/usr/include/OpenMS/ANALYSIS/MAPMATCHING/LabeledPairFinder.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;
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// --------------------------------------------------------------------------
// $Maintainer: $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
#ifndef OPENMS_ANALYSIS_MAPMATCHING_LABELEDPAIRFINDER_H
#define OPENMS_ANALYSIS_MAPMATCHING_LABELEDPAIRFINDER_H
#include <OpenMS/ANALYSIS/MAPMATCHING/BaseGroupFinder.h>
#include <boost/math/tr1.hpp>
#include <cmath>
namespace OpenMS
{
/**
@brief The LabeledPairFinder allows the matching of labeled features (features with a fixed distance).
Finds feature pairs that have a defined distance in RT and m/z in the same map.
@htmlinclude OpenMS_LabeledPairFinder.parameters
@todo Implement support for labled MRM experiments, Q1 m/z value and charges. (Andreas)
@todo Implement support for more than one mass delta, e.g. from missed cleavages and so on (Andreas)
@ingroup FeatureGrouping
*/
class OPENMS_DLLAPI LabeledPairFinder :
public BaseGroupFinder
{
public:
/// Default constructor
LabeledPairFinder();
/// Destructor
inline virtual ~LabeledPairFinder()
{
}
/// Returns an instance of this class
static BaseGroupFinder * create()
{
return new LabeledPairFinder();
}
/// Returns the name of this module
static const String getProductName()
{
return "labeled_pair_finder";
}
/**
@brief Run the algorithm
@note Exactly one @em input map has to be provided.
@note The @em output map has to have two file descriptions, containing
the same file name. The file descriptions have to be labeled 'heavy' and 'light'.
@exception Exception::IllegalArgument is thrown if the input data is not valid.
*/
virtual void run(const std::vector<ConsensusMap> & input_maps, ConsensusMap & result_map);
protected:
/// return the p-value at position x for the bi-Gaussian distribution with mean @p m and standard deviation @p sig1 (left) and @p sig2 (right)
inline DoubleReal PValue_(DoubleReal x, DoubleReal m, DoubleReal sig1, DoubleReal sig2)
{
if (m < x)
{
return 1 - boost::math::tr1::erf((x - m) / sig2 / 0.707106781);
}
else
{
return 1 - boost::math::tr1::erf((m - x) / sig1 / 0.707106781);
}
}
private:
/// Copy constructor not implemented => private
LabeledPairFinder(const LabeledPairFinder & source);
/// Assignment operator not implemented => private
LabeledPairFinder & operator=(const LabeledPairFinder & source);
}; // end of class LabeledPairFinder
} // end of namespace OpenMS
#endif // OPENMS_ANALYSIS_MAPMATCHER_LABELEDPAIRFINDER_H
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