Package org.sbml.jsbml.ext.layout

Class Point

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.layout.Point

All Implemented Interfaces:

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

public class Point
extends AbstractNamedSBase
implements UniqueNamedSBase

The representation of a point in the "layout" package.

A Point is specified via the required attributes 'x', 'y' and an optional attribute 'z', all of which are of type double. If the attribute z is not specified, the object is a two dimensional object. The Point class also has an optional attribute id of type SId. While not used in the Layout package, it can be used by programs to refer to the elements.

Since:

1.0

Author:

Nicolas Rodriguez, Sebastian Frölich, Andreas Dräger, Clemens Wrzodek, David Vetter

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

JSBML_WRONG_SBO_TERM

Constructor Summary

Constructors

Constructor	Description
Point()	Creates a new Point instance with all coordinates set to Double.NaN.
Point(double x, double y)	Creates a new Point instance with the given x and y coordinates. z is set to Double.NaN.
Point(double x, double y, double z)	Creates a new Point instance with the given coordinates.
Point(double x, double y, double z, int level, int version)	Creates a new Point instance with the given coordinates and level and version.
Point(int level, int version)	Creates a new Point instance with the given level and version, all coordinates are set to Double.NaN.
Point(Point point)	Creates a new Point instance with all attributes cloned from the given Point.

Method Summary

Modifier and Type	Method	Description
Point	clone()	Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	equals(java.lang.Object object)	Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
java.lang.String	getElementName()	Returns the XML element name of this object.
double	getX()	Gets the x coordinate.
double	getY()	Gets the y coordinate.
double	getZ()	Gets the z coordinate.
int	hashCode()	Returns a hash code value for this SBase instance.
void	initDefaults()	Initializes the default values using the namespace.
boolean	isIdMandatory()	Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.
boolean	isSetElementName()
boolean	isSetX()	Returns true if the x coordinate is set.
boolean	isSetY()	Returns true if the y coordinate is set.
boolean	isSetZ()	Returns true if the z coordinate is set.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)	Sets the given attribute in this SBase.
void	setX(double x)	Sets the x coordinate.
void	setY(double y)	Sets the y coordinate.
void	setZ(double z)	Sets the z coordinate.
void	unsetX()	Unsets the required x coordinate.
void	unsetY()	Unsets the required y coordinate.
void	unsetZ()	Unsets the optional z coordinate.
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.
double	x()	Gets the x coordinate.
double	y()	Gets the y coordinate.
double	z()	Gets the z coordinate.

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, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, 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, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, 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, isLeaf, 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

getClass, notify, notifyAll, wait, wait, wait

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, 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, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, 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

Point

public Point()

Creates a new Point instance with all coordinates set to Double.NaN.

Point

public Point(double x,
             double y)

Creates a new Point instance with the given x and y coordinates. z is set to Double.NaN.

Parameters:

x - the x coordinate

y - the y coordinate

Point

public Point(double x,
             double y,
             double z)

Creates a new Point instance with the given coordinates.

Parameters:

x - the x coordinate

y - the y coordinate

z - the z coordinate

Point

public Point(double x,
             double y,
             double z,
             int level,
             int version)

Creates a new Point instance with the given coordinates and level and version.

Parameters:

x - the x coordinate

y - the y coordinate

z - the z coordinate

level - the SBML level

version - the SBML version

Point

public Point(int level,
             int version)

Creates a new Point instance with the given level and version, all coordinates are set to Double.NaN.

Parameters:

level - the SBML level

version - the SBML version

Point

public Point(Point point)

Creates a new Point instance with all attributes cloned from the given Point.

Parameters:

point - the Point instance to clone.

Method Detail

clone

public Point 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

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

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 AbstractSBase

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.

getElementName

public java.lang.String getElementName()

Description copied from interface: SBase

Returns the XML element name of this object.

Specified by:

getElementName in interface SBase

Overrides:

getElementName in class AbstractSBase

Returns:

the XML element name of this object.

getX

public double getX()

Gets the x coordinate.

Returns Double.NaN if isSetX() return false.

Returns:

the x coordinate.

getY

public double getY()

Gets the y coordinate.

Returns Double.NaN if isSetY() return false.

Returns:

the y coordinate.

getZ

public double getZ()

Gets the z coordinate.

Returns Double.NaN if isSetZ() return false.

Returns:

the z coordinate.

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 AbstractSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: SBase

Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

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.

isSetElementName

public boolean isSetElementName()

Returns:

Whether the xmlElementName attribute is set

isSetX

public boolean isSetX()

Returns true if the x coordinate is set.

Returns:

true if the x coordinate is set.

isSetY

public boolean isSetY()

Returns true if the y coordinate is set.

Returns:

true if the y coordinate is set.

isSetZ

public boolean isSetZ()

Returns true if the z coordinate is set.

Returns:

true if the z coordinate is set.

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 AbstractSBase

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.

setX

public void setX(double x)

Sets the x coordinate.

The general Point class specifies the x, y, and z (optional) attributes which defines the graphical location with respect to the coordinate system of the Layout extension. The x attribute is required.

Parameters:

x - the x coordinate to be set.

setY

public void setY(double y)

Sets the y coordinate.

The y attribute is required. For a more general description of the dimension attributes, see setX(double).

Parameters:

y - the y coordinate to be set.

setZ

public void setZ(double z)

Sets the z coordinate.

The z attribute is optional. The layout is 2-dimensional if the z attribute is not specified.

Parameters:

z - the z coordinate to be set.

unsetX

public void unsetX()

Unsets the required x coordinate.

unsetY

public void unsetY()

Unsets the required y coordinate.

unsetZ

public void unsetZ()

Unsets the optional z coordinate.

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 AbstractSBase

Returns:

a Map containing the XML attributes of this object.

x

public double x()

Gets the x coordinate.

Returns:

the x coordinate.

See Also:

getX()

Note: this method is kept here as it exist in libSBML.

y

public double y()

Gets the y coordinate.

Returns:

the y coordinate.

See Also:

getY()

Note: this method is kept here as it exist in libSBML.

z

public double z()

Gets the z coordinate.

Returns:

the z coordinate.

See Also:

getZ()

Note: this method is kept here as it exist in libSBML.