gov.nih.nlm.umls.meta.impl
Class AtomImpl

java.lang.Object
  gov.nih.nlm.umls.meta.impl.PlaceholderAtom
      gov.nih.nlm.umls.meta.impl.AtomImpl

All Implemented Interfaces:

Atom, ConceptElement, ContentViewElement, SourceElement, SuppressibleElement, Comparable

public class AtomImpl
extends PlaceholderAtom

Default implementation of the Atom interface.

Author:

Brian Carlsen, Deborah Shapiro

Nested Class Summary

Nested classes/interfaces inherited from interface gov.nih.nlm.umls.meta.Atom

Atom.AtomRankComparator, Atom.ByLanguageRestrictor

Nested classes/interfaces inherited from interface gov.nih.nlm.umls.meta.SourceElement

SourceElement.BySourceComparator, SourceElement.BySourceRestrictor

Field Summary

Fields inherited from class gov.nih.nlm.umls.meta.impl.PlaceholderAtom

aui, code, concept, cvf, ispref, key_fields, key_fields_flag, lat, lui, saui, scui, sdui, source, str, stt, sui, suppress, ts, tty

Constructor Summary

AtomImpl()
Instantiates an empty Atom.

AtomImpl(Atom atom)
Instantiates an Atom from the specified Atom.

Method Summary

void	addAttribute(AtomAttribute att) Adds the specified AtomAttribute.
void	addContext(Context cxt) Adds the specified Context.
void	addCoocurrence(Coocurrence coc) Adds the specified Coocurrence.
void	addDefinition(Definition def) Adds the specified Definition.
void	addLocator(Locator loc) Add the specified Locator.
void	addRelationship(Relationship rel) Adds the specified Relationship.
void	clearAttributes() Remove all AtomAttributes.
void	clearContexts() Remove all Contexts.
void	clearCoocurrences() Remove all Coocurrences.
void	clearDefinitions() Remove all Definitions.
void	clearLocators() Remove all Locators.
void	clearRelationships() Remove all Relationships.
AtomAttribute[]	getAttributes() Returns the AtomAttributes.
List	getAttributesAsList() Returns the AtomAttributes as a List.
Context[]	getContexts() Return the Contexts.
List	getContextsAsList() Returns the Contexts as a List.
Coocurrence[]	getCoocurrences() Returns the Coocurrences.
List	getCoocurrencesAsList() Returns the Coocurrences as a List.
Definition[]	getDefinitions() Returns the Definitions.
List	getDefinitionsAsList() Returns the Definitions as a List.
String	getKeyFields() Returns a String key which can be used by equals, compareTo, and hashCode methods.
Locator[]	getLocators() Returns the Locators.
List	getLocatorsAsList() Returns the Locators as a List.
Relationship[]	getRelationships() Returns the Relationships.
Relationship[]	getRelationships(Restrictor restrictor) Returns a subset of this Atom's Relationships.
List	getRelationshipsAsList() Returns the Relationships as a List.
void	removeAttribute(AtomAttribute att) Removes the specified AtomAttribute.
void	removeContext(Context cxt) Removes the specified Context.
void	removeCoocurrence(Coocurrence coc) Removes the specified Coocurrence.
void	removeDefinition(Definition def) Remove the specified Definition.
void	removeLocator(Locator loc) Removes the specified Locator.
void	removeRelationship(Relationship rel) Removes the specified Relationship.
void	setAttributes(AtomAttribute[] atts) Replace AtomAttributes with the ones in the specified array.
void	setAttributes(List atts) Replace AtomAttributes with the ones in the specified List.
void	setContexts(Context[] cxts) Replace Contexts with the ones in the specified array.
void	setContexts(List cxts) Replace Contexts with the ones in the specified List.
void	setCoocurrences(Coocurrence[] cocs) Replace Coocurrences with the ones in the specified array.
void	setCoocurrences(List cocs) Replace Coocurrences with the ones in the specified List.
void	setDefinitions(Definition[] defs) Replace Definitions with the ones in the specified array.
void	setDefinitions(List defs) Replace Definitions with the ones in the specified List.
void	setLocators(List locs) Replace Locators with the ones in the specified List.
void	setLocators(Locator[] locs) Replace Locators with the ones in the specified array.
void	setRelationships(List rels) Replace Relationships of the ones in the specified List.
void	setRelationships(Relationship[] rels) Replace Relationships with the ones in the specified array.

Methods inherited from class gov.nih.nlm.umls.meta.impl.PlaceholderAtom

compareTo, equals, getAtomIdentifier, getAui, getCode, getConcept, getContentView, getCvf, getIspref, getLanguage, getLat, getLui, getName, getSaui, getScui, getSdui, getSource, getSourceAtomIdentifier, getSourceConceptIdentifier, getSourceDescriptor, getStr, getStringIdentifier, getStringType, getStt, getSui, getSuppress, getTermIdentifier, getTermStatus, getTermType, getTs, getTty, hashCode, hasPreferredAtomIdentifier, hasPreferredAui, hasPreferredLui, hasPreferredStringIdentifier, hasPreferredSui, hasPreferredTermIdentifier, isObsolete, isSuppressible, setAtomIdentifier, setAui, setCode, setConcept, setContentView, setCvf, setIspref, setLanguage, setLat, setLui, setName, setSaui, setScui, setSdui, setSource, setSourceAtomIdentifier, setSourceConceptIdentifier, setSourceDescriptor, setStr, setStringIdentifier, setStringType, setStt, setSui, setSuppress, setTermIdentifier, setTermStatus, setTermType, setTs, setTty

Methods inherited from class java.lang.Object

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

Constructor Detail

AtomImpl

public AtomImpl()

Instantiates an empty Atom.

AtomImpl

public AtomImpl(Atom atom)

Instantiates an Atom from the specified Atom.

Parameters:

atom - Atom to be copied

Method Detail

getDefinitions

public Definition[] getDefinitions()

Returns the Definitions.

Specified by:

getDefinitions in interface Atom

Overrides:

getDefinitions in class PlaceholderAtom

Returns:

a Definition []

getDefinitionsAsList

public List getDefinitionsAsList()

Returns the Definitions as a List.

Specified by:

getDefinitionsAsList in interface Atom

Overrides:

getDefinitionsAsList in class PlaceholderAtom

Returns:

the Definitions as a List

addDefinition

public void addDefinition(Definition def)

Adds the specified Definition.

Specified by:

addDefinition in interface Atom

Overrides:

addDefinition in class PlaceholderAtom

Parameters:

def - the Definition to be added

removeDefinition

public void removeDefinition(Definition def)

Remove the specified Definition.

Specified by:

removeDefinition in interface Atom

Overrides:

removeDefinition in class PlaceholderAtom

Parameters:

def - the Definition to be removed

clearDefinitions

public void clearDefinitions()

Remove all Definitions.

Specified by:

clearDefinitions in interface Atom

Overrides:

clearDefinitions in class PlaceholderAtom

setDefinitions

public void setDefinitions(Definition[] defs)

Replace Definitions with the ones in the specified array.

Specified by:

setDefinitions in interface Atom

Overrides:

setDefinitions in class PlaceholderAtom

Parameters:

defs - a Definition []

setDefinitions

public void setDefinitions(List defs)

Replace Definitions with the ones in the specified List.

Specified by:

setDefinitions in interface Atom

Overrides:

setDefinitions in class PlaceholderAtom

Parameters:

defs - a List of Definitions

getLocators

public Locator[] getLocators()

Returns the Locators.

Specified by:

getLocators in interface Atom

Overrides:

getLocators in class PlaceholderAtom

Returns:

a Locator []

getLocatorsAsList

public List getLocatorsAsList()

Returns the Locators as a List.

Specified by:

getLocatorsAsList in interface Atom

Overrides:

getLocatorsAsList in class PlaceholderAtom

Returns:

the Locators as a List

addLocator

public void addLocator(Locator loc)

Add the specified Locator.

Specified by:

addLocator in interface Atom

Overrides:

addLocator in class PlaceholderAtom

Parameters:

loc - the Locator to be added

removeLocator

public void removeLocator(Locator loc)

Removes the specified Locator.

Specified by:

removeLocator in interface Atom

Overrides:

removeLocator in class PlaceholderAtom

Parameters:

loc - the Locator to be removed

clearLocators

public void clearLocators()

Remove all Locators.

Specified by:

clearLocators in interface Atom

Overrides:

clearLocators in class PlaceholderAtom

setLocators

public void setLocators(Locator[] locs)

Replace Locators with the ones in the specified array.

Specified by:

setLocators in interface Atom

Overrides:

setLocators in class PlaceholderAtom

Parameters:

locs - a Locator []

setLocators

public void setLocators(List locs)

Replace Locators with the ones in the specified List.

Specified by:

setLocators in interface Atom

Overrides:

setLocators in class PlaceholderAtom

Parameters:

locs - a List of Locators

getRelationships

public Relationship[] getRelationships()

Returns the Relationships.

Specified by:

getRelationships in interface Atom

Overrides:

getRelationships in class PlaceholderAtom

Returns:

a Relationship []

getRelationshipsAsList

public List getRelationshipsAsList()

Returns the Relationships as a List.

Specified by:

getRelationshipsAsList in interface Atom

Overrides:

getRelationshipsAsList in class PlaceholderAtom

Returns:

the Relationships as a List

addRelationship

public void addRelationship(Relationship rel)

Adds the specified Relationship.

Specified by:

addRelationship in interface Atom

Overrides:

addRelationship in class PlaceholderAtom

Parameters:

rel - the Relationship to be added

removeRelationship

public void removeRelationship(Relationship rel)

Removes the specified Relationship.

Specified by:

removeRelationship in interface Atom

Overrides:

removeRelationship in class PlaceholderAtom

Parameters:

rel - the Relationship to be removed

clearRelationships

public void clearRelationships()

Remove all Relationships.

Specified by:

clearRelationships in interface Atom

Overrides:

clearRelationships in class PlaceholderAtom

setRelationships

public void setRelationships(Relationship[] rels)

Replace Relationships with the ones in the specified array.

Specified by:

setRelationships in interface Atom

Overrides:

setRelationships in class PlaceholderAtom

Parameters:

rels - a Relationship []

setRelationships

public void setRelationships(List rels)

Replace Relationships of the ones in the specified List.

Specified by:

setRelationships in interface Atom

Overrides:

setRelationships in class PlaceholderAtom

Parameters:

rels - a List of Relationships

getCoocurrences

public Coocurrence[] getCoocurrences()

Returns the Coocurrences.

Specified by:

getCoocurrences in interface Atom

Overrides:

getCoocurrences in class PlaceholderAtom

Returns:

a Coocurrence []

getCoocurrencesAsList

public List getCoocurrencesAsList()

Returns the Coocurrences as a List.

Specified by:

getCoocurrencesAsList in interface Atom

Overrides:

getCoocurrencesAsList in class PlaceholderAtom

Returns:

the Coocurrences as a List

addCoocurrence

public void addCoocurrence(Coocurrence coc)

Adds the specified Coocurrence.

Specified by:

addCoocurrence in interface Atom

Overrides:

addCoocurrence in class PlaceholderAtom

Parameters:

coc - the Coocurrence to be added

removeCoocurrence

public void removeCoocurrence(Coocurrence coc)

Removes the specified Coocurrence.

Specified by:

removeCoocurrence in interface Atom

Overrides:

removeCoocurrence in class PlaceholderAtom

Parameters:

coc - the Coocurrence to be removed

clearCoocurrences

public void clearCoocurrences()

Remove all Coocurrences.

Specified by:

clearCoocurrences in interface Atom

Overrides:

clearCoocurrences in class PlaceholderAtom

setCoocurrences

public void setCoocurrences(Coocurrence[] cocs)

Replace Coocurrences with the ones in the specified array.

Specified by:

setCoocurrences in interface Atom

Overrides:

setCoocurrences in class PlaceholderAtom

Parameters:

cocs - a Coocurrence []

setCoocurrences

public void setCoocurrences(List cocs)

Replace Coocurrences with the ones in the specified List.

Specified by:

setCoocurrences in interface Atom

Overrides:

setCoocurrences in class PlaceholderAtom

Parameters:

cocs - a List of Coocurrences

getContexts

public Context[] getContexts()

Return the Contexts.

Specified by:

getContexts in interface Atom

Overrides:

getContexts in class PlaceholderAtom

Returns:

a Context []

getContextsAsList

public List getContextsAsList()

Returns the Contexts as a List.

Specified by:

getContextsAsList in interface Atom

Overrides:

getContextsAsList in class PlaceholderAtom

Returns:

the Contexts as a List

addContext

public void addContext(Context cxt)

Adds the specified Context.

Specified by:

addContext in interface Atom

Overrides:

addContext in class PlaceholderAtom

Parameters:

cxt - the Context to be added

removeContext

public void removeContext(Context cxt)

Removes the specified Context.

Specified by:

removeContext in interface Atom

Overrides:

removeContext in class PlaceholderAtom

Parameters:

cxt - the Context to be removed

clearContexts

public void clearContexts()

Remove all Contexts.

Specified by:

clearContexts in interface Atom

Overrides:

clearContexts in class PlaceholderAtom

setContexts

public void setContexts(Context[] cxts)

Replace Contexts with the ones in the specified array.

Specified by:

setContexts in interface Atom

Overrides:

setContexts in class PlaceholderAtom

Parameters:

cxts - a Context []

setContexts

public void setContexts(List cxts)

Replace Contexts with the ones in the specified List.

Specified by:

setContexts in interface Atom

Overrides:

setContexts in class PlaceholderAtom

Parameters:

cxts - a List of Contexts

getAttributes

public AtomAttribute[] getAttributes()

Returns the AtomAttributes.

Specified by:

getAttributes in interface Atom

Overrides:

getAttributes in class PlaceholderAtom

Returns:

a AtomAttribute []

getAttributesAsList

public List getAttributesAsList()

Returns the AtomAttributes as a List.

Specified by:

getAttributesAsList in interface Atom

Overrides:

getAttributesAsList in class PlaceholderAtom

Returns:

the AtomAttributes as a List

addAttribute

public void addAttribute(AtomAttribute att)

Adds the specified AtomAttribute.

Specified by:

addAttribute in interface Atom

Overrides:

addAttribute in class PlaceholderAtom

Parameters:

att - the AtomAttribute to be added

removeAttribute

public void removeAttribute(AtomAttribute att)

Removes the specified AtomAttribute.

Specified by:

removeAttribute in interface Atom

Overrides:

removeAttribute in class PlaceholderAtom

Parameters:

att - the AtomAttribute to be removed

clearAttributes

public void clearAttributes()

Remove all AtomAttributes.

Specified by:

clearAttributes in interface Atom

Overrides:

clearAttributes in class PlaceholderAtom

setAttributes

public void setAttributes(AtomAttribute[] atts)

Replace AtomAttributes with the ones in the specified array.

Specified by:

setAttributes in interface Atom

Overrides:

setAttributes in class PlaceholderAtom

Parameters:

atts - an AtomAttribute []

setAttributes

public void setAttributes(List atts)

Replace AtomAttributes with the ones in the specified List.

Specified by:

setAttributes in interface Atom

Overrides:

setAttributes in class PlaceholderAtom

Parameters:

atts - a List of AtomAttributes

getRelationships

public Relationship[] getRelationships(Restrictor restrictor)

Returns a subset of this Atom's Relationships. Restricts the return based on the given Restrictor.

Specified by:

getRelationships in interface Atom

Overrides:

getRelationships in class PlaceholderAtom

Parameters:

restrictor - Restrictor

Returns:

Relationship[]

getKeyFields

public String getKeyFields()

Returns a String key which can be used by equals, compareTo, and hashCode methods.

Specified by:

getKeyFields in interface Atom

Overrides:

getKeyFields in class PlaceholderAtom

Returns:

a String composed from the cui, aui, sui, versioned source, tty, and code.