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:

Serializable, Cloneable, 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

Version:

$Rev$

Author:

Nicolas Rodriguez, Sebastian Frölich, Andreas Dräger, Clemens Wrzodek

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 and 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.
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 and Description
Point	clone()
protected void	clonePointAttributes(Point point, Point cloned) Clones the x, y and z coordinates from point to cloned.
boolean	equals(Object object)
String	getElementName()
double	getX() Gets the x coordinate.
double	getY() Gets the y coordinate.
double	getZ() Gets the z coordinate.
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isIdMandatory()
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(String attributeName, String prefix, String value)
void	setX(double x) Sets the x coordinate.
void	setY(double y) Sets the y coordinate.
void	setZ(double z) Sets the z coordinate.
Map<String,String>	writeXMLAttributes()
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, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, 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, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, toString, 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, 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, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, 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

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, getParent, isLeaf

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()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

clonePointAttributes

protected void clonePointAttributes(Point point,
                                    Point cloned)

Clones the x, y and z coordinates from point to cloned.

Parameters:

point -

cloned -

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

equals

public boolean equals(Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

getElementName

public String getElementName()

Specified by:

getElementName in interface SBase

Overrides:

getElementName in class AbstractSBase

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()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

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(String attributeName,
                             String prefix,
                             String value)

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

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.

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

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.