public void test_L3_Compartment_initDefaults()
{
Compartment c = new Compartment(3, 1);
c.setId("A");
assertEquals(true, c.isSetId());
assertEquals(false, c.isSetName());
assertEquals(false, c.isSetSize());
assertEquals(false, c.isSetVolume());
assertEquals(false, c.isSetUnits());
assertEquals(false, c.isSetConstant());
assertEquals(false, c.isSetSpatialDimensions());
c.initDefaults();
assertTrue(("A" == c.getId()));
assertTrue(c.getName() == "");
assertTrue(("litre" == c.getUnits()));
assertTrue(c.getSpatialDimensions() == 3);
assertTrue(c.getSize() == 1);
assertTrue(c.getConstant() == true);
assertEquals(true, c.isSetId());
assertEquals(false, c.isSetName());
assertEquals(false, c.isSetSize());
assertEquals(false, c.isSetVolume());
assertEquals(true, c.isSetUnits());
assertEquals(true, c.isSetConstant());
assertEquals(true, c.isSetSpatialDimensions());
c = null;
}
public void test_L3_Compartment_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1);
sbmlns.addNamespaces(xmlns);
Compartment c = new Compartment(sbmlns);
assertTrue(c.getTypeCode() == libsbml.SBML_COMPARTMENT);
assertTrue(c.getMetaId() == "");
assertTrue(c.getNotes() == null);
assertTrue(c.getAnnotation() == null);
assertTrue(c.getLevel() == 3);
assertTrue(c.getVersion() == 1);
assertTrue(c.getNamespaces() != null);
assertTrue(c.getNamespaces().getLength() == 2);
assertTrue(c.getId() == "");
assertTrue(c.getName() == "");
assertTrue(c.getUnits() == "");
assertTrue(c.getOutside() == "");
assertEquals(true, isnan(c.getSpatialDimensionsAsDouble()));
assertEquals(true, isnan(c.getVolume()));
assertTrue(c.getConstant() == true);
assertEquals(false, c.isSetId());
assertEquals(false, c.isSetSpatialDimensions());
assertEquals(false, c.isSetName());
assertEquals(false, c.isSetSize());
assertEquals(false, c.isSetVolume());
assertEquals(false, c.isSetUnits());
assertEquals(false, c.isSetOutside());
assertEquals(false, c.isSetConstant());
c = null;
}
public void test_Compartment_setId3()
{
Compartment c = new Compartment(2, 2);
int i = c.setId("cell");
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertEquals(true, c.isSetId());
assertTrue(("cell" == c.getId()));
c = null;
}
public void test_L3_Compartment_create()
{
assertTrue(C.getTypeCode() == libsbml.SBML_COMPARTMENT);
assertTrue(C.getMetaId() == "");
assertTrue(C.getNotes() == null);
assertTrue(C.getAnnotation() == null);
assertTrue(C.getId() == "");
assertTrue(C.getName() == "");
assertTrue(C.getUnits() == "");
assertTrue(C.getOutside() == "");
assertEquals(true, isnan(C.getSpatialDimensionsAsDouble()));
assertEquals(true, isnan(C.getVolume()));
assertTrue(C.getConstant() == true);
assertEquals(false, C.isSetId());
assertEquals(false, C.isSetSpatialDimensions());
assertEquals(false, C.isSetName());
assertEquals(false, C.isSetSize());
assertEquals(false, C.isSetVolume());
assertEquals(false, C.isSetUnits());
assertEquals(false, C.isSetOutside());
assertEquals(false, C.isSetConstant());
}
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 void test_Model_getCompartment()
{
Compartment c1 = new Compartment(2, 4);
Compartment c2 = new Compartment(2, 4);
c1.setId("A");
c2.setId("B");
M.addCompartment(c1);
M.addCompartment(c2);
assertTrue(M.getNumCompartments() == 2);
c1 = M.getCompartment(0);
c2 = M.getCompartment(1);
assertTrue(("A" == c1.getId()));
assertTrue(("B" == c2.getId()));
}
public void test_Compartment_copyConstructor()
{
Compartment o1 = new Compartment(2, 4);
o1.setId("c");
o1.setOutside("c2");
assertTrue(o1.getId() == "c");
assertTrue(o1.getOutside() == "c2");
Compartment o2 = new Compartment(o1);
assertTrue(o2.getId() == "c");
assertTrue(o2.getOutside() == "c2");
assertTrue(o2.getParentSBMLObject() == o1.getParentSBMLObject());
o2 = null;
o1 = null;
}
public void test_Compartment_createWith()
{
Compartment c = new Compartment(2, 4);
c.setId("A");
assertTrue(c.getTypeCode() == libsbml.SBML_COMPARTMENT);
assertTrue(c.getMetaId() == "");
assertTrue(c.getNotes() == null);
assertTrue(c.getAnnotation() == null);
assertTrue(c.getName() == "");
assertTrue(c.getSpatialDimensions() == 3);
assertTrue(("A" == c.getId()));
assertTrue(c.getConstant() == true);
assertEquals(true, c.isSetId());
assertEquals(false, c.isSetName());
c = null;
}
public void test_Compartment_assignmentOperator()
{
Compartment o1 = new Compartment(2, 4);
o1.setId("c");
o1.setOutside("c2");
assertTrue(o1.getId() == "c");
assertTrue(o1.getOutside() == "c2");
Compartment o2 = new Compartment(2, 4);
o2 = o1;
assertTrue(o2.getId() == "c");
assertTrue(o2.getOutside() == "c2");
assertTrue(o2.getParentSBMLObject() == o1.getParentSBMLObject());
o2 = null;
o1 = null;
}
/// <summary>
/// Creates a MoBi Container for a SBML compartment.
/// </summary>
public IContainer CreateContainerFromCompartment(Compartment compartment)
{
var container = _objectBaseFactory.Create <IContainer>()
.WithName(compartment.getId())
.WithContainerType(ContainerType.Compartment)
.WithMode(ContainerMode.Physical)
.WithDescription(SBMLConstants.SBML_NOTES + compartment.getNotesString());
CreateMoleculeProperties(container);
container.Add(CreateVolumeParameter());
if (!compartment.isSetSize())
{
return(container);
}
var sizeParameter = CreateSizeParameter(compartment);
container.Add(sizeParameter);
return(container);
}
public static void Main(string[] args)
{
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "layout") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
// SBMLNamespaces sbmlns(3,1,"layout",1,"LAYOUT");
//
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "layout", 1);
//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
// adds a layout package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("layout",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(LayoutExtension::XmlnsL3V1V1,"layout");
//
// (2) Creates a LayoutPkgNamespaces object (SBMLNamespace derived class for
// layout package. The class is basically used for createing an SBase derived
// objects belonging to the layout package) with the given SBML level, version,
// and package version
//
// LayoutPkgNamespaces sbmlns(3,1,1);
//
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// set the "required" attribute of layout package to "true"
document.setPkgRequired("layout", true);
// create the Model
Model model = document.createModel();
model.setId("TestModel");
document.setModel(model);
// create the Compartment
Compartment compartment = model.createCompartment();
compartment.setId("Compartment_1");
compartment.setConstant(true);
// create the Species
Species species1 = model.createSpecies();
species1.setId("Species_1");
species1.setCompartment(compartment.getId());
species1.setHasOnlySubstanceUnits(false);
species1.setBoundaryCondition(false);
species1.setConstant(false);
Species species2 = model.createSpecies();
species2.setId("Species_2");
species2.setCompartment(compartment.getId());
species2.setHasOnlySubstanceUnits(false);
species2.setBoundaryCondition(false);
species2.setConstant(false);
// create the Reactions
Reaction reaction1 = model.createReaction();
reaction1.setId("Reaction_1");
reaction1.setReversible(false);
reaction1.setFast(false);
SpeciesReference reference1 = reaction1.createReactant();
reference1.setSpecies(species1.getId());
reference1.setId("SpeciesReference_1");
reference1.setConstant(false);
SpeciesReference reference2 = reaction1.createProduct();
reference2.setSpecies(species2.getId());
reference2.setId("SpeciesReference_2");
reference2.setConstant(false);
Reaction reaction2 = model.createReaction();
reaction2.setId("Reaction_2");
reaction2.setReversible(false);
reaction2.setFast(false);
SpeciesReference reference3 = reaction2.createReactant();
reference3.setSpecies(species2.getId());
reference3.setId("SpeciesReference_3");
reference3.setConstant(false);
SpeciesReference reference4 = reaction2.createProduct();
reference4.setSpecies(species1.getId());
reference4.setId("SpeciesReference_4");
reference4.setConstant(false);
// create the Layout
//
// set the LayoutPkgNamespaces for Level 3 Version1 Layout Version 1
//
LayoutPkgNamespaces layoutns = new LayoutPkgNamespaces(3, 1, 1);
//
// Get a LayoutModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is SBasePlugin, and
// thus the value needs to be casted for the corresponding derived class.
//
LayoutModelPlugin mplugin = (LayoutModelPlugin)(model.getPlugin("layout"));
if (mplugin == null)
{
Console.Error.WriteLine("[Fatal Error] Layout Extension Level " + layoutns.getLevel() + " Version " + layoutns.getVersion() + " package version " + layoutns.getPackageVersion() + " is not registered.");
Environment.Exit(1);
}
//
// Creates a Layout object via LayoutModelPlugin object.
//
Layout layout = mplugin.createLayout();
layout.setId("Layout_1");
Dimensions dim = new Dimensions(layoutns, 400.0, 220.0);
layout.setDimensions(dim);
// create the CompartmentGlyph
CompartmentGlyph compartmentGlyph = layout.createCompartmentGlyph();
compartmentGlyph.setId("CompartmentGlyph_1");
compartmentGlyph.setCompartmentId(compartment.getId());
BoundingBox bb = new BoundingBox(layoutns, "bb1", 5, 5, 390, 210);
compartmentGlyph.setBoundingBox(bb);
// create the SpeciesGlyphs
SpeciesGlyph speciesGlyph1 = layout.createSpeciesGlyph();
speciesGlyph1.setId("SpeciesGlyph_1");
speciesGlyph1.setSpeciesId(species1.getId());
bb = new BoundingBox(layoutns, "bb2", 80, 26, 240, 24);
speciesGlyph1.setBoundingBox(bb);
TextGlyph textGlyph1 = layout.createTextGlyph();
textGlyph1.setId("TextGlyph_01");
bb = new BoundingBox(layoutns, "bbA", 92, 26, 228, 24);
textGlyph1.setBoundingBox(bb);
textGlyph1.setOriginOfTextId(speciesGlyph1.getId());
textGlyph1.setGraphicalObjectId(speciesGlyph1.getId());
SpeciesGlyph speciesGlyph2 = layout.createSpeciesGlyph();
speciesGlyph2.setId("SpeciesGlyph_2");
speciesGlyph2.setSpeciesId(species2.getId());
bb = new BoundingBox(layoutns, "bb3", 80, 170, 240, 24);
speciesGlyph2.setBoundingBox(bb);
TextGlyph textGlyph2 = layout.createTextGlyph();
textGlyph2.setId("TextGlyph_02");
bb = new BoundingBox(layoutns, "bbB", 92, 170, 228, 24);
textGlyph2.setBoundingBox(bb);
textGlyph2.setOriginOfTextId(speciesGlyph2.getId());
textGlyph2.setGraphicalObjectId(speciesGlyph2.getId());
// create the ReactionGlyphs
ReactionGlyph reactionGlyph1 = layout.createReactionGlyph();
reactionGlyph1.setId("ReactionGlyph_1");
reactionGlyph1.setReactionId(reaction1.getId());
Curve reactionCurve1 = reactionGlyph1.getCurve();
LineSegment ls = reactionCurve1.createLineSegment();
Point p = new Point(layoutns, 165, 105);
ls.setStart(p);
p = new Point(layoutns, 165, 115);
ls.setEnd(p);
ReactionGlyph reactionGlyph2 = layout.createReactionGlyph();
reactionGlyph2.setId("ReactionGlyph_1");
reactionGlyph2.setReactionId(reaction2.getId());
Curve reactionCurve2 = reactionGlyph2.getCurve();
ls = reactionCurve2.createLineSegment();
p = new Point(layoutns, 235, 105);
ls.setStart(p);
p = new Point(layoutns, 235, 115);
ls.setEnd(p);
// add the SpeciesReferenceGlyphs
SpeciesReferenceGlyph speciesReferenceGlyph1 = reactionGlyph1.createSpeciesReferenceGlyph();
speciesReferenceGlyph1.setId("SpeciesReferenceGlyph_1");
speciesReferenceGlyph1.setSpeciesGlyphId(speciesGlyph1.getId());
speciesReferenceGlyph1.setSpeciesReferenceId(reference1.getId());
speciesReferenceGlyph1.setRole(libsbml.SPECIES_ROLE_SUBSTRATE);
Curve speciesReferenceCurve1 = speciesReferenceGlyph1.getCurve();
CubicBezier cb = speciesReferenceCurve1.createCubicBezier();
p = new Point(layoutns, 165, 105);
cb.setStart(p);
p = new Point(layoutns, 165, 90);
cb.setBasePoint1(p);
p = new Point(layoutns, 165, 90);
cb.setBasePoint2(p);
p = new Point(layoutns, 195, 60);
cb.setEnd(p);
SpeciesReferenceGlyph speciesReferenceGlyph2 = reactionGlyph1.createSpeciesReferenceGlyph();
speciesReferenceGlyph2.setId("SpeciesReferenceGlyph_2");
speciesReferenceGlyph2.setSpeciesGlyphId(speciesGlyph2.getId());
speciesReferenceGlyph2.setSpeciesReferenceId(reference2.getId());
speciesReferenceGlyph2.setRole(libsbml.SPECIES_ROLE_PRODUCT);
Curve speciesReferenceCurve2 = speciesReferenceGlyph2.getCurve();
cb = speciesReferenceCurve2.createCubicBezier();
p = new Point(layoutns, 165, 115);
cb.setStart(p);
p = new Point(layoutns, 165, 130);
cb.setBasePoint1(p);
p = new Point(layoutns, 165, 130);
cb.setBasePoint2(p);
p = new Point(layoutns, 195, 160);
cb.setEnd(p);
SpeciesReferenceGlyph speciesReferenceGlyph3 = reactionGlyph2.createSpeciesReferenceGlyph();
speciesReferenceGlyph3.setId("SpeciesReferenceGlyph_3");
speciesReferenceGlyph3.setSpeciesGlyphId(speciesGlyph2.getId());
speciesReferenceGlyph3.setSpeciesReferenceId(reference3.getId());
speciesReferenceGlyph3.setRole(libsbml.SPECIES_ROLE_SUBSTRATE);
Curve speciesReferenceCurve3 = speciesReferenceGlyph3.getCurve();
cb = speciesReferenceCurve3.createCubicBezier();
p = new Point(layoutns, 235, 115);
cb.setStart(p);
p = new Point(layoutns, 235, 130);
cb.setBasePoint1(p);
p = new Point(layoutns, 235, 130);
cb.setBasePoint2(p);
p = new Point(layoutns, 205, 160);
cb.setEnd(p);
SpeciesReferenceGlyph speciesReferenceGlyph4 = reactionGlyph2.createSpeciesReferenceGlyph();
speciesReferenceGlyph4.setId("SpeciesReferenceGlyph_4");
speciesReferenceGlyph4.setSpeciesGlyphId(speciesGlyph1.getId());
speciesReferenceGlyph4.setSpeciesReferenceId(reference4.getId());
speciesReferenceGlyph4.setRole(libsbml.SPECIES_ROLE_PRODUCT);
Curve speciesReferenceCurve4 = speciesReferenceGlyph4.getCurve();
cb = speciesReferenceCurve4.createCubicBezier();
p = new Point(layoutns, 235, 105);
cb.setStart(p);
p = new Point(layoutns, 235, 90);
cb.setBasePoint1(p);
p = new Point(layoutns, 235, 90);
cb.setBasePoint2(p);
p = new Point(layoutns, 205, 60);
cb.setEnd(p);
libsbml.writeSBML(document, "layout_example1_L3-cs.xml");
Console.WriteLine("all done ...");
}