org.biopax.paxtools.pattern.constraint

Class ParticipatesInConv

java.lang.Object

org.biopax.paxtools.pattern.constraint.ConstraintAdapter

org.biopax.paxtools.pattern.constraint.ParticipatesInConv

All Implemented Interfaces:

Constraint

public class ParticipatesInConv
extends ConstraintAdapter

Gets the related Conversion where the PhysicalEntity is input or output, whichever is desired. var0 is a PE var1 is a Conversion

Author:

Ozgun Babur

Field Summary

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

blacklist, size

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
boolean	canGenerate() This is a generative constraint.
Collection<BioPAXElement>	generate(Match match, int... ind) Identifies the conversion direction and 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

ParticipatesInConv

public ParticipatesInConv(RelType type,
                          Blacklist blacklist)

Constructor with parameters.

Parameters:

type - input or output conversion

blacklist - for detecting blacklisted small molecules

ParticipatesInConv

public ParticipatesInConv(RelType type)

Constructor with parameters.

Parameters:

type - input or output conversion

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)

Identifies the conversion direction and gets the related participants.

Specified by:

generate in interface Constraint

Overrides:

generate in class ConstraintAdapter

Parameters:

match - current pattern match

ind - mapped indices

Returns:

input or output participants