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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
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.
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 AtomAttribute s. |
void |
clearContexts()
Remove all Context s. |
void |
clearCoocurrences()
Remove all Coocurrence s. |
void |
clearDefinitions()
Remove all Definition s. |
void |
clearLocators()
Remove all Locator s. |
void |
clearRelationships()
Remove all Relationship s. |
String |
getAtomIdentifier()
Returns the atom unique identifier (AUI). |
AtomAttribute[] |
getAttributes()
Returns the AtomAttribute s. |
List |
getAttributesAsList()
Returns the AtomAttribute s as a List . |
String |
getAui()
Shorthand for getAtomIdentifier() . |
String |
getCode()
Return the code (CODE). |
Context[] |
getContexts()
Return the Context s. |
List |
getContextsAsList()
Returns the Context s as a List . |
Coocurrence[] |
getCoocurrences()
Returns the Coocurrence s. |
List |
getCoocurrencesAsList()
Returns the Coocurrence s as a List . |
Definition[] |
getDefinitions()
Returns the Definition s. |
List |
getDefinitionsAsList()
Returns the Definition s 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 Locator s. |
List |
getLocatorsAsList()
Returns the Locator s as a List . |
String |
getLui()
Returns the term identifier (LUI). |
String |
getName()
Sets the name (STR). |
Relationship[] |
getRelationships()
Returns the Relationship s. |
Relationship[] |
getRelationships(Restrictor restrictor)
Returns a subset of this Atom 's Relationship s. |
List |
getRelationshipsAsList()
Returns the Relationship s 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 AtomAttribute s with the ones in the specified array. |
void |
setAttributes(List atts)
Replace AtomAttribute s 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 Context s with the ones in the specified array. |
void |
setContexts(List cxts)
Replace Context s with the ones in the specified List . |
void |
setCoocurrences(Coocurrence[] cocs)
Replace Coocurrence s with the ones in the specified array. |
void |
setCoocurrences(List cocs)
Replace Coocurrence s with the ones in the specified List . |
void |
setDefinitions(Definition[] defs)
Replace Definition s with the ones in the specified array. |
void |
setDefinitions(List defs)
Replace Definition s 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 Locator s with the ones in the specified List . |
void |
setLocators(Locator[] locs)
Replace Locator s 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 Relationship s of the ones in the specified List . |
void |
setRelationships(Relationship[] rels)
Replace Relationship s 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 |
public String getSaui()
Atom
.
This is shorthand for getSourceAtomIdentifier()
.
public String getSourceAtomIdentifier()
Atom
.
public void setSourceAtomIdentifier(String saui)
Atom
.
saui
- the SAUIpublic void setSaui(String saui)
Atom
.
This is shorthand for setSourceAtomIdentifier(String)
.
saui
- the SAUIpublic TermType getTermType()
TermType
(TTY).
TermType
public TermType getTty()
TermType
(TTY).
This is shorthand for getTermType()
.
TermType
public void setTermType(TermType tty)
TermType
(TTY).
tty
- the TermType
public void setTty(TermType tty)
TermType
(TTY).
This is shorthand for setTermType(TermType)
.
tty
- the TermType
public String getSdui()
getSourceDescriptor()
.
public String getSourceDescriptor()
public void setSourceDescriptor(String sdui)
sdui
- the SDUIpublic void setSdui(String sdui)
setSourceDescriptor(String)
.
sdui
- the SDUIpublic String getScui()
getSourceConceptIdentifier()
.
public String getSourceConceptIdentifier()
public void setScui(String scui)
setSourceConceptIdentifier(String)
.
scui
- the SCUIpublic void setSourceConceptIdentifier(String scui)
scui
- the SCUIpublic String getCode()
public void setCode(String code)
code
- the codepublic String getIspref()
Atom
is preferred (ISPREF).
Atom
is preferredpublic void setIspref(String ispref)
Atom
is preferred (ISPREF).
ispref
- the flag indicating whether or not this Atom
is preferredpublic boolean hasPreferredAtomIdentifier()
Atom
is the preferred atom identifier
for its Concept
and string identifier.
true
if so, false
otherwisepublic boolean hasPreferredAui()
Atom
is the preferred atom identifier
for its Concept
and string identifier. This is shorthand for
hasPreferredAtomIdentifier()
.
true
if so, false
otherwisepublic String getAui()
getAtomIdentifier()
.
public void setAui(String aui)
setAtomIdentifier(String)
.
aui
- the AUIpublic String getAtomIdentifier()
public void setAtomIdentifier(String aui)
aui
- the AUIpublic Language getLanguage()
Language
(LAT).
Language
public Language getLat()
Language
(LAT).
This is shorthand for getLanguage()
.
Language
public void setLanguage(Language lat)
Language
(LAT).
lat
- the Language
public void setLat(Language lat)
Language
(LAT).
This is shorthand for setLanguage(Language)
.
lat
- the Language
public boolean hasPreferredTermIdentifier()
Term
of the Concept
. In other words, does this Atom
have
the same LUI as the preferred Atom
of the Concept
.
true
if so, false
otherwisepublic boolean hasPreferredLui()
Term
of the Concept
. This is shorthand for hasPreferredTermIdentifier()
true
if so, false
otherwisepublic TermStatus getTermStatus()
TermStatus
(TS).
TermStatus
public TermStatus getTs()
TermStatus
(TS).
This is shorthand for getTermStatus()
.
TermStatus
public void setTermStatus(TermStatus ts)
TermStatus
(TS).
ts
- the TermStatus
public void setTs(TermStatus ts)
TermStatus
(TS).
This is shorthand for setTermStatus(TermStatus)
.
ts
- the TermStatus
public String getLui()
getTermIdentifier()
.
public void setLui(String lui)
setTermIdentifier(String)
.
lui
- the LUIpublic String getTermIdentifier()
public void setTermIdentifier(String lui)
lui
- the LUIpublic boolean hasPreferredStringIdentifier()
Term
it is part of. In other words, does this Atom
have
the same SUI as the preferred Atom
of the Term
.
true
if so, false
otherwisepublic boolean hasPreferredSui()
Term
it is part of. This is shorthand for
hasPreferredStringIdentifier()
.
true
if so, false
otherwisepublic StringType getStringType()
StringType
(STT).
StringType
public StringType getStt()
StringType
(STT).
This is shorthand for getStringType()
.
StringType
public void setStringType(StringType stt)
StringType
(STT).
stt
- the STTpublic void setStt(StringType stt)
StringType
(STT).
This is shorthand for setStringType(StringType)
.
stt
- the STTpublic String getSui()
getStringIdentifier()
.
public void setSui(String sui)
setStringIdentifier(String)
.
sui
- the SUIpublic String getStringIdentifier()
public void setStringIdentifier(String sui)
sui
- the SUIpublic String getName()
public String getStr()
getName()
.
public void setName(String str)
str
- the namepublic void setStr(String str)
setName(String)
.
str
- the namepublic Definition[] getDefinitions()
Definition
s.
Definition
[]
public List getDefinitionsAsList()
Definition
s as a List
.
Definition
s as a List
public String getKeyFields()
String
key which can be used
by equals, compareTo, and hashCode methods.
String
composed from key Atom
fieldspublic void addDefinition(Definition def)
Definition
.
def
- the Definition
to be addedpublic void removeDefinition(Definition def)
Definition
.
def
- the Definition
to be removedpublic void clearDefinitions()
Definition
s.
public void setDefinitions(Definition[] defs)
Definition
s with the ones in the specified array.
defs
- a Definition
[]
public void setDefinitions(List defs)
Definition
s with the ones in the specified List
.
defs
- a List
of Definition
spublic Locator[] getLocators()
Locator
s.
Locator
[]
public List getLocatorsAsList()
Locator
s as a List
.
Locator
s as a List
public void addLocator(Locator loc)
Locator
.
loc
- the Locator
to be addedpublic void removeLocator(Locator loc)
Locator
.
loc
- the Locator
to be removedpublic void clearLocators()
Locator
s.
public void setLocators(Locator[] locs)
Locator
s with the ones in the specified array.
locs
- a Locator
[]
public void setLocators(List locs)
Locator
s with the ones in the specified List
.
locs
- a List
of Locator
spublic Relationship[] getRelationships()
Relationship
s.
Relationship
[]
public List getRelationshipsAsList()
Relationship
s as a List
.
Relationship
s as a List
public void addRelationship(Relationship rel)
Relationship
.
rel
- the Relationship
to be addedpublic void removeRelationship(Relationship rel)
Relationship
.
rel
- the Relationship
to be removedpublic void clearRelationships()
Relationship
s.
public void setRelationships(Relationship[] rels)
Relationship
s with the ones in the specified array.
rels
- a Relationship
[]
public void setRelationships(List rels)
Relationship
s of the ones in the specified List
.
rels
- a List
of Relationship
spublic Coocurrence[] getCoocurrences()
Coocurrence
s.
Coocurrence
[]
public List getCoocurrencesAsList()
Coocurrence
s as a List
.
Coocurrence
s as a List
public void addCoocurrence(Coocurrence coc)
Coocurrence
.
coc
- the Coocurrence
to be addedpublic void removeCoocurrence(Coocurrence coc)
Coocurrence
.
coc
- the Coocurrence
to be removedpublic void clearCoocurrences()
Coocurrence
s.
public void setCoocurrences(Coocurrence[] cocs)
Coocurrence
s with the ones in the specified array.
cocs
- a Coocurrence
[]
public void setCoocurrences(List cocs)
Coocurrence
s with the ones in the specified List
.
cocs
- a List
of Coocurrence
spublic Context[] getContexts()
Context
s.
Context
[]
public List getContextsAsList()
Context
s as a List
.
Context
s as a List
public void addContext(Context cxt)
Context
.
cxt
- the Context
to be addedpublic void removeContext(Context cxt)
Context
.
cxt
- the Context
to be removedpublic void clearContexts()
Context
s.
public void setContexts(Context[] cxts)
Context
s with the ones in the specified array.
cxts
- a Context
[]
public void setContexts(List cxts)
Context
s with the ones in the specified List
.
cxts
- a List
of Context
spublic AtomAttribute[] getAttributes()
AtomAttribute
s.
AtomAttribute
[]
public List getAttributesAsList()
AtomAttribute
s as a List
.
AtomAttribute
s as a List
public void addAttribute(AtomAttribute att)
AtomAttribute
.
att
- the AtomAttribute
to be addedpublic void removeAttribute(AtomAttribute att)
AtomAttribute
.
att
- the AtomAttribute
to be removedpublic void clearAttributes()
AtomAttribute
s.
public void setAttributes(AtomAttribute[] atts)
AtomAttribute
s with the ones in the specified array.
atts
- an AtomAttribute
[]
public void setAttributes(List atts)
AtomAttribute
s with the ones in the specified List
.
atts
- a List
of AtomAttribute
spublic Relationship[] getRelationships(Restrictor restrictor)
Atom
's Relationship
s.
Restricts the return based on the given Atom.ByLanguageRestrictor
.
restrictor
- Atom.ByLanguageRestrictor
|
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