SbmlModelReader

Overview

Package

Class

Use

Tree

Deprecated

Help

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

biouml.plugins.sbml
Class SbmlModelReader

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

Direct Known Subclasses:: SbmlModelReader_11, SbmlModelReader_21

public abstract class SbmlModelReader
extends SbmlSupport

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 java.util.Map`	`compartmentMap`
`protected Compartment`	`defaultCompartment`
`protected java.lang.String`	`level`
`protected LinearFormatter`	`linearFormatter`
`protected int`	`maxVisibleVariableNumber`
`protected boolean`	`shouldLayout`
`protected java.util.Map`	`specieMap`
`protected biouml.plugins.sbml.SbmlModelReader.SbmlVariableResolver`	`variableResolver`
`protected java.lang.String`	`version`
`protected int`	`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()`

Method Summary
`protected double`	`convertUnit(java.lang.String unitName, double value)` It converts value to unified unit system.
`protected DiagramType`	`getDiagramType()`
`protected abstract 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 abstract java.lang.String`	`getTitle(org.w3c.dom.Element element)`
`boolean`	`isReaction(DiagramElement de)`
`boolean`	`isSpecie(DiagramElement de)`
`protected abstract boolean`	`isValid(java.lang.String paramName, java.lang.Object element, java.lang.String name)`
`void`	`layout(Compartment compartment)` Stub implimentation for diagram layout.
`void`	`layout(Compartment compartment, int x, int y)` Hierarchically layout compartments and species.
`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)`
`Diagram`	`read(org.w3c.dom.Document document, java.lang.String name, DataCollection origin)`
`protected Compartment`	`readCompartment(org.w3c.dom.Element element, java.lang.String compartmentId, java.lang.String compartmentName)`
`protected void`	`readCompartmentList(org.w3c.dom.Element model)` Read list of compartments.
`protected void`	`readEventList(org.w3c.dom.Element element)`
`protected void`	`readFunctionDefinitionList(org.w3c.dom.Element model)`
`protected void`	`readKineticLaw(org.w3c.dom.Element element, Node reaction)`
`protected abstract void`	`readKineticLawFormula(org.w3c.dom.Element element, Node reaction, KineticLaw law)`
`protected void`	`readModifiers(org.w3c.dom.Element element, Node reaction)`
`java.lang.String`	`readNotes(org.w3c.dom.Element element)`
`protected Variable`	`readParameter(org.w3c.dom.Element element, java.lang.String parameterId, Node reaction)`
`protected void`	`readParameterList(org.w3c.dom.Element parent, Node reaction)` Read list of parameters for the specified element.
`protected void`	`readProducts(org.w3c.dom.Element element, Node reaction)`
`protected void`	`readReactants(org.w3c.dom.Element element, Node reaction)`
`protected Node`	`readReaction(org.w3c.dom.Element element, java.lang.String reactionId, java.lang.String reactionName)`
`protected void`	`readReactionList(org.w3c.dom.Element model)` Read list of reactions.
`protected abstract void`	`readRule(org.w3c.dom.Element model, int i)`
`protected void`	`readRuleList(org.w3c.dom.Element model)`
`protected Node`	`readSpecie(org.w3c.dom.Element element, java.lang.String specieId, java.lang.String specieName)`
`protected void`	`readSpecieList(org.w3c.dom.Element model)` Read list of species.
`protected void`	`readSpecieReference(Node reactionNode, org.w3c.dom.Element element, java.lang.String specieId, java.lang.String role)`
`protected abstract void`	`readStoichiometry(org.w3c.dom.Element element, SpecieReference reference, Node reactionNode)`
`protected void`	`readUnitList(org.w3c.dom.Element model)` Read list of unit definitions.
`protected void`	`validateReaction(Node reaction)`

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

level

protected java.lang.String level

version

protected java.lang.String version

compartmentMap

protected java.util.Map compartmentMap

specieMap

protected java.util.Map specieMap

defaultCompartment

protected Compartment defaultCompartment

shouldLayout

protected boolean shouldLayout

visibleVariableNumber

protected int visibleVariableNumber

maxVisibleVariableNumber

protected int maxVisibleVariableNumber

variableResolver

protected biouml.plugins.sbml.SbmlModelReader.SbmlVariableResolver variableResolver

linearFormatter

protected LinearFormatter linearFormatter

Constructor Detail