Package org.pathvisio.libgpml.model

Class DataNode

java.lang.Object

org.pathvisio.libgpml.model.PathwayObject

org.pathvisio.libgpml.model.PathwayElement

org.pathvisio.libgpml.model.ShapedElement

org.pathvisio.libgpml.model.DataNode

All Implemented Interfaces:

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

public class DataNode
extends ShapedElement
implements Xrefable

This class stores information for a DataNode pathway element.

Author:

finterly

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	DataNode.State	This class stores all information relevant to a State pathway element.

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 Group	aliasRef
private java.util.List<DataNode.State>	states
private java.lang.String	textLabel
private DataNodeType	type
private org.bridgedb.Xref	xref

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

noFire, pathwayModel

Constructor Summary

Constructors

Constructor	Description
DataNode(java.lang.String textLabel, DataNodeType type)	Instantiates a DataNode given all required parameters.
DataNode(java.lang.String textLabel, DataNodeType type, org.bridgedb.Xref xref, Group aliasRef)	Instantiates a DataNode given all possible parameters.

Method Summary

Modifier and Type	Method	Description
DataNode.State	addState(java.lang.String elementId, java.lang.String textLabel, StateType type, double relX, double relY)	Instantiates a state with the given properties including elementId.
DataNode.State	addState(java.lang.String textLabel, StateType type, double relX, double relY)	Instantiates a state with the given properties.
void	addState(DataNode.State state)	Adds given state to states list.
CopyElement	copy()	Copies this pathway element.
void	copyReferencesFrom(PathwayElement srcDataNode)	Copies references from the given source data node, including state references.
void	copyValuesFrom(DataNode src)	Copies values from the given source pathway element.
Group	getAliasRef()	Returns the pathway element to which the data node refers to as an alias.
ObjectType	getObjectType()	Returns the object type of this pathway element.
java.util.List<DataNode.State>	getStates()
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 this datanode.
DataNodeType	getType()	Returns the type of this datanode.
org.bridgedb.Xref	getXref()	Returns the Xref for this datanode.
boolean	hasState(DataNode.State state)	Checks whether states has the given state.
void	removeState(DataNode.State state)	Removes given state from states list.
private void	removeStates()	Removes all states from states list.
void	setAliasRef(Group v)	Sets the group aliasRef to which this data node refers to as an alias.
protected void	setPathwayModelTo(PathwayModel pathwayModel)	Sets the pathway model for this pathway element.
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 this shaped pathway element.
void	setType(DataNodeType v)	Sets the type of this datanode, e.g.
void	setXref(org.bridgedb.Xref v)	Sets the Xref for this datanode.
protected void	terminate()	Terminates this data node and removes all links and references.
void	unsetAliasRef()	Unsets the aliasRef, if any, from this data node.

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

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

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

addAnnotation, addAnnotation, addAnnotation, addCitation, addCitation, addCitation, addComment, addComment, addEvidence, addEvidence, addEvidence, 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 DataNodeType type

states

private java.util.List<DataNode.State> states

xref

private org.bridgedb.Xref xref

aliasRef

private Group aliasRef

Constructor Details

DataNode

public DataNode(java.lang.String textLabel,
DataNodeType type,
org.bridgedb.Xref xref,
Group aliasRef)

Instantiates a DataNode given all possible parameters. A DataNode of type Alias can have an aliasRef which refers to a Group and/or have a textLabel which points to a group somewhere.

Parameters:

textLabel - the text or link of this datanode.

type - the type of datanode, e.g. complex.

xref - the data node Xref.

aliasRef - the group this data node alias refers to.

DataNode

public DataNode(java.lang.String textLabel,
DataNodeType type)

Instantiates a DataNode given all required parameters.

Parameters:

textLabel - the datanode text label.

type - the datanode type.

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.

getTextLabel

public java.lang.String getTextLabel()

Returns the text of this datanode.

Specified by:

getTextLabel in class ShapedElement

Returns:

textLabel the text of this datanode.

setTextLabel

public void setTextLabel(java.lang.String v)

Sets the text of this shaped pathway element.

Specified by:

setTextLabel in class ShapedElement

Parameters:

v - the text to set.

getType

public DataNodeType getType()

Returns the type of this datanode.

Returns:

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

setType

public void setType(DataNodeType v)

Sets the type of this datanode, e.g. complex. NB: Cannot change type if this is an alias data node.

Parameters:

v - the type to set for this datanode.

getXref

public org.bridgedb.Xref getXref()

Returns the Xref for this datanode.

Specified by:

getXref in interface Xrefable

Returns:

xref the xref of this datanode.

setXref

public void setXref(org.bridgedb.Xref v)

Sets the Xref for this datanode.

Specified by:

setXref in interface Xrefable

Parameters:

v - the xref to set for this datanode.

getStates

public java.util.List<DataNode.State> getStates()

hasState

public boolean hasState(DataNode.State state)

Checks whether states has the given state.

Parameters:

state - the state to look for.

Returns:

true if has state, false otherwise.

addState

public void addState(DataNode.State state)

Adds given state to states list. Sets datanode for the given state.

Parameters:

state - the state to be added.

addState

public DataNode.State addState(java.lang.String textLabel,
StateType type,
double relX,
double relY)

Instantiates a state with the given properties. Adds new state to states list and pathway model.

Parameters:

textLabel - the text label of the state.

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

relX - the relative x coordinates.

relY - the relative y coordinates.

Returns:

state the instantiated state.

addState

public DataNode.State addState(java.lang.String elementId,
java.lang.String textLabel,
StateType type,
double relX,
double relY)

Instantiates a state with the given properties including elementId. Adds new state to states list and pathway model.

Parameters:

elementId - the elementId to set for the instantiated state.

textLabel - the text label of the state.

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

relX - the relative x coordinates.

relY - the relative y coordinates.

Returns:

state the instantiated state.

removeState

public void removeState(DataNode.State state)

Removes given state from states list. State ceases to exist and is terminated.

Parameters:

state - the state to be removed.

removeStates

private void removeStates()

Removes all states from states list.

getAliasRef

public Group getAliasRef()

Returns the pathway element to which the data node refers to as an alias. In GPML, this is aliasRef which refers to the elementId of a pathway element (normally gpml:Group).

Returns:

aliasRef the pathway element to which the data node refers.

setAliasRef

public void setAliasRef(Group v)

Sets the group aliasRef to which this data node refers to as an alias. In GPML, this is aliasRef which refers to the elementId of gpml:Group.

NB:

1. This method calls unsetAliasRef() to remove any existing links.
2. This method calls PathwayModel.linkAlias(org.pathvisio.libgpml.model.Group, org.pathvisio.libgpml.model.DataNode) to add information to pathway model.
3. DataNode type must be "Alias".

Parameters:

v - the group to which this data node refers.

unsetAliasRef

public void unsetAliasRef()

Unsets the aliasRef, if any, from this data node. Also removes references in pathway model.

1. This method calls unsetAliasRef() to remove any existing links.
2. This method calls PathwayModel.unlinkAlias(org.pathvisio.libgpml.model.Group, org.pathvisio.libgpml.model.DataNode) to remove information in the pathway model.
3. This method is also called when this data node alias is terminate().

copyValuesFrom

public void copyValuesFrom(DataNode src)

Copies values from the given source pathway element.

NB:

1. AliasRef value is not copied. References to other PathwayObjects are stored in CopyElement by copy().

Parameters:

src - the source pathway element.

copy

public CopyElement copy()

Copies this pathway element.

Specified by:

copy in class PathwayElement

Returns:

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

copyReferencesFrom

public void copyReferencesFrom(PathwayElement srcDataNode)

Copies references from the given source data node, including state references.

NB:

1. For each state, copies references from the corresponding source state.
2. To be called after new data node is added to a pathway model.
3. The source data node may be the immediate copy element source of the new data node, or an older source data node.

Overrides:

copyReferencesFrom in class PathwayElement

Parameters:

srcDataNode - the source element to copy references from.

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.

setPathwayModelTo

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

Sets the pathway model for this pathway element. NB: Only set when a pathway model adds this pathway element. This method is not used directly. 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 data node and removes all links and references.

Overrides:

terminate in class ShapedElement