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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.
//
// --------------------------------------------------------------------------
// $Maintainer: Stephan Aiche$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------
#ifndef OPENMS_SIMULATION_DETECTABILITYSIMULATION_H
#define OPENMS_SIMULATION_DETECTABILITYSIMULATION_H
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/SIMULATION/SimTypes.h>
namespace OpenMS
{
/**
@brief Simulates peptide detectability
The peptide detectability is predicted based on a support-vector machine. Alternativly
the detectability can be set to a default value for all peptides if no model is given.
@htmlinclude OpenMS_DetectabilitySimulation.parameters
@ingroup Simulation
*/
class OPENMS_DLLAPI DetectabilitySimulation :
public DefaultParamHandler
{
public:
/** @name Constructors and Destructors
*/
//@{
/// Constructor taking a random generator
DetectabilitySimulation();
/// Copy constructor
DetectabilitySimulation(const DetectabilitySimulation & source);
/// Destructor
virtual ~DetectabilitySimulation();
//@}
/// Assignment operator
DetectabilitySimulation & operator=(const DetectabilitySimulation & source);
/**
@brief Filters the given peptide features for detectibility
Based on the provided method (SVM or simple) all peptide features are
removed that do not have a sufficient peptide detectibility.
@param features Feature map that will be filtered for detectibility
*/
void filterDetectability(FeatureMapSim & features);
void predictDetectabilities(std::vector<String> & peptides_vector, std::vector<DoubleReal> & labels,
std::vector<DoubleReal> & detectabilities);
private:
/// Set default parameters
void setDefaultParams_();
/// Synchronize members with param class
void updateMembers_();
/// Minimum allowed detectability likelihood of a peptide
DoubleReal min_detect_;
/// Name of the svm model file
OpenMS::String dt_model_file_;
protected:
/// Filter the feature map using a svm model
void svmFilter_(FeatureMapSim &);
/// Do not filter the feature map, just set the detectability to a default value
void noFilter_(FeatureMapSim &);
};
}
#endif
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