org.biopax.paxtools.pattern.constraint

Class Participant

java.lang.Object

org.biopax.paxtools.pattern.constraint.ConstraintAdapter

org.biopax.paxtools.pattern.constraint.Participant

All Implemented Interfaces:

Constraint

public class Participant
extends ConstraintAdapter

Gets input or output participants of a Conversion. if NOT consider Control and NOT considerPathway (default): var0 is a Conversion var1 is a PE else if considerControl and NOT considerPathway var0 is a Control var1 is a Conversion var2 is a PE else if NOT considerControl and considerPathway var0 is a Pathway var1 is a Conversion var2 is a PE else if considerControl and consider pathway var0 is a Pathway var1 is a Control var2 is a Conversion var3 is a PE

Author:

Ozgun Babur

Field Summary

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

blacklist, size

Constructor Summary

Constructors

Constructor and Description
Participant(RelType type) Constructor with parameters.
Participant(RelType type, Blacklist blacklist) Constructor with parameters.
Participant(RelType type, Blacklist blacklist, boolean considerControl) Constructor with parameters.
Participant(RelType type, Blacklist blacklist, boolean considerControl, boolean considerPathway) Constructor with parameters.
Participant(RelType type, boolean considerControl) Constructor with parameters.
Participant(RelType type, boolean considerControl, boolean considerPathway) 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

Participant

public Participant(RelType type,
                   Blacklist blacklist,
                   boolean considerControl,
                   boolean considerPathway)

Constructor with parameters.

Parameters:

type - input or output conversion

blacklist - for detecting ubiquitous small molecules

considerControl - whether there is a Control that we should consider

considerPathway - whether there is a Pathway that we should consider

Participant

public Participant(RelType type)

Constructor with parameters.

Parameters:

type - input or output of the conversion

Participant

public Participant(RelType type,
                   Blacklist blacklist)

Constructor with parameters.

Parameters:

type - input or output conversion

blacklist - for detecting ubiquitous small molecules

Participant

public Participant(RelType type,
                   Blacklist blacklist,
                   boolean considerControl)

Constructor with parameters.

Parameters:

type - input or output conversion

blacklist - for detecting ubiquitous small molecules

considerControl - whether there is a Control that we should consider

Participant

public Participant(RelType type,
                   boolean considerControl)

Constructor with parameters.

Parameters:

type - input or output of the conversion

considerControl - whether there is a Control that we should consider

Participant

public Participant(RelType type,
                   boolean considerControl,
                   boolean considerPathway)

Constructor with parameters.

Parameters:

type - input or output of the conversion

considerControl - whether there is a Control that we should consider

considerPathway - whether there is a Pathway that we should consider

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