org.sbml.jsbml.ext.multi

Class SpeciesTypeState

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.multi.SpeciesTypeState

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, SBase, UniqueNamedSBase, TreeNodeWithChangeSupport

public class SpeciesTypeState
extends AbstractNamedSBase
implements UniqueNamedSBase

Since:

1.0

Version:

$Rev: 1639 $

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.Boolean	connex
private ListOf<ContainedSpeciesType>	listOfContainedSpeciesTypes
private ListOf<StateFeatureInstance>	listOfStateFeatureInstances
private java.lang.Integer	maxOccur
private java.lang.Integer	minOccur
private java.lang.Boolean	saturated
private static long	serialVersionUID Generated serial version identifier.
private java.lang.String	speciesType

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
SpeciesTypeState()

Method Summary

Methods

Modifier and Type	Method and Description
void	addContainedSpeciesType(ContainedSpeciesType containedSpeciesType) Adds a ContainedSpeciesType.
void	addStateFeatureInstance(StateFeatureInstance stateFeatureInstance) Adds a StateFeatureInstance.
AbstractSBase	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
ContainedSpeciesType	createContainedSpeciesType() Creates a new ContainedSpeciesType inside this StateFeature and returns it.
StateFeatureInstance	createStateFeatureInstance() Creates a new StateFeatureInstance inside this SpeciesTypeState and returns it.
StateFeatureInstance	createStateFeatureInstance(java.lang.String id) Creates a new StateFeatureInstance inside this SpeciesTypeState and returns it.
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
boolean	getConnex() Returns if this SpeciesTypeState is connex or not.
ContainedSpeciesType	getContainedSpeciesType(int i) Gets the ith ContainedSpeciesType.
ContainedSpeciesType	getContainedSpeciesType(java.lang.String id) Gets the ContainedSpeciesType that has the given speciesTypeState id.
ListOf<ContainedSpeciesType>	getListOfContainedSpeciesTypes() Returns the listOfContainedSpeciesTypes
ListOf<StateFeatureInstance>	getListOfStateFeatureInstances() Returns the listOfStateFeatureInstances
int	getMaxOccur() Returns the maxOccur.
int	getMinOccur() Returns the minOccur.
boolean	getSaturated() Returns if this SpeciesTypeState is saturated or not.
java.lang.String	getSpeciesType() Returns the speciesType.
StateFeatureInstance	getStateFeatureInstance(int i) Gets the ith StateFeatureInstance.
StateFeatureInstance	getStateFeatureInstance(java.lang.String id) Gets the StateFeatureInstance that has the given id.
void	initDefaults()
boolean	isConnex() Returns if this SpeciesTypeState is connex or not.
boolean	isIdMandatory() This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.
boolean	isSaturated() Returns if this SpeciesTypeState is saturated or not.
boolean	isSetConnex() Returns true if connex is not null.
boolean	isSetListOfContainedSpeciesTypes() Returns true if the listOfContainedSpeciesType is set.
boolean	isSetListOfStateFeatureInstances() Returns true if the listOfStateFeatureInstance is set.
boolean	isSetMaxOccur() Returns true if maxOccur is not null.
boolean	isSetMinOccur() Returns true if minOccur is not null.
boolean	isSetSaturated() Returns true if saturated is not null.
boolean	isSetSpeciesType() Returns true if the speciesType is defined.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setConnex(boolean connex) Sets the connex
void	setMaxOccur(int maxOccur) Sets the maxOccur.
void	setMinOccur(int minOccur) Sets the minOccur.
void	setSaturated(boolean saturated) Sets the saturated.
void	setSpeciesType(java.lang.String speciesType) Sets the speciesType.
boolean	unsetListOfContainedSpeciesTypes() Sets the listOfContainedSpeciesTypes to null
boolean	unsetListOfStateFeatureInstances() Sets the listOfStateFeatureInstances to null
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes() Returns a map with all the attributes of this SBase that need to be written out in XML.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

equals, getId, getName, hashCode, isSetId, isSetName, isValidId, setId, setName, toString, unsetId, unsetName

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.NamedSBase

getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, equals, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getAllowsChildren, getIndex, getParent, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

speciesType

private java.lang.String speciesType

minOccur

private java.lang.Integer minOccur

maxOccur

private java.lang.Integer maxOccur

connex

private java.lang.Boolean connex

saturated

private java.lang.Boolean saturated

listOfStateFeatureInstances

private ListOf<StateFeatureInstance> listOfStateFeatureInstances

listOfContainedSpeciesTypes

private ListOf<ContainedSpeciesType> listOfContainedSpeciesTypes

Constructor Detail

SpeciesTypeState

public SpeciesTypeState()

Method Detail

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: NamedSBase

This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

Returns:

true if the identifier of this element must be set in order to create a valid SBML representation. false otherwise, i.e., if the identifier can be understood as an optional attribute.

clone

public AbstractSBase clone()

Description copied from interface: SBase

Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

Returns:

a copy of this object

getSpeciesType

public java.lang.String getSpeciesType()

Returns the speciesType.

Returns:

the speciesType

setSpeciesType

public void setSpeciesType(java.lang.String speciesType)

Sets the speciesType.

Parameters:

speciesType - the speciesType to set

isSetSpeciesType

public boolean isSetSpeciesType()

Returns true if the speciesType is defined.

Returns:

true if the speciesType is defined, false otherwise.

getMinOccur

public int getMinOccur()

Returns the minOccur.

Returns:

the minOccur

setMinOccur

public void setMinOccur(int minOccur)

Sets the minOccur.

Parameters:

minOccur - the minOccur to set

isSetMinOccur

public boolean isSetMinOccur()

Returns true if minOccur is not null.

Returns:

true if minOccur is not null.

getMaxOccur

public int getMaxOccur()

Returns the maxOccur.

Returns:

the maxOccur

setMaxOccur

public void setMaxOccur(int maxOccur)

Sets the maxOccur.

Parameters:

maxOccur - the maxOccur to set

isSetMaxOccur

public boolean isSetMaxOccur()

Returns true if maxOccur is not null.

Returns:

true if maxOccur is not null.

isConnex

public boolean isConnex()

Returns if this SpeciesTypeState is connex or not.

Returns:

the connex

getConnex

public boolean getConnex()

Returns if this SpeciesTypeState is connex or not.

Returns:

the connex

setConnex

public void setConnex(boolean connex)

Sets the connex

Parameters:

connex - the connex to set

isSetConnex

public boolean isSetConnex()

Returns true if connex is not null.

Returns:

true if connex is not null.

isSaturated

public boolean isSaturated()

Returns if this SpeciesTypeState is saturated or not.

Returns:

the saturated

getSaturated

public boolean getSaturated()

Returns if this SpeciesTypeState is saturated or not.

Returns:

the saturated

setSaturated

public void setSaturated(boolean saturated)

Sets the saturated.

Parameters:

saturated - the saturated to set

isSetSaturated

public boolean isSetSaturated()

Returns true if saturated is not null.

Returns:

true if saturated is not null.

getListOfStateFeatureInstances

public ListOf<StateFeatureInstance> getListOfStateFeatureInstances()

Returns the listOfStateFeatureInstances

Returns:

the listOfStateFeatureInstances

addStateFeatureInstance

public void addStateFeatureInstance(StateFeatureInstance stateFeatureInstance)

Adds a StateFeatureInstance.

Parameters:

stateFeatureInstance - the StateFeatureInstance to add

createStateFeatureInstance

public StateFeatureInstance createStateFeatureInstance()

Creates a new StateFeatureInstance inside this SpeciesTypeState and returns it.

Returns:

the StateFeatureInstance object created

See Also:

addStateFeatureInstance(StateFeatureInstance r)

createStateFeatureInstance

public StateFeatureInstance createStateFeatureInstance(java.lang.String id)

Creates a new StateFeatureInstance inside this SpeciesTypeState and returns it.

Parameters:

id - the id of the new element to create

Returns:

the StateFeatureInstance object created

getStateFeatureInstance

public StateFeatureInstance getStateFeatureInstance(int i)

Gets the ith StateFeatureInstance.

Parameters:

i -

Returns:

the ith StateFeatureInstance

Throws:

java.lang.IndexOutOfBoundsException - if the index is invalid.

getStateFeatureInstance

public StateFeatureInstance getStateFeatureInstance(java.lang.String id)

Gets the StateFeatureInstance that has the given id.

Parameters:

id -

Returns:

the StateFeatureInstance that has the given id or null if no StateFeatureInstance are found that match id.

isSetListOfStateFeatureInstances

public boolean isSetListOfStateFeatureInstances()

Returns true if the listOfStateFeatureInstance is set.

Returns:

true if the listOfStateFeatureInstance is set.

unsetListOfStateFeatureInstances

public boolean unsetListOfStateFeatureInstances()

Sets the listOfStateFeatureInstances to null

Returns:

true is successful

getListOfContainedSpeciesTypes

public ListOf<ContainedSpeciesType> getListOfContainedSpeciesTypes()

Returns the listOfContainedSpeciesTypes

Returns:

the listOfContainedSpeciesTypes

addContainedSpeciesType

public void addContainedSpeciesType(ContainedSpeciesType containedSpeciesType)

Adds a ContainedSpeciesType.

Parameters:

containedSpeciesType - the ContainedSpeciesType to add

createContainedSpeciesType

public ContainedSpeciesType createContainedSpeciesType()

Creates a new ContainedSpeciesType inside this StateFeature and returns it.

Returns:

the ContainedSpeciesType object created

getContainedSpeciesType

public ContainedSpeciesType getContainedSpeciesType(int i)

Gets the ith ContainedSpeciesType.

Parameters:

i -

Returns:

the ith ContainedSpeciesType

Throws:

java.lang.IndexOutOfBoundsException - if the index is invalid.

getContainedSpeciesType

public ContainedSpeciesType getContainedSpeciesType(java.lang.String id)

Gets the ContainedSpeciesType that has the given speciesTypeState id.

Parameters:

id -

Returns:

the ContainedSpeciesType that has the given speciesTypeState id or null if no ContainedSpeciesType are found that match id.

isSetListOfContainedSpeciesTypes

public boolean isSetListOfContainedSpeciesTypes()

Returns true if the listOfContainedSpeciesType is set.

Returns:

true if the listOfContainedSpeciesType is set.

unsetListOfContainedSpeciesTypes

public boolean unsetListOfContainedSpeciesTypes()

Sets the listOfContainedSpeciesTypes to null

Returns:

true is successful

initDefaults

public void initDefaults()

getChildAt

public javax.swing.tree.TreeNode getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class AbstractSBase

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractNamedSBase

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBase

Returns a map with all the attributes of this SBase that need to be written out in XML.

The attribute name is used as a key and the attribute value as value. If a prefix is needed for the attribute name, it need to be set directly in this map.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractNamedSBase

Returns:

a Map containing the XML attributes of this object.