org.biopax.paxtools.impl.level3
Class ProteinImpl

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.ProteinImpl

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, BioPAXElement, Controller, Entity, Level3Element, Named, Observable, PhysicalEntity, Protein, SimplePhysicalEntity, XReferrable

@Entity
@Indexed
public class ProteinImpl
extends SimplePhysicalEntityImpl
implements Protein

See Also:

Serialized Form

Field Summary

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

SEARCH_FIELD_AVAILABILITY, SEARCH_FIELD_COMMENT, SEARCH_FIELD_EC_NUMBER, SEARCH_FIELD_KEYWORD, SEARCH_FIELD_NAME, SEARCH_FIELD_SEQUENCE, SEARCH_FIELD_TERM, SEARCH_FIELD_XREF_DB, SEARCH_FIELD_XREF_ID, SEARCH_INDEX_NAME

Constructor Summary

ProteinImpl()

Method Summary

java.lang.Class<? extends Protein>

getModelInterface() Overridden to provide better downcasting

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

equivalenceCode, getEntityReference, getEntityReferenceX, getGenericEntityReferences, semanticallyEquivalent, setEntityReference, setEntityReferenceX

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

addFeature, addMemberPhysicalEntity, addNotFeature, 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, getNameX, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setNameX, setStandardName, setStandardNameX

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

addXref, getXref, hasCommonUnificationXref, 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

getAnnotations, getProxyId, getRDFId, getVersion, isEquivalent, setProxyId, setRDFId, setVersion, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

getEntityReference, getGenericEntityReferences, setEntityReference

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, setStandardName

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

addXref, getXref, removeXref

Constructor Detail

ProteinImpl

public ProteinImpl()

Method Detail

getModelInterface

public java.lang.Class<? extends Protein> 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.