Package org.biopax.paxtools.pattern.constraint

Class ConversionSide

java.lang.Object

org.biopax.paxtools.pattern.constraint.ConstraintAdapter

org.biopax.paxtools.pattern.constraint.ConversionSide

All Implemented Interfaces:

Constraint

public class ConversionSide
extends ConstraintAdapter

Given Conversion and its one of the participants (at the left or right), traverses to either the participants at the other side or the same side. var0 is a PE (PE1) var1 is a Conv var2 is a PE (PE2) Prerequisite: PE1 is either at left or right of Conv

Author:

Ozgun Babur

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	ConversionSide.Type	This enum tells if the user want to traverse towards other side of the conversion or stay at the same side.

Field Summary

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

blacklist, size

Constructor Summary

Constructors

Constructor	Description
ConversionSide(ConversionSide.Type type)	Constructor.
ConversionSide(ConversionSide.Type type, Blacklist blacklist, RelType relType)	Constructor.

Method Summary

Modifier and Type	Method	Description
boolean	canGenerate()	This is a generative constraint.
Collection<BioPAXElement>	generate(Match match, int... ind)	Checks which side is the first PhysicalEntity, and gathers participants on either the other side or the same side.

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 Details

ConversionSide

public ConversionSide(ConversionSide.Type type)

Constructor.

Parameters:

type - side type (same side or the other)

ConversionSide

public ConversionSide(ConversionSide.Type type,
 Blacklist blacklist,
 RelType relType)

Constructor. The relType parameter is using during blacklisting, and only if the blacklist is not null.

Parameters:

type - side type

blacklist - blacklist of ubiquitous molecules

relType - relationship type (used together with and during blacklisting)

Method Details

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)

Checks which side is the first PhysicalEntity, and gathers participants on either the other side or the same side.

Specified by:

generate in interface Constraint

Overrides:

generate in class ConstraintAdapter

Parameters:

match - current pattern match

ind - mapped indices

Returns:

participants at the desired side