SbmlModelWriter

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biouml.plugins.sbml
Class SbmlModelWriter

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

Direct Known Subclasses:: SbmlModelWriter_21, SbmlModelWriter_L1

public abstract class SbmlModelWriter
extends SbmlSupport

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 species names.

Pendung:: SName validation, warn if species list or reaction list is empty.

Field Summary
`protected java.util.List`	`compartmentList`
`protected org.w3c.dom.Document`	`document`
`protected boolean`	`doProductStub`
`protected boolean`	`doReactantStub`
`protected org.w3c.dom.Element`	`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()`

Method Summary
`org.w3c.dom.Document`	`createDOM(Diagram sourceDiagram)`
`protected abstract org.w3c.dom.Element`	`createSpecieElement()`
`protected void`	`fillCompartmentList(Compartment compartment, boolean includeItself)`
`protected abstract void`	`initContext()` Initializes context of the writer.
`protected boolean`	`parseAsSpecie(java.lang.String token, java.lang.StringBuffer result)`
`protected abstract 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 abstract void`	`setLevel(org.w3c.dom.Element sbmlElement)`
`protected abstract void`	`setVersion(org.w3c.dom.Element sbmlElement)`
`protected abstract boolean`	`validCompartmentList(java.util.List compartmentList)` Returns true if compartment list is valid according to given version of SBML specification.
`protected abstract boolean`	`validReaction(Node reaction)` Returns true if reaction is valid according to given version of SBML specification.
`protected void`	`writeCompartment(org.w3c.dom.Element compartmentListElement, Compartment compartment)`
`protected org.w3c.dom.Element`	`writeCompartmentList(org.w3c.dom.Element model)`
`protected void`	`writeDiagram(org.w3c.dom.Element sbml)`
`protected abstract void`	`writeEventList(org.w3c.dom.Element model)`
`protected abstract void`	`writeFormula(java.lang.String formula, Node reaction, org.w3c.dom.Element kineticLawElement)`
`protected abstract void`	`writeFunctionDefinitionList(org.w3c.dom.Element model)` Function definitions are only supported since level 2
`protected void`	`writeKineticLaw(org.w3c.dom.Element reactionElement, Node reaction)`
`void`	`writeNotes(org.w3c.dom.Element element, java.lang.String notes)`
`protected void`	`writeParameter(org.w3c.dom.Element parameterListElement, Variable parameter)`
`protected void`	`writeParameterList(org.w3c.dom.Element element)`
`protected void`	`writeProducts(org.w3c.dom.Element reactionElement, Node reaction)`
`protected void`	`writeReactants(org.w3c.dom.Element reactionElement, Node reaction)`
`protected void`	`writeReaction(org.w3c.dom.Element reactionListElement, Node reaction)`
`protected org.w3c.dom.Element`	`writeReactionList(org.w3c.dom.Element model)`
`protected void`	`writeReactionList(org.w3c.dom.Element reactionListElement, Compartment compartment)`
`protected abstract void`	`writeRuleList(org.w3c.dom.Element model)` Writes list of rules, that are not rules derived from reactions
`protected void`	`writeSpecie(org.w3c.dom.Element speciesListElement, Node species)`
`protected org.w3c.dom.Element`	`writeSpecieList(org.w3c.dom.Element model)`
`protected void`	`writeSpecieList(org.w3c.dom.Element speciesListElement, Compartment compartment)`
`protected boolean`	`writeSpecieReferences(org.w3c.dom.Element listElement, Node reaction, java.lang.String role)`
`protected void`	`writeSpecieStub(org.w3c.dom.Element speciesListElement, java.lang.String stubName, java.lang.String messageKey)`
`protected void`	`writeStubReference(org.w3c.dom.Element listElement, Node reaction, java.lang.String stubName)`
`protected abstract void`	`writeUnitList(org.w3c.dom.Element model)`

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

Field Detail

document

protected org.w3c.dom.Document document

compartmentList

protected java.util.List compartmentList

speciesListElement

protected org.w3c.dom.Element speciesListElement

doReactantStub

protected boolean doReactantStub

doProductStub

protected boolean doProductStub

Constructor Detail