#ifndef FORMATGUESS_EX__HPP
#define FORMATGUESS_EX__HPP

/*  $Id: format_guess_ex.hpp 657768 2022-10-17 14:08:26Z ludwigf $
 * ===========================================================================
 *
 *                            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.
 *
 * ===========================================================================
 *
 * Author: Nathan Bouk
 *
 * File Description: wrapper and extention to CFormatGuess, using
 *     actual file readers CFormatGuess fails
 *
 */

#include <corelib/ncbistd.hpp>
#include <serial/typeinfo.hpp>
#include <bitset>
#include <util/format_guess.hpp>
#include <sstream>

BEGIN_NCBI_SCOPE

//  ============================================================================
struct CFileContentInfoNone
//  ============================================================================
{
};

//  ============================================================================
struct CFileContentInfoGenbank
//  ============================================================================
{
    CFileContentInfoGenbank(): 
        mTypeInfo(nullptr), 
        mObjectType("unknown") 
    {};

    TTypeInfo mTypeInfo;
    string mObjectType;
};

//  ============================================================================
struct CFileContentInfoGff3
//  ============================================================================
{
    enum EContentType {
        eContentUnknown,
        eContentFeatureTable,
        eContentAlignment,
        eContentVariations,
    };

    CFileContentInfoGff3(): mContentType(eContentUnknown) {};

    EContentType mContentType;
};

//  ============================================================================
struct CFileContentInfoAlign
//  ============================================================================
{
    enum EAlignFormat {
        eFormatUnknown,
        eFormatClustal,
        eFormatPhyllip,
        eFormatNexus,
        // ...
    };

    CFileContentInfoAlign(): mAlignFormat(eFormatUnknown) {};

    EAlignFormat mAlignFormat;
};

//  ============================================================================
union CFileContentInfo
//  ============================================================================
{
    CFileContentInfo(): mInfoNone() {};
    ~CFileContentInfo() {};

    CFileContentInfoNone mInfoNone;
    CFileContentInfoGenbank mInfoGenbank;
    CFileContentInfoGff3 mInfoGff3;
    CFileContentInfoAlign mInfoAlign;
};

//////////////////////////////////////////////////////////////////
///
/// Wraps CFormatGuess, and if CFormatGuess's result is Unknown,
///  it tries every file reader until one works.
///

class NCBI_XOBJREAD_EXPORT CFormatGuessEx
{
    //  Construction, destruction
public:
    CFormatGuessEx();

    CFormatGuessEx(
        const string& /* file name */ );

    CFormatGuessEx(
        CNcbiIstream& );

    ~CFormatGuessEx();

    //  Interface:
public:
    static set<TTypeInfo> sDefaultRecognizedGenbankObjectTypes;
    void SetRecognizedGenbankTypes(
        const set<TTypeInfo>& recognizedGenbankTypes);
    CFormatGuess::EFormat GuessFormat();
    CFormatGuess::EFormat GuessFormatAndContent(
        CFileContentInfo& contentInfo);

    bool TestFormat(CFormatGuess::EFormat );

    /// Get format hints
    CFormatGuess::CFormatHints& GetFormatHints(void)
        { return m_Guesser->GetFormatHints(); }

protected:
    unique_ptr<CFormatGuess> m_Guesser;
    std::stringstream m_LocalBuffer;
    const set<TTypeInfo>* m_pEffectiveRecognizedGenbankObjectTypes;

    bool x_FillLocalBuffer(CNcbiIstream& In);
    bool x_TryFormat(CFormatGuess::EFormat Format);

    // bool x_TryBinaryAsn();
    bool x_TryRmo();
    bool x_TryAgp();
    // bool x_TryXml();
    bool x_TryWiggle();
    bool x_TryBed();
    bool x_TryBed15();
    bool x_TryFasta();
    bool x_TryTextAsn();
    bool x_TryGtf();
    bool x_TryGff3();
    bool x_TryGff2();
    //  bool x_TryHgvs();

    TTypeInfo xGuessGenbankObjectType(
        CFormatGuess::EFormat baseFormat);
};


END_NCBI_SCOPE

#endif
