Package org.biopax.paxtools.impl.level3

Class SmallMoleculeImpl

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.PhysicalEntityImpl

org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl

org.biopax.paxtools.impl.level3.SmallMoleculeImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, Controller, Entity, Level3Element, Named, Observable, PhysicalEntity, SimplePhysicalEntity, SmallMolecule, XReferrable

public class SmallMoleculeImpl
extends SimplePhysicalEntityImpl
implements SmallMolecule

See Also:

• Serialized Form

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor	Description
SmallMoleculeImpl()

Method Summary

Modifier and Type	Method	Description
void	addFeature(EntityFeature feature)
void	addNotFeature(EntityFeature feature)
Class<? extends PhysicalEntity>	getModelInterface()	Overridden to provide better downcasting
void	setEntityReference(EntityReference entityReference)	Reference entity for this physical entity.

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

equivalenceCode, getEntityReference, getGenericEntityReferences, semanticallyEquivalent

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

addMemberPhysicalEntity, getCellularLocation, getComponentOf, getControllerOf, getFeature, getMemberPhysicalEntity, getMemberPhysicalEntityOf, getNotFeature, hasEquivalentCellularLocation, hasEquivalentFeatures, locationAndFeatureCode, removeFeature, removeMemberPhysicalEntity, removeNotFeature, setCellularLocation

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

addAvailability, addDataSource, addEvidence, getAvailability, getDataSource, getEvidence, getParticipantOf, removeAvailability, removeDataSource, removeEvidence, setDataSource

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

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName

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, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

equals, getAnnotations, getUri, 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.BioPAXElement

equivalenceCode, getAnnotations, getUri, isEquivalent

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

getControllerOf

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.Level3Element

addComment, getComment, removeComment

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.Observable

addEvidence, getEvidence, removeEvidence

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

addMemberPhysicalEntity, getCellularLocation, getComponentOf, getFeature, getMemberPhysicalEntity, getMemberPhysicalEntityOf, getNotFeature, hasEquivalentCellularLocation, hasEquivalentFeatures, removeFeature, removeMemberPhysicalEntity, removeNotFeature, setCellularLocation

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

getEntityReference, getGenericEntityReferences

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

addXref, getXref, removeXref

Constructor Details

SmallMoleculeImpl

public SmallMoleculeImpl()

Method Details

getModelInterface

public Class<? extends PhysicalEntity> getModelInterface()

Description copied from interface: PhysicalEntity

Overridden to provide better downcasting

Specified by:

getModelInterface in interface BioPAXElement

Specified by:

getModelInterface in interface PhysicalEntity

Overrides:

getModelInterface in class PhysicalEntityImpl

Returns:

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

addFeature

public void addFeature(EntityFeature feature)

Specified by:

addFeature in interface PhysicalEntity

Overrides:

addFeature in class PhysicalEntityImpl

addNotFeature

public void addNotFeature(EntityFeature feature)

Specified by:

addNotFeature in interface PhysicalEntity

Overrides:

addNotFeature in class PhysicalEntityImpl

setEntityReference

public void setEntityReference(EntityReference entityReference)

Description copied from interface: SimplePhysicalEntity

Reference entity for this physical entity.

Specified by:

setEntityReference in interface SimplePhysicalEntity

Overrides:

setEntityReference in class SimplePhysicalEntityImpl

Parameters:

entityReference - a BioPAX EntityReference object (usually a more specific subclass of)