fr.curie.BiNoM.pathways.biopax
Interface sequenceFeature

All Superinterfaces:

com.ibm.adtech.jastor.Thing, utilityClass

All Known Implementing Classes:

sequenceFeatureImpl

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

Interface for sequenceFeature 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#sequenceFeature)

RDF Schema Standard Properties
comment : Definition: A feature on a sequence relevant to an interaction, such as a binding site or post-translational modification. Examples: A phosphorylation on a protein.^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	FEATURE_DASH_LOCATIONProperty The Jena Property for FEATURE_DASH_LOCATION
static com.hp.hpl.jena.rdf.model.Property	FEATURE_DASH_TYPEProperty The Jena Property for FEATURE_DASH_TYPE
static com.hp.hpl.jena.rdf.model.Property	NAMEProperty The Jena Property for NAME
static com.hp.hpl.jena.rdf.model.Property	SHORT_DASH_NAMEProperty The Jena Property for SHORT_DASH_NAME
static com.hp.hpl.jena.rdf.model.Property	SYNONYMSProperty The Jena Property for SYNONYMS
static com.hp.hpl.jena.rdf.model.Resource	TYPE The rdf:type for this ontology class
static com.hp.hpl.jena.rdf.model.Property	XREFProperty The Jena Property for XREF

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

COMMENTProperty

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

copyright

Method Summary

sequenceLocation	addFEATURE_DASH_LOCATION() Adds an anonymous value for the 'FEATURE_DASH_LOCATION' property
sequenceLocation	addFEATURE_DASH_LOCATION(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'FEATURE_DASH_LOCATION' property.
void	addFEATURE_DASH_LOCATION(sequenceLocation FEATURE_DASH_LOCATION) Adds a value for the 'FEATURE_DASH_LOCATION' property
void	addSYNONYMS(java.lang.String SYNONYMS) Add a 'SYNONYMS' property value
xref	addXREF() Adds an anonymous value for the 'XREF' property
xref	addXREF(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'XREF' property.
void	addXREF(xref XREF) Adds a value for the 'XREF' property
java.util.Iterator	getFEATURE_DASH_LOCATION() Get an Iterator the 'FEATURE_DASH_LOCATION' property values.
openControlledVocabulary	getFEATURE_DASH_TYPE() Gets the 'FEATURE_DASH_TYPE' property value
java.lang.String	getNAME() Gets the 'NAME' property value
java.lang.String	getSHORT_DASH_NAME() Gets the 'SHORT_DASH_NAME' property value
java.util.Iterator	getSYNONYMS() Iterates through the 'SYNONYMS' property values.
java.util.Iterator	getXREF() Get an Iterator the 'XREF' property values.
void	removeFEATURE_DASH_LOCATION(sequenceLocation FEATURE_DASH_LOCATION) Removes a value for the 'FEATURE_DASH_LOCATION' property.
void	removeSYNONYMS(java.lang.String SYNONYMS) Remove a 'SYNONYMS' property value.
void	removeXREF(xref XREF) Removes a value for the 'XREF' property.
openControlledVocabulary	setFEATURE_DASH_TYPE() Sets the 'FEATURE_DASH_TYPE' property value to an anonymous node
void	setFEATURE_DASH_TYPE(openControlledVocabulary FEATURE_DASH_TYPE) Sets the 'FEATURE_DASH_TYPE' property value
openControlledVocabulary	setFEATURE_DASH_TYPE(com.hp.hpl.jena.rdf.model.Resource resource) Sets the 'FEATURE_DASH_TYPE' property value to the given resource, and add's rdf:type properties.
void	setNAME(java.lang.String NAME) Sets the 'NAME' property value
void	setSHORT_DASH_NAME(java.lang.String SHORT_DASH_NAME) Sets the 'SHORT_DASH_NAME' property value

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

FEATURE_DASH_TYPEProperty

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

The Jena Property for FEATURE_DASH_TYPE

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

RDF Schema Standard Properties
comment : Description and classification of the feature.^^http://www.w3.org/2001/XMLSchema#string

FEATURE_DASH_LOCATIONProperty

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

The Jena Property for FEATURE_DASH_LOCATION

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

RDF Schema Standard Properties
comment : Location of the feature on the sequence of the interactor. One feature may have more than one location, used e.g. for features which involve sequence positions close in the folded, three-dimensional state of a protein, but non-continuous along the sequence.^^http://www.w3.org/2001/XMLSchema#string

SHORT_DASH_NAMEProperty

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

The Jena Property for SHORT_DASH_NAME

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

RDF Schema Standard Properties
comment : An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application.^^http://www.w3.org/2001/XMLSchema#string

SYNONYMSProperty

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

The Jena Property for SYNONYMS

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

RDF Schema Standard Properties
comment : One or more synonyms for the name of this entity. This should include the values of the NAME and SHORT-NAME property so that it is easy to find all known names in one place.@en

NAMEProperty

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

The Jena Property for NAME

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

RDF Schema Standard Properties
comment : The preferred full name for this entity.@en

XREFProperty

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

The Jena Property for XREF

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

RDF Schema Standard Properties
comment : Values of this property define external cross-references from this entity to entities in external databases.@en

Method Detail

getFEATURE_DASH_TYPE

openControlledVocabulary getFEATURE_DASH_TYPE()
                                              throws com.ibm.adtech.jastor.JastorException

Gets the 'FEATURE_DASH_TYPE' property value

Returns:

openControlledVocabulary

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

FEATURE_DASH_TYPEProperty

setFEATURE_DASH_TYPE

void setFEATURE_DASH_TYPE(openControlledVocabulary FEATURE_DASH_TYPE)
                          throws com.ibm.adtech.jastor.JastorException

Sets the 'FEATURE_DASH_TYPE' property value

Parameters:

{@link - fr.curie.BiNoM.pathways.biopax.openControlledVocabulary}

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

FEATURE_DASH_TYPEProperty

setFEATURE_DASH_TYPE

openControlledVocabulary setFEATURE_DASH_TYPE()
                                              throws com.ibm.adtech.jastor.JastorException

Sets the 'FEATURE_DASH_TYPE' property value to an anonymous node

Returns:

openControlledVocabulary, the created value

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

FEATURE_DASH_TYPEProperty

setFEATURE_DASH_TYPE

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

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

Parameters:

{@link - com.hp.hpl.jena.rdf.model.Resource} must not be be null.

Returns:

openControlledVocabulary, the newly created value

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

FEATURE_DASH_TYPEProperty

getFEATURE_DASH_LOCATION

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

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

Returns:

Iterator of sequenceLocation

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

FEATURE_DASH_LOCATIONProperty

addFEATURE_DASH_LOCATION

void addFEATURE_DASH_LOCATION(sequenceLocation FEATURE_DASH_LOCATION)
                              throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'FEATURE_DASH_LOCATION' property

Parameters:

The - sequenceLocation to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

FEATURE_DASH_LOCATIONProperty

addFEATURE_DASH_LOCATION

sequenceLocation addFEATURE_DASH_LOCATION()
                                          throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'FEATURE_DASH_LOCATION' property

Returns:

The anoymous sequenceLocation created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

FEATURE_DASH_LOCATIONProperty

addFEATURE_DASH_LOCATION

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

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

FEATURE_DASH_LOCATIONProperty

removeFEATURE_DASH_LOCATION

void removeFEATURE_DASH_LOCATION(sequenceLocation FEATURE_DASH_LOCATION)
                                 throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'FEATURE_DASH_LOCATION' 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 - sequenceLocation to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

FEATURE_DASH_LOCATIONProperty

getSHORT_DASH_NAME

java.lang.String getSHORT_DASH_NAME()
                                    throws com.ibm.adtech.jastor.JastorException

Gets the 'SHORT_DASH_NAME' property value

Returns:

String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

SHORT_DASH_NAMEProperty

setSHORT_DASH_NAME

void setSHORT_DASH_NAME(java.lang.String SHORT_DASH_NAME)
                        throws com.ibm.adtech.jastor.JastorException

Sets the 'SHORT_DASH_NAME' property value

Parameters:

{@link - java.lang.String}

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

SHORT_DASH_NAMEProperty

getSYNONYMS

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

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

Returns:

Iterator of String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

SYNONYMSProperty

addSYNONYMS

void addSYNONYMS(java.lang.String SYNONYMS)
                 throws com.ibm.adtech.jastor.JastorException

Add a 'SYNONYMS' property value

Parameters:

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

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

SYNONYMSProperty

removeSYNONYMS

void removeSYNONYMS(java.lang.String SYNONYMS)
                    throws com.ibm.adtech.jastor.JastorException

Remove a 'SYNONYMS' 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:

SYNONYMSProperty

getNAME

java.lang.String getNAME()
                         throws com.ibm.adtech.jastor.JastorException

Gets the 'NAME' property value

Returns:

String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

NAMEProperty

setNAME

void setNAME(java.lang.String NAME)
             throws com.ibm.adtech.jastor.JastorException

Sets the 'NAME' property value

Parameters:

{@link - java.lang.String}

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

NAMEProperty

getXREF

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

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

Returns:

Iterator of xref

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

XREFProperty

addXREF

void addXREF(xref XREF)
             throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'XREF' property

Parameters:

The - xref to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

XREFProperty

addXREF

xref addXREF()
             throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'XREF' property

Returns:

The anoymous xref created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

XREFProperty

addXREF

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

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

XREFProperty

removeXREF

void removeXREF(xref XREF)
                throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'XREF' 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 - xref to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

XREFProperty