protected override void Context()
{
var obf = IoC.Resolve <IObjectBaseFactory>();
var opf = IoC.Resolve <IObjectPathFactory>();
var mdf = IoC.Resolve <IMoBiDimensionFactory>();
var ac = IoC.Resolve <IAliasCreator>();
var sI = new SBMLInformation();
sut = new ASTHandler(obf, opf, ac, mdf);
}
protected override void Context()
{
base.Context();
_sbmlModel = new Model(3, 1);
_sbmlInformation = new SBMLInformation();
//one compartment reaction
_reaction = _sbmlModel.createReaction();
_reaction.setId("r1");
//reaction partner
var s1 = _sbmlModel.createSpecies();
s1.setId("s1");
s1.setCompartment("default");
var s2 = _sbmlModel.createSpecies();
s2.setId("s2");
s2.setCompartment("default");
var m = new MoleculeInformation(s1);
var m2 = new MoleculeInformation(s2);
_sbmlInformation.MoleculeInformation.Add(m);
_sbmlInformation.MoleculeInformation.Add(m2);
//SRef
var s1Ref = _reaction.createReactant();
s1Ref.setSpecies("s1");
s1Ref.setStoichiometry(1);
var s2Ref = _reaction.createProduct();
s2Ref.setSpecies("s2");
s2Ref.setStoichiometry(2);
_reaction.addProduct(s2Ref);
//Modifier
var mod = _reaction.createModifier();
mod.setId("mod");
mod.setName("mod");
mod.setSpecies("s1");
//Kinetic Law
var kl = _reaction.createKineticLaw();
kl.setId("kl");
kl.setMath(libsbml.parseFormula("2*3"));
}
public void DoImport(Model sbmlModel, IMoBiProject moBiProject, SBMLInformation sbmlInformation, ICommandCollector command)
{
_sbmlProject = moBiProject;
_sbmlInformation = sbmlInformation;
_command = command;
try
{
Import(sbmlModel);
}
finally
{
_sbmlProject = null;
_sbmlInformation = null;
_command = null;
}
}
/// <summary>
/// Parses a SBML MathML expression into a MoBi Formula.
/// </summary>
/// <param name="rootNode"></param>
/// <param name="rootObjectId"> The id of the parent object of the rootNode to set the name of </param>
/// <param name="isRateRule"></param>
/// <param name="sbmlProject"></param>
/// <param name="sbmlInformation"></param>
public IFormula Parse(ASTNode rootNode, string rootObjectId, bool isRateRule, IMoBiProject sbmlProject,
SBMLInformation sbmlInformation)
{
try
{
_sbmlProject = sbmlProject;
_sbmlInformation = sbmlInformation;
_objectPaths.Clear();
_counter++;
var formulaString = Eval(rootNode);
if (string.IsNullOrEmpty(formulaString))
{
return(null);
}
var formula = _objectBaseFactory.Create <ExplicitFormula>()
.WithName(rootObjectId + _counter)
.WithFormulaString(formulaString);
if (isRateRule)
{
getObjectPathName(ObjectPath.PARENT_CONTAINER, rootObjectId);
}
foreach (var path in _objectPaths.Where(path => path != null))
{
formula.AddObjectPath(path);
}
if (string.IsNullOrEmpty(formula?.FormulaString))
{
createErrorMsg(rootNode);
return(null);
}
else
{
return(formula);
}
}
finally
{
_sbmlProject = null;
_sbmlInformation = null;
}
}
/// <summary>
/// Parses a SBML MathML expression from a SBML Event Assignment into a MoBi Formula.
/// </summary>
/// <param name="rootNode"> The MathMl Expression of the SBML Event Assignment the assignmentVariable should be assigned with.</param>
/// <param name="eventAssignmentBuilder"> The MoBi Event Assignment Builder the SBML Event Assigment should be build with. </param>
/// <param name="assignmentVariable"> The Parameter, Molecule, Species or SpeciesReference that should be assigned when the Event is triggered. </param>
/// <param name="sbmlProject"></param>
/// <param name="sbmlInformation"></param>
public IFormula Parse(ASTNode rootNode, IEventAssignmentBuilder eventAssignmentBuilder, string assignmentVariable,
IMoBiProject sbmlProject, SBMLInformation sbmlInformation)
{
try
{
_sbmlProject = sbmlProject;
_sbmlInformation = sbmlInformation;
_counter++;
var formulaString = Eval(rootNode);
if (string.IsNullOrEmpty(formulaString))
{
return(null);
}
var formula = _objectBaseFactory.Create <ExplicitFormula>()
.WithName(SBMLConstants.SBML_EVENT_ASSIGNMENT + assignmentVariable + _counter)
.WithFormulaString(formulaString);
foreach (var opath in _objectPaths.Where(opath => opath != null))
{
formula.AddObjectPath(opath);
}
var path = getObjectPathForAssignment(assignmentVariable);
if (path != null)
{
eventAssignmentBuilder.ObjectPath = path;
}
if (string.IsNullOrEmpty(formula?.FormulaString))
{
createErrorMsg(rootNode);
return(null);
}
else
{
return(formula);
}
}
finally
{
_sbmlProject = null;
_sbmlInformation = null;
}
}
/// <summary>
/// Parses a SBML MathML expression from a SBML Reaction into a MoBi Formula.
/// </summary>
/// <param name="rootNode"> The root of the MathMl expression. </param>
/// <param name="reactionBuilder"> The MoBi reactionBuilder the SBML reaction should be build with. </param>
/// <param name="sbmlProject"></param>
/// <param name="sbmlInformation"></param>
public IFormula Parse(ASTNode rootNode, IReactionBuilder reactionBuilder, IMoBiProject sbmlProject,
SBMLInformation sbmlInformation)
{
try
{
_objectPaths.Clear();
_sbmlProject = sbmlProject;
_sbmlInformation = sbmlInformation;
_reactionBuilder = reactionBuilder;
var formulaString = Eval(rootNode);
if (string.IsNullOrEmpty(formulaString))
{
return(null);
}
var formula = _objectBaseFactory.Create <ExplicitFormula>()
.WithName(SBMLConstants.SBML_KINETIC_LAW + reactionBuilder.Name)
.WithFormulaString(formulaString);
foreach (var path in _objectPaths.Where(path => path != null))
{
formula.AddObjectPath(path);
}
if (string.IsNullOrEmpty(formula?.FormulaString))
{
createErrorMsg(rootNode);
return(null);
}
else
{
return(formula);
}
}
finally
{
_reactionBuilder = null;
_sbmlProject = null;
_sbmlInformation = null;
}
}
/// <summary>
/// Saves additional Information and important Information that is necessary for the Import.
/// </summary>
public SBMLInformation SaveSBMLInformation(Model sbmlModel, SBMLDocument sbmlDoc)
{
SBMLInformation = new SBMLInformation();
SBMLInformation.Initialize(sbmlModel, sbmlDoc);
return(SBMLInformation);
}