biouml.plugins.cellml
Class CellMLModelWriter

java.lang.Object
  biouml.plugins.cellml.CellMLSupport
      biouml.plugins.cellml.CellMLModelWriter

All Implemented Interfaces:

CellMLConstants

public class CellMLModelWriter

extends CellMLSupport

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

• SbmlDiagramType
• PathwaySimulationDiagramType. This standard BioUML diagram type is most closely corresponds to SBML diagram type
• PathwayDiagramType

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.

Pendung:

SName validation, warn if specie list or reaction list is empty.

Field Summary

protected java.util.List	compartmentList
protected org.w3c.dom.Document	document

Fields inherited from class biouml.plugins.cellml.CellMLSupport

diagram, file, log, modelName, module, resources

Fields inherited from interface biouml.plugins.cellml.CellMLConstants

BIOUML_COMPARTMENT_INFO_ELEMENT, BIOUML_EDGE_INFO_ELEMENT, BIOUML_NODE_INFO_ELEMENT, BIOUML_SPECIES_INFO_ELEMENT, BIOUML_SPECIES_TYPE_ATTR, BIOUML_XMLNS_ATTR, BIOUML_XMLNS_VALUE, COMPONENT_1_ATTR, COMPONENT_2_ATTR, COMPONENT_ELEMENT, CONNECTION_ELEMENT, DIRECTION_ATTR, ENVIRONMENT, INITIAL_VALUE_ATTR, MAP_COMPONENTS_ELEMENT, MATH_ELEMENT, MODEL_ELEMENT, NAME_ATTR, PUBLIC_INTERFACE_ATTR, PUBLIC_INTERFACE_NONE, RDF_ELEMENT, REACTION_ELEMENT, REACTION_REVERSIBLE_ATTR, ROLE_ACTIVATOR, ROLE_ATTR, ROLE_CATALYST, ROLE_ELEMENT, ROLE_INHIBITOR, ROLE_MODIFIER, ROLE_PRODUCT, ROLE_RATE, ROLE_REACTANT, STOICHIOMETRY_ATTR, UNITS_ATTR, VARIABLE_ATTR, VARIABLE_ELEMENT, VARIABLE_REF_ELEMENT

Constructor Summary

CellMLModelWriter(java.io.File outFile)

Method Summary

void	write(Diagram sourceDiagram)
void	write(Diagram sourceDiagram, javax.xml.transform.Transformer transformer)
protected void	writeDiagram(org.w3c.dom.Element sbml)

Methods inherited from class biouml.plugins.cellml.CellMLSupport

error, getElement, warn

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

document

protected org.w3c.dom.Document document

compartmentList

protected java.util.List compartmentList

Constructor Detail

CellMLModelWriter

public CellMLModelWriter(java.io.File outFile)
                  throws java.lang.Exception

Method Detail

write

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

Throws:

java.lang.Exception

write

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

Throws:

java.lang.Exception

writeDiagram

protected void writeDiagram(org.w3c.dom.Element sbml)
                     throws java.lang.Exception

Throws:

java.lang.Exception