text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2015.
  //
  // This software is released under a three-clause BSD license:
  //  * 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 any author or any participating institution
  //    may be used to endorse or promote products derived from this software
  //    without specific prior written permission.
  // For a full list of authors, refer to the file AUTHORS.
  // --------------------------------------------------------------------------
  // 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 ANY OF THE AUTHORS OR THE CONTRIBUTING
  // INSTITUTIONS 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.
  //
  // --------------------------------------------------------------------------
  // $Maintainer: Clemens Groepl,Andreas Bertsch$
  // $Authors: $
  // --------------------------------------------------------------------------
  
  #include <OpenMS/DATASTRUCTURES/BigString.h>
  #include <OpenMS/CONCEPT/Exception.h>
  #include <OpenMS/config.h>
  
  #include <iostream>
  
  namespace OpenMS
  {
  
    typedef std::pair<String, String> FASTAEntry;
  
    BigString::BigString() :
      big_string_("$"),
      separator_('$'),
      count_(1),
      len_(1)
    {
      sep_indices_.push_back(0);
      FASTA_header_.push_back("");
    }
  
    BigString::BigString(const BigString& bs) :
      big_string_(bs.big_string_),
      separator_(bs.separator_),
      count_(bs.count_),
      len_(bs.len_),
      sep_indices_(bs.sep_indices_),
      FASTA_header_(bs.FASTA_header_)
    {
  
    }
  
    BigString::~BigString()
    {
  
    }
  
    void BigString::add(FASTAEntry const& new_entry)
    {
      big_string_ += new_entry.second;
      big_string_ += separator_;
      ++count_;
      len_ += new_entry.second.length() + 1;
      sep_indices_.push_back(len_ - 1);
      FASTA_header_.push_back(new_entry.first);
    }
  
    void BigString::setSeparator(const char sep)
    {
      separator_ = sep;
    }
  
    char BigString::getSeparator()
    {
      return separator_;
    }
  
    Size BigString::size()
    {
      return count_;
    }
  
    Size BigString::length()
    {
      return len_;
    }
  
    void BigString::getPeptide(FASTAEntry& entry, Size start, Size length)
    {
      Size index_start = getIndex_(start);
      if (index_start != getIndex_(start + length))
      {
        throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "desired peptide is part of 2 fasta entries", "");
      }
      entry.first = FASTA_header_[index_start];
      entry.second = big_string_.substr(start, length);
      return;
    }
  
    const String& BigString::getBigString() const
    {
      return big_string_;
    }
  
    Size BigString::getIndex_(Size index, Size start, Size end)
    {
      if (end - start <= 1)
      {
        if (sep_indices_[start] >= index)
        {
          return start;
        }
        else
        {
          return start + 1;
        }
      }
      Size half = (Size) ((end - start) / 2) + start;
  
      if (index > sep_indices_[half])
      {
        return getIndex_(index, half, end);
      }
      else if (index < sep_indices_[half])
      {
        return getIndex_(index, start, half);
      }
      else
      {
        return half;
      }
    }
  
    Size BigString::getIndex_(Size index)
    {
      return getIndex_(index, 0, sep_indices_.size());
    }
  
  }
  