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();
_functionDefDictionary.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);
}
