org.biopax.paxtools.pattern.constraint

Class PEChainsIntersect

java.lang.Object

org.biopax.paxtools.pattern.constraint.ConstraintAdapter

org.biopax.paxtools.pattern.constraint.PEChainsIntersect

All Implemented Interfaces:

Constraint

public class PEChainsIntersect
extends ConstraintAdapter

This constraint checks if two chains of linked physical entities are intersecting or not. Var0 First (simpler) PhysicalEntity in the first chain Var1 Last (complexer) PhysicalEntity in the first chain Var2 First PhysicalEntity in the second chain Var3 Last PhysicalEntity in the second chain

Author:

Ozgun Babur

Field Summary

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

blacklist, size

Constructor Summary

Constructors

Constructor and Description
PEChainsIntersect(boolean intersectionDesired) Constructor with the desired result.
PEChainsIntersect(boolean intersectionDesired, boolean ignoreEndPoints) Constructor with the desired result and endpoint ignore option.

Method Summary

Modifier and Type	Method and Description
boolean	satisfies(Match match, int... ind) Creates two PhysicalEntity chains with the given endpoints, and checks if they are intersecting.

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

assertIndLength, canGenerate, convertStepDirection, findDirectionInCatalysis, findDirectionInPathways, generate, getCatalysisDirection, getControlChain, getConvParticipants, getDirection, getDirection, getDirection, getDirection, getVariableSize, setSize

Methods inherited from class java.lang.Object

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

Constructor Detail

PEChainsIntersect

public PEChainsIntersect(boolean intersectionDesired)

Constructor with the desired result.

Parameters:

intersectionDesired - desired result

PEChainsIntersect

public PEChainsIntersect(boolean intersectionDesired,
                         boolean ignoreEndPoints)

Constructor with the desired result and endpoint ignore option.

Parameters:

intersectionDesired - desired result

ignoreEndPoints - option to ignore intersection at the endpoints of the chains

Method Detail

satisfies

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

Creates two PhysicalEntity chains with the given endpoints, and checks if they are intersecting.

Specified by:

satisfies in interface Constraint

Overrides:

satisfies in class ConstraintAdapter

Parameters:

match - current pattern match

ind - mapped indices

Returns:

true if the chains are intersecting or not intersecting as desired