org.biopax.paxtools.pattern.constraint

Class InterToPartER

java.lang.Object

org.biopax.paxtools.pattern.constraint.ConstraintAdapter

org.biopax.paxtools.pattern.constraint.InterToPartER

All Implemented Interfaces:

Constraint

public class InterToPartER
extends ConstraintAdapter

This constraint is used to collect related EntityReference of the participant physical entities. The constraint let's users to set some participants as taboo, and they are excluded from analysis. Var0 - Interaction Var1 - Taboo element number 1 ... Var(numTabooElements+1) - Last taboo element Var(numTabooElements+2) - The related EntityReference

Author:

Ozgun Babur

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	InterToPartER.Direction

Field Summary

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

blacklist, size

Constructor Summary

Constructors

Constructor and Description
InterToPartER() Constructor without parameters.
InterToPartER(int numOfTabooElements) Constructor with parameters.
InterToPartER(InterToPartER.Direction direction) Constructor with direction.
InterToPartER(InterToPartER.Direction direction, int numOfTabooElements) Constructor with parameters.

Method Summary

Modifier and Type	Method and Description
boolean	canGenerate() This is a generative constraint.
protected Collection<BioPAXElement>	generate(Conversion conv, InterToPartER.Direction direction, Set<Entity> taboo) Gets the related entity references of the given interaction,
protected Collection<BioPAXElement>	generate(Interaction inter, Set<Entity> taboo) Gets the related entity references of the given interaction.
Collection<BioPAXElement>	generate(Match match, int... ind) Iterated over non-taboo participants and collectes related ER.

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

InterToPartER

public InterToPartER(int numOfTabooElements)

Constructor with parameters. A taboo element is the participant that we want to exclude from the analysis. User should provide the number of taboo elements, then during execution, these elements will be fetched from the current match.

Parameters:

numOfTabooElements - the number of entities to exclude from the analysis

InterToPartER

public InterToPartER(InterToPartER.Direction direction,
                     int numOfTabooElements)

Constructor with parameters. A taboo element is the participant that we want to exclude from the analysis. User should provide the number of taboo elements, then during execution, these elements will be fetched from the current match. The direction is left, or right, or both sides of the Conversion.

Parameters:

direction - ide(s) of an interaction to consider

numOfTabooElements - the number of entities to exclude from the analysis

InterToPartER

public InterToPartER()

Constructor without parameters. There are no taboo elements.

InterToPartER

public InterToPartER(InterToPartER.Direction direction)

Constructor with direction. There are no taboo elements.

Parameters:

direction - - side(s) of an interaction to consider; see InterToPartER.Direction

Method Detail

canGenerate

public boolean canGenerate()

This is a generative constraint.

Specified by:

canGenerate in interface Constraint

Overrides:

canGenerate in class ConstraintAdapter

Returns:

true if the constraint can generate candidates

generate

public Collection<BioPAXElement> generate(Match match,
                                          int... ind)

Iterated over non-taboo participants and collectes related ER.

Specified by:

generate in interface Constraint

Overrides:

generate in class ConstraintAdapter

Parameters:

match - current pattern match

ind - mapped indices

Returns:

related participants

generate

protected Collection<BioPAXElement> generate(Interaction inter,
                                             Set<Entity> taboo)

Gets the related entity references of the given interaction.

Parameters:

inter - interaction

taboo - entities to ignore/skip

Returns:

entity references

generate

protected Collection<BioPAXElement> generate(Conversion conv,
                                             InterToPartER.Direction direction,
                                             Set<Entity> taboo)

Gets the related entity references of the given interaction,

Parameters:

conv - conversion interaction

direction - which side(s) participants of the conversion to consider

taboo - skip list of entities

Returns:

entity references