org.biopax.paxtools.pattern.constraint

Class SelfOrThis

java.lang.Object

org.biopax.paxtools.pattern.constraint.ConstraintAdapter

org.biopax.paxtools.pattern.constraint.SelfOrThis

All Implemented Interfaces:

Constraint

public class SelfOrThis
extends ConstraintAdapter

When a constraint excludes the origin element, but it is needed to be among them, use this constraint. The wrapped constraint must have size 2.

Author:

Ozgun Babur

Field Summary

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

blacklist, size

Constructor Summary

Constructors

Constructor and Description
SelfOrThis(Constraint con) Constructor with the wrapped constraint.
SelfOrThis(Constraint con, int selfIndex) Constructor with the wrapped constraint and index of self.

Method Summary

Modifier and Type	Method and Description
boolean	canGenerate() This is a generative constraint.
Collection<BioPAXElement>	generate(Match match, int... ind) Gets the first mapped element along with the generated elements of wrapped constraint.
int	getVariableSize() Returns size of the wrapped constraint.
boolean	satisfies(Match match, int... ind) Checks if the last index is either generated or equal to the first element.

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

assertIndLength, convertStepDirection, findDirectionInCatalysis, findDirectionInPathways, getCatalysisDirection, getControlChain, getConvParticipants, getDirection, getDirection, getDirection, getDirection, setSize

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SelfOrThis

public SelfOrThis(Constraint con)

Constructor with the wrapped constraint. Index of self is 0 by default.

Parameters:

con - wrapped constraint

SelfOrThis

public SelfOrThis(Constraint con,
                  int selfIndex)

Constructor with the wrapped constraint and index of self. This index cannot map to the last element, but has to map one of the previous ones.

Parameters:

con - wrapped constraint

selfIndex - index of self

Method Detail

getVariableSize

public int getVariableSize()

Returns size of the wrapped constraint.

Specified by:

getVariableSize in interface Constraint

Overrides:

getVariableSize in class ConstraintAdapter

Returns:

size of the wrapped constraint

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)

Gets the first mapped element along with the generated elements of wrapped constraint.

Specified by:

generate in interface Constraint

Overrides:

generate in class ConstraintAdapter

Parameters:

match - current pattern match

ind - mapped indices

Returns:

first mapped element along with the generated elements of wrapped constraint

satisfies

public boolean satisfies(Match match,
                         int... ind)

Checks if the last index is either generated or equal to the first element.

Specified by:

satisfies in interface Constraint

Overrides:

satisfies in class ConstraintAdapter

Parameters:

match - current pattern match

ind - mapped indices

Returns:

true if the last index is either generated or equal to the first element