public static int Main(string[] args)
{
if (args.Length != 2)
{
Console.WriteLine("Usage: inlineInitialAssignments filename outFile");
return(1);
}
string filename = args[0];
string outFile = args[1];
long current = DateTime.Now.Ticks;
SBMLDocument document = libsbml.readSBML(filename);
if (document.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0)
{
Console.WriteLine("The models contains errors, please correct them before continuing.");
document.printErrors();
return(1);
}
var model = document.getModel();
SBMLTransforms.expandInitialAssignments(model);
libsbml.writeSBML(document, outFile);
return(0);
}
public static int Main(string[] args)
{
if (args.Length != 4)
{
Console.WriteLine("Usage: replaceOneFD filename functionDefinitionId reactionId outfile");
return(1);
}
string filename = args[0];
string outFile = args[3];
string functionDefinitionId = args[1];
string reactionId = args[2];
long current = DateTime.Now.Ticks;
SBMLDocument document = libsbml.readSBML(filename);
if (document.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0)
{
Console.WriteLine("The models contains errors, please correct them before continuing.");
document.printErrors();
return(1);
}
var model = document.getModel();
var functionDefinition = model.getFunctionDefinition(functionDefinitionId);
if (functionDefinition == null)
{
Console.WriteLine();
Console.WriteLine("No functiondefinition with the given id can be found.");
return(1);
}
var reaction = model.getReaction(reactionId);
if (reaction == null)
{
Console.WriteLine();
Console.WriteLine("No reaction with the given id can be found.");
return(1);
}
if (!reaction.isSetKineticLaw() || !reaction.getKineticLaw().isSetMath())
{
Console.WriteLine();
Console.WriteLine("The reaction has no math set. ");
return(1);
}
// Until here it was all setup, all we needed was an ASTNode, in which we wanted to
// replace calls to a function definition, with the function definitions content.
//
SBMLTransforms.replaceFD(reaction.getKineticLaw().getMath(), functionDefinition);
// finally write to file
libsbml.writeSBML(document, outFile);
return(0);
}
public static int Main(string[] args)
{
if (args.Length < 1)
{
Console.WriteLine("Usage: evaluateCustomMath formula [model containing values]");
return(1);
}
string formula = args[0];
string filename = args.Length == 2 ? args[1] : null;
var math = libsbml.parseFormula(formula);
if (math == null)
{
Console.WriteLine("Invalid formula, aborting.");
return(1);
}
SBMLDocument doc = null;
if (filename != null)
{
doc = libsbml.readSBML(filename);
if (doc.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0)
{
Console.WriteLine("The models contains errors, please correct them before continuing.");
doc.printErrors();
return(1);
}
// the following maps a list of ids to their corresponding model values
// this makes it possible to evaluate expressions involving SIds.
SBMLTransforms.mapComponentValues(doc.getModel());
}
else
{
// create dummy document
doc = new SBMLDocument(3, 1);
}
var result = SBMLTransforms.evaluateASTNode(math, doc.getModel());
Console.WriteLine("{0} = {1}", formula, result);
return(0);
}
