SpectrumAlignment.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
//
// 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: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
//
#ifndef OPENMS_COMPARISON_SPECTRA_SPECTRUMALIGNMENT_H
#define OPENMS_COMPARISON_SPECTRA_SPECTRUMALIGNMENT_H

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

#include <vector>
#include <map>
#include <utility>
#include <algorithm>

#define ALIGNMENT_DEBUG
#undef  ALIGNMENT_DEBUG

namespace OpenMS
{

  class OPENMS_DLLAPI SpectrumAlignment :
    public DefaultParamHandler
  {
public:

    // @name Constructors and Destructors
    // @{
    SpectrumAlignment();

    SpectrumAlignment(const SpectrumAlignment & source);

    virtual ~SpectrumAlignment();

    SpectrumAlignment & operator=(const SpectrumAlignment & source);
    // @}

    template <typename SpectrumType>
    void getSpectrumAlignment(std::vector<std::pair<Size, Size> > & alignment, const SpectrumType & s1, const SpectrumType & s2) const
    {
      if (!s1.isSorted() || !s2.isSorted())
      {
        throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Input to SpectrumAlignment is not sorted!");
      }
      // clear result
      alignment.clear();

      double tolerance = (double)param_.getValue("tolerance");
      std::map<Size, std::map<Size, std::pair<Size, Size> > > traceback;
      std::map<Size, std::map<Size, double> > matrix;

      // init the matrix with "gap costs" tolerance
      matrix[0][0] = 0;
      for (Size i = 1; i <= s1.size(); ++i)
      {
        matrix[i][0] = i * tolerance;
        traceback[i][0]  = std::make_pair(i - 1, 0);
      }
      for (Size j = 1; j <= s2.size(); ++j)
      {
        matrix[0][j] = j * tolerance;
        traceback[0][j] = std::make_pair(0, j - 1);
      }

      // fill in the matrix
      Size left_ptr(1);
      Size last_i(0), last_j(0);

      //Size off_band_counter(0);
      for (Size i = 1; i <= s1.size(); ++i)
      {
        double pos1(s1[i - 1].getMZ());

        for (Size j = left_ptr; j <= s2.size(); ++j)
        {
          bool off_band(false);
          // find min of the three possible directions
          double pos2(s2[j - 1].getMZ());
          double diff_align = fabs(pos1 - pos2);

          // running off the right border of the band?
          if (pos2 > pos1 && diff_align > tolerance)
          {
            if (i < s1.size() && j < s2.size() && s1[i].getMZ() < pos2)
            {
              off_band = true;
            }
          }

          // can we tighten the left border of the band?
          if (pos1 > pos2 && diff_align > tolerance && j > left_ptr + 1)
          {
            ++left_ptr;
          }

          double score_align = diff_align;

          if (matrix.find(i - 1) != matrix.end() && matrix[i - 1].find(j - 1) != matrix[i - 1].end())
          {
            score_align += matrix[i - 1][j - 1];
          }
          else
          {
            score_align += (i - 1 + j - 1) * tolerance;
          }

          double score_up = tolerance;
          if (matrix.find(i) != matrix.end() && matrix[i].find(j - 1) != matrix[i].end())
          {
            score_up += matrix[i][j - 1];
          }
          else
          {
            score_up += (i + j - 1) * tolerance;
          }

          double score_left = tolerance;
          if (matrix.find(i - 1) != matrix.end() && matrix[i - 1].find(j) != matrix[i - 1].end())
          {
            score_left += matrix[i - 1][j];
          }
          else
          {
            score_left += (i - 1 + j) * tolerance;
          }

#ifdef ALIGNMENT_DEBUG
          cerr << i << " " << j << " " << left_ptr << " " << pos1 << " " << pos2 << " " << score_align << " " << score_left << " " << score_up << endl;
#endif

          if (score_align <= score_up && score_align <= score_left && diff_align <= tolerance)
          {
            matrix[i][j] = score_align;
            traceback[i][j] = std::make_pair(i - 1, j - 1);
            last_i = i;
            last_j = j;
          }
          else
          {
            if (score_up <= score_left)
            {
              matrix[i][j] = score_up;
              traceback[i][j] = std::make_pair(i, j - 1);
            }
            else
            {
              matrix[i][j] = score_left;
              traceback[i][j] = std::make_pair(i - 1, j);
            }
          }

          if (off_band)
          {
            break;
          }
        }
      }

      //last_i = s1.size() + 1;
      //last_j = s2.size() + 1;

      //cerr << last_i << " " << last_j << endl;

#ifdef ALIGNMENT_DEBUG
#if 0
      cerr << "TheMatrix: " << endl << " \t  \t";
      for (Size j = 0; j != s2.size(); ++j)
      {
        cerr << s2[j].getPosition()[0] << " \t";
      }
      cerr << endl;
      for (Size i = 0; i <= s1.size(); ++i)
      {
        if (i != 0)
        {
          cerr << s1[i - 1].getPosition()[0] << " \t";
        }
        else
        {
          cerr << " \t";
        }
        for (Size j = 0; j <= s2.size(); ++j)
        {
          if (matrix.has(i) && matrix[i].has(j))
          {
            if (traceback[i][j].first == i - 1 && traceback[i][j].second == j - 1)
            {
              cerr << "\\";
            }
            else
            {
              if (traceback[i][j].first == i - 1 && traceback[i][j].second == j)
              {
                cerr << "|";
              }
              else
              {
                cerr << "-";
              }
            }

            cerr << matrix[i][j] << "  \t";
          }
          else
          {
            cerr << "-1  \t";
          }
        }
        cerr << endl;
      }
#endif
#endif

      // do traceback
      Size i = last_i;
      Size j = last_j;

      while (i >= 1 && j >= 1)
      {
        if (traceback[i][j].first == i - 1 && traceback[i][j].second == j - 1)
        {
          alignment.push_back(std::make_pair(i - 1, j - 1));
        }
        Size new_i = traceback[i][j].first;
        Size new_j = traceback[i][j].second;

        i = new_i;
        j = new_j;
      }

      std::reverse(alignment.begin(), alignment.end());

#ifdef ALIGNMENT_DEBUG
#if 0
      // print alignment
      cerr << "Alignment (size=" << alignment.size() << "): " << endl;

      Size i_s1(0), i_s2(0);
      for (vector<pair<Size, Size> >::const_reverse_iterator it = alignment.rbegin(); it != alignment.rend(); ++it, ++i_s1, ++i_s2)
      {
        while (i_s1 < it->first - 1)
        {
          cerr << i_s1 << " " << s1[i_s1].getPosition()[0] << " " << s1[i_s1].getIntensity() << endl;
          i_s1++;
        }
        while (i_s2 < it->second - 1)
        {
          cerr << " \t " <<  i_s2 << " " << s2[i_s2].getPosition()[0] << " " << s2[i_s2].getIntensity() << endl;
          i_s2++;
        }
        cerr << "(" << s1[it->first - 1].getPosition()[0] << " <-> " << s2[it->second - 1].getPosition()[0] << ") ("
             << it->first << "|" << it->second << ") (" << s1[it->first - 1].getIntensity() << "|" << s2[it->second - 1].getIntensity() << ")" << endl;
      }
#endif
#endif

    }

  };

}
#endif //OPENMS_COMPARISON_SPECTRA_SPECTRUMALIGNMENT_H