SwathFile.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// 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,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/KERNEL/StandardTypes.h>

#include <vector>
#include <boost/shared_ptr.hpp>

namespace OpenMS
{
  class ExperimentalSettings;

  class OPENMS_DLLAPI SwathFile :
    public ProgressLogger
  {
public:

    std::vector<OpenSwath::SwathMap> loadSplit(StringList file_list, String tmp,
                                               boost::shared_ptr<ExperimentalSettings>& exp_meta, 
                                               String readoptions = "normal");

    std::vector<OpenSwath::SwathMap> loadMzML(String file, 
                                              String tmp,
                                              boost::shared_ptr<ExperimentalSettings>& exp_meta,
                                              String readoptions = "normal");

    std::vector<OpenSwath::SwathMap> loadMzXML(String file, 
                                               String tmp,
                                               boost::shared_ptr<ExperimentalSettings>& exp_meta,
                                               String readoptions = "normal");

    std::vector<OpenSwath::SwathMap> loadSqMass(String file, boost::shared_ptr<ExperimentalSettings>& /* exp_meta */);

protected:

    OpenSwath::SpectrumAccessPtr doCacheFile_(const String& in, const String& tmp, const String& tmp_fname,
                                              boost::shared_ptr<PeakMap > experiment_metadata);

    boost::shared_ptr< PeakMap > populateMetaData_(const String& file);

    void countScansInSwath_(const std::vector<MSSpectrum>& exp,
                            std::vector<int>& swath_counter, int& nr_ms1_spectra, 
                            std::vector<OpenSwath::SwathMap>& known_window_boundaries);

  };
}