org.jscience.ml.sbml
Class Model

java.lang.Object
  org.jscience.ml.sbml.SBase
      org.jscience.ml.sbml.SBaseId
          org.jscience.ml.sbml.Model

public class Model
extends SBaseId

This class defines a grouping of components - MathDefinitions, Compartments, Species, Reactions, Parameters, Events, Rules, and UnitDefinitions. This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.

Field Summary

Fields inherited from class org.jscience.ml.sbml.SBaseId

id, name

Constructor Summary

Model()
Creates a new instance of Model

Model(java.lang.String name)
Creates a new Model object.

Method Summary

void	addCompartment(Compartment compartment) DOCUMENT ME!
void	addFunctionDefinition(FunctionDefinition definition) DOCUMENT ME!
void	addParameter(Parameter parameter) DOCUMENT ME!
void	addReaction(Reaction reaction) DOCUMENT ME!
void	addSpecies(Species s) DOCUMENT ME!
java.util.Vector	getCompartments() Getter for property compartments.
SBase	getCompartmentsElement() Getter for property compartmentsElement.
java.util.Vector	getEvents() Getter for property events.
SBase	getEventsElement() Getter for property eventsElement.
java.util.Vector	getFunctionDefinitions() Getter for property functionDefinitions.
SBase	getFunctionDefinitionsElement() Getter for property functionDefinitionsElement.
java.util.Vector	getParameters() Getter for property parameters.
SBase	getParametersElement() Getter for property parametersElement.
java.util.Vector	getReactions() Getter for property reactions.
SBase	getReactionsElement() Getter for property reactionsElement.
java.util.Vector	getRules() Getter for property rules.
SBase	getRulesElement() Getter for property rulesElement.
SBase	getSbmlElement() Getter for property sbmlElement.
java.util.Vector	getSpecies() Getter for property species.
SBase	getSpeciesElement() Getter for property speciesElement.
java.util.List	getUnitDefinitions() Getter for property unitDefinitions.
SBase	getUnitDefinitionsElement() Getter for property unitDefinitionsElement.
boolean	hasLocalParameters() DOCUMENT ME!
void	setCompartments(java.util.Vector compartments) Setter for property compartments.
void	setCompartmentsElement(SBase compartmentsElement) Setter for property compartmentsElement.
void	setEvents(java.util.Vector events) Setter for property events.
void	setEventsElement(SBase eventsElement) Setter for property eventsElement.
void	setFunctionDefinitions(java.util.Vector functionDefinitions) Setter for property functionDefinitions.
void	setFunctionDefinitionsElement(SBase functionDefinitionsElement) Setter for property functionDefinitionsElement.
void	setParameters(java.util.Vector parameters) Setter for property parameters.
void	setParametersElement(SBase parametersElement) Setter for property parametersElement.
void	setReactions(java.util.Vector reactions) Setter for property reactions.
void	setReactionsElement(SBase reactionsElement) Setter for property reactionsElement.
void	setRules(java.util.Vector rules) Setter for property rules.
void	setRulesElement(SBase rulesElement) Setter for property rulesElement.
void	setSbmlElement(SBase sbmlElement) Setter for property sbmlElement.
void	setSpecies(java.util.Vector species) Setter for property species.
void	setSpeciesElement(SBase speciesElement) Setter for property speciesElement.
void	setUnitDefinitionsElement(SBase unitDefinitionsElement) Setter for property unitDefinitionsElement.
java.lang.String	toString() Get the SBML representation for this class.

Methods inherited from class org.jscience.ml.sbml.SBaseId

getId, getName, setId, setName

Methods inherited from class org.jscience.ml.sbml.SBase

getAnnotations, getMetaid, getNotes, getRDF, printList, printShortForm, setMetaid, setRDF, setRDF

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Model

public Model(java.lang.String name)

Creates a new Model object.

Parameters:

name - DOCUMENT ME!

Model

public Model()

Creates a new instance of Model

Method Detail

addCompartment

public void addCompartment(Compartment compartment)

DOCUMENT ME!

Parameters:

compartment - DOCUMENT ME!

addFunctionDefinition

public void addFunctionDefinition(FunctionDefinition definition)

DOCUMENT ME!

Parameters:

definition - DOCUMENT ME!

addParameter

public void addParameter(Parameter parameter)

DOCUMENT ME!

Parameters:

parameter - DOCUMENT ME!

addReaction

public void addReaction(Reaction reaction)

DOCUMENT ME!

Parameters:

reaction - DOCUMENT ME!

addSpecies

public void addSpecies(Species s)

DOCUMENT ME!

Parameters:

s - DOCUMENT ME!

getCompartments

public java.util.Vector getCompartments()

Getter for property compartments.

Returns:

Value of property compartments.

getCompartmentsElement

public SBase getCompartmentsElement()

Getter for property compartmentsElement.

Returns:

Value of property compartmentsElement.

getEvents

public java.util.Vector getEvents()

Getter for property events.

Returns:

Value of property events.

getEventsElement

public SBase getEventsElement()

Getter for property eventsElement.

Returns:

Value of property eventsElement.

getFunctionDefinitions

public java.util.Vector getFunctionDefinitions()

Getter for property functionDefinitions.

Returns:

Value of property functionDefinitions.

getFunctionDefinitionsElement

public SBase getFunctionDefinitionsElement()

Getter for property functionDefinitionsElement.

Returns:

Value of property functionDefinitionsElement.

getParameters

public java.util.Vector getParameters()

Getter for property parameters.

Returns:

Value of property parameters.

getParametersElement

public SBase getParametersElement()

Getter for property parametersElement.

Returns:

Value of property parametersElement.

getReactions

public java.util.Vector getReactions()

Getter for property reactions.

Returns:

Value of property reactions.

getReactionsElement

public SBase getReactionsElement()

Getter for property reactionsElement.

Returns:

Value of property reactionsElement.

getRules

public java.util.Vector getRules()

Getter for property rules.

Returns:

Value of property rules.

getRulesElement

public SBase getRulesElement()

Getter for property rulesElement.

Returns:

Value of property rulesElement.

getSbmlElement

public SBase getSbmlElement()

Getter for property sbmlElement.

Returns:

Value of property sbmlElement.

getSpecies

public java.util.Vector getSpecies()

Getter for property species.

Returns:

Value of property species.

getSpeciesElement

public SBase getSpeciesElement()

Getter for property speciesElement.

Returns:

Value of property speciesElement.

getUnitDefinitions

public java.util.List getUnitDefinitions()

Getter for property unitDefinitions.

Returns:

Value of property unitDefinitions.

getUnitDefinitionsElement

public SBase getUnitDefinitionsElement()

Getter for property unitDefinitionsElement.

Returns:

Value of property unitDefinitionsElement.

hasLocalParameters

public boolean hasLocalParameters()

DOCUMENT ME!

Returns:

DOCUMENT ME!

setCompartments

public void setCompartments(java.util.Vector compartments)

Setter for property compartments.

Parameters:

compartments - New value of property compartments.

setCompartmentsElement

public void setCompartmentsElement(SBase compartmentsElement)

Setter for property compartmentsElement.

Parameters:

compartmentsElement - New value of property compartmentsElement.

setEvents

public void setEvents(java.util.Vector events)

Setter for property events.

Parameters:

events - New value of property events.

setEventsElement

public void setEventsElement(SBase eventsElement)

Setter for property eventsElement.

Parameters:

eventsElement - New value of property eventsElement.

setFunctionDefinitions

public void setFunctionDefinitions(java.util.Vector functionDefinitions)

Setter for property functionDefinitions.

Parameters:

functionDefinitions - New value of property functionDefinitions.

setFunctionDefinitionsElement

public void setFunctionDefinitionsElement(SBase functionDefinitionsElement)

Setter for property functionDefinitionsElement.

Parameters:

functionDefinitionsElement - New value of property functionDefinitionsElement.

setParameters

public void setParameters(java.util.Vector parameters)

Setter for property parameters.

Parameters:

parameters - New value of property parameters.

setParametersElement

public void setParametersElement(SBase parametersElement)

Setter for property parametersElement.

Parameters:

parametersElement - New value of property parametersElement.

setReactions

public void setReactions(java.util.Vector reactions)

Setter for property reactions.

Parameters:

reactions - New value of property reactions.

setReactionsElement

public void setReactionsElement(SBase reactionsElement)

Setter for property reactionsElement.

Parameters:

reactionsElement - New value of property reactionsElement.

setRules

public void setRules(java.util.Vector rules)

Setter for property rules.

Parameters:

rules - New value of property rules.

setRulesElement

public void setRulesElement(SBase rulesElement)

Setter for property rulesElement.

Parameters:

rulesElement - New value of property rulesElement.

setSbmlElement

public void setSbmlElement(SBase sbmlElement)

Setter for property sbmlElement.

Parameters:

sbmlElement - New value of property sbmlElement.

setSpecies

public void setSpecies(java.util.Vector species)

Setter for property species.

Parameters:

species - New value of property species.

setSpeciesElement

public void setSpeciesElement(SBase speciesElement)

Setter for property speciesElement.

Parameters:

speciesElement - New value of property speciesElement.

setUnitDefinitionsElement

public void setUnitDefinitionsElement(SBase unitDefinitionsElement)

Setter for property unitDefinitionsElement.

Parameters:

unitDefinitionsElement - New value of property unitDefinitionsElement.

toString

public java.lang.String toString()

Get the SBML representation for this class.

Overrides:

toString in class SBase

Returns:

The class's SBML representation