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biouml.plugins.sbml
Class SbmlModelReader

biouml.plugins.sbml.SbmlConstants
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  +--biouml.plugins.sbml.SbmlSupport
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        +--biouml.plugins.sbml.SbmlModelReader
Direct Known Subclasses:
SbmlModelReader_11, SbmlModelReader_21
public abstract class SbmlModelReader
extends SbmlSupport

todo read Units, read Rules, functions support
pending generation of name for parameters defined in reaction. Currently name is generated as reactioName_parameterName., name validations that they are valid SNames
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()
           

Method Summary
 booleanisReaction(DiagramElement de)
           
 booleanisSpecie(DiagramElement de)
           
 voidlayout(Compartment compartment)
          Stub implimentation for diagram layout.
 voidlayout(Compartment compartment, int x, int y)
          Hierarchically layout compartments and species.
 Diagramread(Document document, String name, DataCollection origin)
           
 StringreadNotes(Element element)
           

Methods inherited from class biouml.plugins.sbml.SbmlSupport
getElement, parseFormula, readXhtml, writeXhtml

Methods inherited from class biouml.plugins.sbml.SbmlConstants
DEFAULT_SPATIAL_SIZE_UNITS

Constructor Detail

SbmlModelReader

public SbmlModelReader()
Method Detail

isReaction

public boolean isReaction(DiagramElement de)

isSpecie

public boolean isSpecie(DiagramElement de)

layout

public void layout(Compartment compartment)
Stub implimentation for diagram layout.

layout

public void layout(Compartment compartment, int x, int y)
Hierarchically layout compartments and species.
pending currently we use ApplicationFrame to get Graphics object

read

public Diagram read(Document document, String name, DataCollection origin)
              throws java.lang.Exception

readNotes

public String readNotes(Element element)

Association Links

to Class java.lang.String

to Class java.lang.String

to Class java.util.Map

to Class java.util.Map

to Class biouml.model.Compartment

to Class biouml.plugins.sbml.SbmlModelReader.SbmlVariableResolver

to Class ru.biosoft.math.model.LinearFormatter

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