Package org.sbml.jsbml.ext.multi

Class BindingSiteSpeciesType

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.SpeciesType

org.sbml.jsbml.ext.multi.MultiSpeciesType

org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

All Implemented Interfaces:

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

public class BindingSiteSpeciesType
extends MultiSpeciesType

A BindingSiteSpeciesType object is a binding site, and therefore its instance can further define the bindingStatus attribute and can participate a binding internally and explicitly in an InSpeciesTypeBond object, or externally and implicitly defined by an OutwardBindingSite object. A binding site must be an atomic component which means that a BindingSiteSpeciesType object cannot contain a ListOfSpeciesTypeInstances subobject.

Note:
In the Multi package, a binding site can only participate in one binding at a time. That means a binding site cannot bind two partners at the same time. The binding relationship is one-to-one.

Since:

1.0

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor	Description
BindingSiteSpeciesType()	Creates a new BindingSiteSpeciesType instance.
BindingSiteSpeciesType(int level, int version)	Creates a new BindingSiteSpeciesType instance.
BindingSiteSpeciesType(java.lang.String id)	Creates a new BindingSiteSpeciesType instance.
BindingSiteSpeciesType(java.lang.String id, int level, int version)	Creates a new BindingSiteSpeciesType instance.
BindingSiteSpeciesType(java.lang.String id, java.lang.String name, int level, int version)	Creates a new BindingSiteSpeciesType instance.
BindingSiteSpeciesType(BindingSiteSpeciesType obj)	Creates a new BindingSiteSpeciesType instance, cloned from the given object.

Method Summary

Modifier and Type	Method	Description
BindingSiteSpeciesType	clone()	Creates a new BindingSiteSpeciesType instance, cloned from itself.
java.lang.String	getElementName()
void	initDefaults()	Initializes the default values using the namespace.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAllowsChildren, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, 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, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class org.sbml.jsbml.ext.multi.MultiSpeciesType

addInSpeciesTypeBond, addSpeciesFeatureType, addSpeciesTypeComponentIndex, addSpeciesTypeInstance, createInSpeciesTypeBond, createInSpeciesTypeBond, createSpeciesFeatureType, createSpeciesFeatureType, createSpeciesTypeComponentIndex, createSpeciesTypeComponentIndex, createSpeciesTypeInstance, createSpeciesTypeInstance, equals, getChildAt, getChildCount, getCompartment, getCompartmentInstance, getInSpeciesTypeBond, getInSpeciesTypeBond, getInSpeciesTypeBondCount, getListOfInSpeciesTypeBonds, getListOfSpeciesFeatureTypes, getListOfSpeciesTypeComponentIndexes, getListOfSpeciesTypeInstances, getNumInSpeciesTypeBonds, getNumSpeciesFeatureTypes, getNumSpeciesTypeComponentIndexes, getNumSpeciesTypeInstances, getSpeciesFeatureType, getSpeciesFeatureType, getSpeciesFeatureTypeCount, getSpeciesTypeComponentIndex, getSpeciesTypeComponentIndex, getSpeciesTypeComponentIndexCount, getSpeciesTypeInstance, getSpeciesTypeInstance, getSpeciesTypeInstanceCount, hashCode, isCompartmentMandatory, isIdMandatory, isSetCompartment, isSetCompartmentInstance, isSetListOfInSpeciesTypeBonds, isSetListOfSpeciesFeatureTypes, isSetListOfSpeciesTypeComponentIndexes, isSetListOfSpeciesTypeInstances, readAttribute, removeInSpeciesTypeBond, removeInSpeciesTypeBond, removeInSpeciesTypeBond, removeSpeciesFeatureType, removeSpeciesFeatureType, removeSpeciesFeatureType, removeSpeciesTypeComponentIndex, removeSpeciesTypeComponentIndex, removeSpeciesTypeComponentIndex, removeSpeciesTypeInstance, removeSpeciesTypeInstance, removeSpeciesTypeInstance, setCompartment, setCompartment, setListOfInSpeciesTypeBonds, setListOfSpeciesFeatureTypes, setListOfSpeciesTypeComponentIndexes, setListOfSpeciesTypeInstances, unsetCompartment, unsetListOfInSpeciesTypeBonds, unsetListOfSpeciesFeatureTypes, unsetListOfSpeciesTypeComponentIndexes, unsetListOfSpeciesTypeInstances, writeXMLAttributes

Methods inherited from interface org.sbml.jsbml.NamedSBase

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.sbml.jsbml.SBase

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

Methods inherited from class org.sbml.jsbml.SpeciesType

getParent

Methods inherited from interface javax.swing.tree.TreeNode

children, getAllowsChildren, getIndex, getParent, isLeaf

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

Constructor Detail

BindingSiteSpeciesType

public BindingSiteSpeciesType()

Creates a new BindingSiteSpeciesType instance.

BindingSiteSpeciesType

public BindingSiteSpeciesType(int level,
                              int version)

Creates a new BindingSiteSpeciesType instance.

Parameters:

level - the SBML level

version - the SBML version

BindingSiteSpeciesType

public BindingSiteSpeciesType(BindingSiteSpeciesType obj)

Creates a new BindingSiteSpeciesType instance, cloned from the given object.

Parameters:

obj - the BindingSiteSpeciesType instance to clone.

BindingSiteSpeciesType

public BindingSiteSpeciesType(java.lang.String id)

Creates a new BindingSiteSpeciesType instance.

Parameters:

id - the identifier for this element.

BindingSiteSpeciesType

public BindingSiteSpeciesType(java.lang.String id,
                              int level,
                              int version)

Creates a new BindingSiteSpeciesType instance.

Parameters:

id - the identifier for this element.

level - the SBML level

version - the SBML version

BindingSiteSpeciesType

public BindingSiteSpeciesType(java.lang.String id,
                              java.lang.String name,
                              int level,
                              int version)

Creates a new BindingSiteSpeciesType instance.

Parameters:

id - the identifier for this element.

name - a human-readable name for this element that can be used for display purposes.

level - the SBML level

version - the SBML version

Method Detail

clone

public BindingSiteSpeciesType clone()

Creates a new BindingSiteSpeciesType instance, cloned from itself.

Specified by:

clone in interface SBase

Overrides:

clone in class MultiSpeciesType

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

Overrides:

initDefaults in class MultiSpeciesType

getElementName

public java.lang.String getElementName()

Specified by:

getElementName in interface SBase

Overrides:

getElementName in class MultiSpeciesType