SbmlModelReader

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biouml.plugins.sbml
Class SbmlModelReader_11

java.lang.Object
  biouml.plugins.sbml.SbmlConstants
      biouml.plugins.sbml.SbmlSupport
          biouml.plugins.sbml.SbmlModelReader
              biouml.plugins.sbml.SbmlModelReader_11

Direct Known Subclasses:: SbmlModelReader_12

public class SbmlModelReader_11
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 Parser`	`parser`
`protected DefaultParserContext`	`parserContext`

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_11()`

Method Summary
`protected DiagramType`	`getDiagramType()`
`protected java.lang.String`	`getId(org.w3c.dom.Element element)`
`protected java.lang.String`	`getSpecieAttribute(org.w3c.dom.Element specieRef)`
`protected org.w3c.dom.NodeList`	`getSpecieElement(org.w3c.dom.Element specieList)`
`protected org.w3c.dom.NodeList`	`getSpecieReference(org.w3c.dom.Element list)`
`protected java.lang.String`	`getTitle(org.w3c.dom.Element element)`
`protected void`	`initParser()`
`protected boolean`	`isValid(java.lang.String elementName, java.lang.Object element, java.lang.String name)`
`protected void`	`readKineticLawFormula(org.w3c.dom.Element kineticLawElement, Node reaction, KineticLaw law)`
`protected java.lang.String`	`readMath(java.lang.String formula, DiagramElement de)`
`protected void`	`readRule(org.w3c.dom.Element ruleElement, int i)`
`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 errorMissing, java.lang.String errorEmpty, java.lang.String name)`
`protected void`	`validateReaction(Node reaction)`

Methods inherited from class biouml.plugins.sbml.SbmlModelReader

convertUnit, isReaction, isSpecie, layout, layout, parseAsCompartment, parseAsParameter, parseAsSpecie, read, readCompartment, readCompartmentList, readEventList, readFunctionDefinitionList, readKineticLaw, readModifiers, readNotes, readParameter, readParameterList, readProducts, readReactants, readReaction, readReactionList, readRuleList, readSpecie, 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

parser

protected Parser parser

parserContext

protected DefaultParserContext parserContext

Constructor Detail