Package bio.singa.simulation.reactions.reactors

Class AbstractGraphComplexReactor

java.lang.Object

bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

All Implemented Interfaces:

ComplexReactor

Direct Known Subclasses:

OneToOneReactor, OneToTwoReactor, TwoToOneReactor

public abstract class AbstractGraphComplexReactor
extends Object
implements ComplexReactor

Author:

cl

Field Summary

Fields

Modifier and Type	Field	Description
protected static org.slf4j.Logger	logger

Constructor Summary

Constructors

Constructor	Description
AbstractGraphComplexReactor()

Method Summary

Modifier and Type	Method	Description
void	clear()
protected List<ComplexEntity>	filterCandidates(List<ComplexEntity> complexes, List<CandidateCondition> conditions)
Map.Entry<BindingSite,bio.singa.core.utility.Pair<ChemicalEntity>>	getBindingSite()
ComplexEntityModification	getModification()
List<CandidateCondition>	getPrimaryCandidateConditions()
List<ComplexEntity>	getPrimaryProducts()
List<ComplexEntity>	getPrimarySubstrates()
void	setModification(ComplexEntityModification modification)
void	setPrimaryCandidateConditions(List<CandidateCondition> primaryCandidateConditions)
void	setPrimaryProducts(List<ComplexEntity> primaryProducts)
void	setPrimarySubstrates(List<ComplexEntity> primarySubstrates)

Methods inherited from class java.lang.Object

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

Methods inherited from interface bio.singa.simulation.reactions.reactors.ComplexReactor

apply, collectCandidates, getProducts, invert

Field Detail

logger

protected static final org.slf4j.Logger logger

Constructor Detail

AbstractGraphComplexReactor

public AbstractGraphComplexReactor()

Method Detail

filterCandidates

protected List<ComplexEntity> filterCandidates(List<ComplexEntity> complexes,
                                               List<CandidateCondition> conditions)

getBindingSite

public Map.Entry<BindingSite,bio.singa.core.utility.Pair<ChemicalEntity>> getBindingSite()

Specified by:

getBindingSite in interface ComplexReactor

getModification

public ComplexEntityModification getModification()

Specified by:

getModification in interface ComplexReactor

setModification

public void setModification(ComplexEntityModification modification)

getPrimaryCandidateConditions

public List<CandidateCondition> getPrimaryCandidateConditions()

setPrimaryCandidateConditions

public void setPrimaryCandidateConditions(List<CandidateCondition> primaryCandidateConditions)

getPrimarySubstrates

public List<ComplexEntity> getPrimarySubstrates()

setPrimarySubstrates

public void setPrimarySubstrates(List<ComplexEntity> primarySubstrates)

getPrimaryProducts

public List<ComplexEntity> getPrimaryProducts()

setPrimaryProducts

public void setPrimaryProducts(List<ComplexEntity> primaryProducts)

clear

public void clear()

Specified by:

clear in interface ComplexReactor