org.biopax.paxtools.model.level3

Interface SequenceEntityReference

All Superinterfaces:

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

All Known Subinterfaces:

DnaReference, DnaRegionReference, NucleicAcidReference, NucleicAcidRegionReference, ProteinReference, RnaReference, RnaRegionReference

All Known Implementing Classes:

DnaReferenceImpl, DnaRegionReferenceImpl, NucleicAcidReferenceImpl, NucleicAcidRegionReferenceImpl, ProteinReferenceImpl, RnaReferenceImpl, RnaRegionReferenceImpl, SequenceEntityReferenceImpl

public interface SequenceEntityReference
extends EntityReference

Tagger interface for protein, dna and rna entities

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

Modifier and Type	Method and Description
BioSource	getOrganism() An organism, e.g.
String	getSequence() Polymer sequence in uppercase letters.
void	setOrganism(BioSource source) An organism, e.g.
void	setSequence(String sequence) Polymer sequence in uppercase letters.

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, 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, getModelInterface, getUri, isEquivalent

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

addEvidence, getEvidence, removeEvidence

Method Detail

getOrganism

BioSource getOrganism()

An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.

Returns:

the organism for this gene.

setOrganism

void setOrganism(BioSource source)

An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.

Parameters:

source - new organism for this gene

getSequence

String getSequence()

Polymer sequence in uppercase letters. For DNA, usually A,C,G,T letters representing the nucleosides of adenine, cytosine, guanine and thymine, respectively; for RNA, usually A, C, U, G; for protein, usually the letters corresponding to the 20 letter IUPAC amino acid code.

Returns:

sequence - primary structure of a biopolymer.

setSequence

void setSequence(String sequence)

Polymer sequence in uppercase letters. For DNA, usually A,C,G,T letters representing the nucleosides of adenine, cytosine, guanine and thymine, respectively; for RNA, usually A, C, U, G; for protein, usually the letters corresponding to the 20 letter IUPAC amino acid code.

Parameters:

sequence - Polymer sequence in uppercase letters.