// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
//     * Redistributions of source code must retain the above copyright
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above copyright
//       notice, this list of conditions and the following disclaimer in the
//       documentation and/or other materials provided with the distribution.
//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
//       its contributors may be used to endorse or promote products derived
//       from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Stream Benchmark Demo.  This demo shows how to use different stream types
// for reading and writing FASTA files.  The time required for this is
// printed, and thus this demo can be used as a benchmark tool.
// ==========================================================================

// #define SEQAN_NEW_IO

#include <cstdio>
//#include <fstream>
#if SEQAN_HAS_ZLIB
#include <zlib.h>
#endif  // #if SEQAN_HAS_ZLIB
#if SEQAN_HAS_BZIP2
#include <bzlib.h>
#endif  // #if SEQAN_HAS_BZIP2

#include <seqan/basic.h>
#include <seqan/stream.h>
#include <seqan/seq_io.h>
#include <seqan/stream.h>
#include <seqan/sequence.h>
#include <seqan/arg_parse.h>

using namespace seqan2;

// Setting buffer size to 4MB, such that the overhead for jumping buffers and
// such only occurs every 4M chars.
//const unsigned int BUFFER_SIZE = 1024 * 1024 * 4;

typedef Dna5String TSequence;

struct Options
{
    bool doublePass;
    bool cstdio;
    bool fstream;
    bool mmapString;
    bool gzip;
    bool bzip2;
    bool documentMMap;
    bool nonConcat;
    bool multiSeq;

    Options() :
        doublePass(false), cstdio(false), fstream(false),
        mmapString(false), gzip(false), bzip2(false), documentMMap(false),
        nonConcat(false), multiSeq(false)
    {}
};

//int readFileMultiSeqFile(char const * filename, Options const & /*options*/)
//{
//    typedef StringSet<CharString> TSequenceIds;
//    typedef StringSet<TSequence> TSequences;
//    typedef Iterator<TSequenceIds>::Type TSequenceIdsIter;
//    typedef Iterator<TSequences>::Type TSequencesIter;
//    TSequenceIds sequenceIds;
//    TSequences sequences;
//
//    double before = sysTime();
//    std::cerr << "READING\tWHOLE\tOWNER";
//    std::cerr << "\tmultiseq" << std::flush;
//
//    MultiSeqFile multiSeqFile;
//    if (!open(multiSeqFile.concat, filename, OPEN_RDONLY))
//    {
//        std::cerr << std::endl << "Could not open mmap file for reading." << std::endl;
//        return 1;
//    }
//
//    AutoSeqFormat format;
//    guessFormat(multiSeqFile.concat, format);
//    split(multiSeqFile, format);
//
//    unsigned seqCount = length(multiSeqFile);
//    StringSet<TSequence> seqs;
//    StringSet<CharString> seqIDs;
//    reserve(seqs, seqCount, Exact());
//    reserve(seqIDs, seqCount, Exact());
//
//    TSequence seq;
//    // CharString qual;
//    CharString id;
//    for (unsigned i = 0; i < seqCount; ++i)
//    {
//        assignSeq(seq, multiSeqFile[i], format);    // read sequence
//        // assignQual(qual, multiSeqFile[i], format);  // read ascii quality values
//        assignSeqId(id, multiSeqFile[i], format);   // read sequence id
//
//        // convert ascii to values from 0..62
//        // store dna and quality together in Dna5Q
//        // for (unsigned j = 0; j < length(qual) && j < length(seq); ++j)
//        //     assignQualityValue(seq[j], (int)(ordValue(qual[j]) - 33));
//        // we use reserve and append, as assign is not supported
//        // by StringSet<..., Owner<ConcatDirect<> > >
//        appendValue(seqs, seq, Generous());
//        appendValue(seqIDs, id, Generous());
//    }
//
//    double after = sysTime();
//    fprintf(stderr, "\t%f\n", after - before);
//    return 0;
//}

template <typename TSpec>
int readFileMMapDocument(char const * filename, Options const & /*options*/, TSpec const & /*tag*/)
{
    typedef StringSet<CharString, TSpec> TSequenceIds;
    typedef StringSet<TSequence, TSpec> TSequences;
//     typedef typename Iterator<TSequenceIds>::Type TSequenceIdsIter;
//     typedef typename Iterator<TSequences>::Type TSequencesIter;
    TSequenceIds sequenceIds;
    TSequences sequences;

    double before = sysTime();
    std::cerr << "READING\tWHOLE\t";
    if (IsSameType<TSpec, Owner<> >::VALUE)
        std::cerr << "OWNER";
    else
        std::cerr << "CONCAT";
    std::cerr << "\tmmap" << std::flush;
    // fprintf(stderr, "\t%f\n", after - before);
    /*typedef File<Async<> > TFile;
    typedef String<char, MMap< ExternalConfig<TFile> > > TMMapString;
    TMMapString myString;
    if (!open(myString, filename, OPEN_RDONLY)) {
        std::cerr << std::endl << "Could not open mmap file for reading." << std::endl;
        return 1;
    }
    RecordReader<TMMapString, DoublePass<StringReader> > reader(myString, BUFFER_SIZE);
    */
    SeqFileIn reader(filename);
    readRecords(sequenceIds, sequences, reader);
    SEQAN_ASSERT_EQ(length(sequenceIds), length(sequences));

    // TSequenceIdsIter itId = begin(sequenceIds);
    // TSequencesIter itSeq = begin(sequences);
    // for (; !atEnd(itId); ++itId, ++itSeq) {
    //std::cout << value(itId) << "\t" << value(itSeq) << "\n";
    // }

    double after = sysTime();
    fprintf(stderr, "\t%f\n", after - before);
    return 0;
}

int readFileMMapDocument(char const * filename, Options const & options)
{
    if (options.nonConcat)
        return readFileMMapDocument(filename, options, Owner<Default>());

    //else
    //return readFileMMapDocument(filename, options, Owner<ConcatDirect<> >());
    return 0;
}

int readFastaFile(StringSet<CharString> & sequenceIds,
                  StringSet<TSequence> & sequences,
                  SeqFileIn & file)
{
    (void)sequenceIds;
    (void)sequences;

    CharString meta;
    TSequence seq;
    while (!atEnd(file))
        readRecord(meta, seq, file);

    return 0;
}

template <typename TFile>
int readFastaFile(StringSet<CharString> & sequenceIds,
                  StringSet<TSequence> & sequences,
                  TFile & file)
{
    (void)sequenceIds;
    (void)sequences;

    typename DirectionIterator<TFile, Input>::Type iter;
    iter = begin(file);

    CharString meta;
    TSequence seq;
    while (!atEnd(iter))
        readRecord(meta, seq, iter, Fasta());

    return 0;
}

void readFileMMap(char const * filename, Options const & /*options*/)
{
    StringSet<CharString> sequenceIds;
    StringSet<TSequence> sequences;

    double before = sysTime();
    std::cerr << "READING\tRECORD\t" << std::flush;

    typedef File<Async<> > TFile;
    String<char, MMap<ExternalConfig<TFile> > > myString;
    if (!open(myString, filename, OPEN_RDONLY))
    {
        std::cerr << std::endl << "Could not open mmap file for reading." << std::endl;
        return;
    }
    readFastaFile(sequenceIds, sequences, myString);

    double after = sysTime();
    fprintf(stderr, "\t%f\n", after - before);
}

void readFileDefault(char const * filename, Options const & options)
{
    StringSet<CharString> sequenceIds;
    StringSet<TSequence> sequences;

    std::cerr << "READING\tRECORD\t" << std::flush;
    double before = sysTime();
    if (options.cstdio)
    {
        std::cerr << "cstdio" << std::flush;
        FILE * f = fopen(filename, "rb");
        if (!f)
        {
            std::cerr << std::endl << "ERROR: Could not open input file!" << std::endl;
            return;
        }
        //readFastaFile(sequenceIds, sequences, f);
        fclose(f);
    }
    else if (options.fstream)
    {
        std::cerr << "fstream" << std::flush;
        std::ifstream f(filename, std::ios_base::in | std::ios_base::binary);
        if (!f.is_open())
        {
            std::cerr << std::endl << "ERROR: Could not open input file!" << std::endl;
            return;
        }
        //readFastaFile(sequenceIds, sequences, f);
#if SEQAN_HAS_ZLIB
    }
    else if (options.gzip)
    {
        std::cerr << "gzip" << std::flush;
        SeqFileIn f;
        if (!open(f, filename))
        {
            std::cerr << "Could not open input file!" << std::endl;
            return;
        }
        readFastaFile(sequenceIds, sequences, f);
#endif  // #if SEQAN_HAS_ZLIB
#if SEQAN_HAS_BZIP2
    }
    else if (options.bzip2)
    {
        std::cerr << "bzip2" << std::flush;
        SeqFileIn f;
        if (!open(f, filename))
        {
            std::cerr << "Could not open input file!" << std::endl;
            return;
        }
        //readFastaFile(sequenceIds, sequences, f);
#endif  // #if SEQAN_HAS_BZIP2
    }
    else
    {
        SEQAN_ASSERT_FAIL("SHOULD NEVER REACH HERE!");
    }
    double after = sysTime();
    fprintf(stderr, "\t%f\n", after - before);
}

int main(int argc, char const ** argv)
{
    Options options;

    // -----------------------------------------------------------------------
    // Setup Command Line Parser
    // -----------------------------------------------------------------------

    ArgumentParser parser("demo_benchmark_stream");
    setCategory(parser, "Demo");
    setShortDescription(parser, "Just a demo for a simple file io benchmark.");

    addUsageLine(parser, "benchmark_stream [OPTIONS] INPUT OUTPUT");
    addSection(parser, "Read Variant");
    addOption(parser, ArgParseOption("d", "double-pass", "Use double-pass parsing."));
    addSection(parser, "Stream Type Options");
    addOption(parser, ArgParseOption("c", "cstdio", "Use <cstdio> stream."));
    addOption(parser, ArgParseOption("f", "fstream", "Use <fstream> stream."));
#if SEQAN_HAS_ZLIB
    addOption(parser, ArgParseOption("g", "gzip", "Use gzip stream."));
#endif  // #if SEQAN_HAS_ZLIB
#if SEQAN_HAS_BZIP2
    addOption(parser, ArgParseOption("b", "bzip2", "Use bzlib stream."));
#endif  // #if SEQAN_HAS_BZIP2
    addOption(parser, ArgParseOption("m", "memory-mapped", "Use memory mapped I/O."));
    addOption(parser, ArgParseOption("w", "document-mmapped", "Read whole document at once with memory mapped I/O."));
    addOption(parser, ArgParseOption("n", "non-concat", "Do not use concat direct string for document-mmapped version."));
    addOption(parser, ArgParseOption("s", "multi-seq", "Use MultiSeqFile to read input."));

    addArgument(parser, ArgParseArgument(ArgParseArgument::INPUT_FILE, "IN"));

    // -----------------------------------------------------------------------
    // Parse And Check Command Line Parameters
    // -----------------------------------------------------------------------

    bool stop = !parse(parser, argc, argv);
    if (stop)
    {
        if (isSet(parser, "help"))
            return 0;

        return 1;
    }

    if (isSet(parser, "double-pass"))
        options.doublePass = true;
    if (isSet(parser, "cstdio"))
        options.cstdio = true;
    if (isSet(parser, "fstream"))
        options.fstream = true;
#if SEQAN_HAS_ZLIB
    if (isSet(parser, "gzip"))
        options.gzip = true;
#endif  // #if SEQAN_HAS_ZLIB
#if SEQAN_HAS_BZIP2
    if (isSet(parser, "bzip2"))
        options.bzip2 = true;
#endif  // #if SEQAN_HAS_BZIP2
    if (isSet(parser, "memory-mapped"))
        options.mmapString = true;
    if (isSet(parser, "document-mmapped"))
        options.documentMMap = true;
    if (isSet(parser, "non-concat"))
        options.nonConcat = true;
    if (isSet(parser, "multi-seq"))
        options.multiSeq = true;

    if (options.cstdio + options.fstream + options.gzip + options.bzip2 + options.mmapString +
        options.documentMMap + options.multiSeq == 0)
    {
        std::cerr << "You have to select exactly one stream type!" << std::endl;
        return 1;
    }
    else if (options.cstdio + options.fstream + options.gzip + options.bzip2 + options.mmapString + options.documentMMap > 1)
    {
        std::cerr << "Only one stream type can be selected!" << std::endl;
        return 1;
    }
    if (options.documentMMap && options.doublePass)
    {
        std::cerr << "Double-pass I/O is implicit with document-mapped." << std::endl;
        return 1;
    }

    // -----------------------------------------------------------------------
    // Read And Write FASTA file.
    // -----------------------------------------------------------------------
    String<char> inputFileName;
    getArgumentValue(inputFileName, parser, 0);

    if (options.multiSeq)
    {
        //readFileMultiSeqFile(toCString(getArgumentValue(parser, 0)), options);
    }
    else if (options.documentMMap)
    {
        readFileMMapDocument(toCString(inputFileName), options);
    }
    else
    {
        if (options.mmapString)
            ;
        //readFileMMap(toCString(inputFileName), options);
        else
            readFileDefault(toCString(inputFileName), options);
    }

    // for (unsigned i = 0; i < length(sequenceIds); ++i) {
    //     std::cerr << '>' << sequenceIds[i] << '\n';
    //     std::cerr << sequences[i] << '\n';
    // }

    return 0;
}
