org.biopax.paxtools.impl.level3

Class SequenceEntityReferenceImpl

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.impl.level3.SequenceEntityReferenceImpl

All Implemented Interfaces:

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

Direct Known Subclasses:

NucleicAcidReferenceImpl, ProteinReferenceImpl

@Entity
public abstract class SequenceEntityReferenceImpl
extends EntityReferenceImpl
implements SequenceEntityReference

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
SequenceEntityReferenceImpl()

Method Summary

Modifier and Type	Method and Description
int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
BioSource	getOrganism() An organism, e.g.
String	getSequence() Polymer sequence in uppercase letters.
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setOrganism(BioSource organism) An organism, e.g.
void	setSequence(String sequence) Polymer sequence in uppercase letters.

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

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.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

getAnnotations, getModelInterface, getRDFId, isEquivalent

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

addEvidence, getEvidence, removeEvidence

Constructor Detail

SequenceEntityReferenceImpl

public SequenceEntityReferenceImpl()

Method Detail

getOrganism

public BioSource getOrganism()

Description copied from interface: SequenceEntityReference

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.

Specified by:

getOrganism in interface SequenceEntityReference

Returns:

the organism for this gene.

setOrganism

public void setOrganism(BioSource organism)

Description copied from interface: SequenceEntityReference

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.

Specified by:

setOrganism in interface SequenceEntityReference

Parameters:

organism - new organism for this gene

getSequence

@Field(name="sequence",
       analyze=YES)
public String getSequence()

Description copied from interface: SequenceEntityReference

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.

Specified by:

getSequence in interface SequenceEntityReference

Returns:

sequence - primary structure of a biopolymer.

setSequence

public void setSequence(String sequence)

Description copied from interface: SequenceEntityReference

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.

Specified by:

setSequence in interface SequenceEntityReference

Parameters:

sequence - Polymer sequence in uppercase letters.

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class BioPAXElementImpl

equivalenceCode

public int equivalenceCode()

Description copied from interface: BioPAXElement

If two elements are equivalent, then their equivalence code should be the same.

Specified by:

equivalenceCode in interface BioPAXElement

Overrides:

equivalenceCode in class XReferrableImpl

Returns:

an integer that is same across all equivalent entities.