Selector (jsbml-multi 1.0 API)

java.lang.Object
- org.sbml.jsbml.AbstractTreeNode
- - org.sbml.jsbml.AbstractSBase
  - - org.sbml.jsbml.AbstractNamedSBase
    - - org.sbml.jsbml.ext.multi.Selector

All Implemented Interfaces:

Serializable, Cloneable, 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:

$Rev$

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary
- 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)

Constructors
Constructor and Description
`Selector()`
`Selector(Selector selector)`

Method Summary

All Methods Instance Methods Concrete 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()`
`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(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(String id)` Gets the `Bond` that has the given id.
`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(String id)` Gets the `SpeciesTypeState` that has the given id.
`BindingSiteReference`	`getUnboundBindingSite(int i)` Gets the ith unbound binding site (`BindingSiteReference`).
`BindingSiteReference`	`getUnboundBindingSite(String id)` Gets the unbound binding site `BindingSiteReference` that has the given speciesTypeState id.
`void`	`initDefaults()`
`boolean`	`isIdMandatory()`
`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
`Map<String,String>`	`writeXMLAttributes()`

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 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 javax.swing.tree.TreeNode
children, getAllowsChildren, getIndex, getParent, isLeaf

- Constructor Detail
  - Selector
```
public Selector()
```
  - Selector
```
public Selector(Selector selector)
```
    Parameters:
    
    selector -
- Method Detail
  - clone
```
public Selector clone()
```
    Specified by:
    
    clone in interface SBase
    
    Overrides:
    
    clone in class AbstractSBase
  - isIdMandatory
```
public boolean isIdMandatory()
```
    Specified by:
    
    isIdMandatory in interface NamedSBase
  - 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(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:
    
    IndexOutOfBoundsException - if the index is invalid.
  - getSpeciesTypeState
```
public SpeciesTypeState getSpeciesTypeState(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:
    
    IndexOutOfBoundsException - if the index is invalid.
  - getBond
```
public Bond getBond(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.
    
    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:
    
    IndexOutOfBoundsException - if the index is invalid.
  - getUnboundBindingSite
```
public BindingSiteReference getUnboundBindingSite(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 TreeNode getChildAt(int index)
```
    Specified by:
    
    getChildAt in interface TreeNode
    
    Overrides:
    
    getChildAt in class AbstractSBase
  - getChildCount
```
public int getChildCount()
```
    Specified by:
    
    getChildCount in interface TreeNode
    
    Overrides:
    
    getChildCount in class AbstractSBase
  - writeXMLAttributes
```
public Map<String,String> writeXMLAttributes()
```
    Specified by:
    
    writeXMLAttributes in interface SBase
    
    Overrides:
    
    writeXMLAttributes in class AbstractNamedSBase

Class Selector

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

Constructor Summary

Method Summary

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

Methods inherited from class org.sbml.jsbml.AbstractSBase

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

Methods inherited from class java.lang.Object

Methods inherited from interface org.sbml.jsbml.NamedSBase

Methods inherited from interface org.sbml.jsbml.SBase

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

Methods inherited from interface javax.swing.tree.TreeNode

Constructor Detail

Selector

Selector

Method Detail

clone

isIdMandatory

getListOfSpeciesTypeStates

addSpeciesTypeState

createSpeciesTypeState

createSpeciesTypeState

getSpeciesTypeState

getSpeciesTypeState

isSetListOfSpeciesTypeStates

unsetListOfSpeciesTypeStates

getListOfBonds

addBond

createBond

getBond

getBond

isSetListOfBonds

unsetListOfBonds

getListOfUnboundBindingSites

addUnboundBindingSite

createUnboundBindingSite

getUnboundBindingSite

getUnboundBindingSite

isSetListOfUnboundBindingSites

unsetListOfUnboundBindingSites

initDefaults

getChildAt

getChildCount

writeXMLAttributes