fr.curie.BiNoM.pathways.biopax
Interface pathwayStep

All Superinterfaces:

com.ibm.adtech.jastor.Thing, utilityClass

All Known Implementing Classes:

pathwayStepImpl

public interface pathwayStep
extends utilityClass, com.ibm.adtech.jastor.Thing

Interface for pathwayStep 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#pathwayStep)

RDF Schema Standard Properties
comment : Definition: A step in a pathway. Comment: Multiple interactions may occur in a pathway step, each should be listed in the STEP-INTERACTIONS property. Order relationships between pathway steps may be established with the NEXT-STEP slot. This order may not be temporally meaningful for specific steps, such as for a pathway loop or a reversible reaction, but represents a directed graph of step relationships that can be useful for describing the overall flow of a pathway, as may be useful in a pathway diagram. Example: A metabolic pathway may contain a pathway step composed of one biochemical reaction (BR1) and one catalysis (CAT1) instance, where CAT1 describes the catalysis of BR1.^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	NEXT_DASH_STEPProperty The Jena Property for NEXT_DASH_STEP
static com.hp.hpl.jena.rdf.model.Property	STEP_DASH_INTERACTIONSProperty The Jena Property for STEP_DASH_INTERACTIONS
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.utilityClass

COMMENTProperty

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

copyright

Method Summary

pathwayStep	addNEXT_DASH_STEP() Adds an anonymous value for the 'NEXT_DASH_STEP' property
void	addNEXT_DASH_STEP(pathwayStep NEXT_DASH_STEP) Adds a value for the 'NEXT_DASH_STEP' property
pathwayStep	addNEXT_DASH_STEP(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'NEXT_DASH_STEP' property.
interaction	addSTEP_DASH_INTERACTIONS_asinteraction() Adds an anonymous value for the 'STEP_DASH_INTERACTIONS' property
interaction	addSTEP_DASH_INTERACTIONS_asinteraction(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'STEP_DASH_INTERACTIONS' property.
pathway	addSTEP_DASH_INTERACTIONS_aspathway() Adds an anonymous value for the 'STEP_DASH_INTERACTIONS' property
pathway	addSTEP_DASH_INTERACTIONS_aspathway(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'STEP_DASH_INTERACTIONS' property.
void	addSTEP_DASH_INTERACTIONS(interaction STEP_DASH_INTERACTIONS) Adds a value for the 'STEP_DASH_INTERACTIONS' property
void	addSTEP_DASH_INTERACTIONS(pathway STEP_DASH_INTERACTIONS) Adds a value for the 'STEP_DASH_INTERACTIONS' property
java.util.Iterator	getNEXT_DASH_STEP() Get an Iterator the 'NEXT_DASH_STEP' property values.
java.util.Iterator	getSTEP_DASH_INTERACTIONS_asinteraction() Get an Iterator the 'STEP_DASH_INTERACTIONS' property values.
java.util.Iterator	getSTEP_DASH_INTERACTIONS_aspathway() Get an Iterator the 'STEP_DASH_INTERACTIONS' property values.
void	removeNEXT_DASH_STEP(pathwayStep NEXT_DASH_STEP) Removes a value for the 'NEXT_DASH_STEP' property.
void	removeSTEP_DASH_INTERACTIONS(interaction STEP_DASH_INTERACTIONS) Removes a value for the 'STEP_DASH_INTERACTIONS' property.
void	removeSTEP_DASH_INTERACTIONS(pathway STEP_DASH_INTERACTIONS) Removes a value for the 'STEP_DASH_INTERACTIONS' property.

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

addCOMMENT, getCOMMENT, removeCOMMENT

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

NEXT_DASH_STEPProperty

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

The Jena Property for NEXT_DASH_STEP

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

RDF Schema Standard Properties
comment : The next step(s) of the pathway. Contains zero or more pathwayStep instances. If there is no next step, this property is empty.^^http://www.w3.org/2001/XMLSchema#string

STEP_DASH_INTERACTIONSProperty

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

The Jena Property for STEP_DASH_INTERACTIONS

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

RDF Schema Standard Properties
comment : The interactions that take place at this step of the pathway.^^http://www.w3.org/2001/XMLSchema#string

Method Detail

getNEXT_DASH_STEP

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

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

Returns:

Iterator of pathwayStep

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

NEXT_DASH_STEPProperty

addNEXT_DASH_STEP

void addNEXT_DASH_STEP(pathwayStep NEXT_DASH_STEP)
                       throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'NEXT_DASH_STEP' property

Parameters:

The - pathwayStep to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

NEXT_DASH_STEPProperty

addNEXT_DASH_STEP

pathwayStep addNEXT_DASH_STEP()
                              throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'NEXT_DASH_STEP' property

Returns:

The anoymous pathwayStep created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

NEXT_DASH_STEPProperty

addNEXT_DASH_STEP

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

Adds a value for the 'NEXT_DASH_STEP' property. This method is equivalent constructing a new instance of pathwayStep with the factory and calling addNEXT_DASH_STEP(fr.curie.BiNoM.pathways.biopax.pathwayStep NEXT_DASH_STEP) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#pathwayStep. 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:

NEXT_DASH_STEPProperty

removeNEXT_DASH_STEP

void removeNEXT_DASH_STEP(pathwayStep NEXT_DASH_STEP)
                          throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'NEXT_DASH_STEP' 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 - pathwayStep to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

NEXT_DASH_STEPProperty

getSTEP_DASH_INTERACTIONS_asinteraction

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

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

Returns:

Iterator of interaction

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STEP_DASH_INTERACTIONSProperty

addSTEP_DASH_INTERACTIONS

void addSTEP_DASH_INTERACTIONS(interaction STEP_DASH_INTERACTIONS)
                               throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'STEP_DASH_INTERACTIONS' property

Parameters:

The - interaction to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STEP_DASH_INTERACTIONSProperty

addSTEP_DASH_INTERACTIONS_asinteraction

interaction addSTEP_DASH_INTERACTIONS_asinteraction()
                                                    throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'STEP_DASH_INTERACTIONS' property

Returns:

The anoymous interaction created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STEP_DASH_INTERACTIONSProperty

addSTEP_DASH_INTERACTIONS_asinteraction

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

Adds a value for the 'STEP_DASH_INTERACTIONS' property. This method is equivalent constructing a new instance of interaction with the factory and calling addSTEP_DASH_INTERACTIONS(fr.curie.BiNoM.pathways.biopax.interaction STEP_DASH_INTERACTIONS) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#interaction. 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:

STEP_DASH_INTERACTIONSProperty

removeSTEP_DASH_INTERACTIONS

void removeSTEP_DASH_INTERACTIONS(interaction STEP_DASH_INTERACTIONS)
                                  throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'STEP_DASH_INTERACTIONS' 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 - interaction to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STEP_DASH_INTERACTIONSProperty

getSTEP_DASH_INTERACTIONS_aspathway

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

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

Returns:

Iterator of pathway

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STEP_DASH_INTERACTIONSProperty

addSTEP_DASH_INTERACTIONS

void addSTEP_DASH_INTERACTIONS(pathway STEP_DASH_INTERACTIONS)
                               throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'STEP_DASH_INTERACTIONS' property

Parameters:

The - pathway to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STEP_DASH_INTERACTIONSProperty

addSTEP_DASH_INTERACTIONS_aspathway

pathway addSTEP_DASH_INTERACTIONS_aspathway()
                                            throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'STEP_DASH_INTERACTIONS' property

Returns:

The anoymous pathway created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STEP_DASH_INTERACTIONSProperty

addSTEP_DASH_INTERACTIONS_aspathway

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

Adds a value for the 'STEP_DASH_INTERACTIONS' property. This method is equivalent constructing a new instance of pathway with the factory and calling addSTEP_DASH_INTERACTIONS(fr.curie.BiNoM.pathways.biopax.pathway STEP_DASH_INTERACTIONS) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#pathway. 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:

STEP_DASH_INTERACTIONSProperty

removeSTEP_DASH_INTERACTIONS

void removeSTEP_DASH_INTERACTIONS(pathway STEP_DASH_INTERACTIONS)
                                  throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'STEP_DASH_INTERACTIONS' 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 - pathway to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STEP_DASH_INTERACTIONSProperty