public static int Main(string[] args)
{
if (args.Length != 1)
{
Console.WriteLine("Usage: create_sedml output-filename.");
return(2);
}
// create the document
SedDocument doc = new SedDocument();
doc.setLevel(1);
doc.setVersion(1);
{
// create a first model referencing an sbml file
SedModel model = doc.createModel();
model.setId("model1");
model.setSource("file.xml");
model.setLanguage("urn:sedml:sbml");
// create a second model modifying a variable of that other sbml file
model = doc.createModel();
model.setId("model2");
model.setSource("model1");
model.setLanguage("urn:sedml:sbml");
// change a paramerter 'k' to 0.1
SedChangeAttribute change = model.createChangeAttribute();
change.setTarget("/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='k']/@value");
change.setNewValue("0.1");
// remove species 's1'
SedRemoveXML remove = model.createRemoveXML();
remove.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']");
// now for something tricky we want to update the initialConcentration of 'S2' to be
// half what it was in the original model
SedComputeChange compute = model.createComputeChange();
compute.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id="S2"]/@initialConcentration");
SedVariable variable = compute.createVariable();
variable.setId("S2");
variable.setModelReference("model1");
variable.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S2']");
compute.setMath(libsedml.parseFormula("S2 / 2"));
}
// create simulation
SedUniformTimeCourse tc = doc.createUniformTimeCourse();
tc.setId("sim1");
tc.setInitialTime(0.0);
tc.setOutputStartTime(0.0);
tc.setOutputEndTime(10.0);
tc.setNumberOfPoints(1000);
// need to set the correct KISAO Term
SedAlgorithm alg = tc.createAlgorithm();
alg.setKisaoID("KISAO:0000019");
// create a task that uses the simulation and the model above
SedTask task = doc.createTask();
task.setId("task1");
task.setModelReference("model1");
task.setSimulationReference("sim1");
// add a DataGenerator to hold the output for time
SedDataGenerator dg = doc.createDataGenerator();
dg.setId("time");
dg.setName("time");
SedVariable var = dg.createVariable();
var.setId("v0");
var.setName("time");
var.setTaskReference("task1");
var.setSymbol("urn:sedml:symbol:time");
dg.setMath(libsedml.parseFormula("v0"));
// and one for S1
dg = doc.createDataGenerator();
dg.setId("S1");
dg.setName("S1");
var = dg.createVariable();
var.setId("v1");
var.setName("S1");
var.setTaskReference("task1");
var.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']");
dg.setMath(libsedml.parseFormula("v1"));
// add a report
SedReport report = doc.createReport();
report.setId("r1");
report.setName("report 1");
SedDataSet set = report.createDataSet();
set.setId("ds1");
set.setLabel("time");
set.setDataReference("time");
set = report.createDataSet();
set.setId("ds2");
set.setLabel("S1");
set.setDataReference("S1");
// add a 2d plot
SedPlot2D plot = doc.createPlot2D();
plot.setId("p1");
plot.setName("S1 Timecourse");
SedCurve curve = plot.createCurve();
curve.setId("c1");
curve.setName("S1");
curve.setLogX(false);
curve.setLogY(false);
curve.setXDataReference("time");
curve.setYDataReference("S1");
// add a 3D Plot
SedPlot3D plot2 = doc.createPlot3D();
plot2.setId("p2");
plot2.setName("dunno");
SedSurface surf = plot2.createSurface();
surf.setId("surf1");
surf.setName("S1");
surf.setLogX(false);
surf.setLogY(false);
surf.setLogZ(false);
surf.setXDataReference("time");
surf.setYDataReference("S1");
surf.setZDataReference("S1");
// write the document
libsedml.writeSedML(doc, args[0]);
return(0);
}
public static int Main(string[] args)
{
if (args.Length != 1)
{
Console.WriteLine("{0}Usage: print_sedml input-filename{0}{0}", Environment.NewLine);
return(2);
}
SedDocument doc = libsedml.readSedML(args[0]);
if (doc.getErrorLog().getNumFailsWithSeverity(libsedml.LIBSEDML_SEV_ERROR) > 0)
{
Console.WriteLine(doc.getErrorLog().toString());
return(2);
}
Console.WriteLine("The document has " + doc.getNumSimulations() + " simulation(s)." + Environment.NewLine);
for (int i = 0; i < doc.getNumSimulations(); ++i)
{
SedSimulation current = doc.getSimulation(i);
switch (current.getTypeCode())
{
case libsedml.SEDML_SIMULATION_UNIFORMTIMECOURSE:
{
SedUniformTimeCourse tc = (SedUniformTimeCourse)(current);
Console.WriteLine("\tTimecourse id=" + tc.getId() + " start=" + tc.getOutputStartTime() + " end=" + tc.getOutputEndTime() + " numPoints=" + tc.getNumberOfPoints() + " kisao=" + (tc.isSetAlgorithm() ? tc.getAlgorithm().getKisaoID() : "none") + Environment.NewLine);
break;
}
default:
Console.WriteLine("\tUncountered unknown simulation. " + current.getId() + Environment.NewLine);
break;
}
}
Console.WriteLine(Environment.NewLine);
Console.WriteLine("The document has " + doc.getNumModels() + " model(s)." + Environment.NewLine);
for (int i = 0; i < doc.getNumModels(); ++i)
{
SedModel current = doc.getModel(i);
Console.WriteLine("\tModel id=" + current.getId() + " language=" + current.getLanguage() + " source=" + current.getSource() + " numChanges=" + current.getNumChanges() + Environment.NewLine);
}
Console.WriteLine(Environment.NewLine);
Console.WriteLine("The document has " + doc.getNumTasks() + " task(s)." + Environment.NewLine);
for (int i = 0; i < doc.getNumTasks(); ++i)
{
SedTask current = doc.getTask(i);
Console.WriteLine("\tTask id=" + current.getId() + " model=" + current.getModelReference() + " sim=" + current.getSimulationReference() + Environment.NewLine);
}
Console.WriteLine(Environment.NewLine);
Console.WriteLine("The document has " + doc.getNumDataGenerators() + " datagenerators(s)." + Environment.NewLine);
for (int i = 0; i < doc.getNumDataGenerators(); ++i)
{
SedDataGenerator current = doc.getDataGenerator(i);
Console.WriteLine("\tDG id=" + current.getId() + " math=" + libsedml.formulaToString(current.getMath()) + Environment.NewLine);
}
Console.WriteLine(Environment.NewLine);
Console.WriteLine("The document has " + doc.getNumOutputs() + " output(s)." + Environment.NewLine);
for (int i = 0; i < doc.getNumOutputs(); ++i)
{
SedOutput current = doc.getOutput(i);
switch (current.getTypeCode())
{
case libsedml.SEDML_OUTPUT_REPORT:
{
SedReport r = (SedReport)(current);
Console.WriteLine("\tReport id=" + current.getId() + " numDataSets=" + r.getNumDataSets() + Environment.NewLine);
break;
}
case libsedml.SEDML_OUTPUT_PLOT2D:
{
SedPlot2D p = (SedPlot2D)(current);
Console.WriteLine("\tPlot2d id=" + current.getId() + " numCurves=" + p.getNumCurves() + Environment.NewLine);
break;
}
case libsedml.SEDML_OUTPUT_PLOT3D:
{
SedPlot3D p = (SedPlot3D)(current);
Console.WriteLine("\tPlot3d id=" + current.getId() + " numSurfaces=" + p.getNumSurfaces() + Environment.NewLine);
break;
}
default:
Console.WriteLine("\tEncountered unknown output " + current.getId() + Environment.NewLine);
break;
}
}
return(0);
}