/// <summary>
/// Convert the specified outFile.
/// </summary>
/// <param name='outFile'>
/// Out file.
/// </param>
public void Convert(string outFile)
{
OutputFile = outFile;
var path = Path.GetDirectoryName(OutputFile);
var baseName = Path.GetFileNameWithoutExtension(OutputFile);
if (path == null)
{
path = Environment.CurrentDirectory;
}
var sbmlFile = Path.Combine(path, baseName + "-sbml.xml");
CCopasiRootContainer.init();
var dataModel = CCopasiRootContainer.addDatamodel();
dataModel.loadModel(CopasiFile);
// write sbml model
dataModel.exportSBML(sbmlFile, true);
// construct SED-ML
SedML = new SedMLInfo();
SedML.ListOfModels.Add(new Model(
"model1", sbmlFile));
SedML.ListOfModels[0].ModelContent = File.ReadAllText(sbmlFile);
var trajectory = (CTrajectoryTask)dataModel.getTask("Time-Course");
if (trajectory != null)
{
var problem = (CTrajectoryProblem)trajectory.getProblem();
var method = (CTrajectoryMethod)trajectory.getMethod();
var startTime = problem.getOutputStartTime();
var steps = (int)problem.getStepNumber();
var initial = dataModel.getModel().getInitialTime();
var endTime = startTime + steps * problem.getStepSize();
var kisao = method.getSubType() == CCopasiMethod.deterministic
? Algorithm.DeterministicAlgorithm
: Algorithm.StochasticAlgorithm;
var simulation = new UniformTimeCourse("sim1", initial, startTime, endTime, steps)
{
Algorithm = kisao
};
SedML.ListOfSimulations.Add(simulation);
SedML.ListOfTasks.Add(new Task("task1", "sim1", "model1"));
for (int i = 0; i < dataModel.getPlotDefinitionList().size(); i++)
{
var current = dataModel.getPlotSpecification((uint)i);
var plot = CreatePlot(dataModel, current);
if (plot.ListOfCurves.Count > 0)
SedML.ListOfOutputs.Add(plot);
}
CreateDataGenerators(SedML);
}
SedML.FixCommonErrors();
}
/// <summary>
/// Creates the data generators.
/// </summary>
/// <param name='info'>
/// Info.
/// </param>
void CreateDataGenerators(SedMLInfo info)
{
info.UpdateStores();
foreach (var item in dataIds)
{
info.ListOfDataGenerators.Add(new DataGenerator
{
Id = item,
Name = names[item],
ListOfVariables = new List<Variable>
{
new Variable ("v", "task1", SBMLLanguage.GetXPath (types [item], item))
},
MathML = "v"
}
);
}
}
