biouml.plugins.sbml
Class SbmlModelWriter_21

java.lang.Object
  biouml.plugins.sbml.SbmlConstants
      biouml.plugins.sbml.SbmlSupport
          biouml.plugins.sbml.SbmlModelWriter
              biouml.plugins.sbml.SbmlModelWriter_21

public class SbmlModelWriter_21

extends SbmlModelWriter

Field Summary

Fields inherited from class biouml.plugins.sbml.SbmlModelWriter

compartmentList, document, doProductStub, doReactantStub, speciesListElement

Fields inherited from class biouml.plugins.sbml.SbmlSupport

diagram, emodel, log, modelName

Fields inherited from class biouml.plugins.sbml.SbmlConstants

ANNOTATION_ELEMENT, ASSIGNEMENT_ELEMENT, ASSIGNEMENT_LIST_ELEMENT, ASSIGNEMENT_VARIABLE_ATTR, BIOUML_COMPARTMENT_INFO_ELEMENT, BIOUML_EDGE_INFO_ELEMENT, BIOUML_NODE_INFO_ELEMENT, BIOUML_SPECIE_INFO_ELEMENT, BIOUML_SPECIE_TYPE_ATTR, BIOUML_XMLNS_ATTR, BIOUML_XMLNS_VALUE, COMPARTMENT_ATTR, COMPARTMENT_DIMENTION_ATTR, COMPARTMENT_ELEMENT, COMPARTMENT_LIST_ELEMENT, COMPARTMENT_OUTSIDE_ATTR, COMPARTMENT_VOLUME_ATTR, CONSTANT_ATTR, DELAY_ELEMENT, DENOMINATOR_ATTR, EVENT_ELEMENT, EVENT_LIST_ELEMENT, FORMULA_ATTR, FUNCTION_DEFINITION_ELEMENT, FUNCTION_LIST_ELEMENT, ID_ATTR, KINETIC_LAW_ELEMENT, MATH_ATTR, MATH_ELEMENT, MODEL_ELEMENT, MODIFIER_LIST_ELEMENT, NAME_ATTR, NOTES_ELEMENT, PARAMETER_ELEMENT, PARAMETER_LIST_ELEMENT, PARAMETER_VALUE_ATTR, PRODUCT_LIST_ELEMENT, PRODUCT_STUB, REACTANT_LIST_ELEMENT, REACTANT_STUB, REACTION_ELEMENT, REACTION_FAST_ATTR, REACTION_LIST_ELEMENT, REACTION_REVERSIBLE_ATTR, RULE_ALGEBRAIC_ELEMENT, RULE_ASSIGNEMENT_ELEMENT, RULE_COMMENT_ATTR, RULE_COMPARTMENT_VOLUME_ELEMENT, RULE_FORMULA_ATTR, RULE_LIST_ELEMENT, RULE_PARAMETER_ELEMENT, RULE_RATE_ELEMENT, RULE_SPECIE_CONCENTRATION_ELEMENT, RULE_VARIABLE_ATTR, SBML_ELEMENT, SBML_LEVEL_ATTR, SBML_LEVEL_VALUE_1, SBML_LEVEL_VALUE_2, SBML_VERSION_ATTR, SBML_VERSION_VALUE_1, SBML_VERSION_VALUE_2, SBML_XMLNS_VALUE, SPECIE_ATTR, SPECIE_ATTR_11, SPECIE_BOUNDARY_CONDITION_ATTR, SPECIE_CHARGE_ATTR, SPECIE_DEFAULT_SUBSTANCE_UNITS, SPECIE_ELEMENT, SPECIE_ELEMENT_11, SPECIE_HAS_ONLY_SUBSTANCE_UNITS_ATTR, SPECIE_INITIAL_AMOUNT_ATTR, SPECIE_INITIAL_CONCENTRATION_ATTR, SPECIE_LIST_ELEMENT, SPECIE_REFERENCE_ELEMENT, SPECIE_REFERENCE_ELEMENT_11, SPECIE_SPATIAL_SIZE_UNITS_ATTR, SPECIE_SUBSTANCE_UNITS_ATTR, STOICHIOMETRY_ATTR, STOICHIOMETRY_MATH_ELEMENT, SUBSTANCE_UNITS_ATTR, TIME_UNITS_ATTR, TRIGGER_ELEMENT, TYPE_ATTR, UNIT_LIST_ELEMENT, UNIT_SUBSTANCE, UNIT_TIME, UNIT_VOLUME, UNITS_ATTR, XMLNS_ATTR

Constructor Summary

SbmlModelWriter_21()

Method Summary

protected void	appendMathChild(org.w3c.dom.Element element, java.lang.String formula, Role role)
protected org.w3c.dom.Element	createSpecieElement()
protected void	initContext() Initializes context of the writer.
static boolean	isValidModel(Diagram diagram) Checks if the model represented by diagram is representable in SBML level 1 version 1 model.
protected void	setId(org.w3c.dom.Element element, java.lang.String id) Sets 'id' or 'name' attribute (according to level and version) equal to given string.
protected void	setLevel(org.w3c.dom.Element sbmlElement)
protected void	setVersion(org.w3c.dom.Element sbmlElement)
protected boolean	validCompartmentList(java.util.List compartmentList) Returns true if compartment list is valid according to given version of SBML specification.
protected boolean	validReaction(Node reaction) Returns true if reaction is valid according to given version of SBML specification.
protected void	writeAssignment(Assignment assignment, org.w3c.dom.Element eventAssignmentListElement)
protected org.w3c.dom.Element	writeCompartmentList(org.w3c.dom.Element model)
protected void	writeEvent(Event event, org.w3c.dom.Element eventListElement)
protected void	writeEventAssignmentList(Event event, org.w3c.dom.Element eventElement)
protected void	writeEventList(org.w3c.dom.Element modelElement)
protected void	writeFormula(java.lang.String formula, Node reaction, org.w3c.dom.Element kineticLawElement)
protected void	writeFunction(Function function, org.w3c.dom.Element functionListElement)
protected void	writeFunctionDefinitionList(org.w3c.dom.Element modelElement) Function definitions are only supported since level 2
protected org.w3c.dom.Element	writeReactionList(org.w3c.dom.Element model)
protected void	writeRule(Equation equation, org.w3c.dom.Element ruleListElement)
protected void	writeRuleList(org.w3c.dom.Element modelElement) Writes list of rules, that are not rules derived from reactions
protected org.w3c.dom.Element	writeSpecieList(org.w3c.dom.Element model)
protected void	writeStoichiometry(org.w3c.dom.Element specieReferenceElement, SpecieReference species, Node reaction)
protected void	writeUnitList(org.w3c.dom.Element modelElement)

Methods inherited from class biouml.plugins.sbml.SbmlModelWriter

createDOM, fillCompartmentList, parseAsSpecie, writeCompartment, writeDiagram, writeKineticLaw, writeNotes, writeParameter, writeParameterList, writeProducts, writeReactants, writeReaction, writeReactionList, writeSpecie, writeSpecieList, writeSpecieReferences, writeSpecieStub, writeStubReference

Methods inherited from class biouml.plugins.sbml.SbmlSupport

error, getElement, parseAsCompartment, parseAsParameter, parseFormula, readXhtml, warn, writeXhtml

Methods inherited from class biouml.plugins.sbml.SbmlConstants

DEFAULT_SPATIAL_SIZE_UNITS

Methods inherited from class java.lang.Object

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

Constructor Detail

SbmlModelWriter_21

public SbmlModelWriter_21()

Method Detail

initContext

protected void initContext()

Description copied from class: SbmlModelWriter

Initializes context of the writer.

Specified by:

initContext in class SbmlModelWriter

createSpecieElement

protected org.w3c.dom.Element createSpecieElement()

Specified by:

createSpecieElement in class SbmlModelWriter

setLevel

protected void setLevel(org.w3c.dom.Element sbmlElement)

Specified by:

setLevel in class SbmlModelWriter

setVersion

protected void setVersion(org.w3c.dom.Element sbmlElement)

Specified by:

setVersion in class SbmlModelWriter

setId

protected void setId(org.w3c.dom.Element element,
                     java.lang.String id)

Description copied from class: SbmlModelWriter

Sets 'id' or 'name' attribute (according to level and version) equal to given string.

Specified by:

setId in class SbmlModelWriter

validCompartmentList

protected boolean validCompartmentList(java.util.List compartmentList)

Description copied from class: SbmlModelWriter

Returns true if compartment list is valid according to given version of SBML specification.

Specified by:

validCompartmentList in class SbmlModelWriter

validReaction

protected boolean validReaction(Node reaction)

Description copied from class: SbmlModelWriter

Returns true if reaction is valid according to given version of SBML specification.

Specified by:

validReaction in class SbmlModelWriter

appendMathChild

protected void appendMathChild(org.w3c.dom.Element element,
                               java.lang.String formula,
                               Role role)

writeFunctionDefinitionList

protected void writeFunctionDefinitionList(org.w3c.dom.Element modelElement)

Description copied from class: SbmlModelWriter

Function definitions are only supported since level 2

Specified by:

writeFunctionDefinitionList in class SbmlModelWriter

writeFunction

protected void writeFunction(Function function,
                             org.w3c.dom.Element functionListElement)

writeUnitList

protected void writeUnitList(org.w3c.dom.Element modelElement)

Specified by:

writeUnitList in class SbmlModelWriter

To do:

Implement it

writeCompartmentList

protected org.w3c.dom.Element writeCompartmentList(org.w3c.dom.Element model)

Overrides:

writeCompartmentList in class SbmlModelWriter

writeSpecieList

protected org.w3c.dom.Element writeSpecieList(org.w3c.dom.Element model)

Overrides:

writeSpecieList in class SbmlModelWriter

writeReactionList

protected org.w3c.dom.Element writeReactionList(org.w3c.dom.Element model)

Overrides:

writeReactionList in class SbmlModelWriter

writeRuleList

protected void writeRuleList(org.w3c.dom.Element modelElement)

Description copied from class: SbmlModelWriter

Writes list of rules, that are not rules derived from reactions

Specified by:

writeRuleList in class SbmlModelWriter

writeRule

protected void writeRule(Equation equation,
                         org.w3c.dom.Element ruleListElement)

writeEventList

protected void writeEventList(org.w3c.dom.Element modelElement)

Specified by:

writeEventList in class SbmlModelWriter

writeEvent

protected void writeEvent(Event event,
                          org.w3c.dom.Element eventListElement)

writeEventAssignmentList

protected void writeEventAssignmentList(Event event,
                                        org.w3c.dom.Element eventElement)

writeAssignment

protected void writeAssignment(Assignment assignment,
                               org.w3c.dom.Element eventAssignmentListElement)

writeFormula

protected void writeFormula(java.lang.String formula,
                            Node reaction,
                            org.w3c.dom.Element kineticLawElement)

Specified by:

writeFormula in class SbmlModelWriter

writeStoichiometry

protected void writeStoichiometry(org.w3c.dom.Element specieReferenceElement,
                                  SpecieReference species,
                                  Node reaction)

To do:

- use math formatter

isValidModel

public static boolean isValidModel(Diagram diagram)

Checks if the model represented by diagram is representable in SBML level 1 version 1 model.