/// <summary>
/// Converts a SBML document to the latest version (3.1) that is supported.
/// </summary>
private void convertSBML(SBMLDocument sbmlDoc)
{
var latestLevel = SBMLDocument.getDefaultLevel();
var latestVersion = SBMLDocument.getDefaultVersion();
if (sbmlDoc.getLevel() == latestLevel || sbmlDoc.getVersion() == latestVersion)
{
return;
}
var success = sbmlDoc.setLevelAndVersion(latestLevel, latestVersion);
if (!success)
{
throw new MoBiException(SBMLConstants.CouldNotConvertToActualLevel(latestLevel, latestVersion,
sbmlDoc.getLevel(), sbmlDoc.getVersion()));
}
}
public static int Main(string[] args)
{
int latestLevel = (int)SBMLDocument.getDefaultLevel();
int latestVersion = (int)SBMLDocument.getDefaultVersion();
if (args.Length != 2)
{
Console.Write("Usage: convertSBML input-filename output-filename" + Environment.NewLine
+ "This program will attempt to convert a model either to" + Environment.NewLine
+ "SBML Level " + latestLevel + " Version " + latestVersion
+ " (if the model is not already) or, if " + Environment.NewLine
+ "the model is already expressed in Level " + latestLevel
+ " Version " + latestVersion + ", this" + Environment.NewLine
+ "program will attempt to convert the model to Level 1 Version 2."
+ Environment.NewLine);
return(1);
}
string inputFile = args[0];
string outputFile = args[1];
SBMLDocument document = libsbml.readSBML(inputFile);
long errors = document.getNumErrors();
if (errors > 0)
{
Console.Error.Write("Encountered the following SBML errors:" + Environment.NewLine);
document.printErrors();
Console.Error.Write("Conversion skipped. Please correct the problems above first."
+ Environment.NewLine);
return((int)errors);
}
/**
* If the given model is not already L2v4, assume that the user wants to
* convert it to the latest release of SBML (which is L2v4 currently).
* If the model is already L2v4, assume that the user wants to attempt to
* convert it down to Level 1 (specifically L1v2).
*/
int olevel = (int)document.getLevel();
int oversion = (int)document.getVersion();
bool success;
if (olevel < latestLevel || oversion < latestVersion)
{
Console.Write("Attempting to convert Level " + olevel + " Version " + oversion
+ " model to Level " + latestLevel
+ " Version " + latestVersion + "." + Environment.NewLine);
success = document.setLevelAndVersion(latestLevel, latestVersion);
}
else
{
Console.Write("Attempting to convert Level " + olevel + " Version " + oversion
+ " model to Level 1 Version 2." + Environment.NewLine);
success = document.setLevelAndVersion(1, 2);
}
errors = document.getNumErrors();
if (!success)
{
Console.Error.Write("Unable to perform conversion due to the following:" + Environment.NewLine);
document.printErrors();
Console.Write(Environment.NewLine);
Console.Write("Conversion skipped. Either libSBML does not (yet)" + Environment.NewLine
+ "have the ability to convert this model or (automatic)" + Environment.NewLine
+ "conversion is not possible in this case." + Environment.NewLine);
return((int)errors);
}
else if (errors > 0)
{
Console.Write("Information may have been lost in conversion; but a valid model ");
Console.Write("was produced by the conversion.\nThe following information ");
Console.Write("was provided:\n");
document.printErrors();
libsbml.writeSBML(document, outputFile);
}
else
{
Console.Write("Conversion completed." + Environment.NewLine);
libsbml.writeSBML(document, outputFile);
}
return(0);
}