org.biopax.paxtools.io.sif.level3

Class Group

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.EntityReferenceImpl

org.biopax.paxtools.io.sif.level3.Group

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, EntityReference, Level3Element, Named, Observable, UtilityClass, XReferrable

public class Group
extends EntityReferenceImpl

This class represents a grouping of EntityReferences strictly used by SIF rules for handling generics and complexes.

Author:

Emek Demir

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

Method Summary

Modifier and Type	Method and Description
void	addMember(EntityReference member)
void	addSubgroup(Group subgroup)
boolean	equals(Object o)
int	equivalenceCode()
Set<EntityReference>	getAllSimpleMembers()
Map<String,Object>	getAnnotations()
String	getRDFId()
String	groupTypeToString()
int	hashCode()
boolean	isComplex()
boolean	isEmpty()
boolean	isEquivalent(BioPAXElement element)
String	toString()

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

addEntityFeature, addEntityReferenceType, addEvidence, addMemberEntityReference, getEntityFeature, getEntityReferenceOf, getEntityReferenceType, getEvidence, getMemberEntityReference, getMemberEntityReferenceOf, getModelInterface, removeEntityFeature, removeEntityReferenceType, removeEvidence, removeMemberEntityReference, setEntityFeature, setEntityReferenceOf, setEntityReferenceType, setEvidence, setMemberEntity, setMemberEntityReference, setMemberEntityReferenceOf

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

getPk, semanticallyEquivalent

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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

Method Detail

getRDFId

public String getRDFId()

Specified by:

getRDFId in interface BioPAXElement

Overrides:

getRDFId in class BioPAXElementImpl

isEquivalent

public boolean isEquivalent(BioPAXElement element)

Specified by:

isEquivalent in interface BioPAXElement

Overrides:

isEquivalent in class BioPAXElementImpl

equivalenceCode

public int equivalenceCode()

Specified by:

equivalenceCode in interface BioPAXElement

Overrides:

equivalenceCode in class XReferrableImpl

addMember

public void addMember(EntityReference member)

addSubgroup

public void addSubgroup(Group subgroup)

isComplex

public boolean isComplex()

equals

public boolean equals(Object o)

Overrides:

equals in class BioPAXElementImpl

hashCode

public int hashCode()

Overrides:

hashCode in class BioPAXElementImpl

isEmpty

public boolean isEmpty()

toString

public String toString()

Overrides:

toString in class BioPAXElementImpl

getAnnotations

public Map<String,Object> getAnnotations()

Specified by:

getAnnotations in interface BioPAXElement

Overrides:

getAnnotations in class BioPAXElementImpl

groupTypeToString

public String groupTypeToString()

getAllSimpleMembers

public Set<EntityReference> getAllSimpleMembers()