org.biopax.paxtools.impl.level3

Class CatalysisImpl

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.ControlImpl

org.biopax.paxtools.impl.level3.CatalysisImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, Catalysis, Control, Entity, Interaction, Level3Element, Named, Observable, Process, XReferrable

@Entity
 @Indexed
public class CatalysisImpl
extends ControlImpl
implements Catalysis

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
CatalysisImpl()

Method Summary

Modifier and Type	Method and Description
void	addCofactor(PhysicalEntity cofactor) Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
void	addController(Controller controller) The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction.
protected boolean	checkControlled(Process controlled)
CatalysisDirectionType	getCatalysisDirection() This property represents the direction of this catalysis under all physiological conditions if there is one.
Set<PhysicalEntity>	getCofactor() Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
Class<? extends Catalysis>	getModelInterface() This method returns the actual model interface that a class implements.
void	removeCofactor(PhysicalEntity cofactor) Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
void	setCatalysisDirection(CatalysisDirectionType catalysisDirection) This property represents the direction of this catalysis under all physiological conditions if there is one.
protected void	setCofactor(Set<PhysicalEntity> cofactor)

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

addControlled, getControlled, getController, getControlType, getPathwayController, getPeController, removeControlled, removeController, setControlled, setControlType, setPathwayController, setPeController

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.Control

addControlled, getControlled, getController, getControlType, removeControlled, removeController, setControlType

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

CatalysisImpl

public CatalysisImpl()

Method Detail

getModelInterface

public Class<? extends Catalysis> 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 ControlImpl

Returns:

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

getCatalysisDirection

public CatalysisDirectionType getCatalysisDirection()

Description copied from interface: Catalysis

This property represents the direction of this catalysis under all physiological conditions if there is one. Note that chemically a catalyst will increase the rate of the reaction in both directions. In biology, however, there are cases where the enzyme is expressed only when the controlled bidirectional conversion is on one side of the chemical equilibrium. olled bidirectional conversion is on one side of the chemical equilibrium. For example E.Coli's lac operon ensures that lacZ gene is only synthesized when there is enough lactose in the medium. If that is the case and the controller, under biological conditions, is always catalyzing the conversion in one direction then this fact can be captured using this property. If the enzyme is active for both directions, or the conversion is not bidirectional, this property should be left empty.

Specified by:

getCatalysisDirection in interface Catalysis

Returns:

direction of this catalysis under all physiological conditions if there is one

setCatalysisDirection

public void setCatalysisDirection(CatalysisDirectionType catalysisDirection)

Description copied from interface: Catalysis

This property represents the direction of this catalysis under all physiological conditions if there is one. Note that chemically a catalyst will increase the rate of the reaction in both directions. In biology, however, there are cases where the enzyme is expressed only when the controlled bidirectional conversion is on one side of the chemical equilibrium. olled bidirectional conversion is on one side of the chemical equilibrium. For example E.Coli's lac operon ensures that lacZ gene is only synthesized when there is enough lactose in the medium. If that is the case and the controller, under biological conditions, is always catalyzing the conversion in one direction then this fact can be captured using this property. If the enzyme is active for both directions, or the conversion is not bidirectional, this property should be left empty.

Specified by:

setCatalysisDirection in interface Catalysis

Parameters:

catalysisDirection - direction of this catalysis under all physiological conditions if there is one

getCofactor

public Set<PhysicalEntity> getCofactor()

Description copied from interface: Catalysis

Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. This is a suproperty of participants.

Specified by:

getCofactor in interface Catalysis

Returns:

cofactor(s) or coenzyme(s) required for catalysis of the conversion

setCofactor

protected void setCofactor(Set<PhysicalEntity> cofactor)

addCofactor

public void addCofactor(PhysicalEntity cofactor)

Description copied from interface: Catalysis

Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. This is a suproperty of participants.

Specified by:

addCofactor in interface Catalysis

Parameters:

cofactor - cofactor(s) or coenzyme(s) required for catalysis of the conversion

removeCofactor

public void removeCofactor(PhysicalEntity cofactor)

Description copied from interface: Catalysis

Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. This is a suproperty of participants.

Specified by:

removeCofactor in interface Catalysis

Parameters:

cofactor - cofactor(s) or coenzyme(s) required for catalysis of the conversion

addController

public void addController(Controller controller)

Description copied from interface: Control

The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction. Controller is a sub-property of participants.

Specified by:

addController in interface Control

Overrides:

addController in class ControlImpl

Parameters:

controller - The controlling entity

checkControlled

protected boolean checkControlled(Process controlled)

Overrides:

checkControlled in class ControlImpl