/usr/include/OpenMS/FORMAT/MSPFile.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 | // --------------------------------------------------------------------------
// 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: $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_MSPFILE_H
#define OPENMS_FORMAT_MSPFILE_H
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <vector>
namespace OpenMS
{
/**
@brief File adapter for MSP files (NIST spectra library)
@htmlinclude OpenMS_MSPFile.parameters
@ingroup FileIO
*/
class OPENMS_DLLAPI MSPFile :
public DefaultParamHandler
{
public:
/** Constructors and destructors
*/
//@{
///Default constructor
MSPFile();
/// Copy constructor
MSPFile(const MSPFile & rhs);
///Destructor
virtual ~MSPFile();
//@}
/// assignment operator
MSPFile & operator=(const MSPFile & rhs);
/**
@brief Loads a map from a MSPFile file.
@param exp RichPeakMap which contains the spectra after reading
@param filename the filename of the experiment
@param ids output parameter which contains the peptide identifications from the spectra anntations
@throw FileNotFound is thrown if the file could not be found
@throw ParseError is thrown if the given file could not be parsed
@throw ElementNotFound is thrown if a annotated modification cannot be found in ModificationsDB (PSI-MOD definitions)
*/
void load(const String & filename, std::vector<PeptideIdentification> & ids, RichPeakMap & exp);
/**
@brief Stores a map in a MSPFile file.
@throw UnableToCreateFile is thrown if the given file could not be created
*/
void store(const String & filename, const RichPeakMap & exp) const;
protected:
/// reads the header information and stores it as metainfo in the spectrum
void parseHeader_(const String & header, RichPeakSpectrum & spec);
};
} // namespace OpenMS
#endif // OPENMS_FORMAT_MSPFILE_H
|