org.biopax.paxtools.impl.level3

Class L3ElementImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, Level3Element

Direct Known Subclasses:

ChemicalConstantImpl, ChemicalStructureImpl, EntityFeatureImpl, ExperimentalFormImpl, PathwayStepImpl, SequenceLocationImpl, StoichiometryImpl, XReferrableImpl, XrefImpl

@Entity
public abstract class L3ElementImpl
extends BioPAXElementImpl
implements Level3Element

Base BioPAX Level3 element.

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
L3ElementImpl()

Method Summary

Modifier and Type	Method and Description
void	addComment(String COMMENT) A textual comment about this individual.
Set<String>	getComment() A textual comment about this individual.
Set<Provenance>	getDatasources() Deprecated. use getAnnotations() instead
Set<String>	getKeywords() Deprecated. use getAnnotations() instead
Set<BioSource>	getOrganisms() Deprecated. use getAnnotations() instead
Set<Pathway>	getParentPathways() Deprecated. use getAnnotations() instead
void	removeComment(String COMMENT) A textual comment about this individual.
void	setComment(Set<String> comment)

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

equals, equivalenceCode, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, semanticallyEquivalent, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Constructor Detail

L3ElementImpl

public L3ElementImpl()

Method Detail

getComment

@Field(name="comment",
       analyze=YES,
       bridge=@FieldBridge(impl=SetStringBridge.class))
public Set<String> getComment()

Description copied from interface: Level3Element

A textual comment about this individual. This property should be used instead of the OWL documentation elements (rdfs:comment) for instances because information in 'comment' is data to be exchanged, whereas the rdfs:comment field is used for metadata about the structure of the BioPAX ontology. Contents of this set should not be modified. Use Add/Remove instead.

Specified by:

getComment in interface Level3Element

Returns:

A textual comment about this individual.

setComment

public void setComment(Set<String> comment)

addComment

public void addComment(String COMMENT)

Description copied from interface: Level3Element

A textual comment about this individual. This property should be used instead of the OWL documentation elements (rdfs:comment) for instances because information in 'comment' is data to be exchanged, whereas the rdfs:comment field is used for metadata about the structure of the BioPAX ontology. Contents of this set should not be modified. Use Add/Remove instead.

Specified by:

addComment in interface Level3Element

Parameters:

COMMENT - A textual comment about this individual.

removeComment

public void removeComment(String COMMENT)

Description copied from interface: Level3Element

A textual comment about this individual. This property should be used instead of the OWL documentation elements (rdfs:comment) for instances because information in 'comment' is data to be exchanged, whereas the rdfs:comment field is used for metadata about the structure of the BioPAX ontology. Contents of this set should not be modified. Use Add/Remove instead.

Specified by:

removeComment in interface Level3Element

Parameters:

COMMENT - A textual comment about this individual.

getKeywords

@Deprecated
 @Field(name="keyword",
       store=YES,
       analyze=YES)
 @FieldBridge(impl=SetStringBridge.class)
public Set<String> getKeywords()

Deprecated. use getAnnotations() instead

A non-public transient method (not stored in the db table) to create the 'keyword' full-text index field by aggregating biopax data field values from all child elements. This method may be called once per biopax element by the Hibernate Search framework (indexer), if it is used, or never called.

Returns:

keywords, annotations associated with the biopax element

getOrganisms

@Deprecated
 @Field(name="organism",
       store=YES,
       analyze=NO)
 @FieldBridge(impl=OrganismFieldBridge.class)
public Set<BioSource> getOrganisms()

Deprecated. use getAnnotations() instead

A transient method (not stored in the db table) to create the 'organism' full-text index field used then both for searching and filtering (important). This method may be called once per biopax element by the Hibernate Search framework (indexer), or never called.

Returns:

organisms (if any set/inferred explicitly by some external app.)

getDatasources

@Deprecated
 @Field(name="dataSource",
       store=YES,
       analyze=NO)
 @FieldBridge(impl=DataSourceFieldBridge.class)
public Set<Provenance> getDatasources()

Deprecated. use getAnnotations() instead

A transient method (not stored in the db table) to create the 'datasource' full-text index field used then both for searching and filtering (important). This method may be called once per biopax element by the Hibernate Search framework (indexer), if used, or never called otherwise.

Returns:

data sources (if set/inferred by some external app.)

getParentPathways

@Deprecated
 @Field(name="pathway",
       store=YES,
       analyze=NO)
 @FieldBridge(impl=ParentPathwayFieldBridge.class)
public Set<Pathway> getParentPathways()

Deprecated. use getAnnotations() instead

An transient method (not stored in the db table), not trivial one, to create the 'pathway' full-text index field used then both for searching and especially annotating search hits. Parent pathways can be inferred and updated once the BioPAX model is built and complete. This method may be called once per biopax element by the Hibernate Search framework (indexer), or never called.

Returns:

parent pathways (if explicitly inferred and set by some external tool)