org.biopax.paxtools.model.level3
Interface Stoichiometry

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, Level3Element, java.io.Serializable, UtilityClass

All Known Implementing Classes:

StoichiometryImpl

public interface Stoichiometry
extends UtilityClass

Stoichiometric coefficient of a physical entity in the context of a conversion or complex. For each participating element there must be 0 or 1 stoichiometry element. A non-existing stoichiometric element is treated as unknown. This is an n-ary bridge for left, right and component properties.

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

PhysicalEntity	getPhysicalEntity()
float	getStoichiometricCoefficient() Stoichiometric coefficient of the physicalEntity specified by getPhysicalEntity() in the context of the owner interaction or complex.
void	setPhysicalEntity(PhysicalEntity physicalEntity)
void	setStoichiometricCoefficient(float newStoichiometricCoefficient) Sets the stoichiometric coefficient of the physicalEntity specified by getPhysicalEntity() in the context of the owner interaction or complex.

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

addComment, getComment, removeComment

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

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Method Detail

getPhysicalEntity

PhysicalEntity getPhysicalEntity()

Returns:

the physical entity to be annotated with stoichiometry.

setPhysicalEntity

void setPhysicalEntity(PhysicalEntity physicalEntity)

Parameters:

physicalEntity - entity to be annotated with stoichiometry.

getStoichiometricCoefficient

float getStoichiometricCoefficient()

Stoichiometric coefficient of the physicalEntity specified by getPhysicalEntity() in the context of the owner interaction or complex. This value can be any rational number. Generic values such as "n" or "n+1" should not be used - polymers are currently not covered.

Returns:

Stoichiometric coefficient for one of the entities in an interaction or complex

setStoichiometricCoefficient

void setStoichiometricCoefficient(float newStoichiometricCoefficient)

Sets the stoichiometric coefficient of the physicalEntity specified by getPhysicalEntity() in the context of the owner interaction or complex. { can be any rational number. Generic values such as "n" or "n+1" should not be used - polymers are currently not covered.

Parameters:

newStoichiometricCoefficient - of the physical entity