/usr/include/OpenMS/FORMAT/PepNovoInfile.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 | // --------------------------------------------------------------------------
// 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: Sandro Andreotti $
// $Authors: $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_PEPNOVOINFILE_H
#define OPENMS_FORMAT_PEPNOVOINFILE_H
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <map>
namespace OpenMS
{
/**
@brief PepNovo input file adapter.
Creates a PepNovo_PTMs.txt file for PepNovo search.
@ingroup FileIO
*/
class OPENMS_DLLAPI PepNovoInfile
{
public:
/// default constructor
PepNovoInfile();
/// copy constructor
PepNovoInfile(const PepNovoInfile & pepnovo_infile);
/// destructor
virtual ~PepNovoInfile();
/// assignment operator
PepNovoInfile & operator=(const PepNovoInfile & pepnovo_infile);
/// equality operator
bool operator==(const PepNovoInfile & pepnovo_infile) const;
/** stores the experiment data in a PepNovo input file that can be used as input for PepNovo shell execution
@param filename the file which the input file is stored into
@throw Exception::UnableToCreateFile is thrown if the given file could not be created
*/
void store(const String & filename);
/** @brief generates the PepNovo Infile for given fixed and variable modifications *
*
* @param fixed_mods StringList of fixed modifications unique identifiers
* @param variable_mods StringList of variable modifications unique identifiers
*/
void setModifications(const StringList & fixed_mods, const StringList & variable_mods);
/** @brief return the modifications.
*
* the modification unique identifiers are mapped to the keys used
* in the PepNovo Infile (origin+rounded monoisotopic mass of modification ).
* (e.g. modification_key_map["K+16"]=="Oxidation (K)" )
*/
void getModifications(std::map<String, String> & modification_key_map) const;
private:
ModificationDefinitionsSet mods_;
std::map<String, String> mods_and_keys_;
TextFile ptm_file_;
/** retrieves the name of modification, and generates the corresponding line for the
PepNovo infile.
@param modification the modification
@param variable should be set to true if it variable
*/
String handlePTMs_(const String & modification, const bool variable);
};
} // namespace OpenMS
#endif // OPENMS_FORMAT_PEPNOVOINFILE_H
|