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biouml.plugins.cellml
Class CellMLModelWriter

biouml.plugins.cellml.CellMLSupport
  |
  +--biouml.plugins.cellml.CellMLModelWriter
public class CellMLModelWriter
extends CellMLSupport

Writes diagram in SBML format. SbmlModelWriter can correctly process following types of diagram:

Reactant and product are obligatory elements of SBML reaction, but it BioUML allows user to create reaction without reactants or products. So to respect SBML requirements REACTANT_STUB or PRODUCT_STUB can be added into reaction and model.

SbmlModelReader can recognise such stubs and remove them from model automatically. Thus "_in_empty_set" (REACTANT_STUB) and "_out_empty_set" are reserved key words that should not be used as specie names.

pending SName validation, warn if specie list or reaction list is empty.
Constructor Summary
CellMLModelWriter(File outFile)
           

Method Summary
 voidwrite(Diagram sourceDiagram)
           
 voidwrite(Diagram sourceDiagram, Transformer transformer)
           

Methods inherited from class biouml.plugins.cellml.CellMLSupport
getElement

Constructor Detail

CellMLModelWriter

public CellMLModelWriter(File outFile)
                    throws java.lang.Exception
Method Detail

write

public void write(Diagram sourceDiagram)
            throws java.lang.Exception

write

public void write(Diagram sourceDiagram, Transformer transformer)
            throws java.lang.Exception

Association Links

to Class java.util.List

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