org.biopax.paxtools.io.sif.level3

Class InteractionSetL3

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractSet<E>

java.util.HashSet<E>

org.biopax.paxtools.util.AccessibleSet<SimpleInteraction>

org.biopax.paxtools.io.sif.InteractionSet

org.biopax.paxtools.io.sif.level3.InteractionSetL3

All Implemented Interfaces:

Serializable, Cloneable, Iterable<SimpleInteraction>, Collection<SimpleInteraction>, Set<SimpleInteraction>

public class InteractionSetL3
extends InteractionSet

Set of inferred interactions. This set handles grouping operations.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
InteractionSetL3(Model model) Constructor with the model.

Method Summary

Modifier and Type	Method and Description
void	convertGroupsToInteractions() Creates membership links between group nodes and members in the generated SIF graph.
void	expandGroups() This method iteratively replaces groups with BioPAX elements
GroupMap	getGroupMap() Getter for the groupMap

Methods inherited from class org.biopax.paxtools.io.sif.InteractionSet

add

Methods inherited from class org.biopax.paxtools.util.AccessibleSet

access

Methods inherited from class java.util.HashSet

clear, clone, contains, isEmpty, iterator, remove, size, spliterator

Methods inherited from class java.util.AbstractSet

equals, hashCode, removeAll

Methods inherited from class java.util.AbstractCollection

addAll, containsAll, retainAll, toArray, toArray, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Set

addAll, containsAll, equals, hashCode, removeAll, retainAll, toArray, toArray

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Constructor Detail

InteractionSetL3

public InteractionSetL3(Model model)

Constructor with the model.

Parameters:

model - model to mine binary interactions

Method Detail

getGroupMap

public GroupMap getGroupMap()

Getter for the groupMap

Returns:

groupMap

convertGroupsToInteractions

public void convertGroupsToInteractions()

Creates membership links between group nodes and members in the generated SIF graph.

expandGroups

public void expandGroups()

This method iteratively replaces groups with BioPAX elements