biouml.plugins.sbml
Class SbmlSupport
biouml.plugins.sbml.SbmlConstants
|
+--biouml.plugins.sbml.SbmlSupport
- Direct Known Subclasses:
- SbmlModelReader, SbmlModelWriter
- public class SbmlSupport
- extends SbmlConstants
| 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 |
| Method Summary |
Element | getElement(Element element, String childName)
|
String | parseFormula(String formula, Node reaction)
General template to cinvert SBML formula into BioUML formula. |
String | readXhtml(Element element)
Reads html section and returns its content as a single string. |
void | writeXhtml(Document document, Element element, String notes)
|
getElement
public Element getElement(Element element, String childName)
parseFormula
public String parseFormula(String formula, Node reaction)
- General template to cinvert SBML formula into BioUML formula.
Convertion rules are specified by corresponding procedures that are redefiened in subclasses:
1) Specie name: specieName $specieName
2) Compartment name: compartmentName $compartmentName
3) Reaction parameter name: parameterName reactionName_parameterName
readXhtml
public String readXhtml(Element element)
- Reads html section and returns its content as a single string.
For apache.crimson we can get the content as:
String html = element.toString();
but it does not works for apache.xerces.
Thus we impliment an approach that has not any assumptions
and should work for all XML DOM parsers.
writeXhtml
public void writeXhtml(Document document, Element element, String notes)
to Class org.apache.log4j.Category
to Class java.lang.String
to Class biouml.model.Diagram
to Class biouml.model.dynamics.EModel
BOTTOM