/usr/include/OpenMS/FORMAT/MascotXMLFile.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: Nico Pfeifer $
// $Authors: Nico Pfeifer $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_MASCOTXMLFILE_H
#define OPENMS_FORMAT_MASCOTXMLFILE_H
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/FORMAT/HANDLERS/MascotXMLHandler.h>
#include <OpenMS/KERNEL/MSExperiment.h>
namespace OpenMS
{
class ProteinIdentification;
/**
@brief Used to load MascotXML files
This class is used to load documents that implement
the schema of MascotXML files.
@ingroup FileIO
*/
class OPENMS_DLLAPI MascotXMLFile :
public Internal::XMLFile
{
public:
typedef Internal::MascotXMLHandler::RTMapping RTMapping;
/// Constructor
MascotXMLFile();
/**
@brief loads data from a Mascot XML file
@param filename the file to be loaded
@param protein_identification protein identifications belonging to the whole experiment
@param id_data the identifications with m/z and RT
@param rt_mapping An optional mapping of scan indices to RT, in case the file only contains scan numbers
@param scan_regex An optional regular expression used to extract the scan numbers
@exception Exception::FileNotFound is thrown if the file does not exists.
@exception Exception::ParseError is thrown if the file does not suit to the standard.
This method serves to read in a Mascot XML file. The information can be
retrieved via the load function.
*/
void load(const String& filename,
ProteinIdentification& protein_identification,
std::vector<PeptideIdentification>& id_data,
const RTMapping& rt_mapping = RTMapping(),
const String& scan_regex = "");
/**
@brief loads data from a Mascot XML file
@param filename the file to be loaded
@param protein_identification protein identifications belonging to the whole experiment
@param id_data the identifications with m/z and RT
@param peptides a map of modified peptides identified by the String title
@param rt_mapping An optional mapping of scan indices to RT, in case the file only contains scan numbers
@param scan_regex An optional regular expression used to extract the scan numbers
@exception Exception::FileNotFound is thrown if the file does not exists.
@exception Exception::ParseError is thrown if the file does not suit to the standard.
This method serves to read in a Mascot XML file. The information can be
retrieved via the load function.
*/
void load(const String& filename,
ProteinIdentification& protein_identification,
std::vector<PeptideIdentification>& id_data,
std::map<String, std::vector<AASequence> >& peptides,
const RTMapping& rt_mapping = RTMapping(),
const String& scan_regex = "");
/**
@brief Generates a mapping between scan numbers and retention times in raw data
@param begin Iterator to the first spectrum
@param end Iterator past the last spectrum
@param rt_mapping Output mapping
The mapping can be used to infer retention times of identifications when a Mascot XML file is loaded.
*/
static void generateRTMapping(const MSExperiment<>::ConstIterator begin,
const MSExperiment<>::ConstIterator end,
RTMapping& rt_mapping);
};
} // namespace OpenMS
#endif // OPENMS_FORMAT_MASCOTXMLFILE_H
|