/usr/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathHelper.h is in libopenms-dev 1.11.1-5.
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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,
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// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
#ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHHELPER_H
#define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHHELPER_H
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
namespace OpenMS
{
/**
@brief A helper class that is used by several OpenSWATH tools
*/
class OPENMS_DLLAPI OpenSwathHelper
{
public:
/// Select transitions between lower and upper and write them into the new TargetedExperiment
static void selectSwathTransitions(const OpenMS::TargetedExperiment& targeted_exp,
OpenMS::TargetedExperiment& transition_exp_used, double min_upper_edge_dist,
double lower, double upper);
/// Get the lower / upper offset for this SWATH map and do some sanity checks
static void checkSwathMap(const OpenMS::MSExperiment<Peak1D>& swath_map,
double& lower, double& upper);
/// Select transitions between lower and upper and write them into the new TargetedExperiment
static void selectSwathTransitions(const OpenSwath::LightTargetedExperiment& targeted_exp,
OpenSwath::LightTargetedExperiment& transition_exp_used, double min_upper_edge_dist,
double lower, double upper);
template <class TargetedExperimentT>
static bool checkSwathMapAndSelectTransitions(const OpenMS::MSExperiment<Peak1D>& exp,
const TargetedExperimentT& targeted_exp, TargetedExperimentT& transition_exp_used, double min_upper_edge_dist)
{
if (exp.size() == 0 || exp[0].getPrecursors().size() == 0)
{
std::cerr << "WARNING: File " << exp.getLoadedFilePath()
<< " does not have any experiments or any precursors. Is it a SWATH map? "
<< "I will move to the next map."
<< std::endl;
return false;
}
double upper, lower;
OpenSwathHelper::checkSwathMap(exp, lower, upper);
OpenSwathHelper::selectSwathTransitions(targeted_exp, transition_exp_used, min_upper_edge_dist, lower, upper);
if (transition_exp_used.getTransitions().size() == 0)
{
std::cerr << "WARNING: For File " << exp.getLoadedFilePath()
<< " no transition were within the precursor window of " << lower << " to " << upper
<< "I will move to the next map."
<< std::endl;
return false;
}
return true;
}
};
}
#endif
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