Gb_qual.hpp

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/* $Id: Gb_qual.hpp 82939 2018-07-17 17:55:27Z bollin $
 * ===========================================================================
 *
 *                            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.
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 *  warranties of performance, merchantability or fitness for any particular
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/// @Gb_qual.hpp
/// User-defined methods of the data storage class.
///
/// This file was originally generated by application DATATOOL
/// using the following specifications:
/// 'seqfeat.asn'.
///
/// New methods or data members can be added to it if needed.
/// See also: Gb_qual_.hpp
 
 
#ifndef OBJECTS_SEQFEAT_GB_QUAL_HPP
#define OBJECTS_SEQFEAT_GB_QUAL_HPP
 
 
// generated includes
#include <objects/seqfeat/Gb_qual_.hpp>
 
// generated classes
 
// other includes
#include <corelib/ncbistd.hpp>
#include <corelib/ncbistr.hpp>
#include <serial/iterator.hpp>
#include <util/static_map.hpp>
 
 
BEGIN_NCBI_SCOPE
 
BEGIN_objects_SCOPE // namespace ncbi::objects::
 
/////////////////////////////////////////////////////////////////////////////
class NCBI_SEQFEAT_EXPORT CGb_qual : public CGb_qual_Base
{
    typedef CGb_qual_Base Tparent;
public:
    // constructors
    CGb_qual(void);
    CGb_qual(const TQual& qual, const TVal& val);
 
    // destructor
    ~CGb_qual(void);
    
    int Compare(const CGb_qual& gbqual) const;
 
    static void ParseExperiment(const string& orig, string& category, string& experiment, string& doi);
    static string BuildExperiment(const string& category, const string& experiment, const string& doi);
 
    static bool CleanupRptUnitSeq(string& val);
    static bool CleanupReplace(string& val);
    static bool CleanupRptUnitRange(string& val);
 
    // for rpt_type qualifiers
    typedef CStaticArraySet<const char *, PNocase_CStr> TLegalRepeatTypeSet;
    static const TLegalRepeatTypeSet &GetSetOfLegalRepeatTypes(void);
    static bool IsValidRptTypeValue(const string& val);
    static bool FixRptTypeValue(string& val);
 
    // for pseudogene qualifiers
    typedef CStaticArraySet<const char *, PNocase_CStr> TLegalPseudogeneSet;
    static const TLegalPseudogeneSet &GetSetOfLegalPseudogenes(void);
    static bool IsValidPseudogeneValue(const string& val);
    static bool FixPseudogeneValue(string& val);
 
    // for misc_recomb qualifiers
    typedef CStaticArraySet<const char *, PNocase_CStr> TLegalRecombinationClassSet;
    static const TLegalRecombinationClassSet &GetSetOfLegalRecombinationClassValues(void);
    static bool FixRecombinationClassValue(string& val);
 
    static bool IsLegalMobileElementValue(const string& val);
    static void GetMobileElementValueElements(const string& val, string& element_type, string& element_name);
    static bool FixMobileElementValue(string& val);
 
    static bool IsIllegalQualName(const string& val);
 
    // for inference qualifiers
    static void ParseInferenceString(string val, string &category, string &type_str, bool &is_same_species, string &database, 
                                     string &accession, string &program, string &version, string &acc_list);
 
    static string CleanupAndRepairInference( const string &orig_inference );
 
    static bool IsLegalInferenceDatabase(const string& db);
 
 
private:
    // Prohibit copy constructor and assignment operator
    CGb_qual(const CGb_qual& value);
    CGb_qual& operator=(const CGb_qual& value);
 
    static bool x_CleanupRptAndReplaceSeq(string& val);
 
};
 
/////////////////// CGb_qual inline methods
 
// constructor
inline
CGb_qual::CGb_qual(void)
{
}
 
inline
CGb_qual::CGb_qual(const TQual& qual, const TVal& val)
{
    SetQual(qual);
    SetVal(val);
}
 
 
inline
int CGb_qual::Compare(const CGb_qual& gbqual) const
{
    if (GetQual() != gbqual.GetQual()) {
        return (GetQual() < gbqual.GetQual() ? -1 : 1);
    }
    if (GetVal() != gbqual.GetVal()) {
        return (GetVal() < gbqual.GetVal() ? -1 : 1);
    }
    return 0;
}
 
 
/////////////////// end of CGb_qual inline methods
 
/////////// inference prefix list
class NCBI_SEQFEAT_EXPORT CInferencePrefixList
{
public:
    // constructors
    CInferencePrefixList(void);
 
    // destructor
    ~CInferencePrefixList(void);
    
    static void GetPrefixAndRemainder (const string& inference, string& prefix, string& remainder);
    
private:
};
 
 
 
END_objects_SCOPE // namespace ncbi::objects::
 
END_NCBI_SCOPE
 
#endif // OBJECTS_SEQFEAT_GB_QUAL_HPP
/* Original file checksum: lines: 94, chars: 2540, CRC32: e99dce88 */