SvmTheoreticalSpectrumGenerator.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 2002-2021.
//
// 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: Sandro Andreotti $
// --------------------------------------------------------------------------
 
 
#pragma once
 
#include <OpenMS/config.h>
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
#include <OpenMS/ANALYSIS/SVM/SVMWrapper.h>
 
#include <OpenMS/KERNEL/StandardDeclarations.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
#include <boost/random/mersenne_twister.hpp>
 
 
 
namespace OpenMS
{
  class OPENMS_DLLAPI SvmTheoreticalSpectrumGenerator :
    public DefaultParamHandler
  {
    friend class SvmTheoreticalSpectrumGeneratorTrainer;
public:
 
    struct IonType
    {
      Residue::ResidueType residue;
      EmpiricalFormula loss;
      Int charge;
 
      //Default constructor
      IonType() :
        residue((Residue::ResidueType) 0),
        loss(),
        charge(0)
      {
      }
 
      //Custom constructor
      IonType(Residue::ResidueType local_residue, EmpiricalFormula local_loss = EmpiricalFormula(), Int local_charge = 1) :
        residue(local_residue),
        loss(local_loss),
        charge(local_charge)
      {
      }
 
      //Copy constructor
      IonType(const IonType & rhs) :
        residue(rhs.residue),
        loss(rhs.loss),
        charge(rhs.charge)
      {
      }
 
      //Assignment operator
      IonType & operator=(const IonType & rhs)
      {
        if (this != &rhs)
        {
          residue = rhs.residue;
          loss = rhs.loss;
          charge = rhs.charge;
        }
        return *this;
      }
 
      bool operator<(const IonType & rhs) const
      {
        if (residue != rhs.residue)
          return residue < rhs.residue;
        else if (loss.toString() != rhs.loss.toString())
          return loss.toString() < rhs.loss.toString();
        else
          return charge < rhs.charge;
      }
 
    };
 
    struct SvmModelParameterSet
    {
      //pointers to the svm classification models (one per ion_type)
      std::vector<boost::shared_ptr<SVMWrapper> > class_models;
 
      //pointers to the svm regression models (one per ion_type)
      std::vector<boost::shared_ptr<SVMWrapper> > reg_models;
 
      //The intensity for each ion type for the SVC mode
      std::map<Residue::ResidueType, double> static_intensities;
 
      //The selected primary IonTypes
      std::vector<IonType> ion_types;
 
      //The selected secondary IonTypes
      std::map<IonType, std::vector<IonType> > secondary_types;
 
      //The number of intensity levels
      Size number_intensity_levels;
 
      //The number of regions for every spectrum
      Size number_regions;
 
      //upper limits (required for scaling)
      std::vector<double> feature_max;
 
      //lower limits (required for scaling)
      std::vector<double> feature_min;
 
      //lower bound for scaling
      double scaling_lower;
 
      //upper bound for scaling
      double scaling_upper;
 
      //border values for binning secondary types intensity
      std::vector<double> intensity_bin_boarders;
 
      //intensity values for binned secondary types intensity
      std::vector<double> intensity_bin_values;
 
      //conditional probabilities for secondary types
      std::map<std::pair<IonType, Size>, std::vector<std::vector<double> > > conditional_prob;
    };
 
 
 
    SvmTheoreticalSpectrumGenerator();
 
    SvmTheoreticalSpectrumGenerator(const SvmTheoreticalSpectrumGenerator & source);
 
    SvmTheoreticalSpectrumGenerator & operator=(const SvmTheoreticalSpectrumGenerator & tsg);
 
 
    ~SvmTheoreticalSpectrumGenerator() override;
 
 
    void simulate(PeakSpectrum & spectrum, const AASequence & peptide, boost::random::mt19937_64& rng, Size precursor_charge);
 
    void load();
 
    const std::vector<IonType> & getIonTypes() const
    {
      return mp_.ion_types;
    }
 
protected:
    struct DescriptorSet
    {
      typedef std::vector<svm_node> DescriptorSetType;
      DescriptorSetType descriptors;
    };
 
    typedef std::map<IonType, double> IntensityMap;
 
    Size precursor_charge_;
 
    SvmModelParameterSet mp_;
 
    static std::map<String, Size> aa_to_index_;
 
    static std::map<String, double> hydrophobicity_;
 
    static std::map<String, double> helicity_;
 
    static std::map<String, double> basicity_;
 
    std::map<IonType, bool> hide_type_;
 
    inline void scaleSingleFeature_(double & value, double feature_min, double feature_max, double lower = -1.0, double upper = 1.0);
 
    void scaleDescriptorSet_(DescriptorSet & desc, double lower, double upper);
 
    Size generateDescriptorSet_(AASequence peptide, Size position, IonType type, Size precursor_charge, DescriptorSet & desc_set);
 
    String ResidueTypeToString_(Residue::ResidueType type);
 
    static void initializeMaps_();
 
    static bool initializedMaps_;
 
    void updateMembers_() override;
  };
 
  void inline SvmTheoreticalSpectrumGenerator::scaleSingleFeature_(double & value, double lower, double upper, double feature_min, double feature_max)
  {
    double prev = value;
    if (feature_max == feature_min)
    {
      return;
    }
 
    if (value <= feature_min)
    {
      value = lower;
    }
    else if (value >= feature_max)
    {
      value = upper;
    }
    else
    {
      value = lower + (upper - lower) *
              (value - feature_min) /
              (feature_max - feature_min);
    }
 
    if (value < 0)
    {
      std::cerr << "negative value!! " << value << "  l: " << lower << " u: " << upper << " fm: " << feature_min << " fma: " << feature_max << "  prev: " << prev << std::endl;
    }
  }
 
} // namespace OpenMS