jp.sbi.celldesigner.plugin

Class PluginSpecies

java.lang.Object

jp.sbi.celldesigner.plugin.PluginSBase

jp.sbi.celldesigner.plugin.PluginSpecies

public class PluginSpecies
extends PluginSBase

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

Author:

The Systems Biology Institute

Field Summary

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

sbase

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	PluginSpecies() Constructor
	PluginSpecies(java.lang.String type, java.lang.String name) Constructor

Method Summary

Modifier and Type	Method and Description
void	addSpeciesAlias(PluginSpeciesAlias alias) Adds the PluginSpeciesAlias to this Species.
boolean	getBoundaryCondition()
int	getCharge()
java.lang.String	getCompartment()
boolean	getConstant()
boolean	getHasOnlySubstanceUnits()
java.lang.String	getId()
double	getInitialAmount()
double	getInitialConcentration()
PluginListOf	getListOfSpeciesAlias()
java.lang.String	getName()
int	getNumSpeciesAlias()
java.lang.String	getPositionToCompartment()
java.lang.String	getSpatialSizeUnits()
PluginSpeciesAlias	getSpeciesAlias(int index)
PluginSpeciesAlias	getSpeciesAlias(java.lang.String aliasId)
java.lang.String	getSpeciesType()
java.lang.String	getSubstanceUnits()
java.lang.String	getUnits()
boolean	isSetInitialAmount()
boolean	isSetInitialConcentration()
void	removeSpeciesAlias(int index) Removes PluginSpeciesAlias from this Species.
void	removeSpeciesAlias(java.lang.String aliasId) Removes PluginSpeciesAlias from this Species.
void	setBoundaryCondition(boolean boundaryCondition) Sets the boundaryCondition of this PluginSpecies.
void	setCharge(int charge) Sets the charge of this PluginSpecies.
void	setCompartment(java.lang.String compartment) Sets the compartment of this PluginSpecies.
void	setConstant(boolean constant) Sets the constant of this PluginSpecies.
void	setHasOnlySubstanceUnits(boolean hasOnlySubstanceUnits) Sets the HasOnlySubstanceUnits of this PluginSpecies.
protected void	setId(java.lang.String id) Sets the id of this PluginSpecies.
void	setInitialAmount(double initialAmount) Sets the InitialAmount of this PluginSpecies.
void	setInitialConcentration(double initialConcentration) Sets the initialConcentration of this PluginSpecies.
void	setListOfSpeciesAlias(PluginListOf listOfPluginSpeciesAlias) Sets listOfPluginSpeciesAlias of this PluginSpecies.
protected void	setName(java.lang.String name) Sets the name of this PluginSpecies.
protected void	setPositionToCompartment(java.lang.String positionToCompartment) Sets the position of this PluginSpecies
void	setSpatialSizeUnits(java.lang.String spatialSizeUnits) Sets the spatialSizeUnits of this PluginSpecies.
void	setSpeciesType(java.lang.String strSpeciesType) Sets the SpeciesType of this PluginSpecies.
void	setSubstanceUnits(java.lang.String substanceUnits) Sets the hasOnlySubstanceUnits field of this PluginSpecies.
void	setUnits(java.lang.String units) Sets the units of this PluginSpecies
void	update(PluginSpecies species) Update all properties of this PluginSpecies to the same as the given PluginSpecies.

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

addCVTerm, ChangeCVTermToMiriamDefinition, getAnnotation, getAnnotationString, getCVTerm, getNotes, getNotesString, getNumCVTerms, getParentSBase, getRelationFromCVTerm, setAnnotation, setAnnotationString, setCVTerm, setNotes, setNotes, setParentSBase, toSBML

Methods inherited from class java.lang.Object

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

Constructor Detail

PluginSpecies

public PluginSpecies(java.lang.String type,
                     java.lang.String name)

Constructor

Parameters:

type - the one of the field of PluginSpeciesSymbolType

name - String

PluginSpecies

protected PluginSpecies()

Constructor

Method Detail

update

public void update(PluginSpecies species)

Update all properties of this PluginSpecies to the same as the given PluginSpecies.

Parameters:

species - PluginSpecies

getId

public java.lang.String getId()

Returns:

the id of this Species

setId

protected void setId(java.lang.String id)

Sets the id of this PluginSpecies.

Parameters:

id - String

getName

public java.lang.String getName()

Returns:

the name of this Species.

setName

protected void setName(java.lang.String name)

Sets the name of this PluginSpecies.

Parameters:

name - String

getSpeciesType

public java.lang.String getSpeciesType()

Returns:

the SpeciesType of this Species.

setSpeciesType

public void setSpeciesType(java.lang.String strSpeciesType)

Sets the SpeciesType of this PluginSpecies.

Parameters:

strSpeciesType - String

getCompartment

public java.lang.String getCompartment()

Returns:

compartment of this Species.

setCompartment

public void setCompartment(java.lang.String compartment)

Sets the compartment of this PluginSpecies.

Parameters:

compartment - String

getInitialAmount

public double getInitialAmount()

Returns:

the initialAmount of this PluginSpecies.

setInitialAmount

public void setInitialAmount(double initialAmount)

Sets the InitialAmount of this PluginSpecies.

Parameters:

initialAmount - double

getInitialConcentration

public double getInitialConcentration()

Returns:

the initialConcentration of this Species.

setInitialConcentration

public void setInitialConcentration(double initialConcentration)

Sets the initialConcentration of this PluginSpecies.

Parameters:

initialConcentration - double

isSetInitialAmount

public boolean isSetInitialAmount()

Returns:

true if the initialAmount of this PluginSpecies has been set, false otherwise.

isSetInitialConcentration

public boolean isSetInitialConcentration()

Returns:

true if the initalConcentration of this PluginSpecies has been set, false otherwise.

getBoundaryCondition

public boolean getBoundaryCondition()

Returns:

the boundaryCondition of this Species.

setBoundaryCondition

public void setBoundaryCondition(boolean boundaryCondition)

Sets the boundaryCondition of this PluginSpecies.

Parameters:

boundaryCondition - boolean

getCharge

public int getCharge()

Returns:

the charge of this PluginSpecies.

setCharge

public void setCharge(int charge)

Sets the charge of this PluginSpecies.

Parameters:

charge - int

getConstant

public boolean getConstant()

Returns:

the constant of this PluginSpecies.

setConstant

public void setConstant(boolean constant)

Sets the constant of this PluginSpecies.

Parameters:

constant - boolean

getHasOnlySubstanceUnits

public boolean getHasOnlySubstanceUnits()

Returns:

true if this Species hasOnlySubstanceUnits, false otherwise.

setHasOnlySubstanceUnits

public void setHasOnlySubstanceUnits(boolean hasOnlySubstanceUnits)

Sets the HasOnlySubstanceUnits of this PluginSpecies.

Parameters:

hasOnlySubstanceUnits - boolean

getSubstanceUnits

public java.lang.String getSubstanceUnits()

Returns:

the SubstanceUnits of this PluginSpecies

setSubstanceUnits

public void setSubstanceUnits(java.lang.String substanceUnits)

Sets the hasOnlySubstanceUnits field of this PluginSpecies.

Parameters:

substanceUnits - String

getSpatialSizeUnits

public java.lang.String getSpatialSizeUnits()

Returns:

the spatialSizeUnits of this PluginSpecies.

setSpatialSizeUnits

public void setSpatialSizeUnits(java.lang.String spatialSizeUnits)

Sets the spatialSizeUnits of this PluginSpecies.

Parameters:

spatialSizeUnits - String

getUnits

public java.lang.String getUnits()

Returns:

the units of this PluginSpecies.

setUnits

public void setUnits(java.lang.String units)

Sets the units of this PluginSpecies

Parameters:

units - String

getPositionToCompartment

public java.lang.String getPositionToCompartment()

Returns:

the position of this Species.

setPositionToCompartment

protected void setPositionToCompartment(java.lang.String positionToCompartment)

Sets the position of this PluginSpecies

Parameters:

positionToCompartment - String

getNumSpeciesAlias

public int getNumSpeciesAlias()

Returns:

the number of speciesAlias.

getListOfSpeciesAlias

public PluginListOf getListOfSpeciesAlias()

Returns:

listOfPluginSpeciesAlias

getSpeciesAlias

public PluginSpeciesAlias getSpeciesAlias(int index)

Parameters:

index - the index of PluginSpeciesAlias.

Returns:

PluginSpeciesAlias

getSpeciesAlias

public PluginSpeciesAlias getSpeciesAlias(java.lang.String aliasId)

Parameters:

aliasId - the id of the PluginSpeciesAlias.

Returns:

PluginSpeciesAlias

addSpeciesAlias

public void addSpeciesAlias(PluginSpeciesAlias alias)

Adds the PluginSpeciesAlias to this Species.

Parameters:

alias - the PluginSpeciesAlias

removeSpeciesAlias

public void removeSpeciesAlias(int index)

Removes PluginSpeciesAlias from this Species.

Parameters:

index - the index of the PluginSpeciesAlias to remove.

removeSpeciesAlias

public void removeSpeciesAlias(java.lang.String aliasId)

Removes PluginSpeciesAlias from this Species.

Parameters:

aliasId - the id of the PluginSpeciesAlias to remove.

setListOfSpeciesAlias

public void setListOfSpeciesAlias(PluginListOf listOfPluginSpeciesAlias)

Sets listOfPluginSpeciesAlias of this PluginSpecies.

Parameters:

listOfPluginSpeciesAlias - PluginListOf