org.biopax.paxtools.impl.level3

Class NamedImpl

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

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, Level3Element, Named, XReferrable

Direct Known Subclasses:

BioSourceImpl, EntityImpl, EntityReferenceImpl, ProvenanceImpl

@Entity
public abstract class NamedImpl
extends XReferrableImpl
implements Named

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
NamedImpl()

Method Summary

Modifier and Type	Method and Description
void	addName(String name) This method adds the given value to the name set.
String	getDisplayName() 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.
protected String	getDisplayNameX()
Set<String>	getName() Names for this entity, including standardName and shortName if defined.
String	getStandardName() The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.
protected String	getStandardNameX()
void	removeName(String name) This method removes the given value from the name set.
void	setDisplayName(String displayName) 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.
protected void	setDisplayNameX(String displayName)
void	setName(Set<String> names) This method is reserved for batch operations and should not be used for normal use.
void	setStandardName(String name) The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.
protected void	setStandardNameX(String name)

Methods inherited from class org.biopax.paxtools.impl.level3.XReferrableImpl

addXref, equivalenceCode, 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, 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.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

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Constructor Detail

NamedImpl

public NamedImpl()

Method Detail

getStandardNameX

@Field(name="name",
       analyze=YES,
       boost=@Boost(value=3.0f))
protected String getStandardNameX()

setStandardNameX

protected void setStandardNameX(String name)

getStandardName

public String getStandardName()

Description copied from interface: Named

The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.

Specified by:

getStandardName in interface Named

Returns:

standard name for this entity

setStandardName

public void setStandardName(String name)

Description copied from interface: Named

The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.

Specified by:

setStandardName in interface Named

Parameters:

name - standard name for this entity

getDisplayNameX

@Field(name="name",
       analyze=YES,
       boost=@Boost(value=2.5f))
protected String getDisplayNameX()

setDisplayNameX

protected void setDisplayNameX(String displayName)

getDisplayName

public String getDisplayName()

Description copied from interface: Named

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.

Specified by:

getDisplayName in interface Named

Returns:

An abbreviated name for this entity

setDisplayName

public void setDisplayName(String displayName)

Description copied from interface: Named

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.

Specified by:

setDisplayName in interface Named

Parameters:

displayName - new display name (preferably a short one)

getName

@Field(name="name",
       analyze=YES,
       boost=@Boost(value=2.5f),
       bridge=@FieldBridge(impl=SetStringBridge.class))
public Set<String> getName()

Description copied from interface: Named

Names for this entity, including standardName and shortName if defined. The contents of this set can be modified directly but semantic consistency is not guaranteed. Using Named.addName(java.lang.String) and Named.removeName(java.lang.String) is recommended.

Specified by:

getName in interface Named

Returns:

Names for this entity, including standardName and shortName if defined.

setName

public void setName(Set<String> names)

Description copied from interface: Named

This method is reserved for batch operations and should not be used for normal use. Use add/remove name methods to manipulate the names instead.

Specified by:

setName in interface Named

Parameters:

names - new names to set (or replace all existing ones)

addName

public void addName(String name)

Description copied from interface: Named

This method adds the given value to the name set.

Specified by:

addName in interface Named

Parameters:

name - a new name to be added

removeName

public void removeName(String name)

Description copied from interface: Named

This method removes the given value from the name set.

Specified by:

removeName in interface Named

Parameters:

name - a new name to be removed