org.biopax.paxtools.impl.level3

Class StoichiometryImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.StoichiometryImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, Level3Element, Stoichiometry, UtilityClass

@Entity
 @Indexed
public class StoichiometryImpl
extends L3ElementImpl
implements Stoichiometry

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
StoichiometryImpl()

Method Summary

Modifier and Type	Method and Description
int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
Class<? extends Stoichiometry>	getModelInterface() This method returns the actual model interface that a class implements.
PhysicalEntity	getPhysicalEntity()
float	getStoichiometricCoefficient() Stoichiometric coefficient of the physicalEntity specified by Stoichiometry.getPhysicalEntity() in the context of the owner interaction or complex.
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setPhysicalEntity(PhysicalEntity PhysicalEntity)
void	setStoichiometricCoefficient(float newStoichiometricCoefficient) Sets the stoichiometric coefficient of the physicalEntity specified by Stoichiometry.getPhysicalEntity() in the context of the owner interaction or complex.

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.Level3Element

addComment, getComment, removeComment

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

getAnnotations, getRDFId, isEquivalent

Constructor Detail

StoichiometryImpl

public StoichiometryImpl()

Method Detail

getModelInterface

public Class<? extends Stoichiometry> getModelInterface()

Description copied from interface: BioPAXElement

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

Specified by:

getModelInterface in interface BioPAXElement

Returns:

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

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class BioPAXElementImpl

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 BioPAXElementImpl

Returns:

an integer that is same across all equivalent entities.

getPhysicalEntity

public PhysicalEntity getPhysicalEntity()

Specified by:

getPhysicalEntity in interface Stoichiometry

Returns:

the physical entity to be annotated with stoichiometry.

setPhysicalEntity

public void setPhysicalEntity(PhysicalEntity PhysicalEntity)

Specified by:

setPhysicalEntity in interface Stoichiometry

Parameters:

PhysicalEntity - entity to be annotated with stoichiometry.

getStoichiometricCoefficient

public float getStoichiometricCoefficient()

Description copied from interface: Stoichiometry

Stoichiometric coefficient of the physicalEntity specified by Stoichiometry.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.

Specified by:

getStoichiometricCoefficient in interface Stoichiometry

Returns:

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

setStoichiometricCoefficient

public void setStoichiometricCoefficient(float newStoichiometricCoefficient)

Description copied from interface: Stoichiometry

Sets the stoichiometric coefficient of the physicalEntity specified by Stoichiometry.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.

Specified by:

setStoichiometricCoefficient in interface Stoichiometry

Parameters:

newStoichiometricCoefficient - of the physical entity