public static void Main(String[] args)
{
if (args.Length == 0)
{
Console.WriteLine("Need one argument, copasi file");
Environment.Exit(1);
}
CDataModel dataModel = CRootContainer.addDatamodel();
if (!dataModel.loadModel(args[0]))
{
Console.WriteLine("Could not open file");
Console.WriteLine(CCopasiMessage.getAllMessageText());
Environment.Exit(1);
}
CModel model = dataModel.getModel();
ModelParameterSetVectorN sets = model.getModelParameterSets();
// if we don't have one, create one
if (sets.size() == 0)
{
CModelParameterSet newSet = new CModelParameterSet("Current State", model);
newSet.createFromModel();
printParameterSet(newSet);
sets.add(newSet);
}
// interrogate the exiting parameter sets
printExistingParametersets(model.getModelParameterSets());
}
public static void Main(String[] args)
{
// create a new datamodel
CDataModel dataModel = CRootContainer.addDatamodel();
if (args.Length != 1)
{
Console.WriteLine("Need one argument: SBML | CPS filename.");
Environment.Exit(1);
}
String filename = args[0];
try
{
String ext = System.IO.Path.GetExtension(filename);
if (ext.Trim().ToLowerInvariant().EndsWith("xml"))
{
// load the model without progress report
dataModel.importSBML(filename);
}
else
{
// load the model without progress report
dataModel.loadModel(filename);
}
}
catch
{
Console.WriteLine("Error while loading the model from file named \"" + filename + "\".");
Environment.Exit(1);
}
try
{
CModel model = dataModel.getModel();
int numAnnotations = model.getNumUnsupportedAnnotations();
Console.WriteLine("The model has: " + numAnnotations + " unsupported annotations.");
if (numAnnotations == 0)
{
Console.WriteLine("adding custom annotation");
// we don't have an annotation, so lets add one
if (!model.addUnsupportedAnnotation("http://myannotation.org", "<test xmlns='http://myannotation.org' value='blaaaahaaa'/>"))
{
Console.WriteLine("couldn't set annotation: ");
Console.WriteLine(CCopasiMessage.getAllMessageText());
}
}
Console.WriteLine("The name of the first is: " + model.getUnsupportedAnnotationName(0));
Console.WriteLine("The raw xml of the first is: " + model.getUnsupportedAnnotation(0));
}
catch (Exception ex)
{
Console.WriteLine("Error: " + ex.Message);
}
}
public static void Main(String[] args)
{
// create a new datamodel
CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel();
if (args.Length != 2)
{
Console.WriteLine("Need two arguments: filename and filter.");
Environment.Exit(1);
}
String filename = args[0];
try
{
String ext = System.IO.Path.GetExtension(filename);
if (ext.Trim().ToLowerInvariant() == "xml")
{
// load the model without progress report
dataModel.importSBML(filename);
}
else
{
// load the model without progress report
dataModel.loadModel(filename);
}
}
catch
{
Console.WriteLine("Error while loading the model from file named \"" + filename + "\".");
Environment.Exit(1);
}
try
{
// clear warnings / error messages
CCopasiMessage.clearDeque();
// convert
String translation = dataModel.exportMathModelToString(args[1]);
// if conversion failed print message
if (string.IsNullOrEmpty(translation))
{
Console.WriteLine("Translation failed: ");
Console.WriteLine(CCopasiMessage.getAllMessageText());
}
// print translation
Console.WriteLine(translation);
}
catch
{
Console.WriteLine("Error. Exporting the model to math failed.");
}
}
static void Main(string[] args)
{
if (args.Length == 0)
{
Console.WriteLine("usage: process_callback <cps file>");
return;
}
var dataModel = CRootContainer.addDatamodel();
if (!dataModel.loadModel(args[0]))
{
Console.WriteLine("Couldn't open the model: ");
Console.WriteLine(CCopasiMessage.getAllMessageText());
return;
}
var progress = new ProcessCallback();
Console.CancelKeyPress += delegate {
Console.WriteLine("Stop requested ... waiting for process to finish");
progress.ShouldProceed = false;
Thread.Sleep(30000);
};
for (uint i = 0; i < dataModel.getNumTasks(); ++i)
{
var task = dataModel.getTask(i);
if (!task.isScheduled())
{
continue;
}
Console.WriteLine(string.Format("Running Scheduled Task: {0}, stop anytime using CTRL+C", task.getObjectName()));
// set progress support
task.setCallBack(progress);
// execute the task
task.process(true);
// unset
task.clearCallBack();
}
}
/// <summary>
/// Simulate a Step and return data
/// </summary>
/// <param name="stepDuration">Step duration in seconds.</param>
public SimulationStep Step(double stepDuration)
{
CTrajectoryTask trajectoryTask = copasi.TrajectoryTask;
CTrajectoryProblem problem = (CTrajectoryProblem)trajectoryTask.getProblem();
problem.setDuration(stepDuration);
currentTime += stepDuration;
try
{
// now we run the actual trajectory
trajectoryTask.processWithOutputFlags(true, (int)CCopasiTask.NO_OUTPUT);
}
catch
{
if (CCopasiMessage.size() > 0)
{
throw new System.Exception("Running the time course simulation failed: " + CCopasiMessage.getAllMessageText(true));
}
throw new System.Exception("Running the time course simulation failed");
}
// Update the species properties that have changed
ReactionCount[] reactionCount = new ReactionCount[reactionList.Count];
for (int i = 0; i < reactionList.Count; i++)
{
CopasiReactionGroup r = reactionList[i];
reactionCount[i] = r.CalcParticleFlux();
}
// clean up
trajectoryTask.restore();
return(new SimulationStep(reactionCount));
}
