/usr/include/OpenMS/FORMAT/MzIdentMLFile.h is in libopenms-dev 1.11.1-5.
This file is owned by root:root, with mode 0o644.
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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,
// 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: Andreas Bertsch $
// $Authors: Andreas Bertsch, Mathias Walzer $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_MZIDENTMLFILE_H
#define OPENMS_FORMAT_MZIDENTMLFILE_H
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/StringList.h>
#include <OpenMS/METADATA/Identification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <vector>
namespace OpenMS
{
/**
@brief File adapter for MzIdentML files
If a critical error occurs due to the missing functionality, Exception::NotImplemented is thrown.
@ingroup FileIO
*/
class OPENMS_DLLAPI MzIdentMLFile :
public Internal::XMLFile,
public ProgressLogger
{
public:
///Default constructor
MzIdentMLFile();
///Destructor
virtual ~MzIdentMLFile();
/**
@brief Loads a map from a MzIdentML file.
@exception Exception::FileNotFound is thrown if the file could not be opened
@exception Exception::ParseError is thrown if an error occurs during parsing
*/
void load(const String & filename, Identification & id);
/**
@brief Stores a map in a MzIdentML file.
@exception Exception::UnableToCreateFile is thrown if the file could not be created
*/
void store(const String & filename, const std::vector<ProteinIdentification> & poid, const std::vector<PeptideIdentification> & peid) const;
/**
@brief Stores a map in a MzIdentML file.
@exception Exception::UnableToCreateFile is thrown if the file could not be created
*/
void store(const String & filename, const Identification & id) const;
/**
@brief Checks if a file is valid with respect to the mapping file and the controlled vocabulary.
@param filename File name of the file to be checked.
@param errors Errors during the validation are returned in this output parameter.
@param warnings Warnings during the validation are returned in this output parameter.
@exception Exception::FileNotFound is thrown if the file could not be opened
*/
bool isSemanticallyValid(const String & filename, StringList & errors, StringList & warnings);
private:
};
} // namespace OpenMS
#endif // OPENMS_FORMAT_MZIDENTMLFILE_H
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