Package org.sbml.jsbml.ext.spatial

Class ParameterType

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.spatial.ParameterType

All Implemented Interfaces:

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

Direct Known Subclasses:

AdvectionCoefficient, BoundaryCondition, DiffusionCoefficient, SpatialSymbolReference

public class ParameterType
extends AbstractSBase

Top level class for all possible child of a SpatialParameterPlugin.

Since:

1.0

Author:

Alex Thomas, Andreas Dräger

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
ParameterType()	Creates a new ParameterType instance.
ParameterType(int level, int version)	Creates a new ParameterType instance.
ParameterType(ParameterType ref)	Creates a new ParameterType instance.

Method Summary

Modifier and Type	Method	Description
ParameterType	clone()
boolean	equals(java.lang.Object object)
boolean	getAllowsChildren()
javax.swing.tree.TreeNode	getChildAt(int childIndex)
int	getChildCount()
Geometry	getGeometryInstance()	Returns the Geometry instance.
Parameter	getParameterInstance()	Returns the Parameter instance associated with variable.
java.lang.String	getSpatialRef()	Returns the spatial reference (id of any element defined in the Geometry of the model).
Species	getSpeciesInstance()	Returns the Species instance associated with variable.
java.lang.String	getSpeciesReference()	Returns the value of variable.
java.lang.String	getSpId()	Returns the spatial reference (id of any element defined in the Geometry of the model).
java.lang.String	getVariable()	Returns the value of variable.
SBase	getVariableInstance()	Returns the Species or Parameter instance associated with variable.
int	hashCode()
void	initDefaults()	Initializes the default values using the namespace.
boolean	isSetSpatialRef()	Returns true is the spatial reference is set.
boolean	isSetSpeciesReference()	Returns whether variable is set.
boolean	isSetSpId()	Returns true is the spatial reference is set.
boolean	isSetVariable()	Returns whether variable is set.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
void	setSpatialRef(java.lang.String spatialRef)	Sets the spatial reference
void	setSpeciesRef(java.lang.String variable)	Sets the value of variable
void	setSpeciesReference(java.lang.String variable)	Sets the value of variable
void	setSpId(java.lang.String spatialRef)	Sets the spatial reference
void	setVariable(java.lang.String variable)	Sets the value of variable
boolean	unsetSpatialRef()	Unsets the spatialRef attribute.
boolean	unsetVariable()	Unsets the variable attribute.
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes()

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, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, 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 java.lang.Object

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

Methods inherited from interface org.sbml.jsbml.SBase

removeTreeNodeChangeListener

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, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Constructor Detail

ParameterType

public ParameterType()

Creates a new ParameterType instance.

ParameterType

public ParameterType(int level,
                     int version)

Creates a new ParameterType instance.

Parameters:

level - the SBML level

version - the SBML version

ParameterType

public ParameterType(ParameterType ref)

Creates a new ParameterType instance.

Parameters:

ref - the instance to clone

Method Detail

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

getGeometryInstance

public Geometry getGeometryInstance()

Returns the Geometry instance.

Returns:

the Geometry instance.

getSpId

public java.lang.String getSpId()

Returns the spatial reference (id of any element defined in the Geometry of the model).

Returns:

the spatial reference

See Also:

getSpatialRef()

getSpatialRef

public java.lang.String getSpatialRef()

Returns the spatial reference (id of any element defined in the Geometry of the model).

Returns:

the spatial reference

isSetSpId

public boolean isSetSpId()

Returns true is the spatial reference is set.

Returns:

true is the spatial reference is set.

See Also:

isSetSpatialRef()

isSetSpatialRef

public boolean isSetSpatialRef()

Returns true is the spatial reference is set.

Returns:

true is the spatial reference is set.

setSpId

public void setSpId(java.lang.String spatialRef)

Sets the spatial reference

Parameters:

spatialRef - the spatialRef to set

See Also:

setSpatialRef(String)

setSpatialRef

public void setSpatialRef(java.lang.String spatialRef)

Sets the spatial reference

Parameters:

spatialRef - the spatialRef to set

getVariable

public java.lang.String getVariable()

Returns the value of variable.

Returns:

the value of variable.

getVariableInstance

public SBase getVariableInstance()

Returns the Species or Parameter instance associated with variable.

Returns:

an SBase associated with variable or null.

getSpeciesInstance

public Species getSpeciesInstance()

Returns the Species instance associated with variable.

Returns:

a Species associated with variable or null.

getSpeciesReference

public java.lang.String getSpeciesReference()

Returns the value of variable.

Returns:

the value of variable.

See Also:

getVariable()

getParameterInstance

public Parameter getParameterInstance()

Returns the Parameter instance associated with variable.

Returns:

a Parameter associated with variable or null.

isSetSpeciesReference

public boolean isSetSpeciesReference()

Returns whether variable is set.

Returns:

whether variable is set.

See Also:

isSetVariable()

isSetVariable

public boolean isSetVariable()

Returns whether variable is set.

Returns:

whether variable is set.

setSpeciesReference

public void setSpeciesReference(java.lang.String variable)

Sets the value of variable

Parameters:

variable - the value of variable to be set.

See Also:

setVariable(String)

setVariable

public void setVariable(java.lang.String variable)

Sets the value of variable

Parameters:

variable - the value of variable to be set.

unsetSpatialRef

public boolean unsetSpatialRef()

Unsets the spatialRef attribute.

Returns:

true if spatialRef was set before, otherwise false.

unsetVariable

public boolean unsetVariable()

Unsets the variable attribute.

Returns:

true if variable was set before, otherwise false.

setSpeciesRef

public void setSpeciesRef(java.lang.String variable)

Sets the value of variable

Parameters:

variable - the value of variable to be set.

See Also:

setVariable(String)

clone

public ParameterType clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

getChildAt

public javax.swing.tree.TreeNode getChildAt(int childIndex)

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

equals

public boolean equals(java.lang.Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase