private static void printCompartmentInfo(Compartment compartment)
{
var plugin = (MultiCompartmentPlugin)compartment.getPlugin("multi");
var name = compartment.isSetName() ? compartment.getName() : compartment.getId();
Console.WriteLine("Compartment {0}: isType = {1}", name, plugin.getIsType());
for (int i = 0; i < plugin.getNumCompartmentReferences(); ++i)
{
var current = plugin.getCompartmentReference(i);
Console.WriteLine(" compartmentReference: {0}", current.getCompartment());
}
Console.WriteLine();
}
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");
}
static void Main(string[] args)
{
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "multi", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// set the required attribute to true
SBMLDocumentPlugin docPlug =
(SBMLDocumentPlugin)(document.getPlugin("multi"));
docPlug.setRequired(true);
// create the Model
Model model = document.createModel();
// create the compartments
Compartment c = model.createCompartment();
c.setId("membrane");
c.setConstant(true);
// set the multi attribute isType via the compartmentPlugin
MultiCompartmentPlugin compPlug =
(MultiCompartmentPlugin)(c.getPlugin("multi"));
compPlug.setIsType(true);
c = model.createCompartment();
c.setId("inter_membrane");
c.setConstant(true);
// set the multi attribute isType via the compartmentPlugin
compPlug =
(MultiCompartmentPlugin)(c.getPlugin("multi"));
compPlug.setIsType(true);
// create the compartmentReferences
CompartmentReference compRef = compPlug.createCompartmentReference();
compRef.setId("m1");
compRef.setCompartment("membrane");
compRef = compPlug.createCompartmentReference();
compRef.setId("m2");
compRef.setCompartment("membrane");
// create the speciesTypes
MultiModelPlugin modelPlug =
(MultiModelPlugin)(model.getPlugin("multi"));
MultiSpeciesType st = modelPlug.createMultiSpeciesType();
st.setId("stX");
st.setCompartment("ct");
st = modelPlug.createMultiSpeciesType();
st.setId("stXXcis");
st.setCompartment("ct");
// create speciesTypeInstances
SpeciesTypeInstance sti = st.createSpeciesTypeInstance();
sti.setId("stiX1");
sti.setSpeciesType("stX");
sti = st.createSpeciesTypeInstance();
sti.setId("stiX2");
sti.setSpeciesType("stX");
// create speciesTypeBond
InSpeciesTypeBond istb = st.createInSpeciesTypeBond();
istb.setBindingSite1("stiX1");
istb.setBindingSite2("stiX2");
// another speciesType
st = modelPlug.createMultiSpeciesType();
st.setId("stXXtrans");
st.setCompartment("cct");
// create speciesTypeInstances
sti = st.createSpeciesTypeInstance();
sti.setId("stiX1");
sti.setSpeciesType("stX");
sti.setCompartmentReference("cr1");
sti = st.createSpeciesTypeInstance();
sti.setId("stiX2");
sti.setSpeciesType("stX");
sti.setCompartmentReference("cr2");
// create speciesTypeBond
istb = st.createInSpeciesTypeBond();
istb.setBindingSite1("stiX1");
istb.setBindingSite2("stiX2");
libsbml.writeSBML(document, "multi_example1.xml");
}
static void Main(string[] args)
{
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "multi", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// set the required attribute to true
SBMLDocumentPlugin docPlug =
(SBMLDocumentPlugin)(document.getPlugin("multi"));
docPlug.setRequired(true);
// create the Model
Model model = document.createModel();
// create a compartment
Compartment c = model.createCompartment();
c.setId("membrane");
c.setConstant(true);
// set the multi attribute isType via the compartmentPlugin
MultiCompartmentPlugin compPlug =
(MultiCompartmentPlugin)(c.getPlugin("multi"));
compPlug.setIsType(true);
// create species
Species s = model.createSpecies();
s.setId("s1");
s.setCompartment("membrane");
s.setBoundaryCondition(false);
s.setHasOnlySubstanceUnits(false);
s.setConstant(false);
// create reaction
Reaction r = model.createReaction();
r.setId("r1");
r.setFast(false);
r.setReversible(false);
// createReactant
SpeciesReference sr = r.createReactant();
sr.setId("sr1");
sr.setSpecies("s1");
sr.setConstant(false);
KineticLaw kl = r.createKineticLaw();
ASTNode ci = new ASTNode(libsbml.AST_NAME);
ci.setName("s1");
MultiASTPlugin astPlugin = (MultiASTPlugin)(ci.getPlugin("multi"));
astPlugin.setSpeciesReference("r1");
ASTNode ci1 = new ASTNode(libsbml.AST_NAME);
MultiASTPlugin astPlugin1 = (MultiASTPlugin)(ci1.getPlugin("multi"));
astPlugin1.setRepresentationType("sum");
ci1.setName("s1");
ASTNode math = new ASTNode(libsbml.AST_TIMES);
math.addChild(ci);
math.addChild(ci1);
kl.setMath(math);
libsbml.writeSBML(document, "multi_example2.xml");
}
static void Main(string[] args)
{
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "multi", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// set the required attribute to true
SBMLDocumentPlugin docPlug =
(SBMLDocumentPlugin)(document.getPlugin("multi"));
docPlug.setRequired(true);
// create the Model
Model model = document.createModel();
// create the compartments
Compartment c = model.createCompartment();
c.setId("membrane");
c.setConstant(true);
// set the multi attribute isType via the compartmentPlugin
MultiCompartmentPlugin compPlug =
(MultiCompartmentPlugin)(c.getPlugin("multi"));
compPlug.setIsType(true);
// create the speciesTypes
MultiModelPlugin modelPlug =
(MultiModelPlugin)(model.getPlugin("multi"));
MultiSpeciesType st = modelPlug.createMultiSpeciesType();
st.setId("stX");
st.setCompartment("membrane");
// create species
Species s = model.createSpecies();
s.setId("s1");
s.setCompartment("membrane");
s.setBoundaryCondition(false);
s.setHasOnlySubstanceUnits(false);
s.setConstant(false);
// set the multi attribute speciesType via the compartmentPlugin
MultiSpeciesPlugin spPlug =
(MultiSpeciesPlugin)(s.getPlugin("multi"));
spPlug.setSpeciesType("stX");
// create species feature
SpeciesFeature sf = spPlug.createSpeciesFeature();
sf.setSpeciesFeatureType("a");
sf.setOccur(1);
sf.setComponent("b");
SpeciesFeatureValue sfv = sf.createSpeciesFeatureValue();
sfv.setValue("c");
// create a subListOfSpeciesFeatures
SubListOfSpeciesFeatures subloSF = spPlug.createSubListOfSpeciesFeatures();
subloSF.setRelation(libsbml.Relation_fromString("and"));
// add speciesFeatures to the subList
SpeciesFeature sf1 = new SpeciesFeature(3, 1, 1);
sf1.setSpeciesFeatureType("a1");
sf1.setOccur(1);
sf1.setComponent("b1");
SpeciesFeatureValue sfv1 = sf1.createSpeciesFeatureValue();
sfv1.setValue("c1");
subloSF.appendAndOwn(sf1);
sf1 = new SpeciesFeature(3, 1, 1);
sf1.setSpeciesFeatureType("a2");
sf1.setOccur(1);
sf1.setComponent("b2");
sfv1 = sf1.createSpeciesFeatureValue();
sfv1.setValue("c2");
subloSF.appendAndOwn(sf1);
// create a second subListOfSpeciesfeatures
subloSF = spPlug.createSubListOfSpeciesFeatures();
subloSF.setRelation(libsbml.Relation_fromString("or"));
sf1 = new SpeciesFeature(3, 1, 1);
sf1.setSpeciesFeatureType("a3");
sf1.setOccur(1);
sf1.setComponent("b3");
sfv1 = sf1.createSpeciesFeatureValue();
sfv1.setValue("c3");
subloSF.appendAndOwn(sf1);
sf1 = new SpeciesFeature(3, 1, 1);
sf1.setSpeciesFeatureType("a4");
sf1.setOccur(1);
sf1.setComponent("b4");
sfv1 = sf1.createSpeciesFeatureValue();
sfv1.setValue("c4");
subloSF.appendAndOwn(sf1);
libsbml.writeSBML(document, "multi_example3.xml");
}
