O18Labeler.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: Stephan Aiche $
// $Authors: Stephan Aiche$
// --------------------------------------------------------------------------

#ifndef OPENMS_SIMULATION_LABELING_O18LABELER_H
#define OPENMS_SIMULATION_LABELING_O18LABELER_H

#include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>

namespace OpenMS
{

  class OPENMS_DLLAPI O18Labeler :
    public BaseLabeler
  {
public:

    O18Labeler();

    virtual ~O18Labeler();

    static BaseLabeler* create()
    {
      return new O18Labeler();
    }

    static const String getProductName()
    {
      return "o18";
    }

    // redeclaration of virtual methods
    void preCheck(Param& param) const;

    void setUpHook(FeatureMapSimVector& /* channels */);

    void postDigestHook(FeatureMapSimVector& /* features_to_simulate */);

    void postRTHook(FeatureMapSimVector& /* features_to_simulate */);

    void postDetectabilityHook(FeatureMapSimVector& /* features_to_simulate */);

    void postIonizationHook(FeatureMapSimVector& /* features_to_simulate */);

    void postRawMSHook(FeatureMapSimVector& /* features_to_simulate */);

    void postRawTandemMSHook(FeatureMapSimVector& /* features_to_simulate */, MSSimExperiment& /* simulated map */);

protected:
    void addModificationToPeptideHit_(Feature& feature, const String& modification) const;

    Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index) const;

private:
    static const int LIGHT_CHANNEL_ID_;
    static const int MEDIUM_CHANNEL_ID_;
    static const int HEAVY_CHANNEL_ID_;
  };
} // namespace OpenMS

#endif //#ifndef OPENMS_SIMULATION_LABELING_O18LABELER_H