DIAPrescoring.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Witold Wolski $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <algorithm>
#include <iterator>
#include <boost/bind.hpp>
#include <boost/lexical_cast.hpp>
 
#include <OpenMS/OPENSWATHALGO/DATAACCESS/DataFrameWriter.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI DiaPrescore :
    public DefaultParamHandler
  {
    double dia_extract_window_; //done
    int nr_isotopes_;
    int nr_charges_;
public:
 
    DiaPrescore();
 
    DiaPrescore(double dia_extract_window, int nr_isotopes = 4, int nr_charges = 4);
 
    void defineDefaults();
 
    void updateMembers_() override;
 
    void score(OpenSwath::SpectrumPtr spec,
               const std::vector<OpenSwath::LightTransition>& lt,
               double& dotprod,
               double& manhattan);
 
    void operator()(OpenSwath::SpectrumAccessPtr swath_ptr,
                    OpenSwath::LightTargetedExperiment& transition_exp_used,
                    OpenSwath::IDataFrameWriter* ivw);
  };
 
 
}