org.sbml.jsbml.ext.spatial

Class CoordinateComponent

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

org.sbml.jsbml.ext.spatial.CoordinateComponent

All Implemented Interfaces:

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

public class CoordinateComponent
extends AbstractSpatialNamedSBase
implements SBaseWithUnit

Since:

1.0

Version:

$Rev: 1980 $

Author:

Alex Thomas, Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private Boundary	boundaryMaximum
private Boundary	boundaryMinimum
private static java.util.ResourceBundle	bundle
private static long	serialVersionUID Generated serial version identifier.
private CoordinateKind	type
private java.lang.String	unit

Fields inherited from class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

spatialId

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
CoordinateComponent()
CoordinateComponent(CoordinateComponent coordComp)
CoordinateComponent(int level, int version)
CoordinateComponent(java.lang.String id, int level, int version)

Method Summary

Methods

Modifier and Type	Method and Description
CoordinateComponent	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	containsUndeclaredUnits() Returns true or false depending on whether this SBaseWithDerivedUnit refers to elements such as parameters or numbers with undeclared units.
boolean	equals(java.lang.Object object) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
Boundary	getBoundaryMaximum() Returns the value of boundaryMaximum
Boundary	getBoundaryMinimum() Returns the value of boundaryMinimum
javax.swing.tree.TreeNode	getChildAt(int childIndex)
int	getChildCount()
UnitDefinition	getDerivedUnitDefinition() Derives the unit of this quantity and tries to identify an equivalent UnitDefinition within the corresponding Model.
java.lang.String	getDerivedUnits() Derives the unit of this quantity.
CoordinateKind	getType() Returns the value of type
java.lang.String	getUnits() Returns the value of unit
UnitDefinition	getUnitsInstance()
int	hashCode() Returns a hash code value for this SBase instance.
boolean	isSetBoundaryMaximum() Returns whether boundaryMaximum is set
boolean	isSetBoundaryMinimum() Returns whether boundaryMinimum is set
boolean	isSetType() Returns whether type is set
boolean	isSetUnits() Returns whether unit is set
boolean	isSetUnitsInstance() Checks whether the element referenced by the unitsID attribute of this SBaseWithUnit is either an existing base Unit, i.e., a simple Unit that can directly be addressed via its Unit.Kind element, or the identifier of an existing UnitDefinition in the Model to which this SBaseWithUnit belongs.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setBoundaryMaximum(Boundary boundaryMaximum) Sets the value of boundaryMaximum
void	setBoundaryMinimum(Boundary boundaryMinimum) Sets the value of boundaryMinimum
void	setType(CoordinateKind type) Sets the value of type
void	setUnits(java.lang.String unit) Sets the value of unit
void	setUnits(Unit.Kind unitKind) Sets the unit of this SBaseWithUnit.
void	setUnits(Unit unit) Sets the Unit of this SBaseWithUnit.
void	setUnits(UnitDefinition units) Set the unit attribute of this SBaseWithUnit to the given unit definition.
java.lang.String	toString()
boolean	unsetBoundaryMaximum() Unsets the variable boundaryMaximum
boolean	unsetBoundaryMinimum() Unsets the variable boundaryMinimum
boolean	unsetType() Unsets the variable type
void	unsetUnits() Unsets the variable unit
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.ext.spatial.AbstractSpatialNamedSBase

getAllowsChildren, getSpatialId, isSetSpatialId, setSpatialId, unsetSpatialId

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, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, 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.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, 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, 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

type

private CoordinateKind type

boundaryMaximum

private Boundary boundaryMaximum

boundaryMinimum

private Boundary boundaryMinimum

unit

private java.lang.String unit

bundle

private static final java.util.ResourceBundle bundle

Constructor Detail

CoordinateComponent

public CoordinateComponent()

CoordinateComponent

public CoordinateComponent(CoordinateComponent coordComp)

Parameters:

coordComp -

CoordinateComponent

public CoordinateComponent(int level,
                   int version)

Parameters:

level -

version -

CoordinateComponent

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

Parameters:

id -

level -

version -

Method Detail

clone

public CoordinateComponent 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

Specified by:

clone in class AbstractSBase

Returns:

a copy of this object

getBoundaryMinimum

public Boundary getBoundaryMinimum()

Returns the value of boundaryMinimum

Returns:

the value of boundaryMinimum

isSetBoundaryMinimum

public boolean isSetBoundaryMinimum()

Returns whether boundaryMinimum is set

Returns:

whether boundaryMinimum is set

setBoundaryMinimum

public void setBoundaryMinimum(Boundary boundaryMinimum)

Sets the value of boundaryMinimum

unsetBoundaryMinimum

public boolean unsetBoundaryMinimum()

Unsets the variable boundaryMinimum

Returns:

true, if boundaryMinimum was set before, otherwise false

getBoundaryMaximum

public Boundary getBoundaryMaximum()

Returns the value of boundaryMaximum

Returns:

the value of boundaryMaximum

isSetBoundaryMaximum

public boolean isSetBoundaryMaximum()

Returns whether boundaryMaximum is set

Returns:

whether boundaryMaximum is set

setBoundaryMaximum

public void setBoundaryMaximum(Boundary boundaryMaximum)

Sets the value of boundaryMaximum

unsetBoundaryMaximum

public boolean unsetBoundaryMaximum()

Unsets the variable boundaryMaximum

Returns:

true, if boundaryMaximum was set before, otherwise false

getType

public CoordinateKind getType()

Returns the value of type

Returns:

the value of type

isSetType

public boolean isSetType()

Returns whether type is set

Returns:

whether type is set

setType

public void setType(CoordinateKind type)

Sets the value of type

unsetType

public boolean unsetType()

Unsets the variable type

Returns:

true, if type was set before, otherwise false

containsUndeclaredUnits

public boolean containsUndeclaredUnits()

Description copied from interface: SBaseWithDerivedUnit

Returns true or false depending on whether this SBaseWithDerivedUnit refers to elements such as parameters or numbers with undeclared units. A return value of true indicates that the UnitDefinition returned by SBaseWithDerivedUnit.getDerivedUnitDefinition() may not accurately represent the units of the expression.

Specified by:

containsUndeclaredUnits in interface SBaseWithDerivedUnit

Returns:

true if the math expression of this SBaseWithDerivedUnit includes parameters/numbers with undeclared units, false otherwise.

equals

public boolean equals(java.lang.Object object)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSpatialNamedSBase

Parameters:

object - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.

getChildAt

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

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractSpatialNamedSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class AbstractSpatialNamedSBase

getUnits

public java.lang.String getUnits()

Returns the value of unit

Specified by:

getUnits in interface SBaseWithUnit

Returns:

the value of unit

isSetUnits

public boolean isSetUnits()

Returns whether unit is set

Specified by:

isSetUnits in interface SBaseWithUnit

Returns:

whether unit is set

setUnits

public void setUnits(java.lang.String unit)

Sets the value of unit

Specified by:

setUnits in interface SBaseWithUnit

Parameters:

unit - the identifier of an already existing UnitDefinition or an Unit.Kind identifier for the current level/version combination of this unit. Passing a null value to this method is equivalent to calling SBaseWithUnit.unsetUnits().

unsetUnits

public void unsetUnits()

Unsets the variable unit

Specified by:

unsetUnits in interface SBaseWithUnit

getDerivedUnitDefinition

public UnitDefinition getDerivedUnitDefinition()

Description copied from interface: SBaseWithDerivedUnit

Derives the unit of this quantity and tries to identify an equivalent UnitDefinition within the corresponding Model. If no equivalent unit definition can be found, a new unit definition will be created that is not part of the model but represents the unit of this quantity. If it is not possible to derive a unit for this quantity, null will be returned.

Specified by:

getDerivedUnitDefinition in interface SBaseWithDerivedUnit

Returns:

a UnitDefinition that represent the derived unit of this quantity, or null if it is not possible to derive a unit.

getDerivedUnits

public java.lang.String getDerivedUnits()

Description copied from interface: SBaseWithDerivedUnit

Derives the unit of this quantity. If the model that contains this quantity already contains a unit that is equivalent to the derived unit, the corresponding identifier will be returned. In case that the unit cannot be derived or that no equivalent unit exists within the model, or if the model has not been defined yet, null will be returned. In case that this quantity represents a basic Unit.Kind this method will return the String representation of this Unit.Kind.

Specified by:

getDerivedUnits in interface SBaseWithDerivedUnit

Returns:

a String that represent the id of a UnitDefinition. This UnitDefinition represent the derived unit of this quantity. If it is not possible to derive a unit for this quantity or if no equivalent UnitDefinition can be found in the Model, null is returned.

getUnitsInstance

public UnitDefinition getUnitsInstance()

Specified by:

getUnitsInstance in interface SBaseWithUnit

Returns:

The UnitDefinition instance which has the unitsID of this SBaseWithUnit as id. Null if it doesn't exist. In case that the unit of this SBaseWithUnit represents a base Unit, a new UnitDefinition will be created and returned by this method. This new UnitDefinition will only contain the one unit represented by the unit identifier in this SBaseWithUnit. Note that the corresponding model will not contain this UnitDefinition. The identifier of this new UnitDefinition will be set to the same value as the name of the base Unit.

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSpatialNamedSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

isSetUnitsInstance

public boolean isSetUnitsInstance()

Description copied from interface: SBaseWithUnit

Checks whether the element referenced by the unitsID attribute of this SBaseWithUnit is either an existing base Unit, i.e., a simple Unit that can directly be addressed via its Unit.Kind element, or the identifier of an existing UnitDefinition in the Model to which this SBaseWithUnit belongs.

Specified by:

isSetUnitsInstance in interface SBaseWithUnit

Returns:

true if either a UnitDefinition, which has the unitsID of this SBaseWithUnit, can be found in the Model to which this SBaseWithUnit belongs, or if this element's unitsID as a corresponding base Unit for the given Level/Version combination.

setUnits

public void setUnits(Unit.Kind unitKind)

Description copied from interface: SBaseWithUnit

Sets the unit of this SBaseWithUnit. A new unit will be created base on this kind.

Specified by:

setUnits in interface SBaseWithUnit

setUnits

public void setUnits(Unit unit)

Description copied from interface: SBaseWithUnit

Sets the Unit of this SBaseWithUnit.

Specified by:

setUnits in interface SBaseWithUnit

setUnits

public void setUnits(UnitDefinition units)

Description copied from interface: SBaseWithUnit

Set the unit attribute of this SBaseWithUnit to the given unit definition.

Specified by:

setUnits in interface SBaseWithUnit

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 AbstractSpatialNamedSBase

Returns:

a Map containing the XML attributes of this object.

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 AbstractSpatialNamedSBase

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.

toString

public java.lang.String toString()

Overrides:

toString in class AbstractSpatialNamedSBase