libSBML Python API  5.8.0
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libsbml.SBMLExternalValidator Class Reference
Inheritance diagram for libsbml.SBMLExternalValidator:
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Detailed Description

Proxy of C++ SBMLExternalValidator class.

Public Member Functions

def addArgument
 
def clearArguments
 
def clearFailures
 
def clone
 
def getArgument
 
def getDocument
 
def getErrorLog
 
def getFailure
 
def getModel
 
def getNumArguments
 
def getNumFailures
 
def getOutputFileName
 
def getProgram
 
def getSBMLFileName
 
def logFailure
 
def setDocument
 
def setOutputFileName
 
def setProgram
 
def setSBMLFileName
 
def validate
 
def validate
 

Member Function Documentation

def libsbml.SBMLExternalValidator.addArgument (   self,
  args 
)

Python method signature(s):

addArgument(SBMLExternalValidator self, string arg)

Adds the given argument to the list of additional arguments

Parameters
argthe argument
def libsbml.SBMLExternalValidator.clearArguments (   self)

Python method signature(s):

clearArguments(SBMLExternalValidator self)

Clear all additional arguments

def libsbml.SBMLValidator.clearFailures (   self)
inherited

Python method signature(s):

clearFailures(SBMLValidator self)

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.

def libsbml.SBMLExternalValidator.clone (   self)

Proxy of C++ SBMLExternalValidator class.

Python method signature(s):

clone(SBMLExternalValidator self)   SBMLValidator

Creates and returns a deep copy of this converter.

Returns
a (deep) copy of this converter.
def libsbml.SBMLExternalValidator.getArgument (   self,
  args 
)

Python method signature(s):

getArgument(SBMLExternalValidator self, long n)   string

Returns the argument for the given index.

Parameters
nthe zero based index of the argument.
Returns
the argument at the given index.
def libsbml.SBMLValidator.getDocument (   self,
  args 
)
inherited

Python method signature(s):

getDocument(SBMLValidator self)   SBMLDocument
getDocument(SBMLValidator self)   SBMLDocument

Returns the current SBML document in use by this validator.

Returns
the current SBML document
See Also
setDocument()
def libsbml.SBMLValidator.getErrorLog (   self)
inherited

Python method signature(s):

getErrorLog(SBMLValidator self)   SBMLErrorLog

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()).

Returns
the SBMLErrorLog used for the SBMLDocument
def libsbml.SBMLValidator.getFailure (   self,
  args 
)
inherited

Python method signature(s):

getFailure(SBMLValidator self, long n)   SBMLError

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.

Parameters
nan integer indicating the index of the object to return from the failures list; index values start at 0.
Returns
the failure at the given index number.
See Also
getNumFailures()
def libsbml.SBMLValidator.getModel (   self,
  args 
)
inherited

Python method signature(s):

getModel(SBMLValidator self)   Model
getModel(SBMLValidator self)   Model

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 None if a model does not yet exist.

Returns
the Model contained in this validator's SBMLDocument object.
See Also
SBMLDocument.setModel()
SBMLDocument.createModel()
def libsbml.SBMLExternalValidator.getNumArguments (   self)

Python method signature(s):

getNumArguments(SBMLExternalValidator self)   long
Returns
the number of arguments.
def libsbml.SBMLValidator.getNumFailures (   self)
inherited

Python method signature(s):

getNumFailures(SBMLValidator self)   long

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.

Returns
the number of errors logged by this validator.
def libsbml.SBMLExternalValidator.getOutputFileName (   self)

Python method signature(s):

getOutputFileName(SBMLExternalValidator self)   string
Returns
the output file name (this is the file the external program will write)
def libsbml.SBMLExternalValidator.getProgram (   self)

Python method signature(s):

getProgram(SBMLExternalValidator self)   string
Returns
the program name of the validator to be run
def libsbml.SBMLExternalValidator.getSBMLFileName (   self)

Python method signature(s):

getSBMLFileName(SBMLExternalValidator self)   string
Returns
the name of the SBML file (the document of this validator will be written to it)
def libsbml.SBMLValidator.logFailure (   self,
  args 
)
inherited

Python method signature(s):

logFailure(SBMLValidator self, SBMLError err)

Adds the given failure to this list of Validators failures.

Parameters
erran SBMLError object representing an error or warning
def libsbml.SBMLValidator.setDocument (   self,
  args 
)
inherited

Python method signature(s):

setDocument(SBMLValidator self, SBMLDocument doc)   int

Sets the current SBML document to the given SBMLDocument object.

Parameters
docthe document to use for this validation
Returns
an integer value indicating the success/failure of the validation. The possible values returned by this function are
See Also
getDocument()
def libsbml.SBMLExternalValidator.setOutputFileName (   self,
  args 
)

Python method signature(s):

setOutputFileName(SBMLExternalValidator self, string outputFileName)

Sets the output file name

Parameters
outputFileNamethe name of the output XML file
def libsbml.SBMLExternalValidator.setProgram (   self,
  args 
)

Python method signature(s):

setProgram(SBMLExternalValidator self, string program)

Sets the name of the program to run

Parameters
programthe program to be started
def libsbml.SBMLExternalValidator.setSBMLFileName (   self,
  args 
)

Python method signature(s):

setSBMLFileName(SBMLExternalValidator self, string sbmlFileName)

Sets the filename for the temporary file to be created

Parameters
sbmlFileNamethe temporary name
def libsbml.SBMLValidator.validate (   self,
  args 
)
inherited

Python method signature(s):

validate(SBMLValidator self)   long
validate(SBMLValidator self, SBMLDocument d)   long
validate(SBMLValidator self, string filename)   long

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:

validate(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.

Parameters
filenamethe path to the file to be read and validated.
Returns
the number of validation failures that occurred. The objects describing the actual failures can be retrieved using getFailures().

Method variant with the following signature:

validate()

Runs this validator on the current SBML document.

Returns
an integer value indicating the success/failure of the validation. The possible values returned by this function are determined by the specific subclasses of this class.

Method variant with the following signature:

validate(SBMLDocument d)

Validates the given SBMLDocument object.

This is identical to calling setDocument() followed by validate().

Parameters
dthe SBML document to validate
Returns
the number of validation failures that occurred. The objects describing the actual failures can be retrieved using getFailures().
def libsbml.SBMLExternalValidator.validate (   self)

Python method signature(s):

validate(SBMLExternalValidator self)   long

the actual conversion

Returns
status code represeting success/failure/conversion impossible