org.pathvisio.model
Class PathwayElement

java.lang.Object
  org.pathvisio.model.PathwayElement

All Implemented Interfaces:

java.lang.Comparable<PathwayElement>, GraphLink.GraphIdContainer

Direct Known Subclasses:

MGroup, MLine, MState

public class PathwayElement
extends java.lang.Object
implements GraphLink.GraphIdContainer, java.lang.Comparable<PathwayElement>

PathwayElement is responsible for maintaining the data for all the individual objects that can appear on a pwy (Lines, GeneProducts, Shapes, etc.)

All PathwayElements have an ObjectType. This ObjectType is specified at creation time and can't be modified. To create a PathwayElement, use the createPathwayElement() function. This is a factory method that returns a different implementation class depending on the specified ObjectType.

PathwayElements have a number of properties which consist of a key, value pair.

There are two types of properties: Static and Dynamic Static properties are one of the properties

Dynamic properties can have any String as key. Their value is always of type String. Dynamic properties are not essential for the functioning of PathVisio and can be used to store arbitrary data. In GPML, dynamic properties are stored in an tag. Internally, dynamic properties are stored in a Map

Static properties must have a key from the StaticProperty enum Their value can be various types which can be obtained from StaticProperty.type(). Static properties can be queried with getStaticProperty (key) and setStaticProperty(key, value), but also specific accessors such as e.g. getTextLabel() and setTextLabel()

Internally, dynamic properties are stored in various fields of the PathwayElement Object. The static properties are a union of all possible fields (e.g it has both start and endpoints for lines, and label text for labels)

the setPropertyEx() and getPropertyEx() functions can be used to access both dynamic and static properties from the same function. If key instanceof String then it's assumed the caller wants a dynamic property, if key instanceof StaticProperty then the static property is used.

most static properties cannot be set to null. Notable exceptions are graphId, startGraphRef and endGraphRef.

Nested Class Summary

class	PathwayElement.Comment A comment in a pathway element: each element can have zero or more comments with it, and each comment has a source and a text.
class	PathwayElement.MAnchor This class represents the Line.Graphics.Anchor element in GPML
class	PathwayElement.MPoint This class represents the Line.Graphics.Point element in GPML.

Field Summary

protected AlignType	align
protected java.util.List<PathwayElement.MAnchor>	anchors
protected java.lang.String	author
protected org.jdom.Document	biopax
protected java.util.List<java.lang.String>	biopaxRefs
protected java.awt.Color	color
protected java.lang.String	copyright
protected java.lang.String	dataNodeType
protected org.bridgedb.DataSource	dataSource The pathway datasource
protected java.lang.String	email
protected LineType	endLineType
protected boolean	fBold
protected java.awt.Color	fillColor a fillcolor of null is equivalent to transparent.
protected boolean	fItalic
protected java.lang.String	fontName
protected boolean	fStrikethru
protected boolean	fUnderline
protected java.lang.String	graphId
protected java.lang.String	graphRef
protected java.lang.String	groupId
protected java.lang.String	groupRef
protected GroupStyle	groupStyle
protected java.lang.String	href
protected java.lang.String	lastModified
protected int	lineStyle
protected java.lang.String	maintainer
protected java.lang.String	mapInfoDataSource
protected java.lang.String	mapInfoName
protected double	mCenterx
protected double	mCentery
protected double	mFontSize
protected double	mHeight
protected double	mWidth
protected ObjectType	objectType
protected java.lang.String	organism
protected Pathway	parent Parent of this object: may be null (for example, when object is in clipboard)
protected double	rotation
protected java.lang.String	setGeneID
protected ShapeType	shapeType
protected LineType	startLineType
protected java.lang.String	textLabel
protected ValignType	valign
protected java.lang.String	version

Constructor Summary

protected

PathwayElement(ObjectType ot)

Method Summary

void	addBiopaxRef(java.lang.String ref)
void	addComment(PathwayElement.Comment comment)
void	addComment(java.lang.String comment, java.lang.String source)
void	addListener(PathwayElementListener v)
PathwayElement.MAnchor	addMAnchor(double position) Add a new anchor to this line at the given position.
int	compareTo(PathwayElement o)
PathwayElement	copy() Copy Object.
void	copyValuesFrom(PathwayElement src) Note: doesn't change parent, only fields Used by UndoAction.
java.lang.String	createGroupId()
static PathwayElement	createPathwayElement(ObjectType ot) Instantiate a pathway element.
java.lang.String	doGetGraphId()
void	dontFireEvents(int times)
java.lang.String	findComment(java.lang.String source) Finds the first comment with a specific source
void	fireObjectModifiedEvent(PathwayElementEvent e)
AlignType	getAlign()
java.lang.String	getAuthor()
org.jdom.Document	getBiopax()
BiopaxReferenceManager	getBiopaxReferenceManager()
java.util.List<java.lang.String>	getBiopaxRefs()
java.awt.Color	getColor()
java.util.List<PathwayElement.Comment>	getComments()
ConnectorType	getConnectorType()
java.lang.String	getCopyright()
java.lang.String	getDataNodeType()
org.bridgedb.DataSource	getDataSource()
java.lang.String	getDynamicProperty(java.lang.String key) get a dynamic property
java.util.Set<java.lang.String>	getDynamicPropertyKeys() get a set of all dynamic property keys
java.lang.String	getEmail()
java.lang.String	getEndGraphRef()
LineType	getEndLineType()
java.awt.Color	getFillColor()
java.lang.String	getFontName()
java.lang.String	getGeneID()
java.lang.String	getGraphId()
java.lang.String	getGraphRef() graphRef property, used by Modification
java.lang.String	getGroupId()
java.lang.String	getGroupRef()
GroupStyle	getGroupStyle()
java.lang.String	getHref()
java.lang.String	getLastModified()
int	getLineStyle()
double	getLineThickness()
java.lang.String	getMaintainer()
java.util.List<PathwayElement.MAnchor>	getMAnchors() Get the anchors for this line.
java.lang.String	getMapInfoDataSource()
java.lang.String	getMapInfoName()
double	getMBoardHeight()
double[]	getMBoardSize() Calculates the drawing size on basis of the location and size of the containing pathway elements
double	getMBoardWidth()
java.awt.geom.Rectangle2D	getMBounds() Get the rectangular bounds of the object without rotation taken into accound
double	getMCenterX()
double	getMCenterY()
PathwayElement.MPoint	getMEnd()
double	getMEndX()
double	getMEndY()
double	getMFontSize()
double	getMHeight()
double	getMLeft()
java.util.List<PathwayElement.MPoint>	getMPoints()
PathwayElement.MPoint	getMStart()
double	getMStartX()
double	getMStartY()
double	getMTop()
double	getMWidth()
ObjectType	getObjectType()
java.lang.String	getOrganism()
int	getOrientation()
Pathway	getParent()
Pathway	getPathway() Get the parent pathway.
java.lang.Object	getPropertyEx(java.lang.Object key)
java.util.Set<java.lang.Object>	getPropertyKeys() Returns keys of available static properties and dynamic properties as an object list
java.awt.geom.Rectangle2D	getRBounds() Get the rectangular bounds of the object after rotation is applied
java.util.Set<GraphLink.GraphRefContainer>	getReferences()
double	getRelX() relX property, used by State.
double	getRelY() relX property, used by State.
double	getRotation()
ShapeType	getShapeType()
java.lang.String	getStartGraphRef()
LineType	getStartLineType()
java.lang.Object	getStaticProperty(StaticProperty key)
java.util.Set<StaticProperty>	getStaticPropertyKeys() get all attributes that are stored as static members.
java.lang.String	getTextLabel()
ValignType	getValign()
java.lang.String	getVersion()
org.bridgedb.Xref	getXref() returns GeneID and datasource combined in an Xref.
int	getZOrder()
boolean	isBold()
boolean	isItalic()
boolean	isStrikethru()
boolean	isTransparent() checks if fill color is equal to null or the alpha value is equal to 0.
boolean	isUnderline()
void	printRefsDebugInfo()
void	removeBiopaxRef(java.lang.String ref)
void	removeComment(PathwayElement.Comment comment)
void	removeListener(PathwayElementListener v)
void	removeMAnchor(PathwayElement.MAnchor anchor) Remove the given anchor
void	setAlign(AlignType v)
void	setAuthor(java.lang.String v)
void	setBiopax(org.jdom.Document bp)
void	setBiopaxRefs(java.util.List<java.lang.String> refs)
void	setBold(boolean v)
void	setColor(java.awt.Color v)
void	setComments(java.util.List<PathwayElement.Comment> value)
void	setConnectorType(ConnectorType type)
void	setCopyright(java.lang.String v)
void	setDataNodeType(DataNodeType type)
void	setDataNodeType(java.lang.String v)
void	setDataSource(org.bridgedb.DataSource v)
void	setDynamicProperty(java.lang.String key, java.lang.String value) set a dynamic property.
void	setEmail(java.lang.String v)
void	setEndGraphRef(java.lang.String ref)
void	setEndLineType(LineType value)
void	setFillColor(java.awt.Color v)
void	setFontName(java.lang.String v)
void	setGeneID(java.lang.String v)
java.lang.String	setGeneratedGraphId() generate a unique graph Id and use that.
void	setGraphId(java.lang.String v) Set graphId.
void	setGraphRef(java.lang.String value) set graphRef property, used by State The new graphRef should exist and point to an existing DataNode
void	setGroupId(java.lang.String w) Set groupId.
void	setGroupRef(java.lang.String s)
void	setGroupStyle(GroupStyle gs)
void	setHref(java.lang.String v)
void	setInitialSize() This sets the object to a suitable default size.
void	setItalic(boolean v)
void	setLastModified(java.lang.String v)
void	setLineStyle(int value)
void	setLineThickness(double v)
void	setMaintainer(java.lang.String v)
void	setMapInfoDataSource(java.lang.String v)
void	setMapInfoName(java.lang.String v)
void	setMCenterX(double v)
void	setMCenterY(double v)
void	setMEnd(PathwayElement.MPoint p)
void	setMEndX(double v)
void	setMEndY(double v)
void	setMFontSize(double v)
void	setMHeight(double v)
void	setMLeft(double v)
void	setMPoints(java.util.List<PathwayElement.MPoint> points)
void	setMStart(PathwayElement.MPoint p)
void	setMStartX(double v)
void	setMStartY(double v)
void	setMTop(double v)
void	setMWidth(double v)
void	setOrganism(java.lang.String v)
void	setOrientation(int orientation)
void	setPropertyEx(java.lang.Object key, java.lang.Object value) Set dynamic or static properties at the same time Will be replaced with setProperty in the future.
void	setRelX(double value) See getRelX
void	setRelY(double value) See getRelX
void	setRotation(double v)
void	setShapeType(ShapeType v)
void	setStartGraphRef(java.lang.String ref)
void	setStartLineType(LineType value)
void	setStaticProperty(StaticProperty key, java.lang.Object value) This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g.
void	setStrikethru(boolean v)
void	setTextLabel(java.lang.String v)
void	setTransparent(boolean v) sets the alpha component of fillColor to 0 if true sets the alpha component of fillColor to 255 if true
void	setUnderline(boolean v)
void	setValign(ValignType v)
void	setVersion(java.lang.String v)
void	setZOrder(int z)
PathwayElement[]	splitLine()
java.awt.geom.Point2D	toAbsoluteCoordinate(java.awt.geom.Point2D p) Convert a point to pathway coordinates (relative to the pathway)
java.awt.geom.Point2D	toRelativeCoordinate(java.awt.geom.Point2D p) Convert a point to shape coordinates (relative to the bounds of the GraphIdContainer)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

parent

protected Pathway parent

Parent of this object: may be null (for example, when object is in clipboard)

objectType

protected ObjectType objectType

lineStyle

protected int lineStyle

endLineType

protected LineType endLineType

startLineType

protected LineType startLineType

anchors

protected java.util.List<PathwayElement.MAnchor> anchors

color

protected java.awt.Color color

fillColor

protected java.awt.Color fillColor

a fillcolor of null is equivalent to transparent.

setGeneID

protected java.lang.String setGeneID

dataNodeType

protected java.lang.String dataNodeType

dataSource

protected org.bridgedb.DataSource dataSource

The pathway datasource

mCenterx

protected double mCenterx

mCentery

protected double mCentery

mWidth

protected double mWidth

mHeight

protected double mHeight

shapeType

protected ShapeType shapeType

rotation

protected double rotation

fBold

protected boolean fBold

fStrikethru

protected boolean fStrikethru

fUnderline

protected boolean fUnderline

fItalic

protected boolean fItalic

fontName

protected java.lang.String fontName

textLabel

protected java.lang.String textLabel

href

protected java.lang.String href

mFontSize

protected double mFontSize

mapInfoName

protected java.lang.String mapInfoName

organism

protected java.lang.String organism

mapInfoDataSource

protected java.lang.String mapInfoDataSource

valign

protected ValignType valign

align

protected AlignType align

version

protected java.lang.String version

author

protected java.lang.String author

maintainer

protected java.lang.String maintainer

email

protected java.lang.String email

copyright

protected java.lang.String copyright

lastModified

protected java.lang.String lastModified

groupId

protected java.lang.String groupId

graphId

protected java.lang.String graphId

groupRef

protected java.lang.String groupRef

groupStyle

protected GroupStyle groupStyle

graphRef

protected java.lang.String graphRef

biopax

protected org.jdom.Document biopax

biopaxRefs

protected java.util.List<java.lang.String> biopaxRefs

Constructor Detail

PathwayElement

protected PathwayElement(ObjectType ot)

Method Detail

getDynamicPropertyKeys

public java.util.Set<java.lang.String> getDynamicPropertyKeys()

get a set of all dynamic property keys

setDynamicProperty

public void setDynamicProperty(java.lang.String key,
                               java.lang.String value)

set a dynamic property. Setting to null means removing this dynamic property altogether

getDynamicProperty

public java.lang.String getDynamicProperty(java.lang.String key)

get a dynamic property

createPathwayElement

public static PathwayElement createPathwayElement(ObjectType ot)

Instantiate a pathway element. The required parameter objectType ensures only objects with a valid type can be created.

Parameters:

ot - Type of object, one of the ObjectType.* fields

getZOrder

public int getZOrder()

setZOrder

public void setZOrder(int z)

getParent

public Pathway getParent()

getPathway

public Pathway getPathway()

Get the parent pathway. Same as getParent(), but necessary to comply to the GraphLink.GraphIdContainer interface.

Specified by:

getPathway in interface GraphLink.GraphIdContainer

getPropertyKeys

public java.util.Set<java.lang.Object> getPropertyKeys()

Returns keys of available static properties and dynamic properties as an object list

getStaticPropertyKeys

public java.util.Set<StaticProperty> getStaticPropertyKeys()

get all attributes that are stored as static members.

setPropertyEx

public void setPropertyEx(java.lang.Object key,
                          java.lang.Object value)

Set dynamic or static properties at the same time Will be replaced with setProperty in the future.

getPropertyEx

public java.lang.Object getPropertyEx(java.lang.Object key)

setStaticProperty

public void setStaticProperty(StaticProperty key,
                              java.lang.Object value)

This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g. graphRef

Parameters:

key -

value -

getStaticProperty

public java.lang.Object getStaticProperty(StaticProperty key)

copyValuesFrom

public void copyValuesFrom(PathwayElement src)

Note: doesn't change parent, only fields Used by UndoAction.

Parameters:

src -

copy

public PathwayElement copy()

Copy Object. The object will not be part of the same Pathway object, it's parent will be set to null. No events will be sent to the parent of the original.

getObjectType

public ObjectType getObjectType()

setMPoints

public void setMPoints(java.util.List<PathwayElement.MPoint> points)

getMStart

public PathwayElement.MPoint getMStart()

setMStart

public void setMStart(PathwayElement.MPoint p)

getMEnd

public PathwayElement.MPoint getMEnd()

setMEnd

public void setMEnd(PathwayElement.MPoint p)

getMPoints

public java.util.List<PathwayElement.MPoint> getMPoints()

getMStartX

public double getMStartX()

setMStartX

public void setMStartX(double v)

getMStartY

public double getMStartY()

setMStartY

public void setMStartY(double v)

getMEndX

public double getMEndX()

setMEndX

public void setMEndX(double v)

getMEndY

public double getMEndY()

setMEndY

public void setMEndY(double v)

getLineStyle

public int getLineStyle()

setLineStyle

public void setLineStyle(int value)

getStartLineType

public LineType getStartLineType()

getEndLineType

public LineType getEndLineType()

setStartLineType

public void setStartLineType(LineType value)

setEndLineType

public void setEndLineType(LineType value)

setConnectorType

public void setConnectorType(ConnectorType type)

getConnectorType

public ConnectorType getConnectorType()

getMAnchors

public java.util.List<PathwayElement.MAnchor> getMAnchors()

Get the anchors for this line.

Returns:

A list with the anchors, or an empty list, if no anchors are defined

addMAnchor

public PathwayElement.MAnchor addMAnchor(double position)

Add a new anchor to this line at the given position.

Parameters:

position - The relative position on the line, between 0 (start) to 1 (end).

removeMAnchor

public void removeMAnchor(PathwayElement.MAnchor anchor)

Remove the given anchor

getColor

public java.awt.Color getColor()

setColor

public void setColor(java.awt.Color v)

getFillColor

public java.awt.Color getFillColor()

setFillColor

public void setFillColor(java.awt.Color v)

isTransparent

public boolean isTransparent()

checks if fill color is equal to null or the alpha value is equal to 0.

setTransparent

public void setTransparent(boolean v)

sets the alpha component of fillColor to 0 if true sets the alpha component of fillColor to 255 if true

getComments

public java.util.List<PathwayElement.Comment> getComments()

setComments

public void setComments(java.util.List<PathwayElement.Comment> value)

addComment

public void addComment(java.lang.String comment,
                       java.lang.String source)

addComment

public void addComment(PathwayElement.Comment comment)

removeComment

public void removeComment(PathwayElement.Comment comment)

findComment

public java.lang.String findComment(java.lang.String source)

Finds the first comment with a specific source

getGeneID

public java.lang.String getGeneID()

setGeneID

public void setGeneID(java.lang.String v)

getDataNodeType

public java.lang.String getDataNodeType()

setDataNodeType

public void setDataNodeType(DataNodeType type)

setDataNodeType

public void setDataNodeType(java.lang.String v)

getDataSource

public org.bridgedb.DataSource getDataSource()

setDataSource

public void setDataSource(org.bridgedb.DataSource v)

getXref

public org.bridgedb.Xref getXref()

returns GeneID and datasource combined in an Xref. Only meaningful for datanodes. Same as new Xref ( pathwayElement.getGeneID(), pathwayElement.getDataSource() );

getMCenterX

public double getMCenterX()

setMCenterX

public void setMCenterX(double v)

getMCenterY

public double getMCenterY()

setMCenterY

public void setMCenterY(double v)

getMWidth

public double getMWidth()

setMWidth

public void setMWidth(double v)

getMHeight

public double getMHeight()

setMHeight

public void setMHeight(double v)

getMTop

public double getMTop()

setMTop

public void setMTop(double v)

getMLeft

public double getMLeft()

setMLeft

public void setMLeft(double v)

getShapeType

public ShapeType getShapeType()

setShapeType

public void setShapeType(ShapeType v)

setOrientation

public void setOrientation(int orientation)

getOrientation

public int getOrientation()

getRotation

public double getRotation()

setRotation

public void setRotation(double v)

getRBounds

public java.awt.geom.Rectangle2D getRBounds()

Get the rectangular bounds of the object after rotation is applied

getMBounds

public java.awt.geom.Rectangle2D getMBounds()

Get the rectangular bounds of the object without rotation taken into accound

isBold

public boolean isBold()

setBold

public void setBold(boolean v)

isStrikethru

public boolean isStrikethru()

setStrikethru

public void setStrikethru(boolean v)

isUnderline

public boolean isUnderline()

setUnderline

public void setUnderline(boolean v)

isItalic

public boolean isItalic()

setItalic

public void setItalic(boolean v)

getFontName

public java.lang.String getFontName()

setFontName

public void setFontName(java.lang.String v)

getTextLabel

public java.lang.String getTextLabel()

setTextLabel

public void setTextLabel(java.lang.String v)

getHref

public java.lang.String getHref()

setHref

public void setHref(java.lang.String v)

getLineThickness

public double getLineThickness()

setLineThickness

public void setLineThickness(double v)

getMFontSize

public double getMFontSize()

setMFontSize

public void setMFontSize(double v)

getMapInfoName

public java.lang.String getMapInfoName()

setMapInfoName

public void setMapInfoName(java.lang.String v)

getOrganism

public java.lang.String getOrganism()

setOrganism

public void setOrganism(java.lang.String v)

getMapInfoDataSource

public java.lang.String getMapInfoDataSource()

setMapInfoDataSource

public void setMapInfoDataSource(java.lang.String v)

setValign

public void setValign(ValignType v)

getValign

public ValignType getValign()

setAlign

public void setAlign(AlignType v)

getAlign

public AlignType getAlign()

getVersion

public java.lang.String getVersion()

setVersion

public void setVersion(java.lang.String v)

getAuthor

public java.lang.String getAuthor()

setAuthor

public void setAuthor(java.lang.String v)

getMaintainer

public java.lang.String getMaintainer()

setMaintainer

public void setMaintainer(java.lang.String v)

getEmail

public java.lang.String getEmail()

setEmail

public void setEmail(java.lang.String v)

getCopyright

public java.lang.String getCopyright()

setCopyright

public void setCopyright(java.lang.String v)

getLastModified

public java.lang.String getLastModified()

setLastModified

public void setLastModified(java.lang.String v)

getMBoardSize

public double[] getMBoardSize()

Calculates the drawing size on basis of the location and size of the containing pathway elements

Returns:

The drawing size

getMBoardWidth

public double getMBoardWidth()

getMBoardHeight

public double getMBoardHeight()

doGetGraphId

public java.lang.String doGetGraphId()

getGroupRef

public java.lang.String getGroupRef()

setGroupRef

public void setGroupRef(java.lang.String s)

getGroupId

public java.lang.String getGroupId()

createGroupId

public java.lang.String createGroupId()

setGroupStyle

public void setGroupStyle(GroupStyle gs)

getGroupStyle

public GroupStyle getGroupStyle()

setGroupId

public void setGroupId(java.lang.String w)

Set groupId. This id must be any string unique within the Pathway object

See Also:

Pathway.getUniqueId(java.util.Set)

getGraphRef

public java.lang.String getGraphRef()

graphRef property, used by Modification

setGraphRef

public void setGraphRef(java.lang.String value)

set graphRef property, used by State The new graphRef should exist and point to an existing DataNode

getRelX

public double getRelX()

relX property, used by State. Should normally be between -1.0 and 1.0, where 1.0 corresponds to the edge of the parent object

setRelX

public void setRelX(double value)

See getRelX

getRelY

public double getRelY()

relX property, used by State. Should normally be between -1.0 and 1.0, where 1.0 corresponds to the edge of the parent object

setRelY

public void setRelY(double value)

See getRelX

getGraphId

public java.lang.String getGraphId()

Specified by:

getGraphId in interface GraphLink.GraphIdContainer

setGraphId

public void setGraphId(java.lang.String v)

Set graphId. This id must be any string unique within the Pathway object

Specified by:

setGraphId in interface GraphLink.GraphIdContainer

See Also:

Pathway.getUniqueId(java.util.Set)

setGeneratedGraphId

public java.lang.String setGeneratedGraphId()

Description copied from interface: GraphLink.GraphIdContainer

generate a unique graph Id and use that.

Specified by:

setGeneratedGraphId in interface GraphLink.GraphIdContainer

getStartGraphRef

public java.lang.String getStartGraphRef()

setStartGraphRef

public void setStartGraphRef(java.lang.String ref)

getEndGraphRef

public java.lang.String getEndGraphRef()

setEndGraphRef

public void setEndGraphRef(java.lang.String ref)

getBiopax

public org.jdom.Document getBiopax()

getBiopaxReferenceManager

public BiopaxReferenceManager getBiopaxReferenceManager()

setBiopax

public void setBiopax(org.jdom.Document bp)

getBiopaxRefs

public java.util.List<java.lang.String> getBiopaxRefs()

setBiopaxRefs

public void setBiopaxRefs(java.util.List<java.lang.String> refs)

addBiopaxRef

public void addBiopaxRef(java.lang.String ref)

removeBiopaxRef

public void removeBiopaxRef(java.lang.String ref)

splitLine

public PathwayElement[] splitLine()

dontFireEvents

public void dontFireEvents(int times)

addListener

public void addListener(PathwayElementListener v)

removeListener

public void removeListener(PathwayElementListener v)

fireObjectModifiedEvent

public void fireObjectModifiedEvent(PathwayElementEvent e)

setInitialSize

public void setInitialSize()

This sets the object to a suitable default size. This method is intended to be called right after the object is placed on the drawing with a click.

getReferences

public java.util.Set<GraphLink.GraphRefContainer> getReferences()

Specified by:

getReferences in interface GraphLink.GraphIdContainer

compareTo

public int compareTo(PathwayElement o)

Specified by:

compareTo in interface java.lang.Comparable<PathwayElement>

toAbsoluteCoordinate

public java.awt.geom.Point2D toAbsoluteCoordinate(java.awt.geom.Point2D p)

Description copied from interface: GraphLink.GraphIdContainer

Convert a point to pathway coordinates (relative to the pathway)

Specified by:

toAbsoluteCoordinate in interface GraphLink.GraphIdContainer

toRelativeCoordinate

public java.awt.geom.Point2D toRelativeCoordinate(java.awt.geom.Point2D p)

Description copied from interface: GraphLink.GraphIdContainer

Convert a point to shape coordinates (relative to the bounds of the GraphIdContainer)

Specified by:

toRelativeCoordinate in interface GraphLink.GraphIdContainer

printRefsDebugInfo

public void printRefsDebugInfo()