/usr/include/sbml/packages/fbc/util/FbcToCobraConverter.h is in libsbml5-dev 5.13.0+dfsg-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 | /**
* @file FbcToCobraConverter.h
* @brief Definition of a fbc 2 cobra converter.
* @author Frank T. Bergmann
*
* <!--------------------------------------------------------------------------
* This file is part of libSBML. Please visit http://sbml.org for more
* information about SBML, and the latest version of libSBML.
*
* Copyright (C) 2013-2016 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
* 3. University of Heidelberg, Heidelberg, Germany
*
* Copyright (C) 2009-2013 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation. A copy of the license agreement is provided
* in the file named "LICENSE.txt" included with this software distribution
* and also available online as http://sbml.org/software/libsbml/license.html
* ---------------------------------------------------------------------- -->
*
* @class FbcToCobraConverter
* @sbmlbrief{fbc} SBML Level 3 “fbc” to COBRA converter.
*
* @htmlinclude libsbml-facility-only-warning.html
*
* This converter takes a model in “fbc” Version 2 format
* and converts it to COBRA format.
*
* FbcToCobraConverter is enabled by creating a ConversionProperties object
* with the option <code>"convert fbc to cobra"</code> (literally that
* full string, including the spaces), and passing this properties object to
* SBMLDocument::convert(@if java ConversionProperties@endif). The converter
* offers one option:
*
* @li @c "overwriteReactionNotes": should gene associations be written into
* the "notes" subelement attached to Reaction objects, even if a Reaction
* already has "notes" content?
*
* @copydetails doc_section_using_sbml_converters
*/
#ifndef FbcToCobraConverter_h
#define FbcToCobraConverter_h
#include <sbml/common/extern.h>
#include <sbml/SBMLNamespaces.h>
#include <sbml/conversion/SBMLConverter.h>
#include <sbml/conversion/SBMLConverterRegister.h>
#ifdef __cplusplus
LIBSBML_CPP_NAMESPACE_BEGIN
class LIBSBML_EXTERN FbcToCobraConverter : public SBMLConverter
{
public:
/** @cond doxygenLibsbmlInternal */
/**
* Register with the ConversionRegistry.
*/
static void init();
/** @endcond */
/**
* Creates a new FbcToCobraConverter object.
*/
FbcToCobraConverter();
/**
* Copy constructor; creates a copy of an FbcToCobraConverter
* object.
*
* @param orig the FbcToCobraConverter object to copy.
*/
FbcToCobraConverter(const FbcToCobraConverter& orig);
/**
* Creates and returns a deep copy of this FbcToCobraConverter object.
*
* @return a (deep) copy of this FbcToCobraConverter.
*/
virtual FbcToCobraConverter* clone() const;
/**
* Destroy this FbcToCobraConverter object.
*/
virtual ~FbcToCobraConverter ();
/**
* Returns @c true if this converter object's properties match the given
* properties.
*
* A typical use of this method involves creating a ConversionProperties
* object, setting the options desired, and then calling this method on
* an FbcToCobraConverter object to find out if the object's
* property values match the given ones. This method is also used by
* SBMLConverterRegistry::getConverterFor(@if java ConversionProperties@endif)
* to search across all registered converters for one matching particular
* properties.
*
* @param props the properties to match.
*
* @return @c true if this converter's properties match, @c false
* otherwise.
*/
virtual bool matchesProperties(const ConversionProperties &props) const;
/**
* Perform the conversion.
*
* This method causes the converter to do the actual conversion work,
* that is, to convert the SBMLDocument object set by
* SBMLConverter::setDocument(@if java SBMLDocument@endif) and
* with the configuration options set by
* SBMLConverter::setProperties(@if java ConversionProperties@endif).
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*/
virtual int convert();
/**
* Returns the default properties of this converter.
*
* A given converter exposes one or more properties that can be adjusted
* in order to influence the behavior of the converter. This method
* returns the @em default property settings for this converter. It is
* meant to be called in order to discover all the settings for the
* converter object.
*
* @return the ConversionProperties object describing the default properties
* for this converter.
*/
virtual ConversionProperties getDefaultProperties() const;
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#ifndef SWIG
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
END_C_DECLS
LIBSBML_CPP_NAMESPACE_END
#endif /* !SWIG */
#endif /* FbcToCobraConverter_h*/
|