@Entity @Indexed public class ConversionImpl extends InteractionImpl implements Conversion
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
UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT
Constructor and Description |
---|
ConversionImpl() |
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.
|
addInteractionType, addParticipant, getInteractionType, getParticipant, removeInteractionType, removeParticipant, setInteractionType, setParticipant
getControlledOf, getPathwayComponentOf, getStepProcessOf, setControlledOf, setPathwayComponentOf, setStepProcessOf
addAvailability, addDataSource, addEvidence, getAvailability, getDataSource, getEvidence, getParticipantOf, removeAvailability, removeDataSource, removeEvidence, setAvailability, setDataSource, setEvidence, setParticipantOf
addName, getDisplayName, getDisplayNameX, getName, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setStandardName, setStandardNameX
addXref, getXref, removeXref, setXref
addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment
equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
addInteractionType, addParticipant, getInteractionType, getParticipant, removeInteractionType, removeParticipant
getControlledOf, getPathwayComponentOf, getStepProcessOf
addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource
addEvidence, getEvidence, removeEvidence
addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName
addXref, getXref, removeXref
addComment, getComment, removeComment
getAnnotations, getRDFId, isEquivalent
public ConversionImpl()
public Class<? extends Conversion> getModelInterface()
BioPAXElement
getModelInterface
in interface BioPAXElement
getModelInterface
in class InteractionImpl
org.biopax.paxtools.model
package
corresponding to a BioPAX class.public Set<PhysicalEntity> getRight()
Conversion
getRight
in interface Conversion
protected void setRight(Set<PhysicalEntity> right)
public void addRight(PhysicalEntity right)
Conversion
addRight
in interface Conversion
right
- participants to be added to the right side of the conversion interaction.public void removeRight(PhysicalEntity right)
Conversion
removeRight
in interface Conversion
right
- participants to be removed from the right side of the conversion interaction.public Set<PhysicalEntity> getLeft()
Conversion
getLeft
in interface Conversion
protected void setLeft(Set<PhysicalEntity> left)
public void addLeft(PhysicalEntity left)
Conversion
addLeft
in interface Conversion
left
- participants to be added to the left side of the conversion interaction.public void removeLeft(PhysicalEntity left)
Conversion
removeLeft
in interface Conversion
left
- participants to be removed from the left side of the conversion interaction.public Boolean getSpontaneous()
Conversion
getSpontaneous
in interface Conversion
public void setSpontaneous(Boolean spontaneous)
Conversion
setSpontaneous
in interface Conversion
spontaneous
- Whether if this conversion is spontaneous.public Set<Stoichiometry> getParticipantStoichiometry()
Conversion
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.getParticipantStoichiometry
in interface Conversion
Conversion.getLeft()
) and right(Conversion.getRight()
) participants.public void addParticipantStoichiometry(Stoichiometry participantStoichiometry)
Conversion
addParticipantStoichiometry
in interface Conversion
participantStoichiometry
- to be addedpublic void removeParticipantStoichiometry(Stoichiometry participantStoichiometry)
Conversion
removeParticipantStoichiometry
in interface Conversion
participantStoichiometry
- to be removedprotected void setParticipantStoichiometry(Set<Stoichiometry> participantStoichiometry)
public ConversionDirectionType getConversionDirection()
Conversion
getConversionDirection
in interface Conversion
public void setConversionDirection(ConversionDirectionType spontanousType)
Conversion
setConversionDirection
in interface Conversion
spontanousType
- One of REVERSIBLE, LEFT-TO-RIGHT or RIGHT-TO-LEFT -- null for unknown.protected boolean semanticallyEquivalent(BioPAXElement element)
semanticallyEquivalent
in class EntityImpl
public int equivalenceCode()
BioPAXElement
equivalenceCode
in interface BioPAXElement
equivalenceCode
in class XReferrableImpl
Copyright © 2015 BioPAX. All rights reserved.