biouml.plugins.sbml
Class SbmlSupport

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

Direct Known Subclasses:

SbmlModelReader, SbmlModelWriter

public class SbmlSupport

extends SbmlConstants

Field Summary

protected Diagram	diagram
protected EModel	emodel
protected org.apache.log4j.Category	log
protected java.lang.String	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

SbmlSupport()

Method Summary

protected void	error(java.lang.String key, java.lang.String[] params)
org.w3c.dom.Element	getElement(org.w3c.dom.Element element, java.lang.String childName)
protected boolean	parseAsCompartment(java.lang.String token, java.lang.StringBuffer result)
protected boolean	parseAsParameter(java.lang.String token, java.lang.StringBuffer result, Node reaction)
protected boolean	parseAsSpecie(java.lang.String token, java.lang.StringBuffer result)
java.lang.String	parseFormula(java.lang.String formula, Node reaction) General template to cinvert SBML formula into BioUML formula.
java.lang.String	readXhtml(org.w3c.dom.Element element) Reads html section and returns its content as a single string.
protected void	warn(java.lang.String key, java.lang.String[] params)
void	writeXhtml(org.w3c.dom.Document document, org.w3c.dom.Element element, java.lang.String notes)

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

log

protected org.apache.log4j.Category log

modelName

protected java.lang.String modelName

diagram

protected Diagram diagram

emodel

protected EModel emodel

Constructor Detail

SbmlSupport

public SbmlSupport()

Method Detail

warn

protected void warn(java.lang.String key,
                    java.lang.String[] params)

error

protected void error(java.lang.String key,
                     java.lang.String[] params)

getElement

public org.w3c.dom.Element getElement(org.w3c.dom.Element element,
                                      java.lang.String childName)

readXhtml

public java.lang.String readXhtml(org.w3c.dom.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(org.w3c.dom.Document document,
                       org.w3c.dom.Element element,
                       java.lang.String notes)

parseFormula

public java.lang.String parseFormula(java.lang.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

parseAsSpecie

protected boolean parseAsSpecie(java.lang.String token,
                                java.lang.StringBuffer result)

parseAsCompartment

protected boolean parseAsCompartment(java.lang.String token,
                                     java.lang.StringBuffer result)

parseAsParameter

protected boolean parseAsParameter(java.lang.String token,
                                   java.lang.StringBuffer result,
                                   Node reaction)