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libSBML C++ API
5.20.2
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This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
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. There are two main interfaces to libSBML's validation facilities, based on the classes Validator and SBMLValidator.
The Validator class is the basis of the system for validating an SBML document against the validation rules defined in the SBML specifications. The scheme used by Validator relies is compact and uses the visitor programming pattern, but it relies on C/C++ features and is not directly accessible from language bindings. SBMLValidator offers a framework for straightforward class-based extensibility, so that user code can subclass SBMLValidator to implement new validation systems, different validators can be introduced or turned off at run-time, and interfaces can be provided in the libSBML language bindings. SBMLValidator can call Validator functionality internally (as is the case in the current implementation of SBMLInternalValidator) or use entirely different implementation approaches, as necessary.
Users of libSBML may already be familiar with the facilities encompassed by the validation system, in the form 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 via SBMLValidator, specifically as methods on the class SBMLInternalValidator.
Authors may use SBMLValidator as the base class for their own validator extensions to libSBML. The class SBMLInternalValidator may serve as a code example for how to implement such things.
Public Member Functions | |
| virtual void | clearFailures () |
| Clears this validator's list of failures. More... | |
| virtual SBMLValidator * | clone () const |
| Creates and returns a deep copy of this SBMLValidator object. More... | |
| virtual SBMLDocument * | getDocument () |
| Returns the current SBML document in use by this validator. More... | |
| virtual const SBMLDocument * | getDocument () const |
| Returns the current SBML document in use by this validator. More... | |
| SBMLErrorLog * | getErrorLog () |
| Returns the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model. More... | |
| SBMLError * | getFailure (unsigned int n) const |
| Returns the failure object at index n in this validator's list of failures logged during the last run. More... | |
| const std::vector< SBMLError > & | getFailures () const |
| Returns a list of SBMLError objects (if any) that were logged by the last run of this validator. More... | |
| Model * | getModel () |
| Returns the Model object stored in the SBMLDocument. More... | |
| const Model * | getModel () const |
| Returns the Model object stored in the SBMLDocument. More... | |
| unsigned int | getNumFailures () const |
| Returns the number of failures encountered in the last validation run. More... | |
| void | logFailure (const SBMLError &err) |
| Adds the given failure to this list of Validators failures. More... | |
| SBMLValidator & | operator= (const SBMLValidator &rhs) |
| Assignment operator for SBMLValidator. More... | |
| SBMLValidator () | |
| Creates a new SBMLValidator. More... | |
| SBMLValidator (const SBMLValidator &orig) | |
| Copy constructor; creates a copy of an SBMLValidator object. More... | |
| virtual int | setDocument (const SBMLDocument *doc) |
| Sets the current SBML document to the given SBMLDocument object. More... | |
| virtual unsigned int | validate () |
| Runs this validator on the current SBML document. More... | |
| unsigned int | validate (const SBMLDocument &d) |
| Validates the given SBMLDocument object. More... | |
| unsigned int | validate (const std::string &filename) |
Validates the SBML document located at the given filename. More... | |
| virtual | ~SBMLValidator () |
| Destroy this object. More... | |
| SBMLValidator::SBMLValidator | ( | ) |
Creates a new SBMLValidator.
| SBMLValidator::SBMLValidator | ( | const SBMLValidator & | orig | ) |
Copy constructor; creates a copy of an SBMLValidator object.
| orig | the object to copy. |
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Destroy this object.
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Clears this validator's list of failures.
If you are validating multiple SBML documents with the same validator, call this method after you have processed the list of failures from the last validation run and before validating the next document.
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Creates and returns a deep copy of this SBMLValidator object.
Reimplemented in SBMLInternalValidator.
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Returns the current SBML document in use by this validator.
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Returns the current SBML document in use by this validator.
| SBMLErrorLog * SBMLValidator::getErrorLog | ( | ) |
Returns the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model.
Note that this refers to the SBMLDocument object's error log (i.e., the list returned by SBMLDocument::getErrorLog()). That list of errors and warnings is separate from the validation failures tracked by this validator (i.e., the list returned by getFailures()).
| SBMLError * SBMLValidator::getFailure | ( | unsigned int | n | ) | const |
Returns the failure object at index n in this validator's list of failures logged during the last run.
Callers should use getNumFailures() first, to find out the number of entries in this validator's list of failures.
| n | an integer indicating the index of the object to return from the failures list; index values start at 0. |
| const std::vector< SBMLError > & SBMLValidator::getFailures | ( | ) | const |
Returns a list of SBMLError objects (if any) that were logged by the last run of this validator.
| Model * SBMLValidator::getModel | ( | ) |
Returns the Model object stored in the SBMLDocument.
It is important to note that this method does not create a Model instance. The model in the SBMLDocument must have been created at some prior time, for example using SBMLDocument::createModel() or SBMLDocument::setModel(). This method returns NULL if a model does not yet exist.
| const Model * SBMLValidator::getModel | ( | ) | const |
Returns the Model object stored in the SBMLDocument.
It is important to note that this method does not create a Model instance. The model in the SBMLDocument must have been created at some prior time, for example using SBMLDocument::createModel() or SBMLDocument::setModel(). This method returns NULL if a model does not yet exist.
| unsigned int SBMLValidator::getNumFailures | ( | ) | const |
Returns the number of failures encountered in the last validation run.
This method returns the number of failures logged by this validator. This number only reflects this validator's actions; the number may not be the same as the number of errors and warnings logged on the SBMLDocument object's error log (i.e., the object returned by SBMLDocument::getErrorLog()), because other parts of libSBML may log errors and warnings beyond those found by this validator.
| void SBMLValidator::logFailure | ( | const SBMLError & | err | ) |
Adds the given failure to this list of Validators failures.
| err | an SBMLError object representing an error or warning. |
| SBMLValidator & SBMLValidator::operator= | ( | const SBMLValidator & | rhs | ) |
Assignment operator for SBMLValidator.
| rhs | the object whose values are used as the basis of the assignment. |
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Sets the current SBML document to the given SBMLDocument object.
| doc | the document to use for this validation. |
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Runs this validator on the current SBML document.
Reimplemented in SBMLInternalValidator.
| unsigned int SBMLValidator::validate | ( | const SBMLDocument & | d | ) |
Validates the given SBMLDocument object.
This is identical to calling setDocument() followed by validate().
| d | the SBML document to validate. |
| unsigned int SBMLValidator::validate | ( | const std::string & | filename | ) |
Validates the SBML document located at the given filename.
This is a convenience method that saves callers the trouble of using SBMLReader to read the document first.
| filename | the path to the file to be read and validated. |