Package org.sbml.jsbml.ext.multi

Class IntraSpeciesReaction

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.Reaction

org.sbml.jsbml.ext.multi.IntraSpeciesReaction

All Implemented Interfaces:

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

public class IntraSpeciesReaction
extends Reaction

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
IntraSpeciesReaction()	Creates an IntraSpeciesReaction instance
IntraSpeciesReaction(int level, int version)	Creates a IntraSpeciesReaction instance with a level and version.
IntraSpeciesReaction(java.lang.String id)	Creates a IntraSpeciesReaction instance with an id.
IntraSpeciesReaction(java.lang.String id, int level, int version)	Creates a IntraSpeciesReaction instance with an id, level, and version.
IntraSpeciesReaction(java.lang.String id, java.lang.String name, int level, int version)	Creates a IntraSpeciesReaction instance with an id, name, level, and version.
IntraSpeciesReaction(IntraSpeciesReaction obj)	Clone constructor

Method Summary

Modifier and Type	Method	Description
IntraSpeciesReaction	clone()	clones this class
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, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, 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 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 class org.sbml.jsbml.Reaction

addModifier, addProduct, addReactant, containsUndeclaredUnits, createKineticLaw, createModifier, createModifier, createModifier, createModifier, createModifier, createProduct, createProduct, createProduct, createProduct, createProduct, createReactant, createReactant, createReactant, createReactant, createReactant, equals, getAllowsChildren, getChildAt, getChildCount, getCompartment, getCompartmentInstance, getDerivedUnitDefinition, getDerivedUnits, getFast, getKineticLaw, getListOfModifiers, getListOfProducts, getListOfReactants, getModifier, getModifier, getModifierCount, getModifierForSpecies, getNumModifiers, getNumProducts, getNumReactants, getParent, getProduct, getProduct, getProductCount, getProductForSpecies, getReactant, getReactant, getReactantCount, getReactantForSpecies, getReversible, hashCode, hasModifier, hasProduct, hasReactant, initDefaults, initDefaults, involves, isCompartmentMandatory, isFast, isIdMandatory, isListOfModifiersEmpty, isListOfProductsEmpty, isListOfReactantsEmpty, isReversible, isSetCompartment, isSetCompartmentInstance, isSetFast, isSetKineticLaw, isSetListOfModifiers, isSetListOfProducts, isSetListOfReactants, isSetReversible, readAttribute, removeModifier, removeModifier, removeModifier, removeProduct, removeProduct, removeProduct, removeReactant, removeReactant, removeReactant, setCompartment, setCompartment, setFast, setKineticLaw, setListOfModifiers, setListOfProducts, setListOfReactants, setReversible, unsetCompartment, unsetFast, unsetKineticLaw, unsetListOfModifiers, unsetListOfProducts, unsetListOfReactants, unsetReversible, writeXMLAttributes

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, getElementName, 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 interface javax.swing.tree.TreeNode

children, getIndex, 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

IntraSpeciesReaction

public IntraSpeciesReaction()

Creates an IntraSpeciesReaction instance

IntraSpeciesReaction

public IntraSpeciesReaction(java.lang.String id)

Creates a IntraSpeciesReaction instance with an id.

Parameters:

id - the identifier for the new element.

IntraSpeciesReaction

public IntraSpeciesReaction(int level,
                            int version)

Creates a IntraSpeciesReaction instance with a level and version.

Parameters:

level - SBML Level

version - SBML Version

IntraSpeciesReaction

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

Creates a IntraSpeciesReaction instance with an id, level, and version.

Parameters:

id - the identifier for this element.

level - the SBML Level

version - the SBML Version

IntraSpeciesReaction

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

Creates a IntraSpeciesReaction instance with an id, name, level, and version.

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

IntraSpeciesReaction

public IntraSpeciesReaction(IntraSpeciesReaction obj)

Clone constructor

Method Detail

clone

public IntraSpeciesReaction clone()

clones this class

Specified by:

clone in interface SBase

Overrides:

clone in class Reaction

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

Overrides:

initDefaults in class Reaction