org.sbml.jsbml

Class SpeciesType

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.SpeciesType

All Implemented Interfaces:

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

Deprecated.

Only valid in SBML Level 2 for Versions 2 through 4.

@Deprecated
public class SpeciesType
extends AbstractNamedSBase
implements UniqueNamedSBase

Represents the speciesType XML element of a SBML file. It is deprecated since level 3 and not defined in SBML before Level 2 Version 2.

Since:

0.8

Version:

$Rev$

Author:

Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private static long	serialVersionUID Deprecated. Generated serial version identifier.

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, lv, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
SpeciesType() Deprecated.
SpeciesType(int level, int version) Deprecated.
SpeciesType(SpeciesType nsb) Deprecated.
SpeciesType(java.lang.String id) Deprecated.
SpeciesType(java.lang.String id, int level, int version) Deprecated.
SpeciesType(java.lang.String id, java.lang.String name, int level, int version) Deprecated.

Method Summary

Modifier and Type	Method and Description
SpeciesType	clone() Deprecated.
ListOf<SpeciesType>	getParent() Deprecated.
private void	initDefaults() Deprecated. Initializes the default settings of this class.
boolean	isIdMandatory() Deprecated.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

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

Methods inherited from class org.sbml.jsbml.AbstractSBase

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

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, getChildAt, getChildCount, getIndex, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Deprecated.

Generated serial version identifier.

See Also:

Constant Field Values

Constructor Detail

SpeciesType

@Deprecated
public SpeciesType()

Deprecated.

Creates a SpeciesType instance.

SpeciesType

@Deprecated
public SpeciesType(int level,
                               int version)

Deprecated.

Creates a SpeciesType instance from a level and version.

Parameters:

level -

version -

SpeciesType

@Deprecated
public SpeciesType(SpeciesType nsb)

Deprecated.

Creates a SpeciesType instance from a given SpeciesType.

Parameters:

nsb -

SpeciesType

@Deprecated
public SpeciesType(java.lang.String id)

Deprecated.

Parameters:

id -

SpeciesType

@Deprecated
public SpeciesType(java.lang.String id,
                               int level,
                               int version)

Deprecated.

Creates a SpeciesType instance from an id, level and version.

Parameters:

id -

level -

version -

SpeciesType

@Deprecated
public SpeciesType(java.lang.String id,
                               java.lang.String name,
                               int level,
                               int version)

Deprecated.

Creates a SpeciesType instance from an id, name, level and version.

Parameters:

id -

name -

level -

version -

Method Detail

clone

@Deprecated
public SpeciesType clone()

Deprecated.

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

getParent

@Deprecated
public ListOf<SpeciesType> getParent()

Deprecated.

Description copied from class: AbstractSBase

This is equivalent to calling AbstractSBase.getParentSBMLObject(), but this method is needed for TreeNode.

Specified by:

getParent in interface javax.swing.tree.TreeNode

Overrides:

getParent in class AbstractSBase

Returns:

the parent element of this element.

See Also:

AbstractSBase.getParentSBMLObject()

initDefaults

private void initDefaults()

Deprecated.

Initializes the default settings of this class. In this case, it checks if this type can actually be used in the defined SBML Level/Version combination.

isIdMandatory

@Deprecated
public boolean isIdMandatory()

Deprecated.

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.