Package 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:

ICurve

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

Modifier and Type	Field	Description
protected java.lang.String	endHead
protected org.sbml.jsbml.ListOf<CurveSegment>	listOfCurveSegments
protected org.sbml.jsbml.ListOf<RenderPoint>	listOfElements
protected java.lang.String	startHead

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

Fields inherited from class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

stroke, strokeDashArray, strokeWidth

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

transform

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	addCurveSegment(int index, CurveSegment element)
boolean	addCurveSegment(CurveSegment curveSegment)	Adds a new CurveSegment to the listOfCurveSegments.
boolean	addElement(RenderPoint element)
RenderCurve	clone()
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)
boolean	getAllowsChildren()
org.sbml.jsbml.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()
java.lang.String	getEndHead()	Returns the value of endHead
org.sbml.jsbml.ListOf<CurveSegment>	getListOfCurveSegments()	Returns the listOfCurveSegments.
org.sbml.jsbml.ListOf<RenderPoint>	getListOfElements()
int	getNumCurveSegments()	Returns the number of CurveSegments in this RenderCurve.
java.lang.String	getStartHead()	Returns the value of startHead
int	hashCode()
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)
CurveSegment	removeCurveSegment(int i)	Removes an element from the listOfCurveSegments at the given index.
boolean	removeCurveSegment(CurveSegment curveSegment)	Removes an element from the listOfCurveSegments.
void	removeElement(int i)
boolean	removeElement(RenderPoint element)
void	setEndHead(java.lang.String endHead)	Sets the value of endHead
void	setListOfCurveSegments(org.sbml.jsbml.ListOf<CurveSegment> listOfCurveSegments)	Sets the given ListOf<CurveSegment>.
void	setListOfElements(org.sbml.jsbml.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()

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, 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 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 java.lang.Object

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

Methods inherited from interface org.sbml.jsbml.SBase

removeTreeNodeChangeListener

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

isSetTransform, setTransform

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

getTransform, unsetTransform

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

Field Detail

startHead

protected java.lang.String startHead

endHead

protected java.lang.String endHead

listOfElements

protected org.sbml.jsbml.ListOf<RenderPoint> listOfElements

listOfCurveSegments

protected org.sbml.jsbml.ListOf<CurveSegment> listOfCurveSegments

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()

Overrides:

clone in class GraphicalPrimitive1D

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()

Overrides:

hashCode in class GraphicalPrimitive1D

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class GraphicalPrimitive1D

getElementName

public java.lang.String getElementName()

Overrides:

getElementName in class org.sbml.jsbml.AbstractSBase

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 org.sbml.jsbml.ListOf<RenderPoint> getListOfElements()

Returns:

the listOfElements

setListOfElements

public void setListOfElements(org.sbml.jsbml.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 org.sbml.jsbml.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(org.sbml.jsbml.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()

Overrides:

writeXMLAttributes in class GraphicalPrimitive1D

readAttribute

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

Overrides:

readAttribute in class GraphicalPrimitive1D

getAllowsChildren

public boolean getAllowsChildren()

Overrides:

getAllowsChildren in class org.sbml.jsbml.AbstractSBase

getChildAt

public org.sbml.jsbml.SBase getChildAt(int childIndex)

Overrides:

getChildAt in class org.sbml.jsbml.AbstractSBase

getChildCount

public int getChildCount()

Overrides:

getChildCount in class org.sbml.jsbml.AbstractSBase