org.biopax.paxtools.io.sif

Class SimpleInteraction

java.lang.Object

org.biopax.paxtools.io.sif.SimpleInteraction

public class SimpleInteraction
extends Object

This class implements a directed binary interaction between two entities. Most bioinformatics software and algorithms consumes such interactions. User: demir Date: Dec 28, 2007 Time: 3:33:45 PM

Constructor Summary

Constructors

Constructor and Description
SimpleInteraction(BioPAXElement source, BioPAXElement target, BinaryInteractionType type) Constructor with parameters, without mediators.
SimpleInteraction(BioPAXElement source, BioPAXElement target, BinaryInteractionType type, BioPAXElement... mediator) Constructor with parameters, with mediators.
SimpleInteraction(BioPAXElement source, BioPAXElement target, BinaryInteractionType type, Collection<BioPAXElement> mediator) Constructor with parameters, with mediators.

Method Summary

Modifier and Type	Method and Description
void	addMediator(BioPAXElement element) Adds a mediator to the interaction.
boolean	equals(Object o) This method checks for source, target and type equality.
String	getANameForSIF(BioPAXElement element) This method is used when we want to use readable names in the simple SIF format instead of IDs.
Set<BioPAXElement>	getMediators() Gets other related elements of the interaction.
String	getRelatedEntrezGeneID(XReferrable obj) Searches for the Entrez Gene ID in the references.
BioPAXElement	getSource() Gets source element.
BioPAXElement	getTarget() Gets target element.
BinaryInteractionType	getType() Gets the type of the interaction.
int	hashCode() This method returns a hashcode based on the source, target and types hashcodes.
void	setSource(BioPAXElement source) Sets source element.
void	setTarget(BioPAXElement target) Sets target element.
void	setType(BinaryInteractionType type) Sets the type of the interaction.
String	toString() Returns "source type target".

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleInteraction

public SimpleInteraction(BioPAXElement source,
                         BioPAXElement target,
                         BinaryInteractionType type)

Constructor with parameters, without mediators.

Parameters:

source - source of the interaction

target - target of the interaction

type - type of the interaction

SimpleInteraction

public SimpleInteraction(BioPAXElement source,
                         BioPAXElement target,
                         BinaryInteractionType type,
                         BioPAXElement... mediator)

Constructor with parameters, with mediators.

Parameters:

source - source of the interaction

target - target of the interaction

type - type of the interaction

mediator - other elements related to the interaction

SimpleInteraction

public SimpleInteraction(BioPAXElement source,
                         BioPAXElement target,
                         BinaryInteractionType type,
                         Collection<BioPAXElement> mediator)

Constructor with parameters, with mediators.

Parameters:

source - source of the interaction

target - target of the interaction

type - type of the interaction

mediator - other elements related to the interaction

Method Detail

getSource

public BioPAXElement getSource()

Gets source element.

Returns:

source element

setSource

public void setSource(BioPAXElement source)

Sets source element.

Parameters:

source - source element

getTarget

public BioPAXElement getTarget()

Gets target element.

Returns:

target element

setTarget

public void setTarget(BioPAXElement target)

Sets target element.

Parameters:

target - target element

getType

public BinaryInteractionType getType()

Gets the type of the interaction.

Returns:

type of the interaction

setType

public void setType(BinaryInteractionType type)

Sets the type of the interaction.

Parameters:

type - type of the interaction

equals

public boolean equals(Object o)

This method checks for source, target and type equality. Provenance and target equality is based on rdfIDs.

Overrides:

equals in class Object

Parameters:

o - other object

Returns:

true if o is a simple interaction and its source, target and type is equal to this'.

hashCode

public int hashCode()

This method returns a hashcode based on the source, target and types hashcodes.

Overrides:

hashCode in class Object

Returns:

a hashcode based on the source, target and types hashcodes.

toString

public String toString()

Returns "source type target".

Overrides:

toString in class Object

Returns:

"source type target"

getANameForSIF

public String getANameForSIF(BioPAXElement element)

This method is used when we want to use readable names in the simple SIF format instead of IDs. Note that those names may not be unique. In that case the file will contain duplicate names. This method iterates fields of the element to find a name.

Parameters:

element - element to get a name.

Returns:

a name to use in SIF

getRelatedEntrezGeneID

public String getRelatedEntrezGeneID(XReferrable obj)

Searches for the Entrez Gene ID in the references.

Parameters:

obj - object to search

Returns:

Entrez Gene ID

getMediators

public Set<BioPAXElement> getMediators()

Gets other related elements of the interaction.

Returns:

mediators

addMediator

public void addMediator(BioPAXElement element)

Adds a mediator to the interaction.

Parameters:

element - mediator