org.biopax.paxtools.model.level3
Interface DnaReference

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, EntityReference, Level3Element, Named, NucleicAcidReference, Observable, SequenceEntityReference, java.io.Serializable, UtilityClass, XReferrable

All Known Implementing Classes:

DnaReferenceImpl

public interface DnaReference
extends NucleicAcidReference

A DNA reference is a grouping of several DNA entities that are common in sequence and genomic position. Members can differ in celular location, sequence features, SNPs, mutations and bound partners. For more detailed information on semantics see EntityReference.

Comments : Note that this is not a reference gene. A gene can possibly span multiple DNA molecules, sometimes even across chromosomes due to regulatory regions. Similarly a gene is not necessarily made up of deoxyribonucleic acid and can be present in multiple copies ( which are different DNA molecules).

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

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

addSubRegion, getSubRegion, removeSubRegion

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

getOrganism, getSequence, setOrganism, setSequence

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

addEntityFeature, addEntityReferenceType, addMemberEntityReference, getEntityFeature, getEntityReferenceOf, getEntityReferenceType, getMemberEntityReference, getMemberEntityReferenceOf, removeEntityFeature, removeEntityReferenceType, removeMemberEntityReference

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

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

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

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

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

addEvidence, getEvidence, removeEvidence