BaseLabeler.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 2002-2023.
//
// 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: Stephan Aiche, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
#include <OpenMS/KERNEL/ConsensusMap.h>
 
#include <OpenMS/SIMULATION/SimTypes.h>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI BaseLabeler :
    public DefaultParamHandler
  {
public:
 
    BaseLabeler();
 
    ~BaseLabeler() override;
 
    static void registerChildren();
 
    virtual Param getDefaultParameters() const;
 
    virtual void setRnd(SimTypes::MutableSimRandomNumberGeneratorPtr rng);
 
    virtual void preCheck(Param& param) const = 0;
 
 
    virtual void setUpHook(SimTypes::FeatureMapSimVector& /* features */) = 0;
 
    virtual void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
 
    virtual void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
 
    virtual void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
 
    virtual void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
 
    virtual void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
 
    virtual void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) = 0;
 
 
    ConsensusMap& getConsensus();
 
    const String& getDescription() const;
 
    String getChannelIntensityName(const Size channel_index) const;
 
 
protected:
    SimTypes::FeatureMapSim mergeProteinIdentificationsMaps_(const SimTypes::FeatureMapSimVector& maps);
 
    void mergeProteinAccessions_(Feature& target, const Feature& source) const;
 
    void recomputeConsensus_(const SimTypes::FeatureMapSim& simulated_features);
 
 
    ConsensusMap consensus_;
 
    SimTypes::MutableSimRandomNumberGeneratorPtr rng_;
 
    String channel_description_;
 
  };
} // namespace OpenMS