org.sbml.jsbml.ext.multi

Class SpeciesType

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.SpeciesType

org.sbml.jsbml.ext.multi.SpeciesType

All Implemented Interfaces:

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

public class SpeciesType
extends SpeciesType
implements UniqueNamedSBase

The element SpeciesType, which is part of SBML Level 2 Version 4 specification, is not part of SBML Level 3 Version 1 Core any more. Instead, it will be defined in the multi package. The SpeciesType element carries not only the basic attributes which it had in SBML Level 2 Version 4 (metaid, id, name), but is also extended for the needs of describing multi-component entities with the attribute bindingSite and for the needs of multistate entities by linking it to a list of StateFeatures

A species type can be used to describe a component of a supra-macromolecular assembly, but also a domain of a macromolecule. Such a domain can be a portion of the macromolecule, a non-connex set of atoms forming a functional domain, or just a conceptual construct suiting the needs of the modeler. The type of component can be specified by referring terms from the subbranch functional entity of the Systems Biology Ontology through the optional sboTerm attribute. The following table provides typical examples of component or domains (the list is absolutely not complete).

SBO identifier	Definition
SBO:0000242	channel
SBO:0000244	receptor
SBO:0000284	transporter
SBO:0000280	ligand
SBO:0000493	functional domain
SBO:0000494	binding site
SBO:0000495	catalytic site
SBO:0000496	transmembrane domain

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
(package private) java.lang.Boolean	bindingSite
(package private) ListOf<StateFeature>	listOfStateFeatures
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
SpeciesType()

Method Summary

Methods

Modifier and Type	Method and Description
void	addStateFeature(StateFeature stateFeature) Adds a StateFeature.
SpeciesType	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
StateFeature	createStateFeature() Creates a new StateFeature inside this SpeciesType and returns it.
StateFeature	createStateFeature(java.lang.String id) Creates a new StateFeature inside this SpeciesType and returns it.
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
ListOf<StateFeature>	getListOfStateFeatures() Returns the listOfStateFeatures
StateFeature	getStateFeature(int i) Gets the ith StateFeature.
StateFeature	getStateFeature(java.lang.String id) Gets the StateFeature that has the given id.
void	initDefaults()
boolean	isBindingSite()
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	isSetBindingSite()
boolean	isSetListOfStateFeatures() Returns true if the listOfStateFeature is set.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setBindingSite(boolean bindingSite)
boolean	unsetListOfStateFeatures() Sets the listOfStateFeatures 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.SpeciesType

getParent

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

equals, getId, getName, hashCode, isSetId, isSetName, isValidId, 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, 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, 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

listOfStateFeatures

ListOf<StateFeature> listOfStateFeatures

bindingSite

java.lang.Boolean bindingSite

Constructor Detail

SpeciesType

public SpeciesType()

Method Detail

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

Overrides:

isIdMandatory in class SpeciesType

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.

clone

public SpeciesType 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

Overrides:

clone in class SpeciesType

Returns:

a copy of this object

getListOfStateFeatures

public ListOf<StateFeature> getListOfStateFeatures()

Returns the listOfStateFeatures

Returns:

the listOfStateFeatures

addStateFeature

public void addStateFeature(StateFeature stateFeature)

Adds a StateFeature.

Parameters:

stateFeature - the stateFeature to add

createStateFeature

public StateFeature createStateFeature()

Creates a new StateFeature inside this SpeciesType and returns it.

Returns:

the StateFeature object created

See Also:

addStateFeature(StateFeature r)

createStateFeature

public StateFeature createStateFeature(java.lang.String id)

Creates a new StateFeature inside this SpeciesType and returns it.

Parameters:

id - the id of the new element to create

Returns:

the StateFeature object created

getStateFeature

public StateFeature getStateFeature(int i)

Gets the ith StateFeature.

Parameters:

i -

Returns:

the ith StateFeature

Throws:

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

getStateFeature

public StateFeature getStateFeature(java.lang.String id)

Gets the StateFeature that has the given id.

Parameters:

id -

Returns:

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

isSetListOfStateFeatures

public boolean isSetListOfStateFeatures()

Returns true if the listOfStateFeature is set.

Returns:

true if the listOfStateFeature is set.

unsetListOfStateFeatures

public boolean unsetListOfStateFeatures()

Sets the listOfStateFeatures to null

Returns:

true is successful

isBindingSite

public boolean isBindingSite()

Returns:

the bindingSite

isSetBindingSite

public boolean isSetBindingSite()

setBindingSite

public void setBindingSite(boolean bindingSite)

Parameters:

bindingSite - the bindingSite to set

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

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractNamedSBase

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

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.