biouml.plugins.sbml
Class SbmlModelReader_12

java.lang.Object
  biouml.plugins.sbml.SbmlConstants
      biouml.plugins.sbml.SbmlSupport
          biouml.plugins.sbml.SbmlModelReader
              biouml.plugins.sbml.SbmlModelReader_11
                  biouml.plugins.sbml.SbmlModelReader_12

public class SbmlModelReader_12

extends SbmlModelReader_11

1.2 version differs only by validation

Field Summary

Fields inherited from class biouml.plugins.sbml.SbmlModelReader_11

parser, 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_12()

Method Summary

protected DiagramType	getDiagramType()
protected boolean	isValid(java.lang.String elementName, java.lang.Object element, java.lang.String name)

Methods inherited from class biouml.plugins.sbml.SbmlModelReader_11

getId, getSpecieAttribute, getSpecieElement, getSpecieReference, getTitle, initParser, readKineticLawFormula, readMath, readRule, readStoichiometry, validateList, validateReaction

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

Constructor Detail

SbmlModelReader_12

public SbmlModelReader_12()

Method Detail

getDiagramType

protected DiagramType getDiagramType()

Overrides:

getDiagramType in class SbmlModelReader_11

isValid

protected boolean isValid(java.lang.String elementName,
                          java.lang.Object element,
                          java.lang.String name)

Overrides:

isValid in class SbmlModelReader_11