// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2016, 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.
//
// ==========================================================================

#ifndef SEQAN_HEADER_GRAPH_UTILITY_PARSING_H
#define SEQAN_HEADER_GRAPH_UTILITY_PARSING_H


#include <fstream>

namespace seqan
{

//////////////////////////////////////////////////////////////////////////////
// File reading
//////////////////////////////////////////////////////////////////////////////

//////////////////////////////////////////////////////////////////////////////

//////////////////////////////////////////////////////////////////////////////

// This is unused and a deletion candidate.
// TODO(singer): Remove this!
/*
template<typename TPath, typename TStringSet, typename TNames>
inline unsigned int
_loadSequences(TPath const& in_path,
               TStringSet& origStrSet,
               TNames& names)
{
//IOREV _nodoc_ uses custom IO, with ifstream, should be adapted to File()
    typedef typename Size<TStringSet>::Type TSize;

    // Count sequences and read names
    TSize seqCount = 0;
    std::ifstream file;
    std::stringstream input;
    input << in_path;
    file.open(input.str().c_str(), std::ios_base::in | std::ios_base::binary);
    if (!file.is_open()) return 0;
    while (!file.eof()) {
        String<char> id;
        readID(file, id, Fasta());
        appendValue(names, id);
        goNext(file, Fasta());
        ++seqCount;
    }

    // Load sequences
    file.clear();
    file.seekg(0, std::ios_base::beg);
    resize(origStrSet, seqCount);
    TSize count = 0;
    for(TSize i = 0; (i < seqCount) && !file.eof(); ++i)     {
        read(file, origStrSet[i], Fasta());
        count += length(origStrSet[i]);
    }
    file.close();

    return count;
}
*/

}// namespace seqan

#endif //#ifndef SEQAN_HEADER_...
