/usr/include/OpenMS/TRANSFORMATIONS/FEATUREFINDER/BaseModel.h is in libopenms-dev 1.11.1-3.
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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: Clemens Groepl $
// $Authors: $
// --------------------------------------------------------------------------
#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_BASEMODEL_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_BASEMODEL_H
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/DPeak.h>
namespace OpenMS
{
/**
@brief Abstract base class for all D-dimensional models.
Every derived class has to implement the static functions
"T* create()" and "const String getProductName()" (see DefaultParamHandler for details)
*/
template <UInt D>
class BaseModel :
public DefaultParamHandler
{
public:
typedef DoubleReal IntensityType;
typedef DoubleReal CoordinateType;
typedef DPosition<D> PositionType;
typedef typename DPeak<D>::Type PeakType;
typedef std::vector<PeakType> SamplesType;
/// Default constructor.
BaseModel() :
DefaultParamHandler("BaseModel")
{
defaults_.setValue("cutoff", 0.0, "Low intensity cutoff of the model. Peaks below this intensity are not considered part of the model.");
}
/// copy constructor
BaseModel(const BaseModel & source) :
DefaultParamHandler(source),
cut_off_(source.cut_off_)
{
}
/// Destructor
virtual ~BaseModel()
{
}
/// assignment operator
virtual BaseModel & operator=(const BaseModel & source)
{
if (&source == this) return *this;
DefaultParamHandler::operator=(source);
cut_off_ = source.cut_off_;
return *this;
}
/// register all derived classes here (implemented in file BaseModel_impl.h)
static void registerChildren();
/// access model predicted intensity at position @p pos
virtual IntensityType getIntensity(const PositionType & pos) const = 0;
/// check if position @p pos is part of the model regarding the models cut-off.
virtual bool isContained(const PositionType & pos) const
{
return getIntensity(pos) >= cut_off_;
}
/**@brief Convenience function to set the intensity of a peak to the
predicted intensity at its current position, calling virtual void
getIntensity().
*/
template <typename PeakType>
void fillIntensity(PeakType & peak) const
{
peak.setIntensity(getIntensity(peak.getPosition()));
}
/**@brief Convenience function that applies fillIntensity() to an iterator
range.
*/
template <class PeakIterator>
void fillIntensities(PeakIterator begin, PeakIterator end) const
{
for (PeakIterator it = begin; it != end; ++it)
{
fillIntensity(*it);
}
}
/// get cutoff value
virtual IntensityType getCutOff() const
{
return cut_off_;
}
/// set cutoff value
virtual void setCutOff(IntensityType cut_off)
{
cut_off_ = cut_off;
param_.setValue("cutoff", cut_off_);
}
/// get reasonable set of samples from the model (i.e. for printing)
virtual void getSamples(SamplesType & cont) const = 0;
/// fill stream with reasonable set of samples from the model (i.e. for printing)
virtual void getSamples(std::ostream & os)
{
SamplesType samples;
getSamples(samples);
for (typename SamplesType::const_iterator it = samples.begin(); it != samples.end(); ++it)
{
os << *it << std::endl;
}
}
protected:
IntensityType cut_off_;
virtual void updateMembers_()
{
cut_off_ = (double)param_.getValue("cutoff");
}
};
}
#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_BASEMODEL_H
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