public RenameEntityCommand(SBase entity, String oldID, String newID, Model.SBML.Model model)
{
this.entity = entity;
this.oldID = oldID;
this.newID = newID;
this.model = model;
}
/// <summary>
/// Add data to the ReferenceLeafNode
/// </summary>
/// <param name="text">
/// A <see cref="System.String"/>
/// </param>
/// <param name="model">
/// A <see cref="Model"/>
/// </param>
public void AddData(string text, Model model)
{
// Retrieve the object from the model
SBase reference = (SBase)model.findObject(text);
if (reference != null)
{
this.idReference = text;
this.data = reference;
}
}
public AssignmentRule(SBase variable)
{
this.variable = variable;
}
public EventAssignment(SBase variable)
{
this.variable = variable;
}
/// <summary>
/// Sets an object as having a duplicate ID to an object already in the model
/// </summary>
/// <param name="original">
/// A <see cref="SBase"/>
/// </param>
public void setHasADuplicateId(SBase original)
{
this.duplicate = true;
this.original = original;
}
/// <summary>
/// Checks all ReferenceLeafNodes so that they point to their SBase object.
/// Used to complete a MathTree generated from MathML after it has been parsed and
/// more about the model is known (such as paramters).
/// </summary>
/// <param name="model">
/// A <see cref="Model"/>
/// </param>
public override void SetSBaseReferences(Model model)
{
if (this.idReference != null)
{
SBase reference = (SBase)model.findObject(this.idReference);
if (reference != null)
{
this.data = reference;
}
}
}
public RateRule(SBase variable)
{
this.variable = variable;
}
/// <summary>
/// Updates the ID of an SBML object in the model, for renaming of SBML objects
/// </summary>
/// <param name="entity">
/// A <see cref="SBase"/>
/// </param>
public void updateID(SBase entity)
{
// If we have an old ID implies it has actully been renamed
// If the model already contains that ID
// and if the new ID is different to the old one
if (entity.getOldID()!=null && this.IdTable.ContainsKey(entity.getOldID()) && entity.ID!=entity.getOldID())
{
if (this.IdTable.ContainsKey(entity.ID))
{
throw new DuplicateSBMLObjectIdException(entity.ID);
}
else
{
this.IdTable.Remove(entity.getOldID());
this.IdTable.Add(entity.ID, entity);
}
}
}
/// <summary>
/// Used when a new ID is found in the SBML document to add it
/// and its object reference to the global IdTable
/// </summary>
/// <param name="id">The id of the object</param>
/// <param name="reference">
/// The SBase <see cref="SBase"/> object with the corresponding id.
/// </param>
public void AddId(string id, SBase reference)
{
// Need to make sure that we don't add a duplicate refernce but add with a slightly different id
// and flag as a possible duplicate for pass at the end
if (this.IdTable.ContainsKey(id))
{
// Duplicate found
// Get the original
SBase original = this.IdTable[id];
original.duplicateCount++;
// Modify duplicates id
reference.ID = reference.ID+"_"+original.duplicateCount;
// Set the original
reference.setHasADuplicateId(original);
// Add to the idtable
this.IdTable.Add(reference.ID, reference);
} else {
this.IdTable.Add(id, reference);
}
}
public InitialAssignment(SBase variable, Hashtable attrs)
{
this.variable = variable;
this.setId(attrs);
}
public InitialAssignment(SBase variable)
{
this.variable = variable;
}
