org.biopax.paxtools.pattern.constraint

Class ParticipatingPE

java.lang.Object

org.biopax.paxtools.pattern.constraint.ConstraintAdapter

org.biopax.paxtools.pattern.constraint.ParticipatingPE

All Implemented Interfaces:

Constraint

Deprecated.

public class ParticipatingPE
extends ConstraintAdapter

This constraint is useful when we want traverse Control-Conversion-PE (input or output). Control and Conversion are prerequisites, PE is generated. Var0 - Control Var1 - Conversion Var2 - input or output PhysicalEntity

Author:

Ozgun Babur

See Also:

Participant

Field Summary

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

blacklist, size

Constructor Summary

Constructors

Constructor and Description
ParticipatingPE(RelType type) Deprecated. Constructor with parameters.
ParticipatingPE(RelType type, Blacklist blacklist) Deprecated. Constructor with parameters.

Method Summary

Modifier and Type	Method and Description
boolean	canGenerate() Deprecated. This is a generative constraint.
Collection<BioPAXElement>	generate(Match match, int... ind) Deprecated. First evaluates the direction that the Control is affecting the Conversion, then gets the related participants.

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

ParticipatingPE

public ParticipatingPE(RelType type,
                       Blacklist blacklist)

Deprecated.

Constructor with parameters.

Parameters:

type - direction from the Conversion - input or output type

blacklist - a skip-list of ubiquitous molecules

ParticipatingPE

public ParticipatingPE(RelType type)

Deprecated.

Constructor with parameters.

Parameters:

type - direction from the Conversion

Method Detail

canGenerate

public boolean canGenerate()

Deprecated.

This is a generative constraint.

Specified by:

canGenerate in interface Constraint

Overrides:

canGenerate in class ConstraintAdapter

Returns:

true if the constraint can generate candidates

generate

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

Deprecated.

First evaluates the direction that the Control is affecting the Conversion, then gets the related participants.

Specified by:

generate in interface Constraint

Overrides:

generate in class ConstraintAdapter

Parameters:

match - current pattern match

ind - mapped indices

Returns:

related participants