/usr/include/OpenMS/SIMULATION/DigestSimulation.h is in libopenms-dev 1.11.1-5.
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// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// 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.
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------
#ifndef OPENMS_SIMULATION_DIGESTSIMULATION_H
#define OPENMS_SIMULATION_DIGESTSIMULATION_H
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/SIMULATION/SimTypes.h>
namespace OpenMS
{
/**
@brief Simulates protein digestion
Supports all enzymes supported by EnzymaticDigestion.h
and additionally incorporates abundance values, which
are distributed evenly among digestion products of each
protein.
@htmlinclude OpenMS_DigestSimulation.parameters
@ingroup Simulation
*/
class OPENMS_DLLAPI DigestSimulation :
public DefaultParamHandler
{
public:
/** @name Constructors and Destructors
*/
//@{
/// Default constructor
DigestSimulation();
/// Copy constructor
DigestSimulation(const DigestSimulation & source);
/// Destructor
virtual ~DigestSimulation();
//@}
/// Assignment operator
DigestSimulation & operator=(const DigestSimulation & source);
/**
@brief Digest a set of proteins into peptides
Digest proteins to peptides, with protein abundance distributes equally among
created sibling peptides (this also applies for peptides with missed cleavages).
Should a peptide be non-unique the abundances of its instances from proteins are summed up.
@param feature_map Input FeatureMap containing the proteins that should be digested as ProteinIdentification
**/
void digest(FeatureMapSim & feature_map);
private:
/// set defaults
void setDefaultParams_();
};
}
#endif
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