validateSBMLdocument: Validate SBML

In SysBioChalmers/sybil-SBML: 'SBML' Integration in Package 'Sybil'

Validate SBML

Description

Validate files written in SBML.

Usage

  validateSBMLdocument(sbmlf)

Arguments

sbmlf

A single character string containing a filename of an SBML file, or an object of class sbmlPtr as returned by openSBMLfile.

Details

The given SBML file is validated by the libSBML function checkConsistency. Errors are retrieved by the libSBML function getError and returned as list.

Value

If argument sbmlf is an object of class character,the function returns TRUE, if no infos, warnings, errors or fatals have been found. Otherwise a the value returned is a list.

infos	Infos
warnings	Warnings
errors	Errors
fatals	Fatals

Each entry of one of these lists is again a list containing the message id, line and column number of the SBML file generating the message and the corresponding message text.

If argument sbmlf is an object of class sbmlPtr, the function returns the number of errors found in the SBML document.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

References

Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008) LibSBML: An API Library for SBML. Bioinformatics 24, 880–881.

See Also

readSBMLmod, openSBMLfile, getSBMLerrors, sbmlPtr

Examples

  dir  <- system.file(package = "sybilSBML", "extdata")
  file <- file.path(dir, "ecoli_core_model.xml")
  err  <- validateSBMLdocument(file)

SysBioChalmers/sybil-SBML documentation built on Aug. 24, 2023, 1:11 p.m.