/usr/include/OpenMS/ANALYSIS/MRM/MRMFragmentSelection.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:
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// 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.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// --------------------------------------------------------------------------
// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
#ifndef OPENMS_ANALYSIS_MRM_MRMFRAGMENTSELECTION_H
#define OPENMS_ANALYSIS_MRM_MRMFRAGMENTSELECTION_H
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <vector>
namespace OpenMS
{
/**
@brief This class can select appropriate fragment ions of an MS/MS spectrum of a peptide
@htmlinclude OpenMS_MRMFragmentSelection.parameters
Several user choices can influence the selection of the ions from the MS/MS spectrum. These
choices can be done using the parameters as described on the parameters page (see below).
Basically there are two different ways of selecting suitable ions. One, using standardized
names, e.g. given in the meta value "IonName" of each peaks of the spectrum (this can be
written from TheoreticalSpectrumGenerator, PILISModel...). The second one is simply using
the most abundant peaks in a specified m/z range.
@ingroup Analysis_MRM
*/
class OPENMS_DLLAPI MRMFragmentSelection :
public DefaultParamHandler
{
public:
/** @name Constructors and destructors
*/
//@{
/// default constructor
MRMFragmentSelection();
/// copy constructor
MRMFragmentSelection(const MRMFragmentSelection & rhs);
/// destructor
virtual ~MRMFragmentSelection();
//@}
/// assignment operator
MRMFragmentSelection & operator=(const MRMFragmentSelection & rhs);
/// selects accordingly to the parameters the best peaks of spec and writes them into selected_peaks
void selectFragments(std::vector<RichPeak1D> & selected_peaks, const RichPeakSpectrum & spec);
protected:
/// returns true if the selection of peak is allowed, according to the parameters set
bool peakselectionIsAllowed_(const RichPeak1D & peak);
};
}
#endif
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