/usr/include/sbml/validator/SBMLInternalValidator.h is in libsbml5-dev 5.16.0+dfsg-1.
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* @file SBMLInternalValidator.h
* @brief Definition of SBMLInternalValidator, the validator for all internal validation performed by libSBML.
* @author Frank 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) 2013-2017 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
* ------------------------------------------------------------------------ -->
*
* @class SBMLInternalValidator
* @sbmlbrief{core} Basic SBML consistency checks and other validations.
*
* @htmlinclude not-sbml-warning.html
*
* LibSBML implements facilities for verifying that a given SBML document is
* valid according to the SBML specifications; it also exposes the validation
* interface so that user programs and SBML Level 3 package authors may
* use the facilities to implement new validators. The entry point for this
* is the SBMLValidator class.
*
* The subclass SBMLInternalValidator embodies the implementation of the
* consistency-checking methods defined on SBMLDocument. The methods
* SBMLDocument::setConsistencyChecks(), SBMLDocument::checkConsistency(),
* SBMLDocument::checkInternalConsistency() and other method of that sort
* are in fact implemented by SBMLInternalValidator. These validations
* are all performed on the internal (in-memory) representation of an SBML
* model.
*
* Users should not need to call SBMLInternalValidator methods directly,
* since the interface is already provided on SBMLDocument. However, this
* class is exposed in case users would like to implement new or additional
* validations by extending this class (SBMLInternalValidator) or using
* this class as an example of how to implement such validators.
*/
#ifndef SBMLInternalValidator_h
#define SBMLInternalValidator_h
#include <sbml/SBMLNamespaces.h>
#include <sbml/validator/SBMLValidator.h>
#include <sbml/SBMLError.h>
#ifdef __cplusplus
LIBSBML_CPP_NAMESPACE_BEGIN
class LIBSBML_EXTERN SBMLInternalValidator : public SBMLValidator
{
public:
/**
* Controls the consistency checks that are performed when
* SBMLDocument::checkConsistency() is called.
*
* This method works by adding or subtracting consistency checks from the
* set of all possible checks that SBMLDocument::checkConsistency() knows
* how to perform. This method may need to be called multiple times in
* order to achieve the desired combination of checks. The first
* argument (@p category) in a call to this method indicates the category
* of consistency/error checks that are to be turned on or off, and the
* second argument (@p apply, a boolean) indicates whether to turn it on
* (value of @c true) or off (value of @c false).
*
* @if clike
* The possible categories (values to the argument @p category) are the
* set of values from the enumeration #SBMLErrorCategory_t.
* The following are the possible choices:
* @endif@if java
* The possible categories (values to the argument @p category) are the
* set of constants whose names begin with the characters <code>LIBSBML_CAT_</code>
* in the interface class {@link libsbmlConstants}.
* The following are the possible choices:
* @endif@if python
* The possible categories (values to the argument @p category) are the
* set of constants whose names begin with the characters <code>LIBSBML_CAT_</code>
* in the interface class @link libsbml libsbml@endlink.
* The following are the possible choices:
* @endif@~
* <ul>
* <li> @sbmlconstant{LIBSBML_CAT_GENERAL_CONSISTENCY, SBMLErrorCategory_t}:
* Correctness and consistency of specific SBML language constructs.
* Performing this set of checks is highly recommended. With respect to
* the SBML specification, these concern failures in applying the
* validation rules numbered 2xxxx in the Level 2
* Versions 2–4 and Level 3 Versions 1–2 specifications.
*
* <li> @sbmlconstant{LIBSBML_CAT_IDENTIFIER_CONSISTENCY, SBMLErrorCategory_t}:
* Correctness and consistency of identifiers used for model entities. An
* example of inconsistency would be using a species identifier in a
* reaction rate formula without first having declared the species. With
* respect to the SBML specification, these concern failures in applying
* the validation rules numbered 103xx in the Level 2
* Versions 2–4 and Level 3 Versions 1–2 specifications.
*
* <li> @sbmlconstant{LIBSBML_CAT_UNITS_CONSISTENCY, SBMLErrorCategory_t}:
* Consistency of measurement units associated with quantities in a model.
* With respect to the SBML specification, these concern failures in
* applying the validation rules numbered 105xx in the Level 2
* Versions 2–4 and Level 3 Versions 1–2 specifications.
*
* <li> @sbmlconstant{LIBSBML_CAT_MATHML_CONSISTENCY, SBMLErrorCategory_t}:
* Syntax of MathML constructs. With respect to the SBML specification,
* these concern failures in applying the validation rules numbered 102xx
* in the Level 2 Versions 2–4 and Level 3
* Versions 1–2 specifications.
*
* <li> @sbmlconstant{LIBSBML_CAT_SBO_CONSISTENCY, SBMLErrorCategory_t}:
* Consistency and validity of %SBO identifiers (if any) used in the model.
* With respect to the SBML specification, these concern failures in
* applying the validation rules numbered 107xx in the Level 2
* Versions 2–4 and Level 3 Versions 1–2 specifications.
*
* <li> @sbmlconstant{LIBSBML_CAT_OVERDETERMINED_MODEL, SBMLErrorCategory_t}:
* Static analysis of whether the system of equations implied by a model is
* mathematically overdetermined. With respect to the SBML specification,
* this is validation rule #10601 in the Level 2
* Versions 2–4 and Level 3 Versions 1–2 specifications.
*
* <li> @sbmlconstant{LIBSBML_CAT_MODELING_PRACTICE, SBMLErrorCategory_t}:
* Additional checks for recommended good modeling practice. (These are
* tests performed by libSBML and do not have equivalent SBML validation
* rules.)
* </ul>
*
* <em>By default, all validation checks are applied</em> to the model in
* an SBMLDocument object @em unless
* SBMLDocument::setConsistencyChecks(@if java int, boolean@endif)
* is called to indicate that only a subset should be applied. Further,
* this default (i.e., performing all checks) applies separately to
* <em>each new SBMLDocument object</em> created. In other words, each
* time a model is read using SBMLReader::readSBML(@if java String@endif),
* SBMLReader::readSBMLFromString(@if java String@endif),
* or the global functions readSBML() and readSBMLFromString(), a new
* SBMLDocument is created and for that document, a call to
* SBMLDocument::checkConsistency() will default to applying all possible checks.
* Calling programs must invoke
* SBMLDocument::setConsistencyChecks(@if java int, boolean@endif)
* for each such new model if they wish to change the consistency checks
* applied.
*
* @param category a value drawn from @if clike #SBMLErrorCategory_t@else
* the set of SBML error categories@endif@~ indicating the
* consistency checking/validation to be turned on or off.
*
* @param apply a boolean indicating whether the checks indicated by
* @p category should be applied or not.
*
* @see SBMLDocument::checkConsistency()
*/
void setConsistencyChecks(SBMLErrorCategory_t category, bool apply);
/**
* Controls the consistency checks that are performed when
* SBMLDocument::setLevelAndVersion(@if java long, long, boolean@endif) is called.
*
* This method works by adding or subtracting consistency checks from the
* set of all possible checks that may be performed to avoid conversion
* to or from an invalid document. This method may need to be called
* multiple times in
* order to achieve the desired combination of checks. The first
* argument (@p category) in a call to this method indicates the category
* of consistency/error checks that are to be turned on or off, and the
* second argument (@p apply, a boolean) indicates whether to turn it on
* (value of @c true) or off (value of @c false).
*
* @if clike
* The possible categories (values to the argument @p category) are the
* set of values from the enumeration #SBMLErrorCategory_t.
* The following are the possible choices:
* @endif@if java
* The possible categories (values to the argument @p category) are the
* set of constants whose names begin with the characters <code>LIBSBML_CAT_</code>
* in the interface class {@link libsbmlConstants}.
* The following are the possible choices:
* @endif@if python
* The possible categories (values to the argument @p category) are the
* set of constants whose names begin with the characters <code>LIBSBML_CAT_</code>
* in the interface class @link libsbml libsbml@endlink.
* The following are the possible choices:
* @endif@~
* <ul>
* <li> @sbmlconstant{LIBSBML_CAT_GENERAL_CONSISTENCY, SBMLErrorCategory_t}:
* Correctness and consistency of specific SBML language constructs.
* Performing this set of checks is highly recommended. With respect to
* the SBML specification, these concern failures in applying the
* validation rules numbered 2xxxx in the Level 2
* Versions 2–4 and Level 3 Versions 1–2 specifications.
*
* <li> @sbmlconstant{LIBSBML_CAT_IDENTIFIER_CONSISTENCY, SBMLErrorCategory_t}:
* Correctness and consistency of identifiers used for model entities. An
* example of inconsistency would be using a species identifier in a
* reaction rate formula without first having declared the species. With
* respect to the SBML specification, these concern failures in applying
* the validation rules numbered 103xx in the Level 2
* Versions 2–4 and Level 3 Versions 1–2 specifications.
*
* <li> @sbmlconstant{LIBSBML_CAT_UNITS_CONSISTENCY, SBMLErrorCategory_t}:
* Consistency of measurement units associated with quantities in a model.
* With respect to the SBML specification, these concern failures in
* applying the validation rules numbered 105xx in the Level 2
* Versions 2–4 and Level 3 Versions 1–2 specifications.
*
* <li> @sbmlconstant{LIBSBML_CAT_MATHML_CONSISTENCY, SBMLErrorCategory_t}:
* Syntax of MathML constructs. With respect to the SBML specification,
* these concern failures in applying the validation rules numbered 102xx
* in the Level 2 Versions 2–4 and Level 3
* Versions 1–2 specifications.
*
* <li> @sbmlconstant{LIBSBML_CAT_SBO_CONSISTENCY, SBMLErrorCategory_t}:
* Consistency and validity of %SBO identifiers (if any) used in the model.
* With respect to the SBML specification, these concern failures in
* applying the validation rules numbered 107xx in the Level 2
* Versions 2–4 and Level 3 Versions 1–2 specifications.
*
* <li> @sbmlconstant{LIBSBML_CAT_OVERDETERMINED_MODEL, SBMLErrorCategory_t}:
* Static analysis of whether the system of equations implied by a model is
* mathematically overdetermined. With respect to the SBML specification,
* this is validation rule #10601 in the Level 2
* Versions 2–4 and Level 3 Versions 1–2 specifications.
*
* <li> @sbmlconstant{LIBSBML_CAT_MODELING_PRACTICE, SBMLErrorCategory_t}:
* Additional checks for recommended good modeling practice. (These are
* tests performed by libSBML and do not have equivalent SBML validation
* rules.)
* </ul>
*
* <em>By default, all validation checks are applied</em> to the model in
* an SBMLDocument object @em unless
* SBMLDocument::setConsistencyChecks(@if java int, boolean@endif)
* is called to indicate that only a subset should be applied. Further,
* this default (i.e., performing all checks) applies separately to
* <em>each new SBMLDocument object</em> created. In other words, each
* time a model is read using SBMLReader::readSBML(@if java String@endif),
* SBMLReader::readSBMLFromString(@if java String@endif),
* or the global functions readSBML() and readSBMLFromString(), a new
* SBMLDocument is created and for that document, a call to
* SBMLDocument::checkConsistency() will default to applying all possible checks.
* Calling programs must invoke
* SBMLDocument::setConsistencyChecks(@if java int, boolean@endif)
* for each such new model if they wish to change the consistency checks
* applied.
*
* @param category a value drawn from @if clike #SBMLErrorCategory_t@else
* the set of SBML error categories@endif@~ indicating the consistency
* checking/validation to be turned on or off.
*
* @param apply a boolean indicating whether the checks indicated by
* @p category should be applied or not.
*
* @see SBMLDocument::setLevelAndVersion(@if java long, long, boolean@endif)
*/
void setConsistencyChecksForConversion(SBMLErrorCategory_t category,
bool apply);
/**
* Performs consistency checking and validation on this SBML document.
*
* If this method returns a nonzero value (meaning, one or more
* consistency checks have failed for SBML document), the failures may be
* due to warnings @em or errors. Callers should inspect the severity
* flag in the individual SBMLError objects returned by
* SBMLDocument::getError(@if java long@endif) to determine the nature of the failures.
*
* @param writeDocument by default checkConsistency will write the document
* in order to determine all errors for the document.
* This will also clear the error log. Setting this
* parameter to false will skip this additional step
* but might not find all errors.
*
* @return the number of failed checks (errors) encountered.
*
* @see SBMLDocument::checkInternalConsistency()
*/
unsigned int checkConsistency (bool writeDocument=false);
/**
* Performs consistency checking on libSBML's internal representation of
* an SBML Model.
*
* Callers should query the results of the consistency check by calling
* SBMLDocument::getError(@if java long@endif).
*
* @return the number of failed checks (errors) encountered.
*
* The distinction between this method and
* SBMLDocument::checkConsistency() is that this method reports on
* fundamental syntactic and structural errors that violate the XML
* Schema for SBML; by contrast, SBMLDocument::checkConsistency()
* performs more elaborate model verifications and also validation
* according to the validation rules written in the appendices of the
* SBML Level 2 Versions 2–4 specification documents.
*
* @see SBMLDocument::checkConsistency()
*/
unsigned int checkInternalConsistency ();
/**
* Performs a set of consistency checks on the document to establish
* whether it is compatible with SBML Level 1 and can be converted
* to Level 1.
*
* Callers should query the results of the consistency check by calling
* SBMLDocument::getError(@if java long@endif).
*
* @return the number of failed checks (errors) encountered.
*/
unsigned int checkL1Compatibility ();
/**
* Performs a set of consistency checks on the document to establish
* whether it is compatible with SBML Level 2 Version 1 and can
* be converted to Level 2 Version 1.
*
* Callers should query the results of the consistency check by calling
* SBMLDocument::getError(@if java long@endif).
*
* @return the number of failed checks (errors) encountered.
*/
unsigned int checkL2v1Compatibility ();
/**
* Performs a set of consistency checks on the document to establish
* whether it is compatible with SBML Level 2 Version 2 and can
* be converted to Level 2 Version 2.
*
* Callers should query the results of the consistency check by calling
* SBMLDocument::getError(@if java long@endif).
*
* @return the number of failed checks (errors) encountered.
*/
unsigned int checkL2v2Compatibility ();
/**
* Performs a set of consistency checks on the document to establish
* whether it is compatible with SBML Level 2 Version 3 and can
* be converted to Level 2 Version 3.
*
* Callers should query the results of the consistency check by calling
* SBMLDocument::getError(@if java long@endif).
*
* @return the number of failed checks (errors) encountered.
*/
unsigned int checkL2v3Compatibility ();
/**
* Performs a set of consistency checks on the document to establish
* whether it is compatible with SBML Level 2 Version 4 and can
* be converted to Level 2 Version 4.
*
* Callers should query the results of the consistency check by calling
* SBMLDocument::getError(@if java long@endif).
*
* @return the number of failed checks (errors) encountered.
*/
unsigned int checkL2v4Compatibility ();
/**
* Performs a set of consistency checks on the document to establish
* whether it is compatible with SBML Level 2 Version 5 and can
* be converted to Level 2 Version 5.
*
* Callers should query the results of the consistency check by calling
* SBMLDocument::getError(@if java long@endif).
*
* @return the number of failed checks (errors) encountered.
*/
unsigned int checkL2v5Compatibility ();
/**
* Performs a set of consistency checks on the document to establish
* whether it is compatible with SBML Level 3 Version 1 and can
* be converted to Level 3 Version 1.
*
* Callers should query the results of the consistency check by calling
* SBMLDocument::getError(@if java long@endif).
*
* @return the number of failed checks (errors) encountered.
*/
unsigned int checkL3v1Compatibility ();
/**
* Performs a set of consistency checks on the document to establish
* whether it is compatible with SBML Level 3 Version 2 and can
* be converted to Level 3 Version 2.
*
* Callers should query the results of the consistency check by calling
* SBMLDocument::getError(@if java long@endif).
*
* @return the number of failed checks (errors) encountered.
*/
unsigned int checkL3v2Compatibility();
/**
* @return the current list of selected validators.
*/
unsigned char getApplicableValidators() const;
/**
* @return the current list of selected validators for conversion.
*/
unsigned char getConversionValidators() const;
/**
* Set the current list of validators to be applied
*
* @param appl the mask of validators to be applied.
*/
void setApplicableValidators(unsigned char appl);
/**
* Set the current list of conversion validators to be applied
*
* @param appl the mask of validators to be applied.
*/
void setConversionValidators(unsigned char appl);
/**
* Constructor.
*/
SBMLInternalValidator();
/**
* Copy constructor; creates a copy of an SBMLInternalValidator object.
*
* @param orig the object to copy.
*/
SBMLInternalValidator(const SBMLInternalValidator& orig);
/**
* Creates and returns a deep copy of this SBMLValidator object.
*
* @return the (deep) copy of this SBMLValidator object.
*/
virtual SBMLValidator* clone() const;
/**
* Destroy this object.
*/
virtual ~SBMLInternalValidator ();
/**
* Runs the validations.
*
* This runs the validations that were previously enabled via methods such as
* SBMLDocument::setConsistencyChecks(@if java int, boolean@endif).
*
* @return the number of validation failures that occurred. The objects
* describing the actual failures can be retrieved using getFailures().
*/
virtual unsigned int validate();
protected:
/** @cond doxygenLibsbmlInternal */
unsigned char mApplicableValidators;
unsigned char mApplicableValidatorsForConversion;
/** @endcond */
private:
/** @cond doxygenLibsbmlInternal */
/** @endcond */
};
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 /* SBMLInternalValidator_h */
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