org.jscience.ml.sbml
Class Model

java.lang.Object
  extended by org.jscience.ml.sbml.SBase
      extended by org.jscience.ml.sbml.SBaseId
          extended by 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