org.biopax.paxtools.pattern.constraint

Class LinkedPE

java.lang.Object

org.biopax.paxtools.pattern.constraint.ConstraintAdapter

org.biopax.paxtools.pattern.constraint.LinkedPE

All Implemented Interfaces:

Constraint

public class LinkedPE
extends ConstraintAdapter

Many times we want to link PhysicalEntities (PE) while traversing a relation. For instance when we have a PE and want to go the Interactions that it participates, we may also want to consider the complexes that the PE is in. Or we also want to traverse homologies (parent or member PEs) This generative constraint gets related generics (member or parent) and either complexes or members recursively. Linking process is a bit confusing. There two modes: TO_COMPLEX and TO_MEMBER. Linking homologies is identical for both cases. IT is either parent PEs recursively, or member PEs recursively. But not parent of a member (recursion do not alternate between parent and member). In TO_COMPLEX mode, only parent complexes are linked recursively, and in TO_MEMBER mode, only the complex member PEs are linked recursively. Homology linking and complex-relation linking can alternate recursively.

Author:

Ozgun Babur

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	LinkedPE.Type Two type of linking between PhysicalEntity.

Field Summary

Fields inherited from class org.biopax.paxtools.pattern.constraint.ConstraintAdapter

blacklist, size

Constructor Summary

Constructors

Constructor and Description
LinkedPE(LinkedPE.Type type) Constructor with the linking type.
LinkedPE(LinkedPE.Type type, Blacklist blacklist) Constructor with the linking type.

Method Summary

Modifier and Type	Method and Description
protected Set	access(PathAccessor pa, Set<BioPAXElement> seed, Set<BioPAXElement> all) Uses the given PathAccessor to access fields of the seed and return only new elements that is not in the given element set (all).
boolean	canGenerate() This is a generative constraint.
protected void	enrichWithCM(Set<BioPAXElement> seed, Set<BioPAXElement> all) Gets parent complexes or complex members recursively according to the type of the linkage.
protected void	enrichWithGenerics(Set<BioPAXElement> seed, Set<BioPAXElement> all) Gets the linked homologies and then switches to complex-relationship mode.
Collection<BioPAXElement>	generate(Match match, int... ind) Gets to the linked PhysicalEntity.
Set<BioPAXElement>	getLinkedElements(PhysicalEntity pe)

Methods inherited from class org.biopax.paxtools.pattern.constraint.ConstraintAdapter

assertIndLength, convertStepDirection, findDirectionInCatalysis, findDirectionInPathways, getCatalysisDirection, getControlChain, getConvParticipants, getDirection, getDirection, getDirection, getDirection, getVariableSize, satisfies, setSize

Methods inherited from class java.lang.Object

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

Constructor Detail

LinkedPE

public LinkedPE(LinkedPE.Type type)

Constructor with the linking type.

Parameters:

type - type of desired linking

LinkedPE

public LinkedPE(LinkedPE.Type type,
                Blacklist blacklist)

Constructor with the linking type.

Parameters:

type - type of desired linking

blacklist - a skip-list of ubiquitous molecules

Method Detail

canGenerate

public boolean canGenerate()

This is a generative constraint.

Specified by:

canGenerate in interface Constraint

Overrides:

canGenerate in class ConstraintAdapter

Returns:

true

generate

public Collection<BioPAXElement> generate(Match match,
                                          int... ind)

Gets to the linked PhysicalEntity.

Specified by:

generate in interface Constraint

Overrides:

generate in class ConstraintAdapter

Parameters:

match - current pattern match

ind - mapped indices

Returns:

linked PhysicalEntity

getLinkedElements

public Set<BioPAXElement> getLinkedElements(PhysicalEntity pe)

enrichWithGenerics

protected void enrichWithGenerics(Set<BioPAXElement> seed,
                                  Set<BioPAXElement> all)

Gets the linked homologies and then switches to complex-relationship mode. These two enrich methods call each other recursively.

Parameters:

seed - to get the linked elements from

all - already found links

enrichWithCM

protected void enrichWithCM(Set<BioPAXElement> seed,
                            Set<BioPAXElement> all)

Gets parent complexes or complex members recursively according to the type of the linkage.

Parameters:

seed - elements to link

all - already found links

access

protected Set access(PathAccessor pa,
                     Set<BioPAXElement> seed,
                     Set<BioPAXElement> all)

Uses the given PathAccessor to access fields of the seed and return only new elements that is not in the given element set (all).

Parameters:

pa - accessor to the filed

seed - entities to get their fields

all - already found values

Returns:

new values