Package org.pathvisio.libgpml.model

Class DataNode.State

java.lang.Object

org.pathvisio.libgpml.model.PathwayObject

org.pathvisio.libgpml.model.PathwayElement

org.pathvisio.libgpml.model.ShapedElement

org.pathvisio.libgpml.model.DataNode.State

All Implemented Interfaces:

java.lang.Cloneable, Drawable, GraphLink.LinkableTo, Groupable, Referenceable, Referenceable.Annotatable, Referenceable.Citable, Referenceable.Evidenceable, Xrefable

Enclosing class:

DataNode

public class DataNode.State
extends ShapedElement
implements Xrefable

This class stores all information relevant to a State pathway element.

Author:

finterly

Nested Class Summary

Nested classes/interfaces inherited from class org.pathvisio.libgpml.model.PathwayElement

PathwayElement.AnnotationRef, PathwayElement.CitationRef, PathwayElement.Comment, PathwayElement.EvidenceRef, PathwayElement.InfoRef

Nested classes/interfaces inherited from interface org.pathvisio.libgpml.model.Referenceable

Referenceable.Annotatable, Referenceable.Citable, Referenceable.Evidenceable

Field Summary

Fields

Modifier and Type	Field	Description
private double	relX
private double	relY
private java.lang.String	textLabel
private StateType	type
private org.bridgedb.Xref	xref

Fields inherited from class org.pathvisio.libgpml.model.PathwayObject

noFire, pathwayModel

Constructor Summary

Constructors

Modifier	Constructor	Description
private	State(java.lang.String textLabel, StateType type, double relX, double relY)	Instantiates a State pathway element given all possible parameters except xref.
private	State(java.lang.String textLabel, StateType type, double relX, double relY, org.bridgedb.Xref xref)	Instantiates a State pathway element given all possible parameters.

Method Summary

Modifier and Type	Method	Description
void	coordinatesChanged()	Updates coordinates, called by PathwayModel.childModified(org.pathvisio.libgpml.model.PathwayObjectEvent)
CopyElement	copy()	Copies this pathway element.
void	copyValuesFrom(DataNode.State src)	Copies values from the given source pathway element.
DataNode	getDataNode()	Returns the parent data node, outer class, to which the state belongs.
Group	getGroupRef()	Returns the parent group of the dataNode of this state.
ObjectType	getObjectType()	Returns the object type of this pathway element.
double	getRelX()	Returns the relative x coordinate.
double	getRelY()	Returns the relative y coordinate.
java.lang.Object	getStaticProperty(StaticProperty key)	Returns static property value for given key.
java.util.Set<StaticProperty>	getStaticPropertyKeys()	Returns all static properties for this pathway object.
java.lang.String	getTextLabel()	Returns the text of of this state.
StateType	getType()	Returns the type of this state.
org.bridgedb.Xref	getXref()	Returns the Xref for this state.
int	getZOrder()	Returns the z-order of this pathway element.
void	setGroupRefTo(Group v)	Do not allow groupRef to be set for this state.
protected void	setPathwayModelTo(PathwayModel pathwayModel)	Sets the pathway model for this pathway element.
void	setRelX(double v)	Sets the relative x coordinate.
void	setRelY(double v)	Sets the relative y coordinate.
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	setTextLabel(java.lang.String v)	Sets the text of of this shaped pathway element.
void	setType(StateType v)	Sets the type of this state.
void	setXref(org.bridgedb.Xref v)	Sets the Xref for this state.
void	setZOrder(int v)	Do nothing.
protected void	terminate()	Terminates this state and removes all links and references.
private void	updateCoordinates()	Updates coordinates.

Methods inherited from class org.pathvisio.libgpml.model.ShapedElement

copyValuesFrom, getBorderColor, getBorderStyle, getBorderWidth, getBounds, getCenterX, getCenterY, getFillColor, getFontDecoration, getFontName, getFontSize, getFontStrikethru, getFontStyle, getFontWeight, getHAlign, getHeight, getLeft, getLinkableFroms, getRotatedBounds, getRotation, getShapeType, getTextColor, getTop, getVAlign, getWidth, hasGroupRef, setBorderColor, setBorderStyle, setBorderWidth, setCenterX, setCenterY, setFillColor, setFontDecoration, setFontName, setFontSize, setFontStrikethru, setFontStyle, setFontWeight, setHAlign, setHeight, setLeft, setRotation, setShapeType, setTextColor, setTop, setVAlign, setWidth, toAbsoluteCoordinate, toRelativeCoordinate, unsetAllLinkableFroms, unsetGroupRef

Methods inherited from class org.pathvisio.libgpml.model.PathwayElement

addAnnotation, addAnnotation, addAnnotation, addCitation, addCitation, addCitation, addComment, addComment, addEvidence, addEvidence, addEvidence, copyReferencesFrom, copyValuesFrom, findComment, getAnnotationRefs, getCitationRefs, getComments, getDynamicProperties, getDynamicProperty, getDynamicPropertyKeys, getEvidenceRefs, getPropertyEx, getPropertyKeys, hasAnnotationRef, hasCitationRef, hasEvidenceRef, removeAnnotationRef, removeAnnotationRefs, removeCitationRef, removeCitationRefs, removeComment, removeEvidenceRef, removeEvidenceRefs, setComments, setDynamicProperty, setPropertyEx

Methods inherited from class org.pathvisio.libgpml.model.PathwayObject

addListener, dontFireEvents, fireObjectModifiedEvent, getElementId, getListeners, getPathwayModel, hasPathwayModel, removeListener, setElementId, setGeneratedElementId, setPathwayModel, unsetPathwayModel

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.pathvisio.libgpml.model.Drawable

getPathwayModel

Methods inherited from interface org.pathvisio.libgpml.model.GraphLink.LinkableTo

getElementId

Field Details

textLabel

private java.lang.String textLabel

type

private StateType type

relX

private double relX

relY

private double relY

xref

private org.bridgedb.Xref xref

Constructor Details

State

private State(java.lang.String textLabel,
StateType type,
double relX,
double relY,
org.bridgedb.Xref xref)

Instantiates a State pathway element given all possible parameters.

Parameters:

textLabel - the text label of the state.

type - the type of the state, e.g. protein modification.

relX - the relative x coordinates on the parent object, where 0,0 is at the center of the object and 1,1 at the bottom-right corner of the object.

relY - the relative y coordinates on the parent object, where 0,0 is at the center of the object and 1,1 at the bottom-right corner of the object.

xref - the state xref.

State

private State(java.lang.String textLabel,
StateType type,
double relX,
double relY)

Instantiates a State pathway element given all possible parameters except xref.

Method Details

getObjectType

public ObjectType getObjectType()

Returns the object type of this pathway element.

Specified by:

getObjectType in interface Drawable

Specified by:

getObjectType in interface GraphLink.LinkableTo

Specified by:

getObjectType in class PathwayObject

Returns:

the object type.

getDataNode

public DataNode getDataNode()

Returns the parent data node, outer class, to which the state belongs.

NB:

1. Returns the parent data node even if this state has been removed from the data node states list.
2. In GPML2013a, elementRef was used to refer to the elementId of parent data node, thus linking state to parent data node.

Returns:

dataNode the parent data node of the state.

getTextLabel

public java.lang.String getTextLabel()

Returns the text of of this state.

Specified by:

getTextLabel in class ShapedElement

Returns:

textLabel the text of of this state.

setTextLabel

public void setTextLabel(java.lang.String v)

Sets the text of of this shaped pathway element.

Specified by:

setTextLabel in class ShapedElement

Parameters:

v - the text to set for this shaped pathway element.

getType

public StateType getType()

Returns the type of this state.

Returns:

type the type of this state, e.g. complex.

setType

public void setType(StateType v)

Sets the type of this state.

Parameters:

v - the type of this state, e.g. complex.

getRelX

public double getRelX()

Returns the relative x coordinate. When the given state is linked to a data node, relX and relY are the relative coordinates on the data node, where 0,0 is at the center of the data node and 1,1 at the bottom right corner of the data node.

Returns:

relX the relative x coordinate.

setRelX

public void setRelX(double v)

Sets the relative x coordinate. When the given state is linked to a data node, relX and relY are the relative coordinates on the data node, where 0,0 is at the center of the data node and 1,1 at the bottom right corner of the data node.

Parameters:

v - the relative x coordinate.

Throws:

java.lang.IllegalArgumentException - if relX is not between -1.0 and 1.0. t

getRelY

public double getRelY()

Returns the relative y coordinate. When the given state is linked to a data node, relX and relY are the relative coordinates on the data node, where 0,0 is at the center of the data node and 1,1 at the bottom right corner of the data node.

Returns:

relY the relative y coordinate.

setRelY

public void setRelY(double v)

Sets the relative y coordinate. When the given state is linked to a data node, relX and relY are the relative coordinates on the data node, where 0,0 is at the center of the data node and 1,1 at the bottom right corner of the data node.

Parameters:

v - the relative y coordinate.

getXref

public org.bridgedb.Xref getXref()

Returns the Xref for this state.

Specified by:

getXref in interface Xrefable

Returns:

xref the xref of this state.

setXref

public void setXref(org.bridgedb.Xref v)

Sets the Xref for this state.

Specified by:

setXref in interface Xrefable

Parameters:

v - the xref of this state.

updateCoordinates

private void updateCoordinates()

Updates coordinates.

coordinatesChanged

public void coordinatesChanged()

Updates coordinates, called by PathwayModel.childModified(org.pathvisio.libgpml.model.PathwayObjectEvent)

getZOrder

public int getZOrder()

Returns the z-order of this pathway element. NB: State z-order is always z-order of parent data node +1. This is because z-order is not written out to the gpml file.

Specified by:

getZOrder in interface Drawable

Overrides:

getZOrder in class ShapedElement

Returns:

zOrder the order of this pathway element.

setZOrder

public void setZOrder(int v)

Do nothing. State z-order is always z-order of parent data node +1. This is because z-order is not written out to the gpml file.

Specified by:

setZOrder in interface Drawable

Overrides:

setZOrder in class ShapedElement

Parameters:

v - the input

getGroupRef

public Group getGroupRef()

Returns the parent group of the dataNode of this state. NB: A state should always belong to the same group as its parent data node.

Specified by:

getGroupRef in interface Groupable

Overrides:

getGroupRef in class ShapedElement

Returns:

the parent group of this state and its parent dataNode.

setGroupRefTo

public void setGroupRefTo(Group v)

Do not allow groupRef to be set for this state. A state will always belong to the same group as its parent data node.

Specified by:

setGroupRefTo in interface Groupable

Overrides:

setGroupRefTo in class ShapedElement

Parameters:

v - the group.

setPathwayModelTo

protected void setPathwayModelTo(PathwayModel pathwayModel)
                          throws java.lang.IllegalArgumentException,
java.lang.IllegalStateException

Sets the pathway model for this pathway element. NB: This method is not used directly. It is called by PathwayModel.addPathwayObject(org.pathvisio.libgpml.model.PathwayObject).

Overrides:

setPathwayModelTo in class PathwayObject

Parameters:

pathwayModel - the parent pathway model.

Throws:

java.lang.IllegalArgumentException

java.lang.IllegalStateException

terminate

protected void terminate()

Terminates this state and removes all links and references.

Overrides:

terminate in class ShapedElement

copyValuesFrom

public void copyValuesFrom(DataNode.State src)

Copies values from the given source pathway element.

Parameters:

src - the source pathway element.

copy

public CopyElement copy()

Copies this pathway element. NB: this method is never actually used.

Specified by:

copy in class PathwayElement

Returns:

the copyElement for the new pathway element and this source pathway element.

getStaticPropertyKeys

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

Returns all static properties for this pathway object.

Overrides:

getStaticPropertyKeys in class ShapedElement

Returns:

result the set of static property for this pathway object.

getStaticProperty

public java.lang.Object getStaticProperty(StaticProperty key)

Returns static property value for given key.

Overrides:

getStaticProperty in class ShapedElement

Parameters:

key - the key.

Returns:

the static property value.

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

Overrides:

setStaticProperty in class ShapedElement

Parameters:

key - the key.

value - the static property value.