Package bio.singa.simulation.reactions.reactors

Class ReactionChainBuilder.AbstractReactorBuilder

java.lang.Object

bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

All Implemented Interfaces:

ReactionChainBuilder.ConnectorStep, ReactionChainBuilder.ReactorChoiceStep

Direct Known Subclasses:

ReactionChainBuilder.AddReactionChainBuilder, ReactionChainBuilder.BindReactionChainBuilder, ReactionChainBuilder.ReleaseReactionChainBuilder, ReactionChainBuilder.RemoveReactionChainBuilder

Enclosing class:

ReactionChainBuilder

public abstract static class ReactionChainBuilder.AbstractReactorBuilder
extends Object
implements ReactionChainBuilder.ReactorChoiceStep, ReactionChainBuilder.ConnectorStep

Field Summary

Fields

Modifier and Type	Field	Description
protected BindingSite	bindingSite
protected boolean	considerInversion
protected ComplexEntityModification	modification
protected List<CandidateCondition>	primaryCandidateConditions
protected ChemicalEntity	primaryEntity
protected List<ComplexReactor>	reactors
protected List<CandidateCondition>	secondaryCandidateConditions
protected ChemicalEntity	secondaryEntity

Constructor Summary

Constructors

Constructor	Description
AbstractReactorBuilder()

Method Summary

Modifier and Type	Method	Description
ReactionChainBuilder.AddReactorSecondarySubstrateStep	add(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.AddReactorSecondarySubstrateStep	add(ChemicalEntity chemicalEntity)
ReactionChainBuilder.ReactorChoiceStep	and()
ReactionChainBuilder.BindReactorPrimaryConditionStep	bind(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.BindReactorPrimaryConditionStep	bind(ChemicalEntity chemicalEntity)
ReactionChain	build()
ReactionChainBuilder.ConnectorStep	considerInversion()
ReactionChainBuilder.ConnectorStep	identifier(String identifier)
protected void	oneToOneAssignment(ChemicalEntity primaryEntity)
ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep	release(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep	release(ChemicalEntity chemicalEntity)
ReactionChainBuilder.RemoveReactorSecondarySubstrateStep	remove(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.RemoveReactorSecondarySubstrateStep	remove(ChemicalEntity chemicalEntity)

Methods inherited from class java.lang.Object

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

Field Detail

reactors

protected List<ComplexReactor> reactors

modification

protected ComplexEntityModification modification

primaryCandidateConditions

protected List<CandidateCondition> primaryCandidateConditions

secondaryCandidateConditions

protected List<CandidateCondition> secondaryCandidateConditions

bindingSite

protected BindingSite bindingSite

primaryEntity

protected ChemicalEntity primaryEntity

secondaryEntity

protected ChemicalEntity secondaryEntity

considerInversion

protected boolean considerInversion

Constructor Detail

AbstractReactorBuilder

public AbstractReactorBuilder()

Method Detail

oneToOneAssignment

protected void oneToOneAssignment(ChemicalEntity primaryEntity)

add

public ReactionChainBuilder.AddReactorSecondarySubstrateStep add(BindingSite bindingSite,
                                                                 ChemicalEntity chemicalEntity)

Specified by:

add in interface ReactionChainBuilder.ReactorChoiceStep

add

public ReactionChainBuilder.AddReactorSecondarySubstrateStep add(ChemicalEntity chemicalEntity)

Specified by:

add in interface ReactionChainBuilder.ReactorChoiceStep

bind

public ReactionChainBuilder.BindReactorPrimaryConditionStep bind(BindingSite bindingSite,
                                                                 ChemicalEntity chemicalEntity)

Specified by:

bind in interface ReactionChainBuilder.ReactorChoiceStep

bind

public ReactionChainBuilder.BindReactorPrimaryConditionStep bind(ChemicalEntity chemicalEntity)

Specified by:

bind in interface ReactionChainBuilder.ReactorChoiceStep

release

public ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep release(BindingSite bindingSite,
                                                                         ChemicalEntity chemicalEntity)

Specified by:

release in interface ReactionChainBuilder.ReactorChoiceStep

release

public ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep release(ChemicalEntity chemicalEntity)

Specified by:

release in interface ReactionChainBuilder.ReactorChoiceStep

remove

public ReactionChainBuilder.RemoveReactorSecondarySubstrateStep remove(BindingSite bindingSite,
                                                                       ChemicalEntity chemicalEntity)

Specified by:

remove in interface ReactionChainBuilder.ReactorChoiceStep

remove

public ReactionChainBuilder.RemoveReactorSecondarySubstrateStep remove(ChemicalEntity chemicalEntity)

Specified by:

remove in interface ReactionChainBuilder.ReactorChoiceStep

and

public ReactionChainBuilder.ReactorChoiceStep and()

Specified by:

and in interface ReactionChainBuilder.ConnectorStep

identifier

public ReactionChainBuilder.ConnectorStep identifier(String identifier)

Specified by:

identifier in interface ReactionChainBuilder.ConnectorStep

considerInversion

public ReactionChainBuilder.ConnectorStep considerInversion()

Specified by:

considerInversion in interface ReactionChainBuilder.ConnectorStep

build

public ReactionChain build()

Specified by:

build in interface ReactionChainBuilder.ConnectorStep