org.sbml.jsbml.ext.render

Class RenderCurve

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.render.Transformation

org.sbml.jsbml.ext.render.Transformation2D

org.sbml.jsbml.ext.render.GraphicalPrimitive1D

org.sbml.jsbml.ext.render.RenderCurve

All Implemented Interfaces:

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

public class RenderCurve
extends GraphicalPrimitive1D
implements ICurve

Implements the curve concept from the SBML render extension.

The curve concept in the SBML render extension is similar to the curves in the SBML layout. Each curve consists of a number of either straight line segments or cubic Bézier elements. The two element types can also be mixed in a single curve object.

In contrast to layout curves, render curves can not have gaps and the individual coordinates of the curve elements can be specified as a combination of absolute and relative values.

Another difference to layout curves is the fact that render curves can specify decorations to be applied to the start and/or the end of the curve (@see LineEnding).

Since RenderCurve is derived from GraphicalPrimitive1D, it inherits all its attributes and methods.

Since:

1.0

Author:

Eugen Netz, Alexander Diamantikos, Jakob Matthes, Jan Rudolph

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

JSBML_WRONG_SBO_TERM

Constructor Summary

Constructors

Constructor and Description
RenderCurve() Creates an Curve instance
RenderCurve(RenderCurve obj) Clone constructor

Method Summary

Modifier and Type	Method and Description
boolean	addCurveSegment(CurveSegment curveSegment) Adds a new CurveSegment to the listOfCurveSegments.
void	addCurveSegment(int index, CurveSegment element)
boolean	addElement(RenderPoint element)
RenderCurve	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
CubicBezier	createCubicBezier() Creates a new CubicBezier instance and adds it to the listOfCurveSegments list.
RenderPoint	createElement() Deprecated. use#createRenderPoint()
LineSegment	createLineSegment() Creates a new LineSegment instance and adds it to the listOfCurveSegments list.
RenderPoint	createRenderCubicBezier() Creates a new RenderCubicBezier instance and adds it to the ListOfElements list
RenderPoint	createRenderPoint() Creates a new RenderPoint instance and adds it to the ListOfElements list
boolean	equals(java.lang.Object obj) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
boolean	getAllowsChildren()
SBase	getChildAt(int childIndex)
int	getChildCount()
CurveSegment	getCurveSegment(int i) Gets an element from the listOfCurveSegments at the given index.
int	getCurveSegmentCount() Returns the number of CurveSegments in this RenderCurve.
java.lang.String	getElementName() Returns the XML element name of this object.
java.lang.String	getEndHead() Returns the value of endHead
ListOf<CurveSegment>	getListOfCurveSegments() Returns the listOfCurveSegments.
ListOf<RenderPoint>	getListOfElements()
int	getNumCurveSegments() Returns the number of CurveSegments in this RenderCurve.
java.lang.String	getStartHead() Returns the value of startHead
int	hashCode() Returns a hash code value for this SBase instance.
void	initDefaults() Initializes the default values using the namespace.
boolean	isListOfCurveSegmentsEmpty()
boolean	isListOfElementsEmpty()
boolean	isSetEndHead() Returns true if endHead is set.
boolean	isSetListOfCurveSegments() Returns true if listOfCurveSegments contains at least one element.
boolean	isSetListOfElements()
boolean	isSetStartHead() Returns true if startHead is set
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
boolean	removeCurveSegment(CurveSegment curveSegment) Removes an element from the listOfCurveSegments.
CurveSegment	removeCurveSegment(int i) Removes an element from the listOfCurveSegments at the given index.
void	removeElement(int i)
boolean	removeElement(RenderPoint element)
void	setEndHead(java.lang.String endHead) Sets the value of endHead
void	setListOfCurveSegments(ListOf<CurveSegment> listOfCurveSegments) Sets the given ListOf<CurveSegment>.
void	setListOfElements(ListOf<RenderPoint> listOfElements)
void	setStartHead(java.lang.String startHead) Sets the value of startHead.
boolean	unsetEndHead() Unsets the variable endHead
boolean	unsetListOfCurveSegments() Returns true if listOfCurveSegments contains at least one element, otherwise false.
boolean	unsetListOfElements()
boolean	unsetStartHead() Unsets the variable startHead
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.render.GraphicalPrimitive1D

addStrokeDash, getStroke, getStrokeDash, getStrokeDashArray, getStrokeWidth, isSetStroke, isSetStrokeDashArray, isSetStrokeWidth, setStroke, setStrokeDashArray, setStrokeDashArray, setStrokeWidth, unsetStroke, unsetStrokeDashArray, unsetStrokeWidth

Methods inherited from class org.sbml.jsbml.ext.render.Transformation2D

getTransform, unsetTransform

Methods inherited from class org.sbml.jsbml.ext.render.Transformation

isSetTransform, setTransform

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAnnotation, getAnnotationString, 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, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, 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 class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.SBase

removeTreeNodeChangeListener

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

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, isLeaf

Constructor Detail

RenderCurve

public RenderCurve()

Creates an Curve instance

RenderCurve

public RenderCurve(RenderCurve obj)

Clone constructor

Parameters:

obj - the RenderCurve to clone

Method Detail

clone

public RenderCurve 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 GraphicalPrimitive1D

Returns:

a copy of this object

initDefaults

public void initDefaults()

Description copied from class: Transformation

Initializes the default values using the namespace.

Overrides:

initDefaults in class GraphicalPrimitive1D

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 GraphicalPrimitive1D

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

equals

public boolean equals(java.lang.Object obj)

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 GraphicalPrimitive1D

Parameters:

obj - 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.

getStartHead

public java.lang.String getStartHead()

Returns the value of startHead

Returns:

the value of startHead

isSetStartHead

public boolean isSetStartHead()

Returns true if startHead is set

Returns:

whether startHead is set

setStartHead

public void setStartHead(java.lang.String startHead)

Sets the value of startHead.

Parameters:

startHead - the start head

unsetStartHead

public boolean unsetStartHead()

Unsets the variable startHead

Returns:

true, if startHead was set before, otherwise false

getEndHead

public java.lang.String getEndHead()

Returns the value of endHead

Returns:

the value of endHead

isSetEndHead

public boolean isSetEndHead()

Returns true if endHead is set.

Returns:

whether endHead is set

setEndHead

public void setEndHead(java.lang.String endHead)

Sets the value of endHead

Parameters:

endHead - the end head

unsetEndHead

public boolean unsetEndHead()

Unsets the variable endHead

Returns:

true, if endHead was set before, otherwise false

isSetListOfElements

public boolean isSetListOfElements()

Returns:

true, if listOfElements contains at least one element, otherwise false

isListOfElementsEmpty

public boolean isListOfElementsEmpty()

Returns:

true iff listOfElements is not null, but empty (relevant for validation)

getListOfElements

public ListOf<RenderPoint> getListOfElements()

Returns:

the listOfElements

setListOfElements

public void setListOfElements(ListOf<RenderPoint> listOfElements)

Parameters:

listOfElements - the list of RenderPoints

unsetListOfElements

public boolean unsetListOfElements()

Returns:

true, if listOfElements contained at least one element, otherwise false

addElement

public boolean addElement(RenderPoint element)

Parameters:

element -

Returns:

removeElement

public boolean removeElement(RenderPoint element)

Parameters:

element -

Returns:

removeElement

public void removeElement(int i)

Parameters:

i -

createElement

public RenderPoint createElement()

Deprecated. use#createRenderPoint()

Creates a new RenderPoint instance and adds it to the ListOfElements list

Returns:

a new RenderPoint instance

createRenderCubicBezier

public RenderPoint createRenderCubicBezier()

Creates a new RenderCubicBezier instance and adds it to the ListOfElements list

Returns:

a new RenderCubicBezier instance

createRenderPoint

public RenderPoint createRenderPoint()

Creates a new RenderPoint instance and adds it to the ListOfElements list

Returns:

a new RenderPoint instance

isSetListOfCurveSegments

public boolean isSetListOfCurveSegments()

Returns true if listOfCurveSegments contains at least one element.

Specified by:

isSetListOfCurveSegments in interface ICurve

Returns:

true if listOfCurveSegments contains at least one element, otherwise false.

isListOfCurveSegmentsEmpty

public boolean isListOfCurveSegmentsEmpty()

Returns:

true iff listOfCurveSegments is not null, but empty (relevant for validation)

getListOfCurveSegments

public ListOf<CurveSegment> getListOfCurveSegments()

Returns the listOfCurveSegments. Creates it if it does not already exist.

Specified by:

getListOfCurveSegments in interface ICurve

Returns:

the listOfCurveSegments.

setListOfCurveSegments

public void setListOfCurveSegments(ListOf<CurveSegment> listOfCurveSegments)

Sets the given ListOf<CurveSegment>. If listOfCurveSegments was defined before and contains some elements, they are all unset.

Specified by:

setListOfCurveSegments in interface ICurve

Parameters:

listOfCurveSegments - the list of CurveSegments

unsetListOfCurveSegments

public boolean unsetListOfCurveSegments()

Returns true if listOfCurveSegments contains at least one element, otherwise false.

Specified by:

unsetListOfCurveSegments in interface ICurve

Returns:

true if listOfCurveSegments contains at least one element, otherwise false.

addCurveSegment

public boolean addCurveSegment(CurveSegment curveSegment)

Adds a new CurveSegment to the listOfCurveSegments.

The listOfCurveSegments is initialized if necessary.

Specified by:

addCurveSegment in interface ICurve

Parameters:

curveSegment - the element to add to the list

Returns:

true (as specified by Collection.add(E))

See Also:

Collection.add(Object)

addCurveSegment

public void addCurveSegment(int index,
                            CurveSegment element)

Specified by:

addCurveSegment in interface ICurve

removeCurveSegment

public boolean removeCurveSegment(CurveSegment curveSegment)

Removes an element from the listOfCurveSegments.

Specified by:

removeCurveSegment in interface ICurve

Parameters:

curveSegment - the element to be removed from the list.

Returns:

true if the list contained the specified element and it was removed.

See Also:

List.remove(Object)

removeCurveSegment

public CurveSegment removeCurveSegment(int i)

Removes an element from the listOfCurveSegments at the given index.

Parameters:

i - the index where to remove the CurveSegment.

Returns:

the specified element if it was successfully found and removed.

Throws:

java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound ((i < 0) || (i > listOfCurveSegments)).

createLineSegment

public LineSegment createLineSegment()

Creates a new LineSegment instance and adds it to the listOfCurveSegments list.

Returns:

the newly created element, i.e., the last item in the listOfCurveSegments

createCubicBezier

public CubicBezier createCubicBezier()

Creates a new CubicBezier instance and adds it to the listOfCurveSegments list.

Specified by:

createCubicBezier in interface ICurve

Returns:

the newly created element, i.e., the last item in the listOfCurveSegments

getCurveSegment

public CurveSegment getCurveSegment(int i)

Gets an element from the listOfCurveSegments at the given index.

Specified by:

getCurveSegment in interface ICurve

Parameters:

i - the index of the CurveSegment element to get.

Returns:

an element from the listOfCurveSegments at the given index.

Throws:

java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).

getCurveSegmentCount

public int getCurveSegmentCount()

Returns the number of CurveSegments in this RenderCurve.

Specified by:

getCurveSegmentCount in interface ICurve

Returns:

the number of CurveSegments in this RenderCurve.

getNumCurveSegments

public int getNumCurveSegments()

Returns the number of CurveSegments in this RenderCurve.

Returns:

the number of CurveSegments in this RenderCurve.

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

same as getCurveSegmentCount()

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 GraphicalPrimitive1D

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 GraphicalPrimitive1D

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.

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

getChildAt

public SBase 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