fr.curie.BiNoM.pathways.biopax
Interface dna

All Superinterfaces:

entity, physicalEntity, com.ibm.adtech.jastor.Thing

All Known Implementing Classes:

dnaImpl

public interface dna
extends physicalEntity, com.ibm.adtech.jastor.Thing

Interface for dna ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

(URI: http://www.biopax.org/release/biopax-level2.owl#dna)

RDF Schema Standard Properties
comment : Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid. Comment: This is not a 'gene', since gene is a genetic concept, not a physical entity. The concept of a gene may be added later in BioPAX. Examples: a chromosome, a plasmid. A specific example is chromosome 7 of Homo sapiens.^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	ORGANISMProperty The Jena Property for ORGANISM
static com.hp.hpl.jena.rdf.model.Property	SEQUENCEProperty The Jena Property for SEQUENCE
static com.hp.hpl.jena.rdf.model.Resource	TYPE The rdf:type for this ontology class

Fields inherited from interface fr.curie.BiNoM.pathways.biopax.entity

AVAILABILITYProperty, COMMENTProperty, DATA_DASH_SOURCEProperty, NAMEProperty, SHORT_DASH_NAMEProperty, SYNONYMSProperty, XREFProperty

Fields inherited from interface com.ibm.adtech.jastor.Thing

copyright

Method Summary

bioSource	addORGANISM() Adds an anonymous value for the 'ORGANISM' property
void	addORGANISM(bioSource ORGANISM) Adds a value for the 'ORGANISM' property
bioSource	addORGANISM(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'ORGANISM' property.
void	addSEQUENCE(java.lang.String SEQUENCE) Add a 'SEQUENCE' property value
java.util.Iterator	getORGANISM() Get an Iterator the 'ORGANISM' property values.
java.util.Iterator	getSEQUENCE() Iterates through the 'SEQUENCE' property values.
void	removeORGANISM(bioSource ORGANISM) Removes a value for the 'ORGANISM' property.
void	removeSEQUENCE(java.lang.String SEQUENCE) Remove a 'SEQUENCE' property value.

Methods inherited from interface fr.curie.BiNoM.pathways.biopax.entity

addAVAILABILITY, addCOMMENT, addDATA_DASH_SOURCE, addDATA_DASH_SOURCE, addDATA_DASH_SOURCE, addSYNONYMS, addXREF, addXREF, addXREF, getAVAILABILITY, getCOMMENT, getDATA_DASH_SOURCE, getNAME, getSHORT_DASH_NAME, getSYNONYMS, getXREF, removeAVAILABILITY, removeCOMMENT, removeDATA_DASH_SOURCE, removeSYNONYMS, removeXREF, setNAME, setSHORT_DASH_NAME

Methods inherited from interface com.ibm.adtech.jastor.Thing

clearCache, isRDFType, listStatements, model, registerListener, removeStatements, resource, unregisterListener, uri

Field Detail

TYPE

static final com.hp.hpl.jena.rdf.model.Resource TYPE

The rdf:type for this ontology class

SEQUENCEProperty

static final com.hp.hpl.jena.rdf.model.Property SEQUENCEProperty

The Jena Property for SEQUENCE

(URI: http://www.biopax.org/release/biopax-level2.owl#SEQUENCE)

RDF Schema Standard Properties
comment : 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.@en

ORGANISMProperty

static final com.hp.hpl.jena.rdf.model.Property ORGANISMProperty

The Jena Property for ORGANISM

(URI: http://www.biopax.org/release/biopax-level2.owl#ORGANISM)

RDF Schema Standard Properties
comment : 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.@en

Method Detail

getSEQUENCE

java.util.Iterator getSEQUENCE()
                               throws com.ibm.adtech.jastor.JastorException

Iterates through the 'SEQUENCE' property values. This Iteartor may be used to remove all such values.

Returns:

Iterator of String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

SEQUENCEProperty

addSEQUENCE

void addSEQUENCE(java.lang.String SEQUENCE)
                 throws com.ibm.adtech.jastor.JastorException

Add a 'SEQUENCE' property value

Parameters:

{@link - java.lang.String}, the value to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

SEQUENCEProperty

removeSEQUENCE

void removeSEQUENCE(java.lang.String SEQUENCE)
                    throws com.ibm.adtech.jastor.JastorException

Remove a 'SEQUENCE' property value. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Parameters:

{@link - java.lang.String}, the value to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

SEQUENCEProperty

getORGANISM

java.util.Iterator getORGANISM()
                               throws com.ibm.adtech.jastor.JastorException

Get an Iterator the 'ORGANISM' property values. This Iteartor may be used to remove all such values.

Returns:

Iterator of bioSource

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty

addORGANISM

void addORGANISM(bioSource ORGANISM)
                 throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'ORGANISM' property

Parameters:

The - bioSource to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty

addORGANISM

bioSource addORGANISM()
                      throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'ORGANISM' property

Returns:

The anoymous bioSource created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty

addORGANISM

bioSource addORGANISM(com.hp.hpl.jena.rdf.model.Resource resource)
                      throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'ORGANISM' property. This method is equivalent constructing a new instance of bioSource with the factory and calling addORGANISM(fr.curie.BiNoM.pathways.biopax.bioSource ORGANISM) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#bioSource. That is, this method should not be used as a shortcut for creating new objects in the model.

Parameters:

The - om.hp.hpl.jena.rdf.model.Resource to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty

removeORGANISM

void removeORGANISM(bioSource ORGANISM)
                    throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'ORGANISM' property. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Parameters:

The - bioSource to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty