public class LinkedPE extends ConstraintAdapter
Modifier and Type | Class and Description |
---|---|
static class |
LinkedPE.Type
Two type of linking between PhysicalEntity.
|
blacklist, size
Constructor and Description |
---|
LinkedPE(LinkedPE.Type type)
Constructor with the linking type.
|
LinkedPE(LinkedPE.Type type,
Blacklist blacklist)
Constructor with the linking type.
|
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) |
assertIndLength, convertStepDirection, findDirectionInCatalysis, findDirectionInPathways, getCatalysisDirection, getControlChain, getConvParticipants, getDirection, getDirection, getDirection, getDirection, getVariableSize, satisfies, setSize
public LinkedPE(LinkedPE.Type type)
type
- type of desired linkingpublic LinkedPE(LinkedPE.Type type, Blacklist blacklist)
type
- type of desired linkingblacklist
- a skip-list of ubiquitous moleculespublic boolean canGenerate()
canGenerate
in interface Constraint
canGenerate
in class ConstraintAdapter
public Collection<BioPAXElement> generate(Match match, int... ind)
generate
in interface Constraint
generate
in class ConstraintAdapter
match
- current pattern matchind
- mapped indicespublic Set<BioPAXElement> getLinkedElements(PhysicalEntity pe)
protected void enrichWithGenerics(Set<BioPAXElement> seed, Set<BioPAXElement> all)
seed
- to get the linked elements fromall
- already found linksprotected void enrichWithCM(Set<BioPAXElement> seed, Set<BioPAXElement> all)
seed
- elements to linkall
- already found linksprotected Set access(PathAccessor pa, Set<BioPAXElement> seed, Set<BioPAXElement> all)
pa
- accessor to the filedseed
- entities to get their fieldsall
- already found valuesCopyright © 2015 BioPAX. All rights reserved.