// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2024, Knut Reinert, FU Berlin
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// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
// Class for reading/writing files in GFF or GTF format.
// ==========================================================================

#ifndef SEQAN_GFF_IO_GFF_FILE_H_
#define SEQAN_GFF_IO_GFF_FILE_H_

namespace seqan2 {

// ============================================================================
// Typedefs
// ============================================================================

// ----------------------------------------------------------------------------
// Typedef GffFileIn
// ----------------------------------------------------------------------------

/*!
 * @class GffFileIn
 * @signature typedef FormattedFile<Gff, Input> GffFileIn;
 * @extends FormattedFileIn
 * @headerfile <seqan/gff_io.h>
 * @brief Class for reading GFF and GTF files.
 *
 * @see GffRecord
 */

typedef FormattedFile<Gff, Input>   GffFileIn;

// ----------------------------------------------------------------------------
// Typedef GffFileOut
// ----------------------------------------------------------------------------

/*!
 * @class GffFileOut
 * @signature typedef FormattedFile<Gff, Output> GffFileOut;
 * @extends FormattedFileOut
 * @headerfile <seqan/gff_io.h>
 * @brief Class for writing GFF and GTF files.
 *
 * @see GffRecord
 */

typedef FormattedFile<Gff, Output>  GffFileOut;

// ============================================================================
// Metafunctions
// ============================================================================

// ----------------------------------------------------------------------------
// Metafunction FormattedFileContext
// ----------------------------------------------------------------------------

template <typename TSpec, typename TStorageSpec>
struct FormattedFileContext<FormattedFile<Gff, Input, TSpec>, TStorageSpec>
{
    typedef CharString Type;
};

// ----------------------------------------------------------------------------
// Metafunction FileFormats
// ----------------------------------------------------------------------------

template <typename TDirection, typename TSpec>
struct FileFormat<FormattedFile<Gff, TDirection, TSpec> >
{
    typedef TagSelector<
                TagList<Gff,
                TagList<Gtf
                > >
            > Type;
};

// ----------------------------------------------------------------------------
// Function readRecord()
// ----------------------------------------------------------------------------

template <typename TForwardIter, typename TFormats>
inline void
readRecord(GffRecord & record,
           CharString & buffer,
           TForwardIter & iter,
           TagSelector<TFormats> const & /* format */)  // format is ignored as it will be autodetected per record
{
    readRecord(record, buffer, iter);
}

// convient GffFile variant
template <typename TSpec>
inline void
readRecord(GffRecord & record, FormattedFile<Gff, Input, TSpec> & file)
{
    readRecord(record, context(file), file.iter, file.format);
}

// ----------------------------------------------------------------------------
// Function writeRecord()
// ----------------------------------------------------------------------------

// support for dynamically chosen file formats
template <typename TTarget>
inline void
writeRecord(TTarget & /* target */,
            GffRecord & /* record */,
            TagSelector<> const & /* format */)
{
    SEQAN_FAIL("GffFileOut: File format not specified.");
}

template <typename TTarget, typename TTagList>
inline void
writeRecord(TTarget & target,
            GffRecord & record,
            TagSelector<TTagList> const & format)
{
    typedef typename TTagList::Type TFormat;

    if (isEqual(format, TFormat()))
        writeRecord(target, record, TFormat());
    else
        writeRecord(target, record, static_cast<typename TagSelector<TTagList>::Base const &>(format));
}

template <typename TSpec>
inline void
writeRecord(FormattedFile<Gff, Output, TSpec> & file, GffRecord & record)
{
    writeRecord(file.iter, record, file.format);
}

}  // namespace seqan2

#endif // SEQAN_GFF_IO_GFF_FILE_H_
