gov.nih.nlm.umls.meta
Interface Atom

All Superinterfaces:

Comparable, ConceptElement, ContentViewElement, SourceElement, SuppressibleElement

All Known Implementing Classes:

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 inherited from class 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() Sets 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

public String getSaui()

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

Returns:

the SAUI

getSourceAtomIdentifier

public String getSourceAtomIdentifier()

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

Returns:

the SAUI

setSourceAtomIdentifier

public void setSourceAtomIdentifier(String saui)

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

Parameters:

saui - the SAUI

setSaui

public void setSaui(String saui)

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

Parameters:

saui - the SAUI

getTermType

public TermType getTermType()

Returns the TermType (TTY).

Returns:

the TermType

getTty

public TermType getTty()

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

Returns:

the TermType

setTermType

public void setTermType(TermType tty)

Sets the TermType (TTY).

Parameters:

tty - the TermType

setTty

public void setTty(TermType tty)

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

Parameters:

tty - the TermType

getSdui

public String getSdui()

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

Returns:

the SDUI

getSourceDescriptor

public String getSourceDescriptor()

Returns the source asserted descriptor (SDUI).

Returns:

the SDUI

setSourceDescriptor

public void setSourceDescriptor(String sdui)

Sets the source asserted descriptor (SDUI).

Parameters:

sdui - the SDUI

setSdui

public void setSdui(String sdui)

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

Parameters:

sdui - the SDUI

getScui

public String getScui()

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

Returns:

the SCUI

getSourceConceptIdentifier

public String getSourceConceptIdentifier()

Returns the source attributed concept identifier (SCUI).

Returns:

the SCUI

setScui

public void setScui(String scui)

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

Parameters:

scui - the SCUI

setSourceConceptIdentifier

public void setSourceConceptIdentifier(String scui)

Sets the source attributed concept identifier (SCUI).

Parameters:

scui - the SCUI

getCode

public String getCode()

Return the code (CODE).

Returns:

the code

setCode

public void setCode(String code)

Sets the code (CODE).

Parameters:

code - the code

getIspref

public 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

public 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

public 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

public 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

public String getAui()

Shorthand for getAtomIdentifier().

Returns:

the AUI

setAui

public void setAui(String aui)

Shorthand for setAtomIdentifier(String).

Parameters:

aui - the AUI

getAtomIdentifier

public String getAtomIdentifier()

Returns the atom unique identifier (AUI).

Returns:

the AUI

setAtomIdentifier

public void setAtomIdentifier(String aui)

Sets the atom unique identifier (AUI).

Parameters:

aui - the AUI

getLanguage

public Language getLanguage()

Returns the Language (LAT).

Returns:

the Language

getLat

public Language getLat()

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

Returns:

Language

setLanguage

public void setLanguage(Language lat)

Sets the Language (LAT).

Parameters:

lat - the Language

setLat

public void setLat(Language lat)

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

Parameters:

lat - the Language

hasPreferredTermIdentifier

public 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

public 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

public TermStatus getTermStatus()

Returns the TermStatus (TS).

Returns:

the TermStatus

getTs

public TermStatus getTs()

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

Returns:

the TermStatus

setTermStatus

public void setTermStatus(TermStatus ts)

Sets the TermStatus (TS).

Parameters:

ts - the TermStatus

setTs

public void setTs(TermStatus ts)

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

Parameters:

ts - the TermStatus

getLui

public String getLui()

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

Returns:

the LUI

setLui

public void setLui(String lui)

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

Parameters:

lui - the LUI

getTermIdentifier

public String getTermIdentifier()

Returns the term identifier (LUI).

Returns:

the LUI

setTermIdentifier

public void setTermIdentifier(String lui)

Sets the term identifier (LUI).

Parameters:

lui - the LUI

hasPreferredStringIdentifier

public 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

public 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

public StringType getStringType()

Returns the StringType (STT).

Returns:

the StringType

getStt

public StringType getStt()

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

Returns:

the StringType

setStringType

public void setStringType(StringType stt)

Sets the StringType (STT).

Parameters:

stt - the STT

setStt

public void setStt(StringType stt)

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

Parameters:

stt - the STT

getSui

public String getSui()

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

Returns:

the SUI

setSui

public void setSui(String sui)

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

Parameters:

sui - the SUI

getStringIdentifier

public String getStringIdentifier()

Return the string identifier (SUI).

Returns:

the SUI

setStringIdentifier

public void setStringIdentifier(String sui)

Sets the string identifier (SUI).

Parameters:

sui - the SUI

getName

public String getName()

Sets the name (STR).

Returns:

the name

getStr

public String getStr()

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

Returns:

the name

setName

public void setName(String str)

Sets the name (STR).

Parameters:

str - the name

setStr

public void setStr(String str)

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

Parameters:

str - the name

getDefinitions

public Definition[] getDefinitions()

Returns the Definitions.

Returns:

a Definition []

getDefinitionsAsList

public List getDefinitionsAsList()

Returns the Definitions as a List.

Returns:

the Definitions as a List

getKeyFields

public 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

public void addDefinition(Definition def)

Adds the specified Definition.

Parameters:

def - the Definition to be added

removeDefinition

public void removeDefinition(Definition def)

Remove the specified Definition.

Parameters:

def - the Definition to be removed

clearDefinitions

public void clearDefinitions()

Remove all Definitions.

setDefinitions

public void setDefinitions(Definition[] defs)

Replace Definitions with the ones in the specified array.

Parameters:

defs - a Definition []

setDefinitions

public void setDefinitions(List defs)

Replace Definitions with the ones in the specified List.

Parameters:

defs - a List of Definitions

getLocators

public Locator[] getLocators()

Returns the Locators.

Returns:

a Locator []

getLocatorsAsList

public List getLocatorsAsList()

Returns the Locators as a List.

Returns:

the Locators as a List

addLocator

public void addLocator(Locator loc)

Add the specified Locator.

Parameters:

loc - the Locator to be added

removeLocator

public void removeLocator(Locator loc)

Removes the specified Locator.

Parameters:

loc - the Locator to be removed

clearLocators

public void clearLocators()

Remove all Locators.

setLocators

public void setLocators(Locator[] locs)

Replace Locators with the ones in the specified array.

Parameters:

locs - a Locator []

setLocators

public void setLocators(List locs)

Replace Locators with the ones in the specified List.

Parameters:

locs - a List of Locators

getRelationships

public Relationship[] getRelationships()

Returns the Relationships.

Returns:

a Relationship []

getRelationshipsAsList

public List getRelationshipsAsList()

Returns the Relationships as a List.

Returns:

the Relationships as a List

addRelationship

public void addRelationship(Relationship rel)

Adds the specified Relationship.

Parameters:

rel - the Relationship to be added

removeRelationship

public void removeRelationship(Relationship rel)

Removes the specified Relationship.

Parameters:

rel - the Relationship to be removed

clearRelationships

public void clearRelationships()

Remove all Relationships.

setRelationships

public void setRelationships(Relationship[] rels)

Replace Relationships with the ones in the specified array.

Parameters:

rels - a Relationship []

setRelationships

public void setRelationships(List rels)

Replace Relationships of the ones in the specified List.

Parameters:

rels - a List of Relationships

getCoocurrences

public Coocurrence[] getCoocurrences()

Returns the Coocurrences.

Returns:

a Coocurrence []

getCoocurrencesAsList

public List getCoocurrencesAsList()

Returns the Coocurrences as a List.

Returns:

the Coocurrences as a List

addCoocurrence

public void addCoocurrence(Coocurrence coc)

Adds the specified Coocurrence.

Parameters:

coc - the Coocurrence to be added

removeCoocurrence

public void removeCoocurrence(Coocurrence coc)

Removes the specified Coocurrence.

Parameters:

coc - the Coocurrence to be removed

clearCoocurrences

public void clearCoocurrences()

Remove all Coocurrences.

setCoocurrences

public void setCoocurrences(Coocurrence[] cocs)

Replace Coocurrences with the ones in the specified array.

Parameters:

cocs - a Coocurrence []

setCoocurrences

public void setCoocurrences(List cocs)

Replace Coocurrences with the ones in the specified List.

Parameters:

cocs - a List of Coocurrences

getContexts

public Context[] getContexts()

Return the Contexts.

Returns:

a Context []

getContextsAsList

public List getContextsAsList()

Returns the Contexts as a List.

Returns:

the Contexts as a List

addContext

public void addContext(Context cxt)

Adds the specified Context.

Parameters:

cxt - the Context to be added

removeContext

public void removeContext(Context cxt)

Removes the specified Context.

Parameters:

cxt - the Context to be removed

clearContexts

public void clearContexts()

Remove all Contexts.

setContexts

public void setContexts(Context[] cxts)

Replace Contexts with the ones in the specified array.

Parameters:

cxts - a Context []

setContexts

public void setContexts(List cxts)

Replace Contexts with the ones in the specified List.

Parameters:

cxts - a List of Contexts

getAttributes

public AtomAttribute[] getAttributes()

Returns the AtomAttributes.

Returns:

a AtomAttribute []

getAttributesAsList

public List getAttributesAsList()

Returns the AtomAttributes as a List.

Returns:

the AtomAttributes as a List

addAttribute

public void addAttribute(AtomAttribute att)

Adds the specified AtomAttribute.

Parameters:

att - the AtomAttribute to be added

removeAttribute

public void removeAttribute(AtomAttribute att)

Removes the specified AtomAttribute.

Parameters:

att - the AtomAttribute to be removed

clearAttributes

public void clearAttributes()

Remove all AtomAttributes.

setAttributes

public void setAttributes(AtomAttribute[] atts)

Replace AtomAttributes with the ones in the specified array.

Parameters:

atts - an AtomAttribute []

setAttributes

public void setAttributes(List atts)

Replace AtomAttributes with the ones in the specified List.

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 Atom.ByLanguageRestrictor.

Parameters:

restrictor - Atom.ByLanguageRestrictor

Returns:

Relationship[]