/usr/include/OpenMS/ANALYSIS/MRM/MRMFragmentSelection.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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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
libopenms-dev 1.11.1-5 / usr / include / OpenMS / ANALYSIS / MRM / MRMFragmentSelection.h
