| public setPackageRequired ( string package, bool flag ) : int | ||
| package | string | |
| flag | bool | |
| return | int | |
public static int Main(string[] args)
{
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "qual", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// mark qual as required
document.setPackageRequired("qual", true);
// create the Model
Model model = document.createModel();
// create the Compartment
Compartment compartment = model.createCompartment();
compartment.setId("c");
compartment.setConstant(true);
// Get a QualModelPlugin object plugged in the model object.
QualModelPlugin mplugin = (QualModelPlugin)(model.getPlugin("qual"));
// create the QualitativeSpecies
QualitativeSpecies qs = mplugin.createQualitativeSpecies();
qs.setId("s1");
qs.setCompartment("c");
qs.setConstant(false);
qs.setInitialLevel(1);
qs.setMaxLevel(4);
qs.setName("sss");
// create the Transition
Transition t = mplugin.createTransition();
t.setId("d");
t.setSBOTerm(1);
Input i = t.createInput();
i.setId("RD");
i.setQualitativeSpecies("s1");
i.setTransitionEffect(libsbml.INPUT_TRANSITION_EFFECT_NONE);
i.setSign(libsbml.INPUT_SIGN_NEGATIVE);
i.setThresholdLevel(2);
i.setName("aa");
Output o = t.createOutput();
o.setId("wd");
o.setQualitativeSpecies("s1");
o.setTransitionEffect(libsbml.OUTPUT_TRANSITION_EFFECT_PRODUCTION);
o.setOutputLevel(2);
o.setName("aa");
FunctionTerm ft = t.createFunctionTerm();
ASTNode math = libsbml.parseL3Formula("geq(s1, 2)");
ft.setResultLevel(1);
ft.setMath(math);
DefaultTerm dt = t.createDefaultTerm();
dt.setResultLevel(2);
int result = libsbml.writeSBML(document, "qual_example1.xml");
if (result == 1)
{
Console.WriteLine("Wrote file");
return 0;
}
else
{
Console.WriteLine("Failed to write");
return 1;
}
}
public static void Main(string[] args)
{
ArraysPkgNamespaces arraysNs = new ArraysPkgNamespaces();
SBMLDocument doc = new SBMLDocument(arraysNs);
doc.setPackageRequired("arrays", true);
Model model = doc.createModel();
// create compartment
Compartment comp = model.createCompartment();
comp.setMetaId("dd");
comp.setId("s");
comp.setConstant(true);
// set dimensions
ArraysSBasePlugin compPlugin = (ArraysSBasePlugin) comp.getPlugin("arrays");
Dimension dim = compPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
// create species
Species species = model.createSpecies();
species.setId("A");
species.setCompartment("s");
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
ArraysSBasePlugin splugin = (ArraysSBasePlugin) species.getPlugin("arrays");
dim = splugin.createDimension();
dim.setId("i");
dim.setSize("n");
species = model.createSpecies();
species.setId("B");
species.setCompartment("s");
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
splugin = (ArraysSBasePlugin) species.getPlugin("arrays");
dim = splugin.createDimension();
dim.setId("i");
dim.setSize("n");
species = model.createSpecies();
species.setId("C");
species.setCompartment("s");
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
splugin = (ArraysSBasePlugin) species.getPlugin("arrays");
dim = splugin.createDimension();
dim.setId("i");
dim.setSize("n");
// create parameter
Parameter param = model.createParameter();
param.setId("n");
param.setValue(100);
param.setConstant(true);
// create reaction
Reaction reaction = model.createReaction();
reaction.setId("reaction1");
reaction.setReversible(false);
reaction.setFast(false);
ArraysSBasePlugin reactionPlugin = (ArraysSBasePlugin) reaction.getPlugin("arrays");
dim = reactionPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
SpeciesReference speciesRef = reaction.createReactant();
speciesRef.setSpecies("A");
speciesRef.setConstant(false);
ArraysSBasePlugin refPlugin = (ArraysSBasePlugin) speciesRef.getPlugin("arrays");
Index index = refPlugin.createIndex();
ASTNode ast = new ASTNode(libsbml.AST_LINEAR_ALGEBRA_SELECTOR);
ASTNode ci = new ASTNode(libsbml.AST_NAME);
ci.setName("A");
ast.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
ast.addChild(ci);
index.setMath(ast);
speciesRef = reaction.createProduct();
speciesRef.setSpecies("C");
speciesRef.setConstant(false);
refPlugin = (ArraysSBasePlugin) speciesRef.getPlugin("arrays");
index = refPlugin.createIndex();
ast = new ASTNode(libsbml.AST_LINEAR_ALGEBRA_SELECTOR);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("C");
ast.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
ast.addChild(ci);
index.setMath(ast);
libsbml.writeSBMLToFile(doc, "arrays1.xml");
}
public static void Main(string[] args)
{
ArraysPkgNamespaces arraysNs = new ArraysPkgNamespaces();
SBMLDocument doc = new SBMLDocument(arraysNs);
doc.setPackageRequired("arrays", true);
Model model = doc.createModel();
// create parameters
Parameter param = model.createParameter();
param.setId("n");
param.setValue(10);
param.setConstant(true);
param = model.createParameter();
param.setId("m");
param.setValue(10);
param.setConstant(true);
param = model.createParameter();
param.setId("x");
param.setValue(5.7);
param.setConstant(true);
ArraysSBasePlugin paramPlugin = (ArraysSBasePlugin) param.getPlugin("arrays");
Dimension dim = paramPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
param = model.createParameter();
param.setId("y");
param.setConstant(false);
paramPlugin = (ArraysSBasePlugin) param.getPlugin("arrays");
dim = paramPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
param = model.createParameter();
param.setId("z");
param.setConstant(false);
paramPlugin = (ArraysSBasePlugin) param.getPlugin("arrays");
dim = paramPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
// create initial assignments
InitialAssignment assignment = model.createInitialAssignment();
assignment.setSymbol("y");
ASTNode ast = new ASTNode(libsbml.AST_REAL);
ast.setValue(3.2);
assignment.setMath(ast);
assignment = model.createInitialAssignment();
assignment.setSymbol("z");
ast = new ASTNode(libsbml.AST_REAL);
ast.setValue(5.7);
assignment.setMath(ast);
ArraysSBasePlugin assignmentPlugin = (ArraysSBasePlugin) assignment.getPlugin("arrays");
dim = assignmentPlugin.createDimension();
dim.setId("i");
dim.setSize("m");
Index index = assignmentPlugin.createIndex();
ASTNode newAst = new ASTNode(libsbml.AST_FUNCTION);
newAst.setName("selector");
ASTNode ci = new ASTNode(libsbml.AST_NAME);
ci.setName("z");
newAst.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
newAst.addChild(ci);
index.setMath(newAst);
assignment = model.createInitialAssignment();
assignment.setSymbol("z");
ast = new ASTNode(libsbml.AST_REAL);
ast.setValue(3.2);
assignment.setMath(ast);
assignmentPlugin = (ArraysSBasePlugin) assignment.getPlugin("arrays");
dim = assignmentPlugin.createDimension();
dim.setId("i");
dim.setSize("m");
index = assignmentPlugin.createIndex();
newAst = new ASTNode(libsbml.AST_LINEAR_ALGEBRA_SELECTOR);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("z");
newAst.addChild(ci);
ASTNode plus = new ASTNode(libsbml.AST_PLUS);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
plus.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("m");
plus.addChild(ci);
newAst.addChild(plus);
index.setMath(newAst);
libsbml.writeSBMLToFile(doc, "arrays2.xml");
}