MRMIonSeries.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 2002-2017.
//
// 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: George Rosenberger $
// $Authors: George Rosenberger $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_OPENSWATH_MRMIONSERIES_H
#define OPENMS_ANALYSIS_OPENSWATH_MRMIONSERIES_H

#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/MATH/MISC/MathFunctions.h>
#include <boost/unordered_map.hpp>
#include <boost/assign.hpp>
#include <boost/lexical_cast.hpp>

// #define DEBUG_MRMIONSERIES

namespace OpenMS
{
  class OPENMS_DLLAPI MRMIonSeries
  {
private:
    TargetedExperiment::Interpretation annotationToCVTermList_(String annotation);

    void annotationToCV_(ReactionMonitoringTransition& tr);

public:
    MRMIonSeries();

    ~MRMIonSeries();

    typedef boost::unordered_map<String, double> IonSeries;

    std::pair<String, double> getIon(IonSeries ionseries, String ionid);

    std::pair<String, double> annotateIon(IonSeries ionseries, double ProductMZ, double mz_threshold);

    void annotateTransitionCV(ReactionMonitoringTransition& tr, String annotation);

    void annotateTransition(ReactionMonitoringTransition& tr, const TargetedExperiment::Peptide peptide, const double precursor_mz_threshold, const double product_mz_threshold, bool enable_reannotation, std::vector<String> fragment_types, std::vector<size_t> fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, int round_decPow = -4);

    IonSeries getIonSeries(AASequence sequence, size_t precursor_charge, std::vector<String> fragment_types, std::vector<size_t> fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, int round_decPow = -4);
  };
}

#endif