org.biopax.paxtools.pattern.constraint

Class RelatedControl

java.lang.Object

org.biopax.paxtools.pattern.constraint.ConstraintAdapter

org.biopax.paxtools.pattern.constraint.RelatedControl

All Implemented Interfaces:

Constraint

public class RelatedControl
extends ConstraintAdapter

After traversing a PhysicalEntity and the Conversion it participates, this constraint takes us to the Control. The given relation between PhysicalEntity and Conversion is used to filter out unrelated controls. Var0 - PhysicalEntity (participant) Var1 - Conversion Var2 - related Control

Author:

Ozgun Babur

Field Summary

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

blacklist, size

Constructor Summary

Constructors

Constructor and Description
RelatedControl(RelType peType) Constructor with the relation type between PhysicalEntity and Conversion.
RelatedControl(RelType peType, Blacklist blacklist) Constructor with the relation type between PhysicalEntity and Conversion, and the blacklist.

Method Summary

Modifier and Type	Method and Description
boolean	canGenerate() This is a generative constraint.
Collection<BioPAXElement>	generate(Match match, int... ind) According to the relation between PhysicalEntity and the Conversion, checks of the Control is relevant.

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

RelatedControl

public RelatedControl(RelType peType)

Constructor with the relation type between PhysicalEntity and Conversion.

Parameters:

peType - relation type between PhysicalEntity and Conversion

RelatedControl

public RelatedControl(RelType peType,
                      Blacklist blacklist)

Constructor with the relation type between PhysicalEntity and Conversion, and the blacklist.

Parameters:

peType - relation type between PhysicalEntity and Conversion

blacklist - to detect ubiquitous small 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)

According to the relation between PhysicalEntity and the Conversion, checks of the Control is relevant. If relevant it is retrieved.

Specified by:

generate in interface Constraint

Overrides:

generate in class ConstraintAdapter

Parameters:

match - current pattern match

ind - mapped indices

Returns:

related controls