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));
}
static void Main()
{
Debug.Assert((CRootContainer.getRoot() != null));
// create a new datamodel
CDataModel dataModel = CRootContainer.addDatamodel();
Debug.Assert((dataModel != null));
Debug.Assert((CRootContainer.getDatamodelList().size() == 1));
// next we import a simple SBML model from a string
// clear the message queue so that we only have error messages from the import in the queue
CCopasiMessage.clearDeque();
bool result = true;
try
{
result = dataModel.importSBMLFromString(MODEL_STRING);
}
catch
{
System.Console.Error.WriteLine("Import of model failed miserably.");
System.Environment.Exit(1);
}
// check if the import was successful
int mostSevere = CCopasiMessage.getHighestSeverity();
// if it was a filtered error, we convert it to an unfiltered type
// the filtered error messages have the same value as the unfiltered, but they
// have the 7th bit set which basically adds 128 to the value
mostSevere = mostSevere & 127;
// we assume that the import succeeded if the return value is true and
// the most severe error message is not an error or an exception
if (result != true && mostSevere < CCopasiMessage.ERROR)
{
System.Console.Error.WriteLine("Sorry. Model could not be imported.");
System.Environment.Exit(1);
}
//
// now we tell the model object to calculate the jacobian
//
CModel model = dataModel.getModel();
Debug.Assert((model != null));
if (model != null)
{
// running a task, e.g. a trajectory will automatically make sure that
// the initial values are transferred to the current state before the calculation begins.
// If we use low level calculation methods like the one to calculate the jacobian, we
// have to make sure the the initial values are applied to the state
model.applyInitialValues();
// we need an array that stores the result
// the size of the matrix does not really matter because
// the calculateJacobian autoamtically resizes it to the correct
// size
FloatMatrix jacobian = new FloatMatrix();
// the first parameter to the calculation function is a reference to
// the matrix where the result is to be stored
// the second parameter is the derivationFactor for the calculation
// it basically represents a relative delta value for the calculation of the derivatives
// the third parameter is a boolean indicating whether the jacobian should
// be calculated from the reduced (true) or full (false) system
model.getMathContainer().calculateJacobian(jacobian, 1e-12, false);
// now we print the result
// the jacobian stores the values in the order they are
// given in the user order in the state template so it is not really straight
// forward to find out which column/row corresponds to which species
CStateTemplate stateTemplate = model.getStateTemplate();
// and we need the user order
SizeTVector userOrder = stateTemplate.getUserOrder();
// from those two, we can construct an new vector that contains
// the names of the entities in the jacobian in the order in which they appear in
// the jacobian
System.Collections.Generic.List <string> nameVector = new System.Collections.Generic.List <string>();
CModelEntity entity = null;
int status;
for (uint i = 0; i < userOrder.size(); ++i)
{
entity = stateTemplate.getEntity(userOrder.get(i));
Debug.Assert((entity != null));
// now we need to check if the entity is actually
// determined by an ODE or a reaction
status = entity.getStatus();
if (status == CModelEntity.Status_ODE ||
(status == CModelEntity.Status_REACTIONS && entity.isUsed()))
{
nameVector.Add(entity.getObjectName());
}
}
Debug.Assert((nameVector.Count == jacobian.numRows()));
// now we print the matrix, for this we assume that no
// entity name is longer then 5 character which is a save bet since
// we know the model
System.Console.Out.NewLine = "";
System.Console.WriteLine(System.String.Format("Jacobian Matrix:{0}", System.Environment.NewLine));
System.Console.WriteLine(System.String.Format("size:{0}x{1}{2}", jacobian.numRows(), jacobian.numCols(), System.Environment.NewLine));
System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine));
System.Console.Out.WriteLine(System.String.Format("{0,7}", " "));
for (int i = 0; i < nameVector.Count; ++i)
{
System.Console.Out.WriteLine(System.String.Format("{0,7}", nameVector[i]));
}
System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine));
for (uint i = 0; i < nameVector.Count; ++i)
{
System.Console.Out.WriteLine(System.String.Format("{0,7}", nameVector[(int)i]));
for (uint j = 0; j < nameVector.Count; ++j)
{
System.Console.Out.WriteLine(System.String.Format("{0,7:0.###}", jacobian.get(i, j)));
}
System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine));
}
// we can also calculate the jacobian of the reduced system
// in a similar way
model.getMathContainer().calculateJacobian(jacobian, 1e-12, true);
// this time generating the output is actually simpler because the rows
// and columns are ordered in the same way as the independent variables of the state temple
System.Console.WriteLine(System.String.Format("{0}{0}", System.Environment.NewLine));
System.Console.WriteLine(System.String.Format("Reduced Jacobian Matrix:{0}{0}", System.Environment.NewLine));
System.Console.Out.WriteLine(System.String.Format("{0:6}", " "));
uint iMax = stateTemplate.getNumIndependent();
for (uint i = 0; i < iMax; ++i)
{
System.Console.Out.WriteLine(System.String.Format("\t{0:7}", stateTemplate.getIndependent(i).getObjectName()));
}
System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine));
for (uint i = 0; i < iMax; ++i)
{
System.Console.Out.WriteLine(System.String.Format("{0:7}", stateTemplate.getIndependent(i).getObjectName()));
for (uint j = 0; j < iMax; ++j)
{
System.Console.Out.WriteLine(System.String.Format("{0,7:0.###}", jacobian.get(i, j)));
}
System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine));
}
}
}
static void Main()
{
// initialize the backend library
// since we are not interested in the arguments
// that are passed to main, we pass 0 and NULL to
// init
Debug.Assert(CCopasiRootContainer.getRoot() != null);
// create a new datamodel
CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel();
Debug.Assert((dataModel != null));
Debug.Assert((CCopasiRootContainer.getDatamodelList().size() == 1));
// next we import a simple SBML model from a string
// clear the message queue so that we only have error messages from the import in the queue
CCopasiMessage.clearDeque();
bool result = true;
try
{
result = dataModel.importSBMLFromString(MODEL_STRING);
}
catch
{
System.Console.Error.WriteLine("An exception has occured during the import of the SBML model");
System.Environment.Exit(1);
}
// check if the import was successful
int mostSevere = CCopasiMessage.getHighestSeverity();
// if it was a filtered error, we convert it to an unfiltered type
// the filtered error messages have the same value as the unfiltered, but they
// have the 7th bit set which basically adds 128 to the value
mostSevere = mostSevere & 127;
// we assume that the import succeeded if the return value is true and
// the most severe error message is not an error or an exception
if (result != true && mostSevere < CCopasiMessage.ERROR)
{
System.Console.Error.WriteLine("Sorry. Model could not be imported.");
System.Environment.Exit(1);
}
// get the trajectory task object
CSteadyStateTask task = (CSteadyStateTask)dataModel.getTask("Steady-State");
CCopasiMessage.clearDeque();
try
{
// now we run the actual trajectory
task.processWithOutputFlags(true, (int)CCopasiTask.ONLY_TIME_SERIES);
}
catch
{
System.Console.Error.WriteLine("Error. Running the scan failed.");
String lastErrors = task.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);
}
// now we can get the result of the steady state calculation, e.g. the jacobian
// matrix of the model at the steady state
// here we can either get the jacobian as we did in example 8 as a matrix with
// getJacobian, or we can use getJacobianAnnotated to get an annotated matrix
// Corresponding methods for the reduced jacobian are getJacobianX and getJacobianXAnnotated
CArrayAnnotation aj = task.getJacobianAnnotated();
Debug.Assert((aj != null));
if (aj != null)
{
// we do the output, but as in contrast to the jacobian in example 8,
// we now have all the information for the output in one place
// first the array annotation can tell us how many dimensions it has.
// Since the matrix is a 2D array, it should have 2 dimensions
Debug.Assert((aj.dimensionality() == 2));
// since the matrix has a dimensionality of 2, the inde for the underlaying abstract array
// object is a vector with two unsigned int elements
// First element is the index for the outer dimension and the second element is the index
// for the inner dimension
SizeTStdVector index = new SizeTStdVector();
// The constructor does not seem to interpret an integer argument
// as the size
// I though that in C# we might be able to achieve this using the Capacity property
// but that didn't work. Maybe I was using it incorrectly since I don't really know C#
// So for now, we just add two elements to the vector which seems to do the trick.
index.Add(0);
index.Add(0);
// since the rows and columns have the same annotation for the jacobian, it doesn't matter
// for which dimension we get the annotations
StringStdVector annotations = aj.getAnnotationsString(1);
System.Console.Out.NewLine = "";
System.Console.WriteLine(System.String.Format("Jacobian Matrix:{0}{0}", System.Environment.NewLine));
System.Console.Out.WriteLine(System.String.Format("{0,7}", " "));
for (int i = 0; i < annotations.Count; ++i)
{
Console.Out.WriteLine(System.String.Format("{0,7}", annotations[i]));
}
Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine));
for (int i = 0; i < annotations.Count; ++i)
{
System.Console.Out.WriteLine(System.String.Format("{0,7} ", annotations[i]));
index[0] = (uint)i;
for (int j = 0; j < annotations.Count; ++j)
{
index[1] = (uint)j;
System.Console.Out.WriteLine(System.String.Format("{0,7:G2} ", aj.array().get(index)));
}
System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine));
}
}
System.Environment.Exit(0);
}
