mod_reader.hpp

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/*  $Id: mod_reader.hpp 100616 2023-08-17 19:44:16Z stakhovv $
 * ===========================================================================
 *
 *                            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.
 *
 * ===========================================================================
 *
 * Authors:  Justin Foley
 *
 */
#ifndef _MOD_READER_HPP_
#define _MOD_READER_HPP_
#include <corelib/ncbistd.hpp>
#include <map>
#include <unordered_map>
#include <unordered_set>
#include <objtools/readers/reader_error_codes.hpp>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
 
class NCBI_XOBJREAD_EXPORT CModData
{
public:
    CModData() = default;
 
    template<typename _T1, typename _T2>
    CModData(_T1&& name, _T2&& value) : m_name{ std::forward<_T1>(name) }, m_value{ std::forward<_T2>(value) }
    {
    }
 
    template<typename _T>
    void SetName(_T&& name)
    {
        m_name = std::forward<_T>(name);
    }
 
    template<typename _T>
    void SetValue(_T&& value)
    {
        m_value = std::forward<_T>(value);
    }
    template<typename _T>
    void SetAttrib(_T&& attrib)
    {
        m_attrib = std::forward<_T>(attrib);
    }
    bool IsSetAttrib(void) const
    {
        return !m_attrib.empty();
    }
 
    const string& GetName(void) const
    {
        return m_name;
    }
    const string& GetValue(void) const
    {
        return m_value;
    }
    const string& GetAttrib(void) const
    {
        return m_attrib;
    }
 
    string m_name, m_value, m_attrib;
};
 
 
 
class NCBI_XOBJREAD_EXPORT CModHandler
{
public:
 
    using TModList = list<CModData>;
 
    enum EHandleExisting {
        eReplace        = 0,
        ePreserve       = 1,
        eAppendReplace  = 2,
        eAppendPreserve = 3
    };
 
    using TMods = map<string, list<CModData>>;
    using TModEntry = TMods::value_type;
    using FReportError = function<void(const CModData& mod, const string& message, EDiagSev severity, EModSubcode subcode)>;
 
    CModHandler();
    void SetExcludedMods(const vector<string>& excluded_mods);
    void SetIgnoredMods(const list<string>& ignored_mods);
 
    void AddMods(const TModList& mods,
                 EHandleExisting handle_existing,
                 TModList& rejected_mods,
                 FReportError fReportError=nullptr);
 
    void SetMods(const TMods& mods);
 
    const TMods& GetMods(void) const;
 
    void Clear(void);
 
    static const string& GetCanonicalName(const TModEntry& mod_entry);
    static const string& AssertReturnSingleValue(const TModEntry& mod_entry);
    static string GetCanonicalName(const string& name);
 
private:
    static string x_GetNormalizedString(const string& name);
    static bool x_MultipleValuesAllowed(const string& canonical_name);
    static bool x_IsDeprecated(const string& canonical_name);
    void x_SaveMods(TMods&& mods, EHandleExisting handle_existing, TMods& dest);
 
    TMods m_Mods;
 
    using TNameMap = unordered_map<string, string>;
    using TNameSet = unordered_set<string>;
    static const TNameMap sm_NameMap;
    static const TNameSet sm_MultipleValuesForbidden;
    static const TNameSet sm_DeprecatedModifiers;
    TNameSet m_ExcludedModifiers;
    TNameSet m_IgnoredModifiers;
};
 
 
class CBioseq;
class CSeq_inst;
class CSeq_loc;
class CModReaderException;
 
 
class NCBI_XOBJREAD_EXPORT CModAdder
{
public:
    using TMods = CModHandler::TMods;
    using TModEntry = CModHandler::TModEntry;
    using TSkippedMods = list<CModData>;
    using FReportError = CModHandler::FReportError;
    using FPostMessage = FReportError;
 
    static void Apply(const CModHandler& mod_handler,
            CBioseq& bioseq,
            TSkippedMods& skipped_mods,
            FPostMessage fPostMessage=nullptr);
 
    static void Apply(const CModHandler& mod_handler,
            CBioseq& bioseq,
            TSkippedMods& skipped_mods,
            bool logInfo,
            FPostMessage fPostMessage=nullptr);
private:
 
    static const string& x_GetModName(const TModEntry& mod_entry);
    static const string& x_GetModValue(const TModEntry& mod_entry);
 
    static bool x_TrySeqInstMod(const TModEntry& mod_entry,
            CSeq_inst& seq_inst,
            TSkippedMods& skipped_mods,
            FPostMessage fPostMessage);
 
    static void x_SetStrand(const TModEntry& mod_entry,
            CSeq_inst& seq_inst,
            TSkippedMods& skipped_mods,
            FPostMessage fPostMessage);
 
    static void x_SetMolecule(const TModEntry& mod_entry,
            CSeq_inst& seq_inst,
            TSkippedMods& skipped_mods,
            FPostMessage fPostMessage);
 
    static void x_SetMoleculeFromMolType(const TModEntry& mod_entry,
            CSeq_inst& seq_inst);
 
    static void x_SetTopology(const TModEntry& mod_entry,
            CSeq_inst& seq_inst,
            TSkippedMods& skipped_mods,
            FPostMessage fPostMessage);
 
    static void x_SetHist(const TModEntry& mod_entry,
            CSeq_inst& seq_inst);
 
    static void x_ReportInvalidValue(const CModData& mod_data,
                                     TSkippedMods& skipped_mods,
                                     FPostMessage fPostMessage);
};
 
 
class IObjtoolsListener;
class NCBI_XOBJREAD_EXPORT CDefaultModErrorReporter
{
public:
    using TModList = list<CModData>;
 
    CDefaultModErrorReporter(
            const string& seqId,
            int lineNum,
            IObjtoolsListener* pMessageListener);
 
    void operator()(
            const CModData& mod,
            const string& msg,
            EDiagSev sev,
            EModSubcode subcode);
 
private:
    string m_SeqId;
    int m_LineNum;
    IObjtoolsListener* m_pMessageListener;
};
 
 
class NCBI_XOBJREAD_EXPORT CTitleParser
{
public:
    using TModList = CModHandler::TModList;
    static void Apply(const CTempString& title, TModList& mods, string& remainder);
    static bool HasMods(const CTempString& title);
private:
    static bool x_FindBrackets(const CTempString& line, size_t& start, size_t& stop, size_t& eq_pos);
};
 
END_SCOPE(objects)
END_NCBI_SCOPE
 
#endif // _MOD_READER_HPP_