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
CDataModel dataModel = CRootContainer.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)
{
Debug.Assert(CRootContainer.getRoot() != null);
// create a new datamodel
CDataModel dataModel = CRootContainer.addDatamodel();
Debug.Assert(CRootContainer.getDatamodelList().size() == 1);
// the only argument to the main routine should be the name of an SBML file
if (args.Length == 1)
{
string filename = args[0];
try
{
// load the model
dataModel.importSBML(filename);
}
catch
{
System.Console.Error.WriteLine("Error while importing the model from file named \"" + filename + "\".");
System.Environment.Exit(1);
}
CModel model = dataModel.getModel();
Debug.Assert(model != null);
// create a report with the correct filename and all the species against
// time.
CReportDefinitionVector reports = dataModel.getReportDefinitionList();
// create a new report definition object
CReportDefinition report = reports.createReportDefinition("Report", "Output for timecourse");
// set the task type for the report definition to timecourse
report.setTaskType(CTaskEnum.Task_timeCourse);
// we don't want a table
report.setIsTable(false);
// the entries in the output should be seperated by a ", "
report.setSeparator(new CCopasiReportSeparator(", "));
// we need a handle to the header and the body
// the header will display the ids of the metabolites and "time" for
// the first column
// the body will contain the actual timecourse data
ReportItemVector header = report.getHeaderAddr();
ReportItemVector body = report.getBodyAddr();
body.Add(new CRegisteredCommonName(model.getObject(new CCommonName("Reference=Time")).getCN().getString()));
body.Add(new CRegisteredCommonName(report.getSeparator().getCN().getString()));
header.Add(new CRegisteredCommonName(new CDataString("time").getCN().getString()));
header.Add(new CRegisteredCommonName(report.getSeparator().getCN().getString()));
uint i, iMax = (uint)model.getMetabolites().size();
for (i = 0; i < iMax; ++i)
{
CMetab metab = model.getMetabolite(i);
Debug.Assert(metab != null);
// we don't want output for FIXED metabolites right now
if (metab.getStatus() != CModelEntity.Status_FIXED)
{
// we want the concentration oin the output
// alternatively, we could use "Reference=Amount" to get the
// particle number
body.Add(new CRegisteredCommonName(metab.getObject(new CCommonName("Reference=Concentration")).getCN().getString()));
// add the corresponding id to the header
header.Add(new CRegisteredCommonName(new CDataString(metab.getSBMLId()).getCN().getString()));
// after each entry, we need a seperator
if (i != iMax - 1)
{
body.Add(new CRegisteredCommonName(report.getSeparator().getCN().getString()));
header.Add(new CRegisteredCommonName(report.getSeparator().getCN().getString()));
}
}
}
// get the trajectory task object
CTrajectoryTask trajectoryTask = (CTrajectoryTask)dataModel.getTask("Time-Course");
// run a deterministic time course
trajectoryTask.setMethodType(CTaskEnum.Method_deterministic);
// pass a pointer of the model to the problem
trajectoryTask.getProblem().setModel(dataModel.getModel());
// actiavate the task so that it will be run when the model is saved
// and passed to CopasiSE
trajectoryTask.setScheduled(true);
// set the report for the task
trajectoryTask.getReport().setReportDefinition(report);
// set the output filename
trajectoryTask.getReport().setTarget("example3.txt");
// don't append output if the file exists, but overwrite the file
trajectoryTask.getReport().setAppend(false);
// get the problem for the task to set some parameters
CTrajectoryProblem problem = (CTrajectoryProblem)trajectoryTask.getProblem();
// simulate 100 steps
problem.setStepNumber(100);
// start at time 0
dataModel.getModel().setInitialTime(0.0);
// simulate a duration of 10 time units
problem.setDuration(10);
// tell the problem to actually generate time series data
problem.setTimeSeriesRequested(true);
// set some parameters for the LSODA method through the method
CTrajectoryMethod method = (CTrajectoryMethod)trajectoryTask.getMethod();
CCopasiParameter parameter = method.getParameter("Absolute Tolerance");
Debug.Assert(parameter != null);
Debug.Assert(parameter.getType() == CCopasiParameter.Type_DOUBLE);
parameter.setDblValue(1.0e-12);
bool result = true;
try
{
// now we run the actual trajectory
result = trajectoryTask.processWithOutputFlags(true, (int)CCopasiTask.ONLY_TIME_SERIES);
}
catch
{
System.Console.Error.WriteLine("Error. Running the time course simulation failed.");
String lastErrors = trajectoryTask.getProcessError();
// check if there are additional error messages
if (!string.IsNullOrEmpty(lastErrors))
{
// print the messages in chronological order
System.Console.Error.WriteLine(lastErrors);
}
System.Environment.Exit(1);
}
if (result == false)
{
System.Console.Error.WriteLine("An error occured while running the time course simulation.");
String lastErrors = trajectoryTask.getProcessError();
// check if there are additional error messages
if (!string.IsNullOrEmpty(lastErrors))
{
// print the messages in chronological order
System.Console.Error.WriteLine(lastErrors);
}
System.Environment.Exit(1);
}
// look at the timeseries
CTimeSeries timeSeries = trajectoryTask.getTimeSeries();
// we simulated 100 steps, including the initial state, this should be
// 101 step in the timeseries
Debug.Assert(timeSeries.getRecordedSteps() == 101);
System.Console.WriteLine("The time series consists of " + System.Convert.ToString(timeSeries.getRecordedSteps()) + ".");
System.Console.WriteLine("Each step contains " + System.Convert.ToString(timeSeries.getNumVariables()) + " variables.");
System.Console.WriteLine("The final state is: ");
iMax = (uint)timeSeries.getNumVariables();
uint lastIndex = (uint)timeSeries.getRecordedSteps() - 1;
for (i = 0; i < iMax; ++i)
{
// here we get the particle number (at least for the species)
// the unit of the other variables may not be particle numbers
// the concentration data can be acquired with getConcentrationData
System.Console.WriteLine(timeSeries.getTitle(i) + ": " + System.Convert.ToString(timeSeries.getData(lastIndex, i)));
}
}
else
{
System.Console.Error.WriteLine("Usage: example3 SBMLFILE");
System.Environment.Exit(1);
}
}