/usr/include/sbml/packages/fbc/validator/constraints/UniqueGeneProductLabels.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 | /**
* @cond doxygenLibsbmlInternal
*
* @file UniqueGeneProductLabels.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
*
* 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 UniqueGeneProductLabels_h
#define UniqueGeneProductLabels_h
#ifdef __cplusplus
#include <string>
#include <sstream>
#include <set>
#include <sbml/validator/VConstraint.h>
LIBSBML_CPP_NAMESPACE_BEGIN
class SBase;
class Validator;
/**
* The UniqueGeneProductLabels 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 UniqueGeneProductLabels: public TConstraint<Model>
{
public:
/**
* Creates a new UniqueGeneProductLabels with the given constraint id.
*/
UniqueGeneProductLabels (unsigned int id, Validator& v);
/**
* Destroys this Constraint.
*/
virtual ~UniqueGeneProductLabels ();
protected:
/**
* Called by check(). Override this method to define your own subset.
*/
void doCheck (const Model& m);
/* ------------------------------------------------------------ */
/* 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);
/**
* Logs a message that the given @p id (and its corresponding object) have
* failed to satisfy this constraint.
*/
void logConflict (const std::string& label, const SBase& object);
typedef std::set<std::string> ExistingLabels;
ExistingLabels mLabels;
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#endif /* UniqueGeneProductLabels_h */
/** @endcond */
|