interaction

Class InteractionNetwork

java.lang.Object

interaction.InteractionNetwork

public class InteractionNetwork
extends java.lang.Object

Class containing all entities and all interactions of the problem.

Author:

lmarmiesse 6 mars 2013

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.List<Interaction>	addedInteractions List of interation added in the interaction file.
private java.util.Map<java.lang.String,parsebionet.biodata.BioEntity>	binaryEntities List of entities with binary values.
private java.util.List<Interaction>	GPRInteractions List of GPR interactions.
private java.util.Map<java.lang.String,parsebionet.biodata.BioEntity>	intEntities List of entities with interger values.
protected java.util.Map<parsebionet.biodata.BioEntity,java.util.List<Interaction>>	interactionsToCheck
private java.util.List<Unique>	notTransformedProbaUnique
private java.util.Map<java.lang.String,parsebionet.biodata.BioEntity>	numEntities List of entities with real values.

Constructor Summary

Constructors

Constructor and Description
InteractionNetwork()

Method Summary

Methods

Modifier and Type	Method and Description
void	addAddedIntercation(Interaction i)
void	addBinaryEntity(parsebionet.biodata.BioEntity e)
void	addGPRIntercation(Interaction i)
void	addIntEntity(parsebionet.biodata.BioEntity e)
void	addInteractionToCheck(Interaction i)
void	addNumEntity(parsebionet.biodata.BioEntity e)
void	addProbaUnique(Unique unique)
void	clear() Clears all lists.
java.util.List<Interaction>	getAddedInteractions()
java.util.Set<parsebionet.biodata.BioEntity>	getBinaryEntities()
java.util.List<parsebionet.biodata.BioEntity>	getEntities()
parsebionet.biodata.BioEntity	getEntity(java.lang.String name)
java.util.List<Interaction>	getGPRInteractions()
java.util.Set<parsebionet.biodata.BioEntity>	getIntEntities()
java.util.Map<parsebionet.biodata.BioEntity,java.util.List<Interaction>>	getInteractionToCheck()
java.util.List<Unique>	getNotTransformedUniques()
java.util.Set<parsebionet.biodata.BioEntity>	getNumEntities()
boolean	isNotTransformedUnique()
Unique	removeNotTransformedUnique()
void	removeNumEntity(parsebionet.biodata.BioEntity entity)

Methods inherited from class java.lang.Object

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

Field Detail

numEntities

private java.util.Map<java.lang.String,parsebionet.biodata.BioEntity> numEntities

List of entities with real values.

intEntities

private java.util.Map<java.lang.String,parsebionet.biodata.BioEntity> intEntities

List of entities with interger values.

binaryEntities

private java.util.Map<java.lang.String,parsebionet.biodata.BioEntity> binaryEntities

List of entities with binary values.

GPRInteractions

private java.util.List<Interaction> GPRInteractions

List of GPR interactions.

addedInteractions

private java.util.List<Interaction> addedInteractions

List of interation added in the interaction file.

notTransformedProbaUnique

private java.util.List<Unique> notTransformedProbaUnique

interactionsToCheck

protected java.util.Map<parsebionet.biodata.BioEntity,java.util.List<Interaction>> interactionsToCheck

Constructor Detail

InteractionNetwork

public InteractionNetwork()

Method Detail

getInteractionToCheck

public java.util.Map<parsebionet.biodata.BioEntity,java.util.List<Interaction>> getInteractionToCheck()

getEntities

public java.util.List<parsebionet.biodata.BioEntity> getEntities()

addInteractionToCheck

public void addInteractionToCheck(Interaction i)

addGPRIntercation

public void addGPRIntercation(Interaction i)

addAddedIntercation

public void addAddedIntercation(Interaction i)

addNumEntity

public void addNumEntity(parsebionet.biodata.BioEntity e)

getNumEntities

public java.util.Set<parsebionet.biodata.BioEntity> getNumEntities()

addIntEntity

public void addIntEntity(parsebionet.biodata.BioEntity e)

getIntEntities

public java.util.Set<parsebionet.biodata.BioEntity> getIntEntities()

addBinaryEntity

public void addBinaryEntity(parsebionet.biodata.BioEntity e)

getBinaryEntities

public java.util.Set<parsebionet.biodata.BioEntity> getBinaryEntities()

getEntity

public parsebionet.biodata.BioEntity getEntity(java.lang.String name)

getGPRInteractions

public java.util.List<Interaction> getGPRInteractions()

getAddedInteractions

public java.util.List<Interaction> getAddedInteractions()

addProbaUnique

public void addProbaUnique(Unique unique)

getNotTransformedUniques

public java.util.List<Unique> getNotTransformedUniques()

removeNotTransformedUnique

public Unique removeNotTransformedUnique()

clear

public void clear()

Clears all lists.

isNotTransformedUnique

public boolean isNotTransformedUnique()

Returns:

True if there are not transformed unique probabilities.

removeNumEntity

public void removeNumEntity(parsebionet.biodata.BioEntity entity)