/usr/include/OpenMS/FORMAT/MzDataFile.h is in libopenms-dev 1.11.1-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 | // --------------------------------------------------------------------------
// 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: Marc Sturm $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_MZDATAFILE_H
#define OPENMS_FORMAT_MZDATAFILE_H
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/FORMAT/HANDLERS/MzDataHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/METADATA/DocumentIdentifier.h>
namespace OpenMS
{
/**
@brief File adapter for MzData files
@ingroup FileIO
*/
class OPENMS_DLLAPI MzDataFile :
public Internal::XMLFile,
public ProgressLogger
{
public:
///Default constructor
MzDataFile();
///Destructor
~MzDataFile();
/// Mutable access to the options for loading/storing
PeakFileOptions & getOptions();
/// Non-mutable access to the options for loading/storing
const PeakFileOptions & getOptions() const;
/// set options for loading/storing
void setOptions(const PeakFileOptions &);
/**
@brief Loads a map from a MzData file.
@p map has to be a MSExperiment or have the same interface.
@exception Exception::FileNotFound is thrown if the file could not be opened
@exception Exception::ParseError is thrown if an error occurs during parsing
*/
template <typename MapType>
void load(const String & filename, MapType & map)
{
map.reset();
//set DocumentIdentifier
map.setLoadedFileType(filename);
map.setLoadedFilePath(filename);
Internal::MzDataHandler<MapType> handler(map, filename, schema_version_, *this);
handler.setOptions(options_);
parse_(filename, &handler);
}
/**
@brief Stores a map in a MzData file.
@p map has to be a MSExperiment or have the same interface.
@exception Exception::UnableToCreateFile is thrown if the file could not be created
*/
template <typename MapType>
void store(const String & filename, const MapType & map) const
{
Internal::MzDataHandler<MapType> handler(map, filename, schema_version_, *this);
handler.setOptions(options_);
save_(filename, &handler);
}
/**
@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:
/// Options for loading / storing
PeakFileOptions options_;
};
} // namespace OpenMS
#endif // OPENMS_FOMAT_MZXMLFILE_H
|