/**
*
* Creates an SBML model represented in "7.2 Example involving units"
* in the SBML Level 2 Version 4 Specification.
*
*/
private static SBMLDocument createExampleInvolvingUnits()
{
int level = Level;
int version = Version;
//---------------------------------------------------------------------------
//
// Creates an SBMLDocument object
//
//---------------------------------------------------------------------------
SBMLDocument sbmlDoc = new SBMLDocument(level, version);
// Adds the namespace for XHTML to the SBMLDocument object. We need this
// because we will add notes to the model. (By default, the SBML document
// created by SBMLDocument only declares the SBML XML namespace.)
sbmlDoc.getNamespaces().add("http://www.w3.org/1999/xhtml", "xhtml");
//---------------------------------------------------------------------------
//
// Creates a Model object inside the SBMLDocument object.
//
//---------------------------------------------------------------------------
Model model = sbmlDoc.createModel();
model.setId("unitsExample");
//---------------------------------------------------------------------------
//
// Creates UnitDefinition objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers (reused more than once below).
UnitDefinition unitdef;
Unit unit;
//---------------------------------------------------------------------------
// (UnitDefinition1) Creates an UnitDefinition object ("substance").
//
// This has the effect of redefining the default unit of subtance for the
// whole model.
//---------------------------------------------------------------------------
unitdef = model.createUnitDefinition();
unitdef.setId("substance");
// Creates an Unit inside the UnitDefinition object
unit = unitdef.createUnit();
unit.setKind(libsbml.UNIT_KIND_MOLE);
unit.setScale(-3);
//--------------------------------------------------------------------------------
// (UnitDefinition2) Creates an UnitDefinition object ("mmls")
//--------------------------------------------------------------------------------
// Note that we can reuse the pointers 'unitdef' and 'unit' because the
// actual UnitDefinition object (along with the Unit objects within it)
// is already attached to the Model object.
unitdef = model.createUnitDefinition();
unitdef.setId("mmls");
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef.createUnit();
unit.setKind(libsbml.UNIT_KIND_MOLE);
unit.setScale(-3);
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef.createUnit();
unit.setKind(libsbml.UNIT_KIND_LITRE);
unit.setExponent(-1);
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef.createUnit();
unit.setKind(libsbml.UNIT_KIND_SECOND);
unit.setExponent(-1);
//--------------------------------------------------------------------------------
// (UnitDefinition3) Creates an UnitDefinition object ("mml")
//--------------------------------------------------------------------------------
unitdef = model.createUnitDefinition();
unitdef.setId("mml");
// Creates an Unit inside the UnitDefinition object ("mml")
unit = unitdef.createUnit();
unit.setKind(libsbml.UNIT_KIND_MOLE);
unit.setScale(-3);
// Creates an Unit inside the UnitDefinition object ("mml")
unit = unitdef.createUnit();
unit.setKind(libsbml.UNIT_KIND_LITRE);
unit.setExponent(-1);
//---------------------------------------------------------------------------
//
// Creates a Compartment object inside the Model object.
//
//---------------------------------------------------------------------------
Compartment comp;
string compName = "cell";
// Creates a Compartment object ("cell")
comp = model.createCompartment();
comp.setId(compName);
// Sets the "size" attribute of the Compartment object.
//
// The units of this Compartment object is the default SBML
// units of volume (litre), and thus we don't have to explicitly invoke
// setUnits("litre") function to set the default units.
//
comp.setSize(1);
//---------------------------------------------------------------------------
//
// Creates Species objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointer (reused more than once below).
Species sp;
//---------------------------------------------------------------------------
// (Species1) Creates a Species object ("x0")
//---------------------------------------------------------------------------
sp = model.createSpecies();
sp.setId("x0");
// Sets the "compartment" attribute of the Species object to identify the
// compartnet in which the Species object located.
sp.setCompartment(compName);
// Sets the "initialConcentration" attribute of the Species object.
//
// The units of this Species object is determined by two attributes of this
// Species object ("substanceUnits" and "hasOnlySubstanceUnits") and the
// "spatialDimensions" attribute of the Compartment object ("cytosol") in which
// this species object is located.
// Since the default values are used for "substanceUnits" (substance (mole))
// and "hasOnlySubstanceUnits" (false) and the value of "spatialDimension" (3)
// is greater than 0, the units of this Species object is moles/liters .
//
sp.setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species2) Creates a Species object ("x1")
//---------------------------------------------------------------------------
sp = model.createSpecies();
sp.setId("x1");
sp.setCompartment(compName);
sp.setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species3) Creates a Species object ("s1")
//---------------------------------------------------------------------------
sp = model.createSpecies();
sp.setCompartment(compName);
sp.setId("s1");
sp.setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species4) Creates a Species object ("s2")
//---------------------------------------------------------------------------
sp = model.createSpecies();
sp.setCompartment(compName);
sp.setId("s2");
sp.setInitialConcentration(1);
//---------------------------------------------------------------------------
//
// Creates global Parameter objects inside the Model object.
//
//---------------------------------------------------------------------------
Parameter para;
// Creates a Parameter ("vm")
para = model.createParameter();
para.setId("vm");
para.setValue(2);
para.setUnits("mmls");
// Creates a Parameter ("km")
para = model.createParameter();
para.setId("km");
para.setValue(2);
para.setUnits("mml");
//---------------------------------------------------------------------------
//
// Creates Reaction objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers.
Reaction reaction;
SpeciesReference spr;
KineticLaw kl;
//---------------------------------------------------------------------------
// (Reaction1) Creates a Reaction object ("v1").
//---------------------------------------------------------------------------
reaction = model.createReaction();
reaction.setId("v1");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v1").
//---------------------------------------------------------------------------
// (Reactant1) Creates a Reactant object that references Species "x0"
// in the model.
spr = reaction.createReactant();
spr.setSpecies("x0");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v1").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "s1" in the model.
spr = reaction.createProduct();
spr.setSpecies("s1");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v1").
//---------------------------------------------------------------------------
kl = reaction.createKineticLaw();
// Creates a <notes> element in the KineticLaw object.
// Here we illustrate how to do it using a literal string. This requires
// known the required syntax of XHTML and the requirements for SBML <notes>
// elements. Later below, we show how to create notes using objects instead
// of strings.
string notesString = "<xhtml:p> ((vm * s1)/(km + s1)) * cell </xhtml:p>";
kl.setNotes(notesString);
//---------------------------------------------------------------------------
// Creates an ASTNode object which represents the following KineticLaw object.
//
// <math xmlns=\"http://www.w3.org/1998/Math/MathML\">
// <apply>
// <times/>
// <apply>
// <divide/>
// <apply>
// <times/>
// <ci> vm </ci>
// <ci> s1 </ci>
// </apply>
// <apply>
// <plus/>
// <ci> km </ci>
// <ci> s1 </ci>
// </apply>
// </apply>
// <ci> cell </ci>
// </apply>
// </math>
//---------------------------------------------------------------------------
//
// In the following code, ASTNode objects, which construct an ASTNode tree
// of the above math, are created and added in the order of preorder traversal
// of the tree (i.e. the order corresponds to the nested structure of the above
// MathML elements), and thus the following code maybe a bit more efficient but
// maybe a bit difficult to read.
//
ASTNode astMath = new ASTNode(libsbml.AST_TIMES);
astMath.addChild(new ASTNode(libsbml.AST_DIVIDE));
ASTNode astDivide = astMath.getLeftChild();
astDivide.addChild(new ASTNode(libsbml.AST_TIMES));
ASTNode astTimes = astDivide.getLeftChild();
astTimes.addChild(new ASTNode(libsbml.AST_NAME));
astTimes.getLeftChild().setName("vm");
astTimes.addChild(new ASTNode(libsbml.AST_NAME));
astTimes.getRightChild().setName("s1");
astDivide.addChild(new ASTNode(libsbml.AST_PLUS));
ASTNode astPlus = astDivide.getRightChild();
astPlus.addChild(new ASTNode(libsbml.AST_NAME));
astPlus.getLeftChild().setName("km");
astPlus.addChild(new ASTNode(libsbml.AST_NAME));
astPlus.getRightChild().setName("s1");
astMath.addChild(new ASTNode(libsbml.AST_NAME));
astMath.getRightChild().setName("cell");
//---------------------------------------------
//
// set the Math element
//
//------------------------------------------------
kl.setMath(astMath);
//---------------------------------------------------------------------------
// (Reaction2) Creates a Reaction object ("v2").
//---------------------------------------------------------------------------
reaction = model.createReaction();
reaction.setId("v2");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v2").
//---------------------------------------------------------------------------
// (Reactant2) Creates a Reactant object that references Species "s1"
// in the model.
spr = reaction.createReactant();
spr.setSpecies("s1");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v2").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "s2" in the model.
spr = reaction.createProduct();
spr.setSpecies("s2");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v2").
//---------------------------------------------------------------------------
kl = reaction.createKineticLaw();
// Sets a notes (by XMLNode) to the KineticLaw object.
//
// The following code is an alternative to using setNotes(const string&).
// The equivalent code would be like this:
//
// notesString = "<xhtml:p>((vm * s2)/(km + s2))*cell</xhtml:p>";
// kl.setNotes(notesString);
// Creates an XMLNode of start element (<xhtml:p>) without attributes.
XMLNode notesXMLNode = new XMLNode(
new XMLTriple("p", "", "xhtml"),
new XMLAttributes());
// Adds a text element to the start element.
notesXMLNode.addChild(new XMLNode(" ((vm * s2)/(km + s2)) * cell "));
// Adds it to the kineticLaw object.
kl.setNotes(notesXMLNode);
//---------------------------------------------------------------------------
// Sets a math (ASTNode object) to the KineticLaw object.
//---------------------------------------------------------------------------
// To create mathematical expressions, one would typically construct
// an ASTNode tree as the above example code which creates a math of another
// KineticLaw object. Here, to save some space and illustrate another approach
// of doing it, we will write out the formula in MathML form and then use a
// libSBML convenience function to create the ASTNode tree for us.
// (This is a bit dangerous; it's very easy to make mistakes when writing MathML
// by hand, so in a real program, we would not really want to do it this way.)
string mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
+ " <apply>"
+ " <times/>"
+ " <apply>"
+ " <divide/>"
+ " <apply>"
+ " <times/>"
+ " <ci> vm </ci>"
+ " <ci> s2 </ci>"
+ " </apply>"
+ " <apply>"
+ " <plus/>"
+ " <ci> km </ci>"
+ " <ci> s2 </ci>"
+ " </apply>"
+ " </apply>"
+ " <ci> cell </ci>"
+ " </apply>"
+ "</math>";
astMath = libsbml.readMathMLFromString(mathXMLString);
kl.setMath(astMath);
//---------------------------------------------------------------------------
// (Reaction3) Creates a Reaction object ("v3").
//---------------------------------------------------------------------------
reaction = model.createReaction();
reaction.setId("v3");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v3").
//---------------------------------------------------------------------------
// (Reactant2) Creates a Reactant object that references Species "s2"
// in the model.
spr = reaction.createReactant();
spr.setSpecies("s2");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v3").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "x1" in the model.
spr = reaction.createProduct();
spr.setSpecies("x1");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v3").
//---------------------------------------------------------------------------
kl = reaction.createKineticLaw();
// Sets a notes (by string) to the KineticLaw object.
notesString = "<xhtml:p> ((vm * x1)/(km + x1)) * cell </xhtml:p>";
kl.setNotes(notesString);
//---------------------------------------------------------------------------
// Sets a math (ASTNode object) to the KineticLaw object.
//---------------------------------------------------------------------------
mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
+ " <apply>"
+ " <times/>"
+ " <apply>"
+ " <divide/>"
+ " <apply>"
+ " <times/>"
+ " <ci> vm </ci>"
+ " <ci> x1 </ci>"
+ " </apply>"
+ " <apply>"
+ " <plus/>"
+ " <ci> km </ci>"
+ " <ci> x1 </ci>"
+ " </apply>"
+ " </apply>"
+ " <ci> cell </ci>"
+ " </apply>"
+ "</math>";
astMath = libsbml.readMathMLFromString(mathXMLString);
kl.setMath(astMath);
// Returns the created SBMLDocument object.
// The returned object must be explicitly deleted by the caller,
// otherwise memory leak will happen.
return sbmlDoc;
}
public void test_SBase_appendNotesWithGlobalNamespace()
{
string notes = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" xmlns:html=\"http://www.w3.org/1999/xhtml\" level=\"2\" version=\"4\">\n" + " <model id=\"test\" name=\"name\">\n" + " <notes>\n" + " <html:p>DATE: 2010/12/08 13:00:00</html:p>\n" + " <html:p>VERSION: 0.99</html:p>\n" + " <html:p>TAXONOMY: 9606</html:p>\n" + " </notes>\n" + " </model>\n" + "</sbml>\n";
SBMLDocument sbmlDoc = new SBMLDocument (2, 4);
sbmlDoc.getNamespaces ().@add ("http://www.w3.org/1999/xhtml", "html");
Model sbmlModel = sbmlDoc.createModel ();
sbmlModel.setId ("test");
sbmlModel.setName ("name");
setOrAppendNotes (sbmlModel, "<html:p>DATE: 2010/12/08 13:00:00</html:p>");
setOrAppendNotes (sbmlModel, "<html:p>VERSION: 0.99</html:p>");
setOrAppendNotes (sbmlModel, "<html:p>TAXONOMY: 9606</html:p>");
SBMLWriter ttt = new SBMLWriter ();
string documentString = ttt.writeToString (sbmlDoc);
assertTrue ((notes == documentString));
}