gov.nih.nlm.umls.meta
Interface Atom

All Superinterfaces:

Comparable, ConceptElement, ContentViewElement, SourceElement, SuppressibleElement

All Known Implementing Classes:

AtomImpl, PlaceholderAtom

public interface Atom
extends Comparable, ConceptElement, ContentViewElement, SuppressibleElement, SourceElement

Represents information about a single named unit of meaning within a Concept.

Following is a UML Class diagram showing the neighborhood around Atom

All data in a row of the MRCONSO file is represented here.

Author:

Brian Carlsen, Deborah Shapiro

Nested Class Summary

static class	Atom.AtomRankComparator Sorts the atoms.
static class	Atom.ByLanguageRestrictor Restrictor that restricts by Language.

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

SourceElement.BySourceComparator, SourceElement.BySourceRestrictor

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.
String	getAtomIdentifier() Returns the atom unique identifier (AUI).
AtomAttribute[]	getAttributes() Returns the AtomAttributes.
List	getAttributesAsList() Returns the AtomAttributes as a List.
String	getAui() Shorthand for getAtomIdentifier().
String	getCode() Return the code (CODE).
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	getIspref() Returns the flag indicating whether or not this Atom is preferred (ISPREF).
String	getKeyFields() Returns a String key which can be used by equals, compareTo, and hashCode methods.
Language	getLanguage() Returns the Language (LAT).
Language	getLat() Returns the Language (LAT).
Locator[]	getLocators() Returns the Locators.
List	getLocatorsAsList() Returns the Locators as a List.
String	getLui() Returns the term identifier (LUI).
String	getName() Returns the name (STR).
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.
String	getSaui() Returns the source asserted identifier (SAUI) for this Atom.
String	getScui() Returns the source attributed concept identifier (SCUI).
String	getSdui() Returns the source asserted descriptor (SDUI).
String	getSourceAtomIdentifier() Returns the source asserted identifier (SAUI) for this Atom.
String	getSourceConceptIdentifier() Returns the source attributed concept identifier (SCUI).
String	getSourceDescriptor() Returns the source asserted descriptor (SDUI).
String	getStr() Returns the name (STR).
String	getStringIdentifier() Return the string identifier (SUI).
StringType	getStringType() Returns the StringType (STT).
StringType	getStt() Returns the StringType (STT).
String	getSui() Return the string identifier (SUI).
String	getTermIdentifier() Returns the term identifier (LUI).
TermStatus	getTermStatus() Returns the TermStatus (TS).
TermType	getTermType() Returns the TermType (TTY).
TermStatus	getTs() Returns the TermStatus (TS).
TermType	getTty() Returns the TermType (TTY).
boolean	hasPreferredAtomIdentifier() Indicates whether or not this Atom is the preferred atom identifier for its Concept and string identifier.
boolean	hasPreferredAui() Indicates whether or not this Atom is the preferred atom identifier for its Concept and string identifier.
boolean	hasPreferredLui() Indicates whether or not this atom is part of the preferred Term of the Concept.
boolean	hasPreferredStringIdentifier() Indicates whether or not this atom has the preferred string identifier of the Term it is part of.
boolean	hasPreferredSui() Indicates whether or not this atom has the preferred string identifier of the Term it is part of.
boolean	hasPreferredTermIdentifier() Indicates whether or not this atom is part of the preferred Term of the Concept.
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	setAtomIdentifier(String aui) Sets the atom unique identifier (AUI).
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	setAui(String aui) Shorthand for setAtomIdentifier(String).
void	setCode(String code) Sets the code (CODE).
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	setIspref(String ispref) Sets the flag indicating whether or not this Atom is preferred (ISPREF).
void	setLanguage(Language lat) Sets the Language (LAT).
void	setLat(Language lat) Sets the Language (LAT).
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	setLui(String lui) Sets the term identifier (LUI).
void	setName(String str) Sets the name (STR).
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.
void	setSaui(String saui) Sets the source asserted identifier (SAUI) for this Atom.
void	setScui(String scui) Sets the source attributed concept identifier (SCUI).
void	setSdui(String sdui) Sets the source asserted descriptor (SDUI).
void	setSourceAtomIdentifier(String saui) Sets the source asserted identifier (SAUI) for this Atom.
void	setSourceConceptIdentifier(String scui) Sets the source attributed concept identifier (SCUI).
void	setSourceDescriptor(String sdui) Sets the source asserted descriptor (SDUI).
void	setStr(String str) Sets the name (STR).
void	setStringIdentifier(String sui) Sets the string identifier (SUI).
void	setStringType(StringType stt) Sets the StringType (STT).
void	setStt(StringType stt) Sets the StringType (STT).
void	setSui(String sui) Sets the string identifier (SUI).
void	setTermIdentifier(String lui) Sets the term identifier (LUI).
void	setTermStatus(TermStatus ts) Sets the TermStatus (TS).
void	setTermType(TermType tty) Sets the TermType (TTY).
void	setTs(TermStatus ts) Sets the TermStatus (TS).
void	setTty(TermType tty) Sets the TermType (TTY).

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface gov.nih.nlm.umls.meta.ConceptElement

getConcept, setConcept

Methods inherited from interface gov.nih.nlm.umls.meta.ContentViewElement

getContentView, getCvf, setContentView, setCvf

Methods inherited from interface gov.nih.nlm.umls.meta.SuppressibleElement

getSuppress, isObsolete, isSuppressible, setSuppress

Methods inherited from interface gov.nih.nlm.umls.meta.SourceElement

getSource, setSource

Method Detail

getSaui

String getSaui()

Returns the source asserted identifier (SAUI) for this Atom. This is shorthand for getSourceAtomIdentifier().

Returns:

the SAUI

getSourceAtomIdentifier

String getSourceAtomIdentifier()

Returns the source asserted identifier (SAUI) for this Atom.

Returns:

the SAUI

setSourceAtomIdentifier

void setSourceAtomIdentifier(String saui)

Sets the source asserted identifier (SAUI) for this Atom.

Parameters:

saui - the SAUI

setSaui

void setSaui(String saui)

Sets the source asserted identifier (SAUI) for this Atom. This is shorthand for setSourceAtomIdentifier(String).

Parameters:

saui - the SAUI

getTermType

TermType getTermType()

Returns the TermType (TTY).

Returns:

the TermType

getTty

TermType getTty()

Returns the TermType (TTY). This is shorthand for getTermType().

Returns:

the TermType

setTermType

void setTermType(TermType tty)

Sets the TermType (TTY).

Parameters:

tty - the TermType

setTty

void setTty(TermType tty)

Sets the TermType (TTY). This is shorthand for setTermType(TermType).

Parameters:

tty - the TermType

getSdui

String getSdui()

Returns the source asserted descriptor (SDUI). This is shorthand for getSourceDescriptor().

Returns:

the SDUI

getSourceDescriptor

String getSourceDescriptor()

Returns the source asserted descriptor (SDUI).

Returns:

the SDUI

setSourceDescriptor

void setSourceDescriptor(String sdui)

Sets the source asserted descriptor (SDUI).

Parameters:

sdui - the SDUI

setSdui

void setSdui(String sdui)

Sets the source asserted descriptor (SDUI). This is shorthand for setSourceDescriptor(String).

Parameters:

sdui - the SDUI

getScui

String getScui()

Returns the source attributed concept identifier (SCUI). This is shorthand for getSourceConceptIdentifier().

Returns:

the SCUI

getSourceConceptIdentifier

String getSourceConceptIdentifier()

Returns the source attributed concept identifier (SCUI).

Returns:

the SCUI

setScui

void setScui(String scui)

Sets the source attributed concept identifier (SCUI). This is shorthand for setSourceConceptIdentifier(String).

Parameters:

scui - the SCUI

setSourceConceptIdentifier

void setSourceConceptIdentifier(String scui)

Sets the source attributed concept identifier (SCUI).

Parameters:

scui - the SCUI

getCode

String getCode()

Return the code (CODE).

Returns:

the code

setCode

void setCode(String code)

Sets the code (CODE).

Parameters:

code - the code

getIspref

String getIspref()

Returns the flag indicating whether or not this Atom is preferred (ISPREF).

Returns:

the flag indicating whether or not this Atom is preferred

setIspref

void setIspref(String ispref)

Sets the flag indicating whether or not this Atom is preferred (ISPREF).

Parameters:

ispref - the flag indicating whether or not this Atom is preferred

hasPreferredAtomIdentifier

boolean hasPreferredAtomIdentifier()

Indicates whether or not this Atom is the preferred atom identifier for its Concept and string identifier.

Returns:

true if so, false otherwise

hasPreferredAui

boolean hasPreferredAui()

Indicates whether or not this Atom is the preferred atom identifier for its Concept and string identifier. This is shorthand for hasPreferredAtomIdentifier().

Returns:

true if so, false otherwise

getAui

String getAui()

Shorthand for getAtomIdentifier().

Returns:

the AUI

setAui

void setAui(String aui)

Shorthand for setAtomIdentifier(String).

Parameters:

aui - the AUI

getAtomIdentifier

String getAtomIdentifier()

Returns the atom unique identifier (AUI).

Returns:

the AUI

setAtomIdentifier

void setAtomIdentifier(String aui)

Sets the atom unique identifier (AUI).

Parameters:

aui - the AUI

getLanguage

Language getLanguage()

Returns the Language (LAT).

Returns:

the Language

getLat

Language getLat()

Returns the Language (LAT). This is shorthand for getLanguage().

Returns:

Language

setLanguage

void setLanguage(Language lat)

Sets the Language (LAT).

Parameters:

lat - the Language

setLat

void setLat(Language lat)

Sets the Language (LAT). This is shorthand for setLanguage(Language).

Parameters:

lat - the Language

hasPreferredTermIdentifier

boolean hasPreferredTermIdentifier()

Indicates whether or not this atom is part of the preferred Term of the Concept. In other words, does this Atom have the same LUI as the preferred Atom of the Concept.

Returns:

true if so, false otherwise

hasPreferredLui

boolean hasPreferredLui()

Indicates whether or not this atom is part of the preferred Term of the Concept. This is shorthand for hasPreferredTermIdentifier()

Returns:

true if so, false otherwise

getTermStatus

TermStatus getTermStatus()

Returns the TermStatus (TS).

Returns:

the TermStatus

getTs

TermStatus getTs()

Returns the TermStatus (TS). This is shorthand for getTermStatus().

Returns:

the TermStatus

setTermStatus

void setTermStatus(TermStatus ts)

Sets the TermStatus (TS).

Parameters:

ts - the TermStatus

setTs

void setTs(TermStatus ts)

Sets the TermStatus (TS). This is shorthand for setTermStatus(TermStatus).

Parameters:

ts - the TermStatus

getLui

String getLui()

Returns the term identifier (LUI). This is shorthand for getTermIdentifier().

Returns:

the LUI

setLui

void setLui(String lui)

Sets the term identifier (LUI). This is shorthand for setTermIdentifier(String).

Parameters:

lui - the LUI

getTermIdentifier

String getTermIdentifier()

Returns the term identifier (LUI).

Returns:

the LUI

setTermIdentifier

void setTermIdentifier(String lui)

Sets the term identifier (LUI).

Parameters:

lui - the LUI

hasPreferredStringIdentifier

boolean hasPreferredStringIdentifier()

Indicates whether or not this atom has the preferred string identifier of the Term it is part of. In other words, does this Atom have the same SUI as the preferred Atom of the Term.

Returns:

true if so, false otherwise

hasPreferredSui

boolean hasPreferredSui()

Indicates whether or not this atom has the preferred string identifier of the Term it is part of. This is shorthand for hasPreferredStringIdentifier().

Returns:

true if so, false otherwise

getStringType

StringType getStringType()

Returns the StringType (STT).

Returns:

the StringType

getStt

StringType getStt()

Returns the StringType (STT). This is shorthand for getStringType().

Returns:

the StringType

setStringType

void setStringType(StringType stt)

Sets the StringType (STT).

Parameters:

stt - the STT

setStt

void setStt(StringType stt)

Sets the StringType (STT). This is shorthand for setStringType(StringType).

Parameters:

stt - the STT

getSui

String getSui()

Return the string identifier (SUI). This is shorthand for getStringIdentifier().

Returns:

the SUI

setSui

void setSui(String sui)

Sets the string identifier (SUI). This is shorthand for setStringIdentifier(String).

Parameters:

sui - the SUI

getStringIdentifier

String getStringIdentifier()

Return the string identifier (SUI).

Returns:

the SUI

setStringIdentifier

void setStringIdentifier(String sui)

Sets the string identifier (SUI).

Parameters:

sui - the SUI

getName

String getName()

Returns the name (STR).

Returns:

the name

getStr

String getStr()

Returns the name (STR). This is shorthand for getName().

Returns:

the name

setName

void setName(String str)

Sets the name (STR).

Parameters:

str - the name

setStr

void setStr(String str)

Sets the name (STR). This is shorthand for setName(String).

Parameters:

str - the name

getDefinitions

Definition[] getDefinitions()

Returns the Definitions.

Returns:

a Definition []

getDefinitionsAsList

List getDefinitionsAsList()

Returns the Definitions as a List.

Returns:

the Definitions as a List

getKeyFields

String getKeyFields()

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

Returns:

a String composed from key Atom fields

addDefinition

void addDefinition(Definition def)

Adds the specified Definition.

Parameters:

def - the Definition to be added

removeDefinition

void removeDefinition(Definition def)

Remove the specified Definition.

Parameters:

def - the Definition to be removed

clearDefinitions

void clearDefinitions()

Remove all Definitions.

setDefinitions

void setDefinitions(Definition[] defs)

Replace Definitions with the ones in the specified array.

Parameters:

defs - a Definition []

setDefinitions

void setDefinitions(List defs)

Replace Definitions with the ones in the specified List.

Parameters:

defs - a List of Definitions

getLocators

Locator[] getLocators()

Returns the Locators.

Returns:

a Locator []

getLocatorsAsList

List getLocatorsAsList()

Returns the Locators as a List.

Returns:

the Locators as a List

addLocator

void addLocator(Locator loc)

Add the specified Locator.

Parameters:

loc - the Locator to be added

removeLocator

void removeLocator(Locator loc)

Removes the specified Locator.

Parameters:

loc - the Locator to be removed

clearLocators

void clearLocators()

Remove all Locators.

setLocators

void setLocators(Locator[] locs)

Replace Locators with the ones in the specified array.

Parameters:

locs - a Locator []

setLocators

void setLocators(List locs)

Replace Locators with the ones in the specified List.

Parameters:

locs - a List of Locators

getRelationships

Relationship[] getRelationships()

Returns the Relationships.

Returns:

a Relationship []

getRelationshipsAsList

List getRelationshipsAsList()

Returns the Relationships as a List.

Returns:

the Relationships as a List

addRelationship

void addRelationship(Relationship rel)

Adds the specified Relationship.

Parameters:

rel - the Relationship to be added

removeRelationship

void removeRelationship(Relationship rel)

Removes the specified Relationship.

Parameters:

rel - the Relationship to be removed

clearRelationships

void clearRelationships()

Remove all Relationships.

setRelationships

void setRelationships(Relationship[] rels)

Replace Relationships with the ones in the specified array.

Parameters:

rels - a Relationship []

setRelationships

void setRelationships(List rels)

Replace Relationships of the ones in the specified List.

Parameters:

rels - a List of Relationships

getCoocurrences

Coocurrence[] getCoocurrences()

Returns the Coocurrences.

Returns:

a Coocurrence []

getCoocurrencesAsList

List getCoocurrencesAsList()

Returns the Coocurrences as a List.

Returns:

the Coocurrences as a List

addCoocurrence

void addCoocurrence(Coocurrence coc)

Adds the specified Coocurrence.

Parameters:

coc - the Coocurrence to be added

removeCoocurrence

void removeCoocurrence(Coocurrence coc)

Removes the specified Coocurrence.

Parameters:

coc - the Coocurrence to be removed

clearCoocurrences

void clearCoocurrences()

Remove all Coocurrences.

setCoocurrences

void setCoocurrences(Coocurrence[] cocs)

Replace Coocurrences with the ones in the specified array.

Parameters:

cocs - a Coocurrence []

setCoocurrences

void setCoocurrences(List cocs)

Replace Coocurrences with the ones in the specified List.

Parameters:

cocs - a List of Coocurrences

getContexts

Context[] getContexts()

Return the Contexts.

Returns:

a Context []

getContextsAsList

List getContextsAsList()

Returns the Contexts as a List.

Returns:

the Contexts as a List

addContext

void addContext(Context cxt)

Adds the specified Context.

Parameters:

cxt - the Context to be added

removeContext

void removeContext(Context cxt)

Removes the specified Context.

Parameters:

cxt - the Context to be removed

clearContexts

void clearContexts()

Remove all Contexts.

setContexts

void setContexts(Context[] cxts)

Replace Contexts with the ones in the specified array.

Parameters:

cxts - a Context []

setContexts

void setContexts(List cxts)

Replace Contexts with the ones in the specified List.

Parameters:

cxts - a List of Contexts

getAttributes

AtomAttribute[] getAttributes()

Returns the AtomAttributes.

Returns:

a AtomAttribute []

getAttributesAsList

List getAttributesAsList()

Returns the AtomAttributes as a List.

Returns:

the AtomAttributes as a List

addAttribute

void addAttribute(AtomAttribute att)

Adds the specified AtomAttribute.

Parameters:

att - the AtomAttribute to be added

removeAttribute

void removeAttribute(AtomAttribute att)

Removes the specified AtomAttribute.

Parameters:

att - the AtomAttribute to be removed

clearAttributes

void clearAttributes()

Remove all AtomAttributes.

setAttributes

void setAttributes(AtomAttribute[] atts)

Replace AtomAttributes with the ones in the specified array.

Parameters:

atts - an AtomAttribute []

setAttributes

void setAttributes(List atts)

Replace AtomAttributes with the ones in the specified List.

Parameters:

atts - a List of AtomAttributes

getRelationships

Relationship[] getRelationships(Restrictor restrictor)

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

Parameters:

restrictor - Atom.ByLanguageRestrictor

Returns:

Relationship[]