/usr/include/sbml/packages/layout/validator/constraints/UniqueIdsLayout.h is in libsbml5-dev 5.16.0+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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 | /**
* @cond doxygenLibsbmlInternal
*
* @file UniqueIdsLayout.h
* @brief Base class for Id constraints
* @author Ben Bornstein
*
* <!--------------------------------------------------------------------------
* This file is part of libSBML. Please visit http://sbml.org for more
* information about SBML, and the latest version of libSBML.
*
* Copyright (C) 2013-2017 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
*
* Copyright (C) 2006-2008 by the California Institute of Technology,
* Pasadena, CA, USA
*
* Copyright (C) 2002-2005 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. Japan Science and Technology Agency, Japan
*
* 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
* ---------------------------------------------------------------------- -->*/
#ifndef UniqueIdsLayout_h
#define UniqueIdsLayout_h
#ifdef __cplusplus
#include <string>
#include <sstream>
#include <map>
#include <sbml/validator/VConstraint.h>
LIBSBML_CPP_NAMESPACE_BEGIN
class SBase;
class Validator;
/**
* The UniqueIdsLayout Constraint is the base class for all SBML id constraints. It
* provides mechanisms for checking only certain subsets of ids within an
* SBML model and tailoring the error messages logged.
*
* To customize:
*
* 1. Override doCheck() to iterate over the SBML objects you are
* interested in and call checkId() for each.
*
* checkId() does the work of extracting the unique identifier
* (whether it be an id or variable name) from the SBML object and
* then delegates to doCheckId().
*
* 2. Override doCheckId() to perform the actual check. If the check
* fails, call logFailure().
*
* 3. Override getMessage() to log error messages. GetMessage() should
* use getPreamble() and getFieldName() when constructing the error
* message.
*
* 4. Override getPreamble() to customize the part of the actual error
* message that remains constant (e.g. the part that doesn't report
* line numbers, SBML object ids and typenames, etc).
*
* 5. Override getFieldName() if you are checking a field that isn't
* called 'id', for instance, the 'variable' field of a Rule.
*
* Finally, if you need the type name of the SBML object that failed,
* e.g. 'Compartment' or 'Species', when constructing an error message,
* call getTypename().
*/
class UniqueIdsLayout: public TConstraint<Model>
{
public:
/**
* Creates a new UniqueIdsLayout with the given constraint id.
*/
UniqueIdsLayout (unsigned int id, Validator& v);
/**
* Destroys this Constraint.
*/
virtual ~UniqueIdsLayout ();
protected:
/**
* Resets the state of this GlobalConstraint by clearing its internal
* list of error messages.
*/
void reset ();
/**
* Called by check(). Override this method to define your own subset.
*/
void doCheck (const Model& m);
/**
* Checks that the id associated with the given object adheres to this
* constraint. If it does not, logFailure is called.
*/
void doCheckId (const std::string& id, const SBase& object);
/**
* Checks that the id associated with the given object adheres to this
* constraint. If it does not, logFailure is called.
*/
void logId (const SBase& object);
/**
* Called by check(). Override this method to define your own subset.
*/
void createExistingMap (const Model& m);
/**
* Returns the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* If at all possible please use getPreamble() and getFieldname() when
* constructing error messages. This will help to make your constraint
* easily customizable.
*
* @return the error message to use when logging constraint violations.
*/
const std::string
getMessage (const std::string& id, const SBase& object);
/* ------------------------------------------------------------ */
/* You should not need to override methods beyond this point. */
/* ------------------------------------------------------------ */
/**
* Checks that all ids for some given subset of the Model adhere to this
* Constraint. Override the doCheck() method to define your own subset.
*/
virtual void check_ (const Model& m, const Model& object);
/**
* Checks that the id associated with the given object is unique. If it
* is not, logFailure is called.
*/
void doCheckId (const SBase& object);
/**
* Returns a non-owning character pointer to the typename of the given SBase
* @p object, as constructed from its typecode and package.
*
* @return the typename of the given SBase object.
*/
const char* getTypename (const SBase& object);
/**
* Logs a message that the given @p id (and its corresponding object) have
* failed to satisfy this constraint.
*/
void logIdConflict (const std::string& id, const SBase& object);
typedef std::map<std::string, const SBase*> IdObjectMap;
IdObjectMap mIdMap;
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#endif /* UniqueIdsLayout_h */
/** @endcond */
|