SbmlModelReader

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biouml.plugins.sbml
Class SbmlModelReader_21

java.lang.Object
  biouml.plugins.sbml.SbmlConstants
      biouml.plugins.sbml.SbmlSupport
          biouml.plugins.sbml.SbmlModelReader
              biouml.plugins.sbml.SbmlModelReader_21

public class SbmlModelReader_21
extends SbmlModelReader

To do:: read Units, read Rules, functions support
Pendung:: generation of name for parameters defined in reaction. Currently name is generated as reactioName_parameterName., name validations that they are valid SNames

Field Summary
`protected MathMLParser`	`mathMLParser`

Fields inherited from class biouml.plugins.sbml.SbmlModelReader

compartmentMap, defaultCompartment, level, linearFormatter, maxVisibleVariableNumber, shouldLayout, specieMap, variableResolver, version, visibleVariableNumber

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
`SbmlModelReader_21()`

Method Summary
`protected DiagramType`	`getDiagramType()`
`protected java.lang.String`	`getId(org.w3c.dom.Element element)`
`protected java.lang.String`	`getTitle(org.w3c.dom.Element element)`
`protected boolean`	`isValid(java.lang.String elementName, java.lang.Object element, java.lang.String name)`
`protected void`	`readAssignmentList(org.w3c.dom.Element eventElement, Event event)`
`protected Compartment`	`readCompartment(org.w3c.dom.Element element, java.lang.String compartmentId, java.lang.String compartmentName)`
`protected void`	`readEvent(org.w3c.dom.Element eventElement, int i)`
`protected void`	`readEventList(org.w3c.dom.Element model)`
`protected void`	`readFunctionDeclaration(org.w3c.dom.Element funcDefElement, java.lang.String funcDefId)`
`protected void`	`readFunctionDefinitionList(org.w3c.dom.Element model)`
`protected void`	`readKineticLawFormula(org.w3c.dom.Element element, Node reaction, KineticLaw kineticLaw)`
`protected java.lang.String`	`readMath(org.w3c.dom.Element element, DiagramElement de)`
`protected void`	`readModifiers(org.w3c.dom.Element element, Node reaction)`
`protected Variable`	`readParameter(org.w3c.dom.Element element, java.lang.String parameterId, Node reaction)`
`protected void`	`readRule(org.w3c.dom.Element ruleElement, int i)`
`protected Node`	`readSpecie(org.w3c.dom.Element element, java.lang.String speciesId, java.lang.String speciesName)`
`protected void`	`readStoichiometry(org.w3c.dom.Element element, SpecieReference reference, Node reaction)`
`protected boolean`	`validateList(java.lang.Object element, java.lang.String tag, java.lang.String name)`
`protected void`	`validateReaction(Node reaction)`

Methods inherited from class biouml.plugins.sbml.SbmlModelReader

convertUnit, getSpecieAttribute, getSpecieElement, getSpecieReference, isReaction, isSpecie, layout, layout, parseAsCompartment, parseAsParameter, parseAsSpecie, read, readCompartmentList, readKineticLaw, readNotes, readParameterList, readProducts, readReactants, readReaction, readReactionList, readRuleList, readSpecieList, readSpecieReference, readUnitList

Methods inherited from class biouml.plugins.sbml.SbmlSupport

error, getElement, 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

mathMLParser

protected MathMLParser mathMLParser

Constructor Detail