org.biopax.paxtools.impl.level3

Class TemplateReactionImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.XReferrableImpl

org.biopax.paxtools.impl.level3.NamedImpl

org.biopax.paxtools.impl.level3.EntityImpl

org.biopax.paxtools.impl.level3.ProcessImpl

org.biopax.paxtools.impl.level3.InteractionImpl

org.biopax.paxtools.impl.level3.TemplateReactionImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, Entity, Interaction, Level3Element, Named, Observable, Process, TemplateReaction, XReferrable

@Entity
 @Indexed
public class TemplateReactionImpl
extends InteractionImpl
implements TemplateReaction

See Also:

Serialized Form

Field Summary

Fields inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_AVAILABILITY, FIELD_COMMENT, FIELD_DATASOURCE, FIELD_ECNUMBER, FIELD_KEYWORD, FIELD_NAME, FIELD_ORGANISM, FIELD_PATHWAY, FIELD_SEQUENCE, FIELD_TERM, FIELD_XREFDB, FIELD_XREFID, FILTER_BY_DATASOURCE, FILTER_BY_ORGANISM

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor and Description
TemplateReactionImpl()

Method Summary

Modifier and Type	Method and Description
void	addProduct(PhysicalEntity product)
Class<? extends TemplateReaction>	getModelInterface() This method returns the actual model interface that a class implements.
Set<PhysicalEntity>	getProduct()
NucleicAcid	getTemplate()
TemplateDirectionType	getTemplateDirection()
protected NucleicAcid	getTemplateX()
void	removeProduct(PhysicalEntity product)
protected void	setProduct(Set<PhysicalEntity> product)
void	setTemplate(NucleicAcid template)
void	setTemplateDirection(TemplateDirectionType templateDirection)
protected void	setTemplateX(NucleicAcid template)

Methods inherited from class org.biopax.paxtools.impl.level3.InteractionImpl

addInteractionType, addParticipant, getInteractionType, getParticipant, removeInteractionType, removeParticipant, setInteractionType, setParticipant

Methods inherited from class org.biopax.paxtools.impl.level3.ProcessImpl

getControlledOf, getPathwayComponentOf, getStepProcessOf, setControlledOf, setPathwayComponentOf, setStepProcessOf

Methods inherited from class org.biopax.paxtools.impl.level3.EntityImpl

addAvailability, addDataSource, addEvidence, getAvailability, getDataSource, getEvidence, getParticipantOf, removeAvailability, removeDataSource, removeEvidence, semanticallyEquivalent, setAvailability, setDataSource, setEvidence, setParticipantOf

Methods inherited from class org.biopax.paxtools.impl.level3.NamedImpl

addName, getDisplayName, getDisplayNameX, getName, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setStandardName, setStandardNameX

Methods inherited from class org.biopax.paxtools.impl.level3.XReferrableImpl

addXref, equivalenceCode, getXref, removeXref, setXref

Methods inherited from class org.biopax.paxtools.impl.level3.L3ElementImpl

addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biopax.paxtools.model.level3.Interaction

addInteractionType, addParticipant, getInteractionType, getParticipant, removeInteractionType, removeParticipant

Methods inherited from interface org.biopax.paxtools.model.level3.Process

getControlledOf, getPathwayComponentOf, getStepProcessOf

Methods inherited from interface org.biopax.paxtools.model.level3.Entity

addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getRDFId, isEquivalent

Constructor Detail

TemplateReactionImpl

public TemplateReactionImpl()

Method Detail

getModelInterface

public Class<? extends TemplateReaction> getModelInterface()

Description copied from interface: BioPAXElement

This method returns the actual model interface that a class implements.

Specified by:

getModelInterface in interface BioPAXElement

Overrides:

getModelInterface in class InteractionImpl

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

getProduct

public Set<PhysicalEntity> getProduct()

Specified by:

getProduct in interface TemplateReaction

setProduct

protected void setProduct(Set<PhysicalEntity> product)

addProduct

public void addProduct(PhysicalEntity product)

Specified by:

addProduct in interface TemplateReaction

removeProduct

public void removeProduct(PhysicalEntity product)

Specified by:

removeProduct in interface TemplateReaction

getTemplateX

protected NucleicAcid getTemplateX()

setTemplateX

protected void setTemplateX(NucleicAcid template)

getTemplate

public NucleicAcid getTemplate()

Specified by:

getTemplate in interface TemplateReaction

setTemplate

public void setTemplate(NucleicAcid template)

Specified by:

setTemplate in interface TemplateReaction

getTemplateDirection

public TemplateDirectionType getTemplateDirection()

Specified by:

getTemplateDirection in interface TemplateReaction

setTemplateDirection

public void setTemplateDirection(TemplateDirectionType templateDirection)

Specified by:

setTemplateDirection in interface TemplateReaction