 
inline
bool CCdd_Base::IsSetChildren(void) const
{
    return m_Children.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetChildren(void) const
{
    return IsSetChildren();
}
 
inline
const CCdd_Base::TChildren& CCdd_Base::GetChildren(void) const
{
    if (!CanGetChildren()) {
        ThrowUnassigned(12);
    }
    return (*m_Children);
}
 
inline
bool CCdd_Base::IsSetSiblings(void) const
{
    return m_Siblings.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetSiblings(void) const
{
    return IsSetSiblings();
}
 
inline
const CCdd_Base::TSiblings& CCdd_Base::GetSiblings(void) const
{
    if (!CanGetSiblings()) {
        ThrowUnassigned(13);
    }
    return (*m_Siblings);
}
 
inline
bool CCdd_Base::IsSetNeighbors(void) const
{
    return m_Neighbors.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetNeighbors(void) const
{
    return IsSetNeighbors();
}
 
inline
const CCdd_Base::TNeighbors& CCdd_Base::GetNeighbors(void) const
{
    if (!CanGetNeighbors()) {
        ThrowUnassigned(14);
    }
    return (*m_Neighbors);
}
 
inline
bool CCdd_Base::IsSetPending(void) const
{
    return ((m_set_State[0] & 0xc0000000) != 0);
}
 
inline
bool CCdd_Base::CanGetPending(void) const
{
    return true;
}
 
inline
const CCdd_Base::TPending& CCdd_Base::GetPending(void) const
{
    return m_Pending;
}
 
inline
CCdd_Base::TPending& CCdd_Base::SetPending(void)
{
    m_set_State[0] |= 0x40000000;
    return m_Pending;
}
 
inline
bool CCdd_Base::IsSetRejects(void) const
{
    return ((m_set_State[1] & 0x3) != 0);
}
 
inline
bool CCdd_Base::CanGetRejects(void) const
{
    return true;
}
 
inline
const CCdd_Base::TRejects& CCdd_Base::GetRejects(void) const
{
    return m_Rejects;
}
 
inline
CCdd_Base::TRejects& CCdd_Base::SetRejects(void)
{
    m_set_State[1] |= 0x1;
    return m_Rejects;
}
 
inline
bool CCdd_Base::IsSetMaster3d(void) const
{
    return ((m_set_State[1] & 0xc) != 0);
}
 
inline
bool CCdd_Base::CanGetMaster3d(void) const
{
    return true;
}
 
inline
const CCdd_Base::TMaster3d& CCdd_Base::GetMaster3d(void) const
{
    return m_Master3d;
}
 
inline
CCdd_Base::TMaster3d& CCdd_Base::SetMaster3d(void)
{
    m_set_State[1] |= 0x4;
    return m_Master3d;
}
 
inline
bool CCdd_Base::IsSetAlignannot(void) const
{
    return m_Alignannot.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetAlignannot(void) const
{
    return IsSetAlignannot();
}
 
inline
const CCdd_Base::TAlignannot& CCdd_Base::GetAlignannot(void) const
{
    if (!CanGetAlignannot()) {
        ThrowUnassigned(18);
    }
    return (*m_Alignannot);
}
 
inline
bool CCdd_Base::IsSetStyle_dictionary(void) const
{
    return m_Style_dictionary.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetStyle_dictionary(void) const
{
    return IsSetStyle_dictionary();
}
 
inline
const CCdd_Base::TStyle_dictionary& CCdd_Base::GetStyle_dictionary(void) const
{
    if (!CanGetStyle_dictionary()) {
        ThrowUnassigned(19);
    }
    return (*m_Style_dictionary);
}
 
inline
bool CCdd_Base::IsSetUser_annotations(void) const
{
    return m_User_annotations.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetUser_annotations(void) const
{
    return IsSetUser_annotations();
}
 
inline
const CCdd_Base::TUser_annotations& CCdd_Base::GetUser_annotations(void) const
{
    if (!CanGetUser_annotations()) {
        ThrowUnassigned(20);
    }
    return (*m_User_annotations);
}
 
inline
bool CCdd_Base::IsSetAncestors(void) const
{
    return ((m_set_State[1] & 0xc00) != 0);
}
 
inline
bool CCdd_Base::CanGetAncestors(void) const
{
    return true;
}
 
inline
const CCdd_Base::TAncestors& CCdd_Base::GetAncestors(void) const
{
    return m_Ancestors;
}
 
inline
CCdd_Base::TAncestors& CCdd_Base::SetAncestors(void)
{
    m_set_State[1] |= 0x400;
    return m_Ancestors;
}
 
inline
bool CCdd_Base::IsSetScoreparams(void) const
{
    return m_Scoreparams.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetScoreparams(void) const
{
    return IsSetScoreparams();
}
 
inline
const CCdd_Base::TScoreparams& CCdd_Base::GetScoreparams(void) const
{
    if (!CanGetScoreparams()) {
        ThrowUnassigned(22);
    }
    return (*m_Scoreparams);
}
 
inline
bool CCdd_Base::IsSetSeqtree(void) const
{
    return m_Seqtree.NotEmpty();
}
 
inline
bool CCdd_Base::CanGetSeqtree(void) const
{
    return IsSetSeqtree();
}
 
inline
const CCdd_Base::TSeqtree& CCdd_Base::GetSeqtree(void) const
{
    if (!CanGetSeqtree()) {
        ThrowUnassigned(23);
    }
    return (*m_Seqtree);
}
 
///////////////////////////////////////////////////////////
////////////////// end of inline methods //////////////////
///////////////////////////////////////////////////////////
 
 
 
 
 
END_objects_SCOPE // namespace ncbi::objects::
 
END_NCBI_SCOPE
 
 
#endif // OBJECTS_CDD_CDD_BASE_HPP