org.sbml.jsbml.ext.multi

Class Selector

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.multi.Selector

All Implemented Interfaces:

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

public class Selector
extends AbstractNamedSBase
implements UniqueNamedSBase

A selector is a mask describing the rules that an entity has to pass in order to be used or rejected. This selector is built of different components, carrying state features. The components can be bound together or not. In a population-based model, the selector, when applied to a pool of entities, permits to filter it, and to obtain a further, more refined, entity pool.

A selector can be reused in various places of a model, to restrict the application of a procedure to a certain set of topologies and states. Selectors can be used to refine the initial conditions of a species, for instance to specify the initial distribution of different states and topologies. They can also be used in a reaction to decide if a this reaction happens, or to modulate its velocity, in function of the state or topology of a reactant.

A selector defines the list of components composing the mask, that are species type existing under a given state (that can be an ensemble of elementary states). In addition to the components, the selector lists the possible or mandatory bonds, as well as the components that must not be bound. It is to be noted that a selector must not necessarily be the most parsimonious. One can use the selectors to describe the fine-grained topology of complexes, even if this topology is not used to decide upon particular reactions.

Since:

1.0

Version:

$Rev: 1639 $

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private ListOf<Bond>	listOfBonds
private ListOf<SpeciesTypeState>	listOfSpeciesTypeStates
private ListOf<BindingSiteReference>	listOfUnboundBindingSites
private static long	serialVersionUID Generated serial version identifier.

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
Selector()
Selector(Selector selector)

Method Summary

Methods

Modifier and Type	Method and Description
void	addBond(Bond bond) Adds a Bond.
void	addSpeciesTypeState(SpeciesTypeState speciesTypeState) Adds a SpeciesTypeState.
void	addUnboundBindingSite(BindingSiteReference unboundBindingSite) Adds an unboundBindingSite.
Selector	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
Bond	createBond() Creates a new Bond inside this Selector and returns it.
SpeciesTypeState	createSpeciesTypeState() Creates a new SpeciesTypeState inside this Selector and returns it.
SpeciesTypeState	createSpeciesTypeState(java.lang.String id) Creates a new SpeciesTypeState inside this Selector and returns it.
BindingSiteReference	createUnboundBindingSite() Creates a new BindingSiteReference inside this Selector list of unbound binding site and returns it.
Bond	getBond(int i) Gets the ith Bond.
Bond	getBond(java.lang.String id) Gets the Bond that has the given id.
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
ListOf<Bond>	getListOfBonds() Returns the listOfBonds
ListOf<SpeciesTypeState>	getListOfSpeciesTypeStates() Returns the listOfSpeciesTypeStates
ListOf<BindingSiteReference>	getListOfUnboundBindingSites() Returns the listOfUnboundBindingSites
SpeciesTypeState	getSpeciesTypeState(int i) Gets the ith SpeciesTypeState.
SpeciesTypeState	getSpeciesTypeState(java.lang.String id) Gets the SpeciesTypeState that has the given id.
BindingSiteReference	getUnboundBindingSite(int i) Gets the ith unbound binding site (BindingSiteReference).
BindingSiteReference	getUnboundBindingSite(java.lang.String id) Gets the unbound binding site BindingSiteReference that has the given speciesTypeState id.
void	initDefaults()
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	isSetListOfBonds() Returns true if the listOfBond is set.
boolean	isSetListOfSpeciesTypeStates() Returns true if the listOfSpeciesTypeState is set.
boolean	isSetListOfUnboundBindingSites() Returns true if the listOfUnBoundBindingSite is set.
boolean	unsetListOfBonds() Sets the listOfBonds to null.
boolean	unsetListOfSpeciesTypeStates() Sets the listOfSpeciesTypeStates to null
boolean	unsetListOfUnboundBindingSites() Sets the listOfUnboundBindingSites 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, readAttribute, 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, readAttribute, 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

listOfSpeciesTypeStates

private ListOf<SpeciesTypeState> listOfSpeciesTypeStates

listOfBonds

private ListOf<Bond> listOfBonds

listOfUnboundBindingSites

private ListOf<BindingSiteReference> listOfUnboundBindingSites

Constructor Detail

Selector

public Selector()

Selector

public Selector(Selector selector)

Parameters:

selector -

Method Detail

clone

public Selector 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

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.

getListOfSpeciesTypeStates

public ListOf<SpeciesTypeState> getListOfSpeciesTypeStates()

Returns the listOfSpeciesTypeStates

Returns:

the listOfSpeciesTypeStates

addSpeciesTypeState

public void addSpeciesTypeState(SpeciesTypeState speciesTypeState)

Adds a SpeciesTypeState.

Parameters:

speciesTypeState - the SpeciesTypeState to add

createSpeciesTypeState

public SpeciesTypeState createSpeciesTypeState()

Creates a new SpeciesTypeState inside this Selector and returns it.

Returns:

the SpeciesTypeState object created

See Also:

addSpeciesTypeState(SpeciesTypeState r)

createSpeciesTypeState

public SpeciesTypeState createSpeciesTypeState(java.lang.String id)

Creates a new SpeciesTypeState inside this Selector and returns it.

Parameters:

id - the id of the new element to create

Returns:

the SpeciesTypeState object created

getSpeciesTypeState

public SpeciesTypeState getSpeciesTypeState(int i)

Gets the ith SpeciesTypeState.

Parameters:

i -

Returns:

the ith SpeciesTypeState

Throws:

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

getSpeciesTypeState

public SpeciesTypeState getSpeciesTypeState(java.lang.String id)

Gets the SpeciesTypeState that has the given id.

Parameters:

id -

Returns:

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

isSetListOfSpeciesTypeStates

public boolean isSetListOfSpeciesTypeStates()

Returns true if the listOfSpeciesTypeState is set.

Returns:

true if the listOfSpeciesTypeState is set.

unsetListOfSpeciesTypeStates

public boolean unsetListOfSpeciesTypeStates()

Sets the listOfSpeciesTypeStates to null

Returns:

true is successful

getListOfBonds

public ListOf<Bond> getListOfBonds()

Returns the listOfBonds

Returns:

the listOfBonds

addBond

public void addBond(Bond bond)

Adds a Bond.

Parameters:

bond - the Bond to add

createBond

public Bond createBond()

Creates a new Bond inside this Selector and returns it.

Returns:

the Bond object created

getBond

public Bond getBond(int i)

Gets the ith Bond.

Parameters:

i -

Returns:

the ith Bond

Throws:

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

getBond

public Bond getBond(java.lang.String id)

Gets the Bond that has the given id.

Parameters:

id -

Returns:

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

isSetListOfBonds

public boolean isSetListOfBonds()

Returns true if the listOfBond is set.

Returns:

true if the listOfBond is set.

unsetListOfBonds

public boolean unsetListOfBonds()

Sets the listOfBonds to null.

Returns:

true is successful

getListOfUnboundBindingSites

public ListOf<BindingSiteReference> getListOfUnboundBindingSites()

Returns the listOfUnboundBindingSites

Returns:

the listOfUnboundBindingSites

addUnboundBindingSite

public void addUnboundBindingSite(BindingSiteReference unboundBindingSite)

Adds an unboundBindingSite.

Parameters:

unboundBindingSite - the UnboundBindingSite to add

createUnboundBindingSite

public BindingSiteReference createUnboundBindingSite()

Creates a new BindingSiteReference inside this Selector list of unbound binding site and returns it.

Parameters:

id - the id of the new element to create

Returns:

the BindingSiteReference object created

getUnboundBindingSite

public BindingSiteReference getUnboundBindingSite(int i)

Gets the ith unbound binding site (BindingSiteReference).

Parameters:

i -

Returns:

the ith BindingSiteReference

Throws:

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

getUnboundBindingSite

public BindingSiteReference getUnboundBindingSite(java.lang.String id)

Gets the unbound binding site BindingSiteReference that has the given speciesTypeState id.

Parameters:

id -

Returns:

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

isSetListOfUnboundBindingSites

public boolean isSetListOfUnboundBindingSites()

Returns true if the listOfUnBoundBindingSite is set.

Returns:

true if the listOfUnBoundBindingSite is set.

unsetListOfUnboundBindingSites

public boolean unsetListOfUnboundBindingSites()

Sets the listOfUnboundBindingSites 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

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.