org.biopax.paxtools.impl.level3

Class ConversionImpl

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.ConversionImpl

All Implemented Interfaces:

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

Direct Known Subclasses:

BiochemicalReactionImpl, ComplexAssemblyImpl, DegradationImpl, TransportImpl

@Entity
 @Indexed
public class ConversionImpl
extends InteractionImpl
implements Conversion

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
ConversionImpl()

Method Summary

Modifier and Type	Method and Description
void	addLeft(PhysicalEntity left) Adds a participant to the left side of the conversion interaction.
void	addParticipantStoichiometry(Stoichiometry participantStoichiometry) This method adds a stoichiometry for one of the participants of this conversion.
void	addRight(PhysicalEntity right) Adds a participant to the right side of the conversion interaction.
int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
ConversionDirectionType	getConversionDirection() This property represents the direction of the reaction.
Set<PhysicalEntity>	getLeft() The participants on the left side of the conversion interaction.
Class<? extends Conversion>	getModelInterface() This method returns the actual model interface that a class implements.
Set<Stoichiometry>	getParticipantStoichiometry() Stoichiometry of the left (Conversion.getLeft()) and right(Conversion.getRight()) participants.
Set<PhysicalEntity>	getRight() The participants on the right side of the conversion interaction.
Boolean	getSpontaneous() Specifies whether a conversion occurs spontaneously or not.
void	removeLeft(PhysicalEntity left) Removes a participant from the left side of the conversion interaction.
void	removeParticipantStoichiometry(Stoichiometry participantStoichiometry) This method removes a stoichiometry for one of the participants of this conversion.
void	removeRight(PhysicalEntity right) Removes a participant from the right side of the conversion interaction.
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setConversionDirection(ConversionDirectionType spontanousType) This property represents the direction of the reaction.
protected void	setLeft(Set<PhysicalEntity> left)
protected void	setParticipantStoichiometry(Set<Stoichiometry> participantStoichiometry)
protected void	setRight(Set<PhysicalEntity> right)
void	setSpontaneous(Boolean spontaneous) Specifies whether a conversion occurs spontaneously or not.

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, 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, 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

getAnnotations, getRDFId, isEquivalent

Constructor Detail

ConversionImpl

public ConversionImpl()

Method Detail

getModelInterface

public Class<? extends Conversion> 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.

getRight

public Set<PhysicalEntity> getRight()

Description copied from interface: Conversion

The participants on the right side of the conversion interaction. Since conversion interactions may proceed in either the right-to-right or right-to-right direction, occupants of the right property may be either reactants or products. right is a sub-property of participants.

Specified by:

getRight in interface Conversion

Returns:

The participants on the right side of the conversion interaction.

setRight

protected void setRight(Set<PhysicalEntity> right)

addRight

public void addRight(PhysicalEntity right)

Description copied from interface: Conversion

Adds a participant to the right side of the conversion interaction. Since conversion interactions may proceed in either the right-to-right or right-to-right direction, occupants of the right property may be either reactants or products. right is a sub-property of participants.

Specified by:

addRight in interface Conversion

Parameters:

right - participants to be added to the right side of the conversion interaction.

removeRight

public void removeRight(PhysicalEntity right)

Description copied from interface: Conversion

Removes a participant from the right side of the conversion interaction. Since conversion interactions may proceed in either the right-to-right or right-to-right direction, occupants of the right property may be either reactants or products. right is a sub-property of participants.

Specified by:

removeRight in interface Conversion

Parameters:

right - participants to be removed from the right side of the conversion interaction.

getLeft

public Set<PhysicalEntity> getLeft()

Description copied from interface: Conversion

The participants on the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the left property may be either reactants or products. left is a sub-property of participants.

Specified by:

getLeft in interface Conversion

Returns:

The participants on the left side of the conversion interaction.

setLeft

protected void setLeft(Set<PhysicalEntity> left)

addLeft

public void addLeft(PhysicalEntity left)

Description copied from interface: Conversion

Adds a participant to the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the left property may be either reactants or products. left is a sub-property of participants.

Specified by:

addLeft in interface Conversion

Parameters:

left - participants to be added to the left side of the conversion interaction.

removeLeft

public void removeLeft(PhysicalEntity left)

Description copied from interface: Conversion

Removes a participant from the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the left property may be either reactants or products. left is a sub-property of participants.

Specified by:

removeLeft in interface Conversion

Parameters:

left - participants to be removed from the left side of the conversion interaction.

getSpontaneous

public Boolean getSpontaneous()

Description copied from interface: Conversion

Specifies whether a conversion occurs spontaneously or not. If the spontaneity is not known,this property should not be specified.

Specified by:

getSpontaneous in interface Conversion

Returns:

whether if this conversion is spontaneous.

setSpontaneous

public void setSpontaneous(Boolean spontaneous)

Description copied from interface: Conversion

Specifies whether a conversion occurs spontaneously or not. If the spontaneity is not known,this property should not be specified.

Specified by:

setSpontaneous in interface Conversion

Parameters:

spontaneous - Whether if this conversion is spontaneous.

getParticipantStoichiometry

public Set<Stoichiometry> getParticipantStoichiometry()

Description copied from interface: Conversion

Stoichiometry of the left (Conversion.getLeft()) and right(Conversion.getRight()) participants. Note: This is a "bridge" workaround for the n-ary relationship problem. There is no default stoichiometry ( e.g. 1). Leaving this out will create reactions with unknown stoichiometry. It is a best practice to define the stoichiometry of each participant. It is invalid to define more than one stoichiometry per participant. It is invalid to reuse stoichiometry instances across conversions.

Specified by:

getParticipantStoichiometry in interface Conversion

Returns:

Stoichiometry of the left (Conversion.getLeft()) and right(Conversion.getRight()) participants.

addParticipantStoichiometry

public void addParticipantStoichiometry(Stoichiometry participantStoichiometry)

Description copied from interface: Conversion

This method adds a stoichiometry for one of the participants of this conversion.

Specified by:

addParticipantStoichiometry in interface Conversion

Parameters:

participantStoichiometry - to be added

removeParticipantStoichiometry

public void removeParticipantStoichiometry(Stoichiometry participantStoichiometry)

Description copied from interface: Conversion

This method removes a stoichiometry for one of the participants of this conversion.

Specified by:

removeParticipantStoichiometry in interface Conversion

Parameters:

participantStoichiometry - to be removed

setParticipantStoichiometry

protected void setParticipantStoichiometry(Set<Stoichiometry> participantStoichiometry)

getConversionDirection

public ConversionDirectionType getConversionDirection()

Description copied from interface: Conversion

This property represents the direction of the reaction. If a reaction will run in a single direction under all biological contexts then it is considered irreversible and has a direction. Otherwise it is reversible.

Specified by:

getConversionDirection in interface Conversion

Returns:

One of REVERSIBLE, LEFT-TO-RIGHT or RIGHT-TO-LEFT

setConversionDirection

public void setConversionDirection(ConversionDirectionType spontanousType)

Description copied from interface: Conversion

This property represents the direction of the reaction. If a reaction will run in a single direction under all biological contexts then it is considered irreversible and has a direction. Otherwise it is reversible.

Specified by:

setConversionDirection in interface Conversion

Parameters:

spontanousType - One of REVERSIBLE, LEFT-TO-RIGHT or RIGHT-TO-LEFT -- null for unknown.

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class EntityImpl

equivalenceCode

public int equivalenceCode()

Description copied from interface: BioPAXElement

If two elements are equivalent, then their equivalence code should be the same.

Specified by:

equivalenceCode in interface BioPAXElement

Overrides:

equivalenceCode in class XReferrableImpl

Returns:

an integer that is same across all equivalent entities.