libSBML Python API
5.8.0
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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 |
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
arg | the argument |
def libsbml.SBMLExternalValidator.clearArguments | ( | self | ) |
Python method signature(s):
clearArguments(SBMLExternalValidator self)
Clear all additional arguments
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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.
def libsbml.SBMLExternalValidator.getArgument | ( | self, | |
args | |||
) |
Python method signature(s):
getArgument(SBMLExternalValidator self, long n)string
Returns the argument for the given index.
n | the zero based index of the argument. |
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inherited |
Python method signature(s):
getDocument(SBMLValidator self)SBMLDocument getDocument(SBMLValidator self)
SBMLDocument
Returns the current SBML document in use by this validator.
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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()).
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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.
n | an integer indicating the index of the object to return from the failures list; index values start at 0. |
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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.
def libsbml.SBMLExternalValidator.getNumArguments | ( | self | ) |
Python method signature(s):
getNumArguments(SBMLExternalValidator self)long
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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.
def libsbml.SBMLExternalValidator.getOutputFileName | ( | self | ) |
Python method signature(s):
getOutputFileName(SBMLExternalValidator self)string
def libsbml.SBMLExternalValidator.getProgram | ( | self | ) |
Python method signature(s):
getProgram(SBMLExternalValidator self)string
def libsbml.SBMLExternalValidator.getSBMLFileName | ( | self | ) |
Python method signature(s):
getSBMLFileName(SBMLExternalValidator self)string
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inherited |
Python method signature(s):
logFailure(SBMLValidator self, SBMLError err)
Adds the given failure to this list of Validators failures.
err | an SBMLError object representing an error or warning |
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inherited |
Python method signature(s):
setDocument(SBMLValidator self, SBMLDocument doc)int
Sets the current SBML document to the given SBMLDocument object.
doc | the document to use for this validation |
def libsbml.SBMLExternalValidator.setOutputFileName | ( | self, | |
args | |||
) |
Python method signature(s):
setOutputFileName(SBMLExternalValidator self, string outputFileName)
Sets the output file name
outputFileName | the 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
program | the 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
sbmlFileName | the temporary name |
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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.
filename | the path to the file to be read and validated. |
Method variant with the following signature:
validate()
Runs this validator on the current SBML document.
Method variant with the following signature:
validate(SBMLDocument d)
Validates the given SBMLDocument object.
This is identical to calling setDocument() followed by validate().
d | the SBML document to validate |
def libsbml.SBMLExternalValidator.validate | ( | self | ) |
Python method signature(s):
validate(SBMLExternalValidator self)long
the actual conversion