jp.sbi.celldesigner.plugin
Class PluginModel

java.lang.Object
  jp.sbi.celldesigner.plugin.PluginSBase
      jp.sbi.celldesigner.plugin.PluginModel

public class PluginModel
extends PluginSBase

This class wraps org.sbml.libsbml.Model for the plug-in.

Author:

Field Summary

Fields inherited from class jp.sbi.celldesigner.plugin.PluginSBase

sbase

Constructor Summary

PluginModel(java.lang.String id)
Constructor

Method Summary

void	addCompartment(PluginCompartment compartment) Adds a PluginCompartment to the list.
void	addEvent(PluginEvent event) Adds the PluginEvent to the list.
void	addFunctionDefinition(PluginFunctionDefinition function) Adds a PluginFunctionDefinition to the list.
void	addParameter(PluginParameter parameter) Adds the PluginParameter to the list.
void	addReaction(PluginReaction reaction) Adds a PluginReaction to the list.
void	addRule(PluginRule rule) Adds a PluginRule to the list.
void	addSpecies(PluginSpecies species) Adds a PluginSpecies to the list in this PluginModel.
void	addUnitDefinition(PluginUnitDefinition unit) Adds a PluginUnitDefinition to the list.
void	appendProtein(PluginProtein protein) Adds the PluginProtein to the list.
PluginAntiSenseRNA	getAntiSenseRNA(java.lang.String id) Gets the PluginAntiSenseRNA with the given id.
PluginCompartment	getCompartment(int index) Gets the PluginCompartment with the given index.
PluginCompartment	getCompartment(java.lang.String id) Gets the PluginCompartment with the given id.
PluginEvent	getEvent(int index) Gets the PluginEvent with the given index.
PluginEvent	getEvent(java.lang.String id) Gets the PluginEvent with the given id.
PluginFunctionDefinition	getFunctionDefinition(int index) Gets the PluginFunctionDefinition with the given index.
PluginFunctionDefinition	getFunctionDefinition(java.lang.String id) Gets the PluginFunctionDefinition with the given id.
PluginGene	getGene(java.lang.String id) Gets the PluginGene with the given id.
java.lang.String	getId()
PluginListOf	getListOfAllSpeciesAlias()
PluginListOf	getListOfAntiSenseRNAs()
PluginListOf	getListOfCompartments()
PluginListOf	getListOfEvents()
PluginListOf	getListOfFunctionDefinitions()
PluginListOf	getListOfGenes()
PluginListOf	getListOfParameters()
PluginListOf	getListOfProteins()
PluginListOf	getListOfReactions()
PluginListOf	getListOfRNAs()
PluginListOf	getListOfRules()
PluginListOf	getListOfSpecies()
PluginListOf	getListOfSpecies(PluginAntiSenseRNA rna)
PluginListOf	getListOfSpecies(PluginGene rna)
PluginListOf	getListOfSpecies(PluginProtein rna) Gets the list of PluginProtein added the given PluginProtein to.
PluginListOf	getListOfSpecies(PluginRNA rna)
PluginListOf	getListOfUnitDefinitions()
java.lang.String	getName()
int	getNumCompartments()
int	getNumEvents()
int	getNumFunctionDefinitions()
int	getNumParameters()
int	getNumReactions()
int	getNumRules()
int	getNumSpecies()
int	getNumUnitDefinitions()
PluginParameter	getParameter(int index) Gets the PluginParameter with the given index.
PluginParameter	getParameter(java.lang.String id) Gets the PluginParameter with the given id.
PluginSpeciesAlias	getPluginSpeciesAlias(java.lang.String aliasID) Gets PluginSpeciesAlias with the given id.
PluginProtein	getProtein(java.lang.String id) Gets the PluginProtein with the given id.
PluginReaction	getReaction(int index) Gets the PluginReaction with the given index.
PluginReaction	getReaction(java.lang.String id) Gets the PluginReaction with the given id.
PluginRNA	getRNA(java.lang.String id) Gets the PluginRNA with the given id.
PluginRule	getRule(int index) Gets the PluginRule with the given index from the list.
PluginSpecies	getSpecies(int index) Gets the PluginSpecies with the given index.
PluginSpecies	getSpecies(java.lang.String id) Gets the PluginSpecies with the given id.
PluginUnitDefinition	getUnitDefinition(int index) Gets the PluginUnitDefinition with the given index.
PluginUnitDefinition	getUnitDefinition(java.lang.String id) Gets the PluginUnitDefinition with the given id.
void	removeAntiSenseRNA(int index) Removes the PluginAntiSenseRNA with the given index from the list.
void	removeAntiSenseRNA(PluginAntiSenseRNA rna) Removes the given PluginAntiSenseRNA from the list.
void	removeCompartment(int index) Removes the PluginCompartment with the given index from the list.
void	removeCompartment(PluginCompartment compartment) Removes the given PluginCompartment from the list.
void	removeCompartment(java.lang.String id) Removes the PluginCompartment with the given id from the list.
void	removeEvent(int index) Removes the PluginEvent with the given index.
void	removeEvent(PluginEvent event) Removes the given PluginEvent from the list.
void	removeEvent(java.lang.String id) Remove the PluginEvent with the given id.
void	removeFunctionDefinition(int index) Removes the PluginFunctionDefinition with the given index from the list.
void	removeFunctionDefinition(PluginFunctionDefinition function) Removes the given PluginFunctionDefinition from the list.
void	removeFunctionDefinition(java.lang.String id) Removes the PluginFunctionDefinition with the given id from the list.
void	removeGene(int index) Removes the PluginGene with the given index from the list.
void	removeGene(PluginGene rna) Removes the given PluginGene from the list.
void	removeParameter(int index) Removes the PluginParameter with the given index to the list.
void	removeParameter(PluginParameter parameter) Remove the given PluginParameter from the list.
void	removeParameter(java.lang.String id) Remove the PluginParameter with the given id.
void	removeProtein(int index) Removes the PluginProtein with the given index.
void	removeProtein(PluginProtein rna) Removes the given PluginProtein from the list.
void	removeReaction(int index) Removes the PluginReaction with the given index from the list.
void	removeReaction(PluginReaction reaction) Removes the given PluginReaction from the list.
void	removeReaction(java.lang.String id) Removes the PluginReaction with the given id from the list.
void	removeRNA(int index) Removes the PluginRNA with the given index from the list.
void	removeRNA(PluginRNA rna) Adds a PluginRNA to the list
void	removeRule(int index) Removes the PluginRule with the given index from the list.
void	removeRule(PluginRule rule) Removes the given PluginRule from the list.
void	removeSpecies(int index) Removes the PluginSpecies with the given index from the list.
void	removeSpecies(java.lang.String id) Removes the PluginSpecies with the given id from the list
void	removeUnitDefinition(int index) Remove the PluginUnitDefinition with the given index from the list.
void	removeUnitDefinition(PluginUnitDefinition unit) Remove the given PluginUnitDefinition from the list.
void	removeUnitDefinition(java.lang.String id) Removes the PluginUnitDefinition with the given id from the list.
void	setListOfAntiSenseRNAs(PluginListOf listOfAntiSenseRNAs) Sets the list of PluginAntiSenseRNA of this PluginModel.
void	setListOfCompartments(PluginListOf listOfCompartments) Sets the list of PluginCompartment of this PluginModel
void	setListOfEvents(PluginListOf listOfEvents) Sets the list of PluginEvent of this PluginModel.
void	setListOfFunctionDefinitions(PluginListOf listOfFunctionDefinitions) Sets the list of PluginFunctionDefinition of this PluginModel.
void	setListOfGenes(PluginListOf listOfGenes) Sets the list of PluginGene of this PluginModel.
void	setListOfParameters(PluginListOf listOfParameters) Sets the list of PluginParameter of this PluginModel.
void	setListOfProteins(PluginListOf listOfProteins) Sets the list of PluginProtein of this PluginModel.
void	setListOfReactions(PluginListOf listOfReactions) Sets the PluginReaction of this PluginModel.
void	setListOfRNAs(PluginListOf listOfRNAs) Sets the list of PluginRNA of this PluginModel.
void	setListOfRules(PluginListOf listOfRules) Sets the list of PluginRule of this PluginModel.
void	setListOfSpecies(PluginListOf listOfSpecies) Sets the list of PluginSpecies of this PluginModel.
void	setListOfUnitDefinitions(PluginListOf listOfUnitDefinitions) Sets the list of PluginUnitDefinition of this PluginModel
void	setName(java.lang.String name) Sets the name of this PluginModel.
void	update(PluginModel model) Update all properties of this PluginModel to the same as the given PluginModel

Methods inherited from class jp.sbi.celldesigner.plugin.PluginSBase

getNotes, getNotesString, getParentSBase, setNotes, setParentSBase, toSBML

Methods inherited from class java.lang.Object

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

Constructor Detail

PluginModel

public PluginModel(java.lang.String id)

Constructor

Parameters:

id -

Method Detail

update

public void update(PluginModel model)

Update all properties of this PluginModel to the same as the given PluginModel

Parameters:

model - PluginModel

getId

public java.lang.String getId()

Returns:

the id of this PluginModel.

getName

public java.lang.String getName()

Returns:

the name of this PluginModel.

setName

public void setName(java.lang.String name)

Sets the name of this PluginModel.

Parameters:

name -

getListOfCompartments

public PluginListOf getListOfCompartments()

Returns:

the list of PluginCompartment of this PluginModel

setListOfCompartments

public void setListOfCompartments(PluginListOf listOfCompartments)

Sets the list of PluginCompartment of this PluginModel

Parameters:

listOfCompartments - the list of PluginCompartment

getListOfEvents

public PluginListOf getListOfEvents()

Returns:

the list of PluginEvent

setListOfEvents

public void setListOfEvents(PluginListOf listOfEvents)

Sets the list of PluginEvent of this PluginModel.

Parameters:

listOfEvents - the list of PluginEvent

getListOfFunctionDefinitions

public PluginListOf getListOfFunctionDefinitions()

Returns:

the list of PluginFunctionDefinition

setListOfFunctionDefinitions

public void setListOfFunctionDefinitions(PluginListOf listOfFunctionDefinitions)

Sets the list of PluginFunctionDefinition of this PluginModel.

Parameters:

listOfFunctionDefinitions - the list of PluginFunctionDefinition

getListOfParameters

public PluginListOf getListOfParameters()

Returns:

the list of PluginParameter of this PluginModel.

setListOfParameters

public void setListOfParameters(PluginListOf listOfParameters)

Sets the list of PluginParameter of this PluginModel.

Parameters:

listOfParameters - the list of PluginParameter

getListOfReactions

public PluginListOf getListOfReactions()

Returns:

the list of PluginReaction

setListOfReactions

public void setListOfReactions(PluginListOf listOfReactions)

Sets the PluginReaction of this PluginModel.

Parameters:

listOfReactions - the list of PluginReaction.

getListOfRules

public PluginListOf getListOfRules()

Returns:

the list of PluginRule of this PluginModel.

setListOfRules

public void setListOfRules(PluginListOf listOfRules)

Sets the list of PluginRule of this PluginModel.

Parameters:

listOfRules - the list of PluginRule

getListOfSpecies

public PluginListOf getListOfSpecies()

Returns:

the list of PluginSpecies

setListOfSpecies

public void setListOfSpecies(PluginListOf listOfSpecies)

Sets the list of PluginSpecies of this PluginModel.

Parameters:

listOfSpecies - the listOfPluginSpecies

getListOfUnitDefinitions

public PluginListOf getListOfUnitDefinitions()

Returns:

the list of PluginUnitDefinition of this PluginModel.

setListOfUnitDefinitions

public void setListOfUnitDefinitions(PluginListOf listOfUnitDefinitions)

Sets the list of PluginUnitDefinition of this PluginModel

Parameters:

listOfUnitDefinitions - the list of PluginUnitDefinition

addSpecies

public void addSpecies(PluginSpecies species)

Adds a PluginSpecies to the list in this PluginModel.

Parameters:

species - PluginSpecies

removeSpecies

public void removeSpecies(java.lang.String id)

Removes the PluginSpecies with the given id from the list

Parameters:

id -

removeSpecies

public void removeSpecies(int index)

Removes the PluginSpecies with the given index from the list.

Parameters:

index -

getSpecies

public PluginSpecies getSpecies(int index)

Gets the PluginSpecies with the given index.

Parameters:

index -

Returns:

PluginSpecies

getSpecies

public PluginSpecies getSpecies(java.lang.String id)

Gets the PluginSpecies with the given id.

Parameters:

id -

Returns:

PluginSpecies

addCompartment

public void addCompartment(PluginCompartment compartment)

Adds a PluginCompartment to the list.

Parameters:

compartment -

removeCompartment

public void removeCompartment(PluginCompartment compartment)

Removes the given PluginCompartment from the list.

Parameters:

compartment -

removeCompartment

public void removeCompartment(java.lang.String id)

Removes the PluginCompartment with the given id from the list.

Parameters:

id -

removeCompartment

public void removeCompartment(int index)

Removes the PluginCompartment with the given index from the list.

Parameters:

index -

getCompartment

public PluginCompartment getCompartment(int index)

Gets the PluginCompartment with the given index.

Parameters:

index -

Returns:

PluginCompartment

getCompartment

public PluginCompartment getCompartment(java.lang.String id)

Gets the PluginCompartment with the given id.

Parameters:

id -

Returns:

PluginCompartment

addReaction

public void addReaction(PluginReaction reaction)

Adds a PluginReaction to the list.

Parameters:

reaction - PluginReaction

removeReaction

public void removeReaction(PluginReaction reaction)

Removes the given PluginReaction from the list.

Parameters:

reaction - PluginReaction

removeReaction

public void removeReaction(java.lang.String id)

Removes the PluginReaction with the given id from the list.

Parameters:

id -

removeReaction

public void removeReaction(int index)

Removes the PluginReaction with the given index from the list.

Parameters:

index -

getReaction

public PluginReaction getReaction(int index)

Gets the PluginReaction with the given index.

Parameters:

index -

Returns:

PluginReaction

getReaction

public PluginReaction getReaction(java.lang.String id)

Gets the PluginReaction with the given id.

Parameters:

id -

Returns:

PluginReaction

addEvent

public void addEvent(PluginEvent event)

Adds the PluginEvent to the list.

Parameters:

event - PluginEvent

removeEvent

public void removeEvent(PluginEvent event)

Removes the given PluginEvent from the list.

Parameters:

event - PluginEvent

removeEvent

public void removeEvent(java.lang.String id)

Remove the PluginEvent with the given id.

Parameters:

id -

removeEvent

public void removeEvent(int index)

Removes the PluginEvent with the given index.

Parameters:

index -

getEvent

public PluginEvent getEvent(int index)

Gets the PluginEvent with the given index.

Parameters:

index -

Returns:

PluginEvent

getEvent

public PluginEvent getEvent(java.lang.String id)

Gets the PluginEvent with the given id.

Parameters:

id -

Returns:

PluginEvent

addParameter

public void addParameter(PluginParameter parameter)

Adds the PluginParameter to the list.

Parameters:

parameter - PluginParameter

removeParameter

public void removeParameter(PluginParameter parameter)

Remove the given PluginParameter from the list.

Parameters:

parameter - PluginParameter

removeParameter

public void removeParameter(java.lang.String id)

Remove the PluginParameter with the given id.

Parameters:

id -

removeParameter

public void removeParameter(int index)

Removes the PluginParameter with the given index to the list.

Parameters:

index -

getParameter

public PluginParameter getParameter(int index)

Gets the PluginParameter with the given index.

Parameters:

index -

Returns:

PluginParameter

getParameter

public PluginParameter getParameter(java.lang.String id)

Gets the PluginParameter with the given id.

Parameters:

id -

Returns:

PluginParameter

addFunctionDefinition

public void addFunctionDefinition(PluginFunctionDefinition function)

Adds a PluginFunctionDefinition to the list.

Parameters:

function - PluginFunctionDefinition.

removeFunctionDefinition

public void removeFunctionDefinition(PluginFunctionDefinition function)

Removes the given PluginFunctionDefinition from the list.

Parameters:

function -

removeFunctionDefinition

public void removeFunctionDefinition(java.lang.String id)

Removes the PluginFunctionDefinition with the given id from the list.

Parameters:

id -

removeFunctionDefinition

public void removeFunctionDefinition(int index)

Removes the PluginFunctionDefinition with the given index from the list.

Parameters:

index - PluginFunctionDefinition

getFunctionDefinition

public PluginFunctionDefinition getFunctionDefinition(int index)

Gets the PluginFunctionDefinition with the given index.

Parameters:

index -

Returns:

PluginFunctionDefinition

getFunctionDefinition

public PluginFunctionDefinition getFunctionDefinition(java.lang.String id)

Gets the PluginFunctionDefinition with the given id.

Parameters:

id -

Returns:

PluginFunctionDefinition

addRule

public void addRule(PluginRule rule)

Adds a PluginRule to the list.

Parameters:

rule -

removeRule

public void removeRule(PluginRule rule)

Removes the given PluginRule from the list.

Parameters:

rule - PluginRule

removeRule

public void removeRule(int index)

Removes the PluginRule with the given index from the list.

Parameters:

index -

getRule

public PluginRule getRule(int index)

Gets the PluginRule with the given index from the list.

Parameters:

index -

Returns:

PluginRule

addUnitDefinition

public void addUnitDefinition(PluginUnitDefinition unit)

Adds a PluginUnitDefinition to the list.

Parameters:

unit -

removeUnitDefinition

public void removeUnitDefinition(PluginUnitDefinition unit)

Remove the given PluginUnitDefinition from the list.

Parameters:

unit - PluginUnitDefinition

removeUnitDefinition

public void removeUnitDefinition(java.lang.String id)

Removes the PluginUnitDefinition with the given id from the list.

Parameters:

id -

removeUnitDefinition

public void removeUnitDefinition(int index)

Remove the PluginUnitDefinition with the given index from the list.

Parameters:

index -

getUnitDefinition

public PluginUnitDefinition getUnitDefinition(int index)

Gets the PluginUnitDefinition with the given index.

Parameters:

index -

Returns:

PluginUnitDefinition

getUnitDefinition

public PluginUnitDefinition getUnitDefinition(java.lang.String id)

Gets the PluginUnitDefinition with the given id.

Parameters:

id -

Returns:

PluginUnitDefinition

getNumSpecies

public int getNumSpecies()

Returns:

the number of PluginSpecies of this PluginModel.

getNumReactions

public int getNumReactions()

Returns:

the number of PluginReaction of this PluginModel.

getNumCompartments

public int getNumCompartments()

Returns:

the number of PluginCompartment of this PluginModel.

getNumEvents

public int getNumEvents()

Returns:

the number of PluginEvent of this PluginModel.

getNumParameters

public int getNumParameters()

Returns:

the number of PluginParameter of this PluginModel.

getNumFunctionDefinitions

public int getNumFunctionDefinitions()

Returns:

the number of PluginFunctionDefinition of this PluginModel

getNumRules

public int getNumRules()

Returns:

the number of PluginRule of this PluginModel.

getNumUnitDefinitions

public int getNumUnitDefinitions()

Returns:

the number of PluginUnitDefinition of this PluginModel.

getAntiSenseRNA

public PluginAntiSenseRNA getAntiSenseRNA(java.lang.String id)

Gets the PluginAntiSenseRNA with the given id.

Parameters:

id -

Returns:

PluginAntiSenseRNA

getListOfAntiSenseRNAs

public PluginListOf getListOfAntiSenseRNAs()

Returns:

the list of PluginAntiSenseRNA

getListOfSpecies

public PluginListOf getListOfSpecies(PluginAntiSenseRNA rna)

Returns:

the list of PluginAntiSenseRNA

setListOfAntiSenseRNAs

public void setListOfAntiSenseRNAs(PluginListOf listOfAntiSenseRNAs)

Sets the list of PluginAntiSenseRNA of this PluginModel.

Parameters:

listOfAntiSenseRNAs - the list of PluginAntiSenseRNA

removeAntiSenseRNA

public void removeAntiSenseRNA(PluginAntiSenseRNA rna)

Removes the given PluginAntiSenseRNA from the list.

Parameters:

rna - PluginAntiSenseRNA

removeAntiSenseRNA

public void removeAntiSenseRNA(int index)

Removes the PluginAntiSenseRNA with the given index from the list.

Parameters:

index -

getGene

public PluginGene getGene(java.lang.String id)

Gets the PluginGene with the given id.

Parameters:

id -

Returns:

getListOfGenes

public PluginListOf getListOfGenes()

Returns:

the list of PluginGene.

getListOfSpecies

public PluginListOf getListOfSpecies(PluginGene rna)

Returns:

the list of PluginGene

setListOfGenes

public void setListOfGenes(PluginListOf listOfGenes)

Sets the list of PluginGene of this PluginModel.

Parameters:

listOfGenes - a list of PluginGene

removeGene

public void removeGene(PluginGene rna)

Removes the given PluginGene from the list.

Parameters:

rna - PluginGene

removeGene

public void removeGene(int index)

Removes the PluginGene with the given index from the list.

Parameters:

index -

appendProtein

public void appendProtein(PluginProtein protein)

Adds the PluginProtein to the list.

Parameters:

protein - PluginProtein

getProtein

public PluginProtein getProtein(java.lang.String id)

Gets the PluginProtein with the given id.

Parameters:

id -

Returns:

PluginProtein

getListOfProteins

public PluginListOf getListOfProteins()

Returns:

the list of PluginProtein

getListOfSpecies

public PluginListOf getListOfSpecies(PluginProtein rna)

Gets the list of PluginProtein added the given PluginProtein to.

Parameters:

rna - PluginProtein

Returns:

the list of PluginProtein

setListOfProteins

public void setListOfProteins(PluginListOf listOfProteins)

Sets the list of PluginProtein of this PluginModel.

Parameters:

listOfProteins - the list of PluginProtein

removeProtein

public void removeProtein(PluginProtein rna)

Removes the given PluginProtein from the list.

Parameters:

rna - PluginProtein

removeProtein

public void removeProtein(int index)

Removes the PluginProtein with the given index.

Parameters:

index -

getRNA

public PluginRNA getRNA(java.lang.String id)

Gets the PluginRNA with the given id.

Parameters:

id -

Returns:

PluginRNA

getListOfRNAs

public PluginListOf getListOfRNAs()

Returns:

the list of PluginRNA

getListOfSpecies

public PluginListOf getListOfSpecies(PluginRNA rna)

Returns:

the list of PluginRNA

setListOfRNAs

public void setListOfRNAs(PluginListOf listOfRNAs)

Sets the list of PluginRNA of this PluginModel.

removeRNA

public void removeRNA(PluginRNA rna)

Adds a PluginRNA to the list

Parameters:

rna - PluginRNA

removeRNA

public void removeRNA(int index)

Removes the PluginRNA with the given index from the list.

Parameters:

index -

getListOfAllSpeciesAlias

public PluginListOf getListOfAllSpeciesAlias()

Returns:

the list of PluginSpeciesAlias.

getPluginSpeciesAlias

public PluginSpeciesAlias getPluginSpeciesAlias(java.lang.String aliasID)

Gets PluginSpeciesAlias with the given id.

Parameters:

aliasID -

Returns:

PluginSpeciesAlias