org.biopax.paxtools.impl.level3

Class ComplexImpl

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.ComplexImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, Complex, Controller, Entity, Level3Element, Named, Observable, PhysicalEntity, XReferrable

@Entity
 @Indexed
public class ComplexImpl
extends PhysicalEntityImpl
implements Complex

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
ComplexImpl()

Method Summary

Modifier and Type	Method and Description
void	addComponent(PhysicalEntity component) Defines the PhysicalEntity subunits of this complex.
void	addComponentStoichiometry(Stoichiometry stoichiometry) The stoichiometry of components in a complex.
protected void	collectSimpleMembersRecursive(PhysicalEntity pe, Set<SimplePhysicalEntity> set)
Set<PhysicalEntity>	getComponent() Defines the PhysicalEntity subunits of this complex.
Set<Stoichiometry>	getComponentStoichiometry() The stoichiometry of components in a complex.
Set<EntityReference>	getMemberReferences() Gets the EntityReferences of the member simple physical entities.
Class<? extends Complex>	getModelInterface() Overridden to provide better downcasting
Class<? extends PhysicalEntity>	getPhysicalEntityClass()
Set<SimplePhysicalEntity>	getSimpleMembers() Gets the member physical entities which are not complex.
protected Set<SimplePhysicalEntity>	getSimpleMembers(Set<SimplePhysicalEntity> set)
void	removeComponent(PhysicalEntity component) Defines the PhysicalEntity subunits of this complex.
void	removeComponentStoichiometry(Stoichiometry stoichiometry) The stoichiometry of components in a complex.
protected boolean	semanticallyEquivalent(BioPAXElement element)
protected void	setComponent(Set<PhysicalEntity> component)
protected void	setComponentStoichiometry(Set<Stoichiometry> stoichiometry)

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

addFeature, addMemberPhysicalEntity, addNotFeature, equivalenceCode, getCellularLocation, getComponentOf, getControllerOf, getFeature, getMemberPhysicalEntity, getMemberPhysicalEntityOf, getNotFeature, hasEquivalentCellularLocation, hasEquivalentFeatures, locationAndFeatureCode, removeFeature, removeMemberPhysicalEntity, removeNotFeature, setCellularLocation, setComponentOf, setControllerOf, setFeature, setMemberPhysicalEntity, setMemberPhysicalEntityOf, setNotFeature

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

addAvailability, addDataSource, addEvidence, getAvailability, getDataSource, getEvidence, getParticipantOf, removeAvailability, removeDataSource, removeEvidence, 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, 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.PhysicalEntity

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

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.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

ComplexImpl

public ComplexImpl()

Method Detail

getModelInterface

public Class<? extends Complex> 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.

getComponent

public Set<PhysicalEntity> getComponent()

Description copied from interface: Complex

Defines the PhysicalEntity subunits of this complex. This property should not contain other complexes, i.e. it should always be a flat representation of the complex. For example, if two protein complexes join to form a single larger complex via a complex assembly interaction, the component of the new complex should be the individual proteins of the smaller complexes, not the two smaller complexes themselves. Exceptions are black-box complexes (i.e. complexes in which the component property is empty), which may be used as component of other complexes because their constituent parts are unknown / unspecified. The reason for keeping complexes flat is to signify that there is no information stored in the way complexes are nested, such as assembly order. Otherwise, the complex assembly order may be implicitly encoded and interpreted by some users, while others created hierarchical complexes randomly, which could lead to data loss. Additionally, the physicalEntityParticipants used in the component property are in the context of the complex, thus should not be reused between complexes. For instance, a protein may participate in two different complexes, but have different conformation in each.

Specified by:

getComponent in interface Complex

Returns:

components of this complex

addComponent

public void addComponent(PhysicalEntity component)

Description copied from interface: Complex

Defines the PhysicalEntity subunits of this complex. This property should not contain other complexes, i.e. it should always be a flat representation of the complex. For example, if two protein complexes join to form a single larger complex via a complex assembly interaction, the component of the new complex should be the individual proteins of the smaller complexes, not the two smaller complexes themselves. Exceptions are black-box complexes (i.e. complexes in which the component property is empty), which may be used as component of other complexes because their constituent parts are unknown / unspecified. The reason for keeping complexes flat is to signify that there is no information stored in the way complexes are nested, such as assembly order. Otherwise, the complex assembly order may be implicitly encoded and interpreted by some users, while others created hierarchical complexes randomly, which could lead to data loss. Additionally, the physicalEntityParticipants used in the component property are in the context of the complex, thus should not be reused between complexes. For instance, a protein may participate in two different complexes, but have different conformation in each.

Specified by:

addComponent in interface Complex

Parameters:

component - to be added as a new member

removeComponent

public void removeComponent(PhysicalEntity component)

Description copied from interface: Complex

Defines the PhysicalEntity subunits of this complex. This property should not contain other complexes, i.e. it should always be a flat representation of the complex. For example, if two protein complexes join to form a single larger complex via a complex assembly interaction, the component of the new complex should be the individual proteins of the smaller complexes, not the two smaller complexes themselves. Exceptions are black-box complexes (i.e. complexes in which the component property is empty), which may be used as component of other complexes because their constituent parts are unknown / unspecified. The reason for keeping complexes flat is to signify that there is no information stored in the way complexes are nested, such as assembly order. Otherwise, the complex assembly order may be implicitly encoded and interpreted by some users, while others created hierarchical complexes randomly, which could lead to data loss. Additionally, the physicalEntityParticipants used in the component property are in the context of the complex, thus should not be reused between complexes. For instance, a protein may participate in two different complexes, but have different conformation in each.

Specified by:

removeComponent in interface Complex

Parameters:

component - to be removed from members.

setComponent

protected void setComponent(Set<PhysicalEntity> component)

getComponentStoichiometry

public Set<Stoichiometry> getComponentStoichiometry()

Description copied from interface: Complex

The stoichiometry of components in a complex.

Specified by:

getComponentStoichiometry in interface Complex

Returns:

the stoichiometry of components in a complex.

addComponentStoichiometry

public void addComponentStoichiometry(Stoichiometry stoichiometry)

Description copied from interface: Complex

The stoichiometry of components in a complex.

Specified by:

addComponentStoichiometry in interface Complex

Parameters:

stoichiometry - add a stoichiometry for the member.

removeComponentStoichiometry

public void removeComponentStoichiometry(Stoichiometry stoichiometry)

Description copied from interface: Complex

The stoichiometry of components in a complex.

Specified by:

removeComponentStoichiometry in interface Complex

Parameters:

stoichiometry - remove a stoichiometry for the member.

setComponentStoichiometry

protected void setComponentStoichiometry(Set<Stoichiometry> stoichiometry)

getSimpleMembers

public Set<SimplePhysicalEntity> getSimpleMembers()

Description copied from interface: Complex

Gets the member physical entities which are not complex. When the complex is nested, members of inner complexes are added to the returned set recursively.

Specified by:

getSimpleMembers in interface Complex

Returns:

non-complex member physical entities

getSimpleMembers

protected Set<SimplePhysicalEntity> getSimpleMembers(Set<SimplePhysicalEntity> set)

collectSimpleMembersRecursive

protected void collectSimpleMembersRecursive(PhysicalEntity pe,
                                             Set<SimplePhysicalEntity> set)

getMemberReferences

public Set<EntityReference> getMemberReferences()

Description copied from interface: Complex

Gets the EntityReferences of the member simple physical entities. When the complex is nested, contents of the member complexes are retrieved recursively.

Specified by:

getMemberReferences in interface Complex

Returns:

non-complex members' entity references

getPhysicalEntityClass

public Class<? extends PhysicalEntity> getPhysicalEntityClass()

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class PhysicalEntityImpl