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A

aasTerm - Variable in class gov.nih.nlm.nls.metamap.ResultImpl.AcronymsAbbrevsImpl
 
ACRONYMS_ABBREVS_INDEX - Static variable in class gov.nih.nlm.nls.metamap.ResultImpl
 
AcronymsAbbrevs - Interface in gov.nih.nlm.nls.metamap
The interface for MetaMap Acronyms and Abbreviations.
AcronymsAbbrevsImpl(PBTerm) - Constructor for class gov.nih.nlm.nls.metamap.ResultImpl.AcronymsAbbrevsImpl
 
actionPerformed(ActionEvent) - Method in class test.TestGUI
 
actionPerformed(ActionEvent) - Method in class test.TestMetaMapGui
 
api - Variable in class examples.CriteriaExample
MetaMap api instance
api - Variable in class examples.CriteriaExample2
MetaMap api instance
api - Variable in class examples.CUIListExample
MetaMap api instance
api - Variable in class examples.CUIListExampleInstrumented
MetaMap api instance
api - Variable in class examples.CUIScoreSemTypesUtterance
MetaMap api instance
api - Variable in class examples.DirectMMO
MetaMap api instance
api - Variable in class examples.Example
MetaMap api instance
api - Variable in class gov.nih.nlm.nls.metamap.MetaMapApiTest
MetaMap api instance
api - Variable in class test.TestMetaMapGui
 
App - Class in gov.nih.nlm.nls
Hello world!
App() - Constructor for class gov.nih.nlm.nls.App
 
AutoGen - Class in gov.nih.nlm.nls.metamap
 
AutoGen() - Constructor for class gov.nih.nlm.nls.metamap.AutoGen
 

C

Candidates - Interface in gov.nih.nlm.nls.metamap
An interface for representing a MetaMap candidate term.
CandidatesImpl(PBTerm) - Constructor for class gov.nih.nlm.nls.metamap.PCMBase.CandidatesImpl
 
candidatesTerm - Variable in class gov.nih.nlm.nls.metamap.PCMBase.CandidatesImpl
 
candidatesTerm - Variable in class gov.nih.nlm.nls.metamap.PCMBase
 
conceptId - Variable in class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl.ConceptPairImpl
 
ConceptPair - Interface in gov.nih.nlm.nls.metamap
A container for a concept id (CUI) and its associated preferred name.
ConceptPairImpl(String, String) - Constructor for class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl.ConceptPairImpl
 
connected - Variable in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
 
createOptionListString(String[]) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
 
createOptionListString(String) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
 
CriteriaExample - Class in examples
 
CriteriaExample() - Constructor for class examples.CriteriaExample
Creates a new CriteriaExample instance.
CriteriaExample2 - Class in examples
 
CriteriaExample2() - Constructor for class examples.CriteriaExample2
Creates a new CriteriaExample2 instance.
CUIListExample - Class in examples
 
CUIListExample() - Constructor for class examples.CUIListExample
Creates a new CUIListExample instance.
CUIListExampleInstrumented - Class in examples
 
CUIListExampleInstrumented() - Constructor for class examples.CUIListExampleInstrumented
Creates a new CUIListExampleInstrumented instance.
CUIScoreSemTypesUtterance - Class in examples
 
CUIScoreSemTypesUtterance() - Constructor for class examples.CUIScoreSemTypesUtterance
Creates a new CUIScoreSemTypesUtterance instance.
CUIScoreSemTypesUtterance(String, int) - Constructor for class examples.CUIScoreSemTypesUtterance
Creates a new CUIScoreSemTypesUtterance instance using specified host and port.
currentOptionListString - Variable in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
 

D

DEFAULT_SERVER_HOST - Static variable in interface gov.nih.nlm.nls.metamap.MetaMapApi
default hostname of MetaMap server
DEFAULT_SERVER_PORT - Static variable in interface gov.nih.nlm.nls.metamap.MetaMapApi
default port of MetaMap server
DEFAULT_TIMEOUT - Static variable in interface gov.nih.nlm.nls.metamap.MetaMapApi
Default time out for api session
DirectMMO - Class in examples
 
DirectMMO() - Constructor for class examples.DirectMMO
This example bypasses translation of the Prolog terms of some parts of the MetaMap Machine Output in an attempt improve performance of client.
DirectMMO.EvImpl - Class in examples
 
DirectMMO.MappingImpl - Class in examples
 
DirectMMO.MatchMapImpl - Class in examples
 
disconnect() - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
disconnect from server.
disconnect() - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Disconnect from Prolog server.

E

eTime - Variable in class examples.CUIListExample
 
eTime - Variable in class examples.CUIListExampleInstrumented
 
eTime - Variable in class examples.DirectMMO
 
Ev - Interface in gov.nih.nlm.nls.metamap
Representation of MetaMap Evaluation (Ev) instance.
evaluate - Variable in class test.TestGUI
 
evaluate - Variable in class test.TestMetaMapGui
 
evCount - Variable in class examples.CUIListExampleInstrumented
 
evCount - Variable in class examples.DirectMMO
 
EvImpl(PBTerm) - Constructor for class examples.DirectMMO.EvImpl
 
EvImpl(PBTerm) - Constructor for class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
evTerm - Variable in class examples.DirectMMO.EvImpl
 
evTerm - Variable in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
Example - Class in examples
 
Example() - Constructor for class examples.Example
Creates a new Example instance.
examples - package examples
 

F

FilterSources - Class in examples
 
FilterSources() - Constructor for class examples.FilterSources
 
finalize() - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
 
FIRST_UTTERANCE_INDEX - Static variable in class gov.nih.nlm.nls.metamap.ResultImpl
 

G

getAcronym() - Method in interface gov.nih.nlm.nls.metamap.AcronymsAbbrevs
Get acronym or abbreviation
getAcronym() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.AcronymsAbbrevsImpl
 
getAcronymsAbbrevs() - Method in interface gov.nih.nlm.nls.metamap.Result
Return a list of Acronym and Abbreviations objects.
getAcronymsAbbrevs() - Method in class gov.nih.nlm.nls.metamap.ResultImpl
Describe getAcronymsAbbrevs method here.
getAcronymsAbbrevsList() - Method in interface gov.nih.nlm.nls.metamap.Result
Return a list of Acronym and Abbreviations objects.
getAcronymsAbbrevsList() - Method in class gov.nih.nlm.nls.metamap.ResultImpl
Describe getAcronymsAbbrevsList method here.
getArgumentAsString(PBTerm, int) - Static method in class gov.nih.nlm.nls.metamap.TermUtils
 
getAtomArgument(PBTerm, int) - Static method in class gov.nih.nlm.nls.metamap.TermUtils
 
getAtomStringListArgument(PBTerm, int) - Static method in class gov.nih.nlm.nls.metamap.TermUtils
 
getCandidateList() - Method in interface gov.nih.nlm.nls.metamap.PCM
Return the Candidate (Ev) list associated with the Phrase.
getCandidateList() - Method in class gov.nih.nlm.nls.metamap.PCMBase
get candidates list
getCandidates() - Method in interface gov.nih.nlm.nls.metamap.PCM
Deprecated. 
getCandidates() - Method in class gov.nih.nlm.nls.metamap.PCMBase
Deprecated. 
getCandidatesInstance() - Method in interface gov.nih.nlm.nls.metamap.PCM
Return the (Candidates) instance associated with the Phrase.
getCandidatesInstance() - Method in class gov.nih.nlm.nls.metamap.PCMBase
Return the Candidates instance associated with the Phrase.
getConceptId() - Method in class examples.DirectMMO.EvImpl
 
getConceptId() - Method in interface gov.nih.nlm.nls.metamap.ConceptPair
 
getConceptId() - Method in interface gov.nih.nlm.nls.metamap.Ev
Returns the UMLS Metathesaurus CUI of the UMLS string identifed.
getConceptId() - Method in interface gov.nih.nlm.nls.metamap.Negation
Deprecated.
The preferred method Negation.getConceptPairList() provides a list of concepts for the negation, each represented by the concept's id (cui) and preferred name.
getConceptId() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
getConceptId() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl.ConceptPairImpl
 
getConceptId() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl
Deprecated. 
getConceptMatchEnd() - Method in class examples.DirectMMO.MatchMapImpl
The position within the concept words of the last matching word
getConceptMatchEnd() - Method in interface gov.nih.nlm.nls.metamap.MatchMap
The position within the concept words of the last matching word
getConceptMatchEnd() - Method in class gov.nih.nlm.nls.metamap.PCMBase.MatchMapImpl
The position within the concept words of the last matching word
getConceptMatchStart() - Method in class examples.DirectMMO.MatchMapImpl
The position within the concept words of the first matching word
getConceptMatchStart() - Method in interface gov.nih.nlm.nls.metamap.MatchMap
The position within the concept words of the first matching word
getConceptMatchStart() - Method in class gov.nih.nlm.nls.metamap.PCMBase.MatchMapImpl
The position within the concept words of the first matching word
getConceptName() - Method in class examples.DirectMMO.EvImpl
 
getConceptName() - Method in interface gov.nih.nlm.nls.metamap.Ev
Returns the Metathesaurus string matched by MetaMap.
getConceptName() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
getConceptPairList() - Method in interface gov.nih.nlm.nls.metamap.Negation
Provides a list of ConceptPair objects for the negation, each represented by the concept's id (cui) and preferred name.
getConceptPairList() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl
 
getConceptPositionList() - Method in interface gov.nih.nlm.nls.metamap.Negation
 
getConceptPositionList() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl
 
getCountList() - Method in interface gov.nih.nlm.nls.metamap.AcronymsAbbrevs
Returns the CountList of the Acronym and Abbreviation Object.
getCountList() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.AcronymsAbbrevsImpl
 
getCUIList() - Method in interface gov.nih.nlm.nls.metamap.AcronymsAbbrevs
Get the concept ids of the acronym or abbreviation
getCUIList() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.AcronymsAbbrevsImpl
 
getEvList() - Method in class examples.DirectMMO.MappingImpl
 
getEvList() - Method in interface gov.nih.nlm.nls.metamap.Candidates
Return the list of candidate (Ev) instances associated with the Candidates instance.
getEvList() - Method in interface gov.nih.nlm.nls.metamap.Mapping
 
getEvList() - Method in class gov.nih.nlm.nls.metamap.PCMBase.CandidatesImpl
 
getEvList() - Method in class gov.nih.nlm.nls.metamap.PCMBase.MappingImpl
 
getExcludedCandidateCount() - Method in interface gov.nih.nlm.nls.metamap.Candidates
Get count of excluded candidates.
getExcludedCandidateCount() - Method in class gov.nih.nlm.nls.metamap.PCMBase.CandidatesImpl
 
getExpansion() - Method in interface gov.nih.nlm.nls.metamap.AcronymsAbbrevs
Get the expansion of the acronym or abbreviation
getExpansion() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.AcronymsAbbrevsImpl
 
getId() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.UtteranceImpl
 
getId() - Method in interface gov.nih.nlm.nls.metamap.Utterance
Get id of utterance.
getInputText() - Method in interface gov.nih.nlm.nls.metamap.Result
Get input text that produced this result.
getInputText() - Method in class gov.nih.nlm.nls.metamap.ResultImpl
 
getIntegerArgument(PBTerm, int) - Static method in class gov.nih.nlm.nls.metamap.TermUtils
 
getIntegerListArgument(PBTerm, int) - Static method in class gov.nih.nlm.nls.metamap.TermUtils
 
getLexMatchVariation() - Method in class examples.DirectMMO.MatchMapImpl
The degree of lexical variation between the words in the candidate concept and the words in the phrase; the computation of this value is explained on pp.
getLexMatchVariation() - Method in interface gov.nih.nlm.nls.metamap.MatchMap
The degree of lexical variation between the words in the candidate concept and the words in the phrase; the computation of this value is explained on pp.
getLexMatchVariation() - Method in class gov.nih.nlm.nls.metamap.PCMBase.MatchMapImpl
The degree of lexical variation between the words in the candidate concept and the words in the phrase; the computation of this value is explained on pp.
getListElement(PBTerm, int) - Static method in class gov.nih.nlm.nls.metamap.TermUtils
 
getListRepr() - Method in class examples.DirectMMO.MatchMapImpl
This returns a list of representation of match map.
getListRepr() - Method in interface gov.nih.nlm.nls.metamap.MatchMap
This returns a list of representation of match map.
getListRepr() - Method in class gov.nih.nlm.nls.metamap.PCMBase.MatchMapImpl
This returns a list of representation of match map.
getLocationFromId(String) - Static method in class gov.nih.nlm.nls.metamap.Utils
Get location portion of metamap id.
getMachineOutput() - Method in interface gov.nih.nlm.nls.metamap.Result
Return the raw string representation of MetaMap machine output.
getMachineOutput() - Method in class gov.nih.nlm.nls.metamap.ResultImpl
 
getMappingList(PBTerm) - Method in class examples.DirectMMO
 
getMappingList() - Method in interface gov.nih.nlm.nls.metamap.PCM
Return the Mapping list associated with the Phrase.
getMappingList() - Method in class gov.nih.nlm.nls.metamap.PCMBase
Return the Mapping list associated with the Phrase.
getMappings() - Method in interface gov.nih.nlm.nls.metamap.PCM
Deprecated. 
getMappings() - Method in class gov.nih.nlm.nls.metamap.PCMBase
Deprecated. 
getMatchedWords() - Method in class examples.DirectMMO.EvImpl
 
getMatchedWords() - Method in interface gov.nih.nlm.nls.metamap.Ev
Returns lowercased list of the words in the input text licensing the concept.
getMatchedWords() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
getMatchMap() - Method in class examples.DirectMMO.EvImpl
This returns a recursive list of objects where the elements can be Integer classes or List classes containing Lists or Integers.
getMatchMap() - Method in interface gov.nih.nlm.nls.metamap.Ev
MatchMap is a list representing (1) the correspondence of words in the candidate concept and words in the original phrase, and (2) any lexical variation in the matching.
getMatchMap() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
This returns a recursive list of objects where the elements can be Integer classes or List classes containing Lists or Integers.
getMatchMapList() - Method in class examples.DirectMMO.EvImpl
This returns a list of MatchMap objects
getMatchMapList() - Method in interface gov.nih.nlm.nls.metamap.Ev
This returns a list of MatchMap objects
getMatchMapList() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
This returns a list of MatchMap objects
getMatchMapTree(PBTerm) - Static method in class gov.nih.nlm.nls.metamap.TermUtils
 
getMincoMan() - Method in interface gov.nih.nlm.nls.metamap.Phrase
Get the result of the syntax analysis of the phrase by the minimal commitment parser as a PrologBeans Term Object
getMincoMan() - Method in class gov.nih.nlm.nls.metamap.PhraseImpl
 
getMincoManAsString() - Method in interface gov.nih.nlm.nls.metamap.Phrase
Get the result of the syntax analysis of the phrase by the minimal commitment parser.
getMincoManAsString() - Method in class gov.nih.nlm.nls.metamap.PhraseImpl
Return the result of the syntax analysis of the phrase by the minimal commitment parser See MetaMap Technical Notes, Preliminary processing (http://skr.nlm.nih.gov/papers/references/metamap.tech.pdf, pp 3-4) for more information
getMMOPBlist() - Method in interface gov.nih.nlm.nls.metamap.Result
Return a prolog beans list of terms representing machine output.
getMMOPBlist() - Method in class gov.nih.nlm.nls.metamap.ResultImpl
 
getMMOPosition() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.UtteranceImpl
 
getNegationList() - Method in interface gov.nih.nlm.nls.metamap.Result
Return a list of Negation objects.
getNegationList() - Method in class gov.nih.nlm.nls.metamap.ResultImpl
Describe getNegationList method here.
getNegations() - Method in interface gov.nih.nlm.nls.metamap.Result
Return a list of Negation objects.
getNegations() - Method in class gov.nih.nlm.nls.metamap.ResultImpl
Describe getNegations method here.
getNegationStatus() - Method in class examples.DirectMMO.EvImpl
 
getNegationStatus() - Method in interface gov.nih.nlm.nls.metamap.Ev
Get negation status of ev term.
getNegationStatus() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
getOptions() - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Get the server's current option settings.
getOptions() - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Get the server's current option settings.
getPCMList(int) - Method in class gov.nih.nlm.nls.metamap.ResultImpl
Deprecated. 
getPCMList() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.UtteranceImpl
Return a list of PCM (Phrase/Candidate/Mapping) objects associated with the utterance.
getPCMList() - Method in interface gov.nih.nlm.nls.metamap.Utterance
Return a list of PCM (Phrase/Candidates/Mappings) container objects associated with the utterance.
getPhrase() - Method in interface gov.nih.nlm.nls.metamap.PCM
Return the Phrase associated with set of Mappings and Candidates.
getPhrase() - Method in class gov.nih.nlm.nls.metamap.PCMBase
Get Phrase associated with Utterance.
getPhraseMatchEnd() - Method in class examples.DirectMMO.MatchMapImpl
The position within the phrase words of the last matching word
getPhraseMatchEnd() - Method in interface gov.nih.nlm.nls.metamap.MatchMap
The position within the phrase words of the last matching word
getPhraseMatchEnd() - Method in class gov.nih.nlm.nls.metamap.PCMBase.MatchMapImpl
The position within the phrase words of the last matching word
getPhraseMatchStart() - Method in class examples.DirectMMO.MatchMapImpl
The position within the phrase words of the first matching word
getPhraseMatchStart() - Method in interface gov.nih.nlm.nls.metamap.MatchMap
The position within the phrase words of the first matching word
getPhraseMatchStart() - Method in class gov.nih.nlm.nls.metamap.PCMBase.MatchMapImpl
The position within the phrase words of the first matching word
getPhraseText() - Method in interface gov.nih.nlm.nls.metamap.Phrase
Get original text of phrase.
getPhraseText() - Method in class gov.nih.nlm.nls.metamap.PhraseImpl
Get original text of phrase.
getPmidFromId(String) - Static method in class gov.nih.nlm.nls.metamap.Utils
Get pmid portion of metamap id.
getPosition() - Method in interface gov.nih.nlm.nls.metamap.Phrase
Get position of phrase in the input text.
getPosition() - Method in class gov.nih.nlm.nls.metamap.PhraseImpl
Get position of phrase in the input text.
getPosition() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.UtteranceImpl
 
getPosition() - Method in interface gov.nih.nlm.nls.metamap.Utterance
Get character position of utterance input text.
getPositionalInfo() - Method in class examples.DirectMMO.EvImpl
 
getPositionalInfo() - Method in interface gov.nih.nlm.nls.metamap.Ev
Returns a list of position instances representing terms of the form StartPos/Length , identifying the starting character position within the input text and and character length of each word in the string.
getPositionalInfo() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
getPositionArgument(PBTerm, int) - Static method in class gov.nih.nlm.nls.metamap.TermUtils
 
getPositionListArgument(PBTerm, int) - Static method in class gov.nih.nlm.nls.metamap.TermUtils
 
getPreferredName() - Method in class examples.DirectMMO.EvImpl
 
getPreferredName() - Method in interface gov.nih.nlm.nls.metamap.ConceptPair
 
getPreferredName() - Method in interface gov.nih.nlm.nls.metamap.Ev
Returns the preferred name of the concept, (which may be the same as the Metathe- saurus string).
getPreferredName() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
getPreferredName() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl.ConceptPairImpl
 
getPrunedCandidateCount() - Method in interface gov.nih.nlm.nls.metamap.Candidates
Get count of pruned candidates.
getPrunedCandidateCount() - Method in class gov.nih.nlm.nls.metamap.PCMBase.CandidatesImpl
 
getPruningStatus() - Method in class examples.DirectMMO.EvImpl
 
getPruningStatus() - Method in interface gov.nih.nlm.nls.metamap.Ev
Get pruning status of ev term.
getPruningStatus() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
getRemainingCandidates() - Method in interface gov.nih.nlm.nls.metamap.Candidates
Get count of remaining candidates.
getRemainingCandidates() - Method in class gov.nih.nlm.nls.metamap.PCMBase.CandidatesImpl
 
getScore() - Method in class examples.DirectMMO.EvImpl
 
getScore() - Method in class examples.DirectMMO.MappingImpl
 
getScore() - Method in interface gov.nih.nlm.nls.metamap.Ev
The score is an integer equal to -1 times the concept's MetaMap score.
getScore() - Method in interface gov.nih.nlm.nls.metamap.Mapping
 
getScore() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
getScore() - Method in class gov.nih.nlm.nls.metamap.PCMBase.MappingImpl
 
getSemanticTypes() - Method in class examples.DirectMMO.EvImpl
 
getSemanticTypes() - Method in interface gov.nih.nlm.nls.metamap.Ev
Returns a list of the short forms of the Semantic Types of the concept.
getSemanticTypes() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
getSequenceNumberFromId(String) - Static method in class gov.nih.nlm.nls.metamap.Utils
Get sequence number portion of metamap id.
getSession() - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Return Prolog session associated with this instance of the API.
getSession() - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Return Prolog session associated with this instance of the API.
getSources() - Method in class examples.DirectMMO.EvImpl
 
getSources() - Method in interface gov.nih.nlm.nls.metamap.Ev
Returns a list of the short forms (RSAB) of the UMLS source vocabularies in which the concept appears.
getSources() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
getString() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.UtteranceImpl
 
getString() - Method in interface gov.nih.nlm.nls.metamap.Utterance
Get content of utterance.
getStringArgument(PBTerm, int) - Static method in class gov.nih.nlm.nls.metamap.TermUtils
 
getStringListArgument(PBTerm, int) - Static method in class gov.nih.nlm.nls.metamap.TermUtils
 
getTerm() - Method in class examples.DirectMMO.EvImpl
get underlying Prolog Term
getTerm() - Method in interface gov.nih.nlm.nls.metamap.Ev
Return ev instance as a PrologBeans term to allow greater processing.
getTerm() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
get underlying Prolog Term
getTotalCandidatesCount() - Method in interface gov.nih.nlm.nls.metamap.Candidates
Get total count of candidates.
getTotalCandidatesCount() - Method in class gov.nih.nlm.nls.metamap.PCMBase.CandidatesImpl
 
getTrigger() - Method in interface gov.nih.nlm.nls.metamap.Negation
 
getTrigger() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl
 
getTriggerPositionList() - Method in interface gov.nih.nlm.nls.metamap.Negation
 
getTriggerPositionList() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl
 
getType() - Method in interface gov.nih.nlm.nls.metamap.Negation
 
getType() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl
 
getUtteranceList() - Method in interface gov.nih.nlm.nls.metamap.Result
Return a list of Utterance objects.
getUtteranceList() - Method in class gov.nih.nlm.nls.metamap.ResultImpl
Describe getUtterances method here.
getX() - Method in interface gov.nih.nlm.nls.metamap.Position
 
getX() - Method in class gov.nih.nlm.nls.metamap.PositionImpl
 
getY() - Method in interface gov.nih.nlm.nls.metamap.Position
 
getY() - Method in class gov.nih.nlm.nls.metamap.PositionImpl
 
gov.nih.nlm.nls - package gov.nih.nlm.nls
 
gov.nih.nlm.nls.metamap - package gov.nih.nlm.nls.metamap
 

I

input - Variable in class test.TestGUI
 
input - Variable in class test.TestMetaMapGui
 
inputText - Variable in class gov.nih.nlm.nls.metamap.ResultImpl
 
inspect(PBTerm, int) - Method in class gov.nih.nlm.nls.metamap.AutoGen
 
invokeSetOptions(String) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Deprecated. 
invokeSetOptions(String) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Deprecated. 
isHead() - Method in class examples.DirectMMO.EvImpl
 
isHead() - Method in interface gov.nih.nlm.nls.metamap.Ev
Returns true if the concept is part of the head of the phrase.
isHead() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
isNegated() - Method in class examples.DirectMMO.EvImpl
 
isNegated() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
isOvermatch() - Method in class examples.DirectMMO.EvImpl
 
isOvermatch() - Method in interface gov.nih.nlm.nls.metamap.Ev
returns true if the concept match is an overmatch.
isOvermatch() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
isPureAscii(String) - Static method in class gov.nih.nlm.nls.metamap.Utils
From Real's howto http://www.rgagnon.com/javadetails/java-0536.html

J

join(List<String>, String) - Static method in class examples.Example
 

L

listArgs(PBTerm) - Method in class examples.MincoManExample
 
listArgs(PBTerm) - Method in class examples.PrologBeansTermExample
 
listAtomTermses(PBTerm) - Method in class examples.MincoManExample
 
listElements(PBTerm) - Method in class examples.MincoManExample
 
listElements(PBTerm) - Method in class examples.PrologBeansTermExample
 
listInputMatches(PBTerm) - Method in class examples.MincoManExample
 
listInputMatches(PBTerm) - Method in class examples.PrologBeansTermExample
 
LongSentenceTest - Class in examples
 
LongSentenceTest() - Constructor for class examples.LongSentenceTest
 

M

main(String[]) - Static method in class examples.CriteriaExample
 
main(String[]) - Static method in class examples.CriteriaExample2
 
main(String[]) - Static method in class examples.CUIListExample
 
main(String[]) - Static method in class examples.CUIListExampleInstrumented
 
main(String[]) - Static method in class examples.CUIScoreSemTypesUtterance
 
main(String[]) - Static method in class examples.DirectMMO
 
main(String[]) - Static method in class examples.Example
 
main(String[]) - Static method in class examples.FilterSources
 
main(String[]) - Static method in class examples.LongSentenceTest
 
main(String[]) - Static method in class examples.MincoManExample
 
main(String[]) - Static method in class examples.PostFilterSources
 
main(String[]) - Static method in class examples.PrologBeansTermExample
 
main(String[]) - Static method in class examples.StringExample
 
main(String[]) - Static method in class examples.TestAPI
 
main(String[]) - Static method in class gov.nih.nlm.nls.App
 
main(String[]) - Static method in class gov.nih.nlm.nls.metamap.AutoGen
 
main(String[]) - Static method in class gov.nih.nlm.nls.metamap.MetaMapApiTest
 
main(String[]) - Static method in class MetaMapToCSV
 
main(String[]) - Static method in class test.TestFE
 
main(String[]) - Static method in class test.TestFE2
 
main(String[]) - Static method in class test.TestGUI
 
main(String[]) - Static method in class test.TestMetaMapGui
 
Map - Interface in gov.nih.nlm.nls.metamap
An interface for representing a MetaMap map term.
mapCount - Variable in class examples.CUIListExampleInstrumented
 
mapCount - Variable in class examples.DirectMMO
 
Mapping - Interface in gov.nih.nlm.nls.metamap
An interface for representing a MetaMap map term.
MappingImpl(PBTerm) - Constructor for class examples.DirectMMO.MappingImpl
 
MappingImpl(PBTerm) - Constructor for class gov.nih.nlm.nls.metamap.PCMBase.MappingImpl
 
mappingsTerm - Variable in class gov.nih.nlm.nls.metamap.PCMBase
 
mapTerm - Variable in class examples.DirectMMO.MappingImpl
 
mapTerm - Variable in class gov.nih.nlm.nls.metamap.PCMBase.MappingImpl
 
MatchMap - Interface in gov.nih.nlm.nls.metamap
Describe interface MatchMap here.
MatchMapImpl(PBTerm) - Constructor for class examples.DirectMMO.MatchMapImpl
 
MatchMapImpl(PBTerm) - Constructor for class gov.nih.nlm.nls.metamap.PCMBase.MatchMapImpl
 
MetaMapApi - Interface in gov.nih.nlm.nls.metamap
This provides a generic interface to access the MetaMap server:
MetaMapApiImpl - Class in gov.nih.nlm.nls.metamap
The default implementation of the MetaMapApi interface.
MetaMapApiImpl() - Constructor for class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Instantiate api using the default timeout.
MetaMapApiImpl(int) - Constructor for class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Instantiate api using specified timeout.
MetaMapApiImpl(String) - Constructor for class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Instantiate api using MetaMap server specified by hostname
MetaMapApiImpl(String, int) - Constructor for class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Instantiate api using MetaMap server specified by hostname
MetaMapApiImpl(String, int, int) - Constructor for class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Instantiate api using MetaMap server specified by hostname with specified timeout.
MetaMapApiTest - Class in gov.nih.nlm.nls.metamap
MetaMapApiTest: An implementation of MetaMapApi Test Class.
MetaMapApiTest() - Constructor for class gov.nih.nlm.nls.metamap.MetaMapApiTest
Creates a new MetaMapApiTest instance.
MetaMapApiTest(String, int) - Constructor for class gov.nih.nlm.nls.metamap.MetaMapApiTest
Creates a new MetaMapApiTest instance using specified host and port.
MetaMapElement - Interface in gov.nih.nlm.nls.metamap
A marker interface for MetaMap elements.
MetaMapToCSV - Class in <Unnamed>
/**
MetaMapToCSV() - Constructor for class MetaMapToCSV
 
MincoManExample - Class in examples
A crude example of accessing the MincoMan term using the modified Phrase and PhraseImpl classes.
MincoManExample() - Constructor for class examples.MincoManExample
 
mmoListPosition - Variable in class gov.nih.nlm.nls.metamap.ResultImpl.UtteranceImpl
 
mmoTermList - Variable in class gov.nih.nlm.nls.metamap.ResultImpl
 

N

Negation - Interface in gov.nih.nlm.nls.metamap
Represention of MetaMap Negation elements.
NegationImpl(PBTerm) - Constructor for class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl
 
NEGATIONLIST_INDEX - Static variable in class gov.nih.nlm.nls.metamap.ResultImpl
 
negTerm - Variable in class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl
 

P

PCM - Interface in gov.nih.nlm.nls.metamap
Interface for container for a Phrase, Candidates, and Mappings set.
PCMBase - Class in gov.nih.nlm.nls.metamap
Implementation of container for a Phrase, Candidates, and Mappings set (PCM).
PCMBase(PBTerm, PBTerm, PBTerm) - Constructor for class gov.nih.nlm.nls.metamap.PCMBase
Creates a new PCMBase instance.
PCMBase.CandidatesImpl - Class in gov.nih.nlm.nls.metamap
 
PCMBase.EvImpl - Class in gov.nih.nlm.nls.metamap
 
PCMBase.MappingImpl - Class in gov.nih.nlm.nls.metamap
 
PCMBase.MatchMapImpl - Class in gov.nih.nlm.nls.metamap
 
Phrase - Interface in gov.nih.nlm.nls.metamap
A representation of MetaMap Phrase structure.
PhraseImpl - Class in gov.nih.nlm.nls.metamap
Implementation class of Phrase interface.
PhraseImpl(PBTerm) - Constructor for class gov.nih.nlm.nls.metamap.PhraseImpl
Creates a new PhraseImpl instance.
phraseTerm - Variable in class gov.nih.nlm.nls.metamap.PCMBase
 
phraseTerm - Variable in class gov.nih.nlm.nls.metamap.PhraseImpl
 
Position - Interface in gov.nih.nlm.nls.metamap
Representation of MetaMap Positional Information.
PositionImpl - Class in gov.nih.nlm.nls.metamap
Position implementation class.
PositionImpl(int, int) - Constructor for class gov.nih.nlm.nls.metamap.PositionImpl
Creates a new Position instance.
PositionImpl(long, long) - Constructor for class gov.nih.nlm.nls.metamap.PositionImpl
Creates a new Position instance.
PositionImpl(PBTerm) - Constructor for class gov.nih.nlm.nls.metamap.PositionImpl
 
PostFilterSources - Class in examples
 
PostFilterSources() - Constructor for class examples.PostFilterSources
 
pprintBracketedList(List<String>, String) - Method in class examples.Example
 
preferredName - Variable in class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl.ConceptPairImpl
 
printHelp() - Static method in class gov.nih.nlm.nls.metamap.MetaMapApiTest
print information about server options
process(String, PrintStream, int) - Method in class examples.CriteriaExample
 
process(String, PrintStream, int) - Method in class examples.CriteriaExample2
 
process(String) - Method in class examples.CUIListExample
 
process(String) - Method in class examples.CUIListExampleInstrumented
 
process(String, PrintStream, int) - Method in class examples.CUIScoreSemTypesUtterance
Process terms using MetaMap API and send results to PrintStream.
process(File, PrintStream, int) - Method in class examples.CUIScoreSemTypesUtterance
 
process(File, PrintStream, List<String>, int) - Method in class examples.CUIScoreSemTypesUtterance
Process terms using MetaMap API and send results to PrintStream.
process(File, PrintStream, String, int) - Method in class examples.CUIScoreSemTypesUtterance
Process terms using MetaMap API and send results to PrintStream.
process(String) - Method in class examples.DirectMMO
 
process(String, String) - Method in class examples.Example
Column 1: File name Column 2: Phrase the CUI came from.
process(String, PrintStream, String, MetaMapApi) - Static method in class examples.FilterSources
 
process(String, PrintStream, String, MetaMapApi) - Static method in class examples.LongSentenceTest
 
process(String, PrintStream, String, MetaMapApi) - Static method in class examples.PostFilterSources
 
process(String, PrintStream, List<String>) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiTest
Process terms using MetaMap API and display result to standard output.
process(String, String) - Method in class test.TestFE
 
process(String, String) - Method in class test.TestFE2
 
processCitationsFromFile(String) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Process a ASCII text file of one or more documents - unicode (utf8) is not supported
processCitationsFromFile(String, String) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Process a ASCII text file of one or more documents - unicode (utf8) is not supported
processCitationsFromFile(String) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Process a ASCII text file of one or more documents - unicode (utf8) is not supported
processCitationsFromFile(String, String) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
 
processCitationsFromReader(Reader) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Process a ASCII text stream reader of one or more documents - unicode (utf8) is not supported
processCitationsFromReader(String, Reader) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Process a ASCII text stream reader of one or more documents - unicode (utf8) is not supported
processCitationsFromReader(Reader) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Process a ASCII text stream reader of one or more documents - unicode (utf8) is not supported.
processCitationsFromReader(String, Reader) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
 
processCitationsFromString(String) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
process a string containing one or more documents - unicode (utf8) is not supported
processCitationsFromString(String, String) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
process a string containing one or more documents - unicode (utf8) is not supported
processCitationsFromString(String) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
process a string containing one or more documents - unicode (utf8) is not supported
processCitationsFromString(String, String) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
 
processCitationsFromStringWithNoOptions(String) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
 
processCitationsFromStringWithOptionListString(String, String) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
 
processString(String) - Method in class gov.nih.nlm.nls.metamap.AutoGen
process a string containing one or more documents - unicode (utf8) is not supported
PrologBeansTermExample - Class in examples
 
PrologBeansTermExample() - Constructor for class examples.PrologBeansTermExample
 
prologList - Variable in class examples.DirectMMO.MatchMapImpl
 
prologList - Variable in class gov.nih.nlm.nls.metamap.PCMBase.MatchMapImpl
 

R

readInputFile(File) - Static method in class gov.nih.nlm.nls.metamap.MetaMapApiTest
 
resetOptions() - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Reset options to defaults
resetOptions() - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Reset options to defaults
Result - Interface in gov.nih.nlm.nls.metamap
A container for the machine output representation of a MetaMap result.
result - Variable in class gov.nih.nlm.nls.metamap.ResultImpl.UtteranceImpl
 
ResultImpl - Class in gov.nih.nlm.nls.metamap
An implemention of the Result interface, a container for the result of a MetaMap query.
ResultImpl() - Constructor for class gov.nih.nlm.nls.metamap.ResultImpl
Creates a new ResultImpl instance.
ResultImpl(PBTerm) - Constructor for class gov.nih.nlm.nls.metamap.ResultImpl
Creates a new ResultImpl instance.
ResultImpl(PBTerm, String) - Constructor for class gov.nih.nlm.nls.metamap.ResultImpl
Creates a new ResultImpl instance.
ResultImpl.AcronymsAbbrevsImpl - Class in gov.nih.nlm.nls.metamap
aas(["ABC"*"American Broadcasting System" *[1,3,5,28]*[], "CBS"*"Columbia Broadcasting System" *[1,3,5,28]*[]]).
ResultImpl.NegationImpl - Class in gov.nih.nlm.nls.metamap
 
ResultImpl.NegationImpl.ConceptPairImpl - Class in gov.nih.nlm.nls.metamap
 
ResultImpl.UtteranceImpl - Class in gov.nih.nlm.nls.metamap
 
rrTime - Variable in class examples.CUIListExample
 
rrTime - Variable in class examples.CUIListExampleInstrumented
 
rrTime - Variable in class examples.DirectMMO
 
run_metamap(String, MetaMapApi, String) - Static method in class MetaMapToCSV
 

S

saveOptions(String) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Save MetaMap server options.
session - Variable in class gov.nih.nlm.nls.metamap.AutoGen
 
session - Variable in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
 
session - Variable in class test.TestFE2
 
session - Variable in class test.TestGUI
 
setHost(String) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Use MetaMap server on specified host
setHost(String) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Use MetaMap server on specified host
setInputText(String) - Method in interface gov.nih.nlm.nls.metamap.Result
Assign inputText that produced this result.
setInputText(String) - Method in class gov.nih.nlm.nls.metamap.ResultImpl
 
setOptions(String) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Set MetaMap server options using a string of form:
setOptions(String[]) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
 
setOptions(List<String>) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Set MetaMap server options.
setOptions(String) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Set MetaMap server options using a string of form:
setOptions(String[]) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Set MetaMap server options using array of form:
setOptions(List<String>) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Set options using list of form:
setPort(int) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Use MetaMap server on specified port
setPort(int) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Use MetaMap server on specified port
setTimeout(int) - Method in class examples.CUIScoreSemTypesUtterance
 
setTimeout(int) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Set time for api prolog session.
setTimeout(int) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Set time for api prolog session.
setTimeout(int) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiTest
 
StringExample - Class in examples
 
StringExample() - Constructor for class examples.StringExample
 

T

TermUtils - Class in gov.nih.nlm.nls.metamap
Utility functions for dealing with Terms.
TermUtils() - Constructor for class gov.nih.nlm.nls.metamap.TermUtils
 
test - package test
 
TestAPI - Class in examples
 
TestAPI() - Constructor for class examples.TestAPI
 
TestFE - Class in test
An example of using the api to read an input file and then writing the result to an output file.
TestFE() - Constructor for class test.TestFE
Creates a new TestFE instance.
TestFE2 - Class in test
An example of reading an input file to a string, passing the string to the api, and then writing the result to an output file in a human readable form .
TestFE2() - Constructor for class test.TestFE2
Creates a new TestFE2 instance.
TestGUI - Class in test
A prologbeans test program
TestGUI() - Constructor for class test.TestGUI
 
TestMetaMapGui - Class in test
 
TestMetaMapGui() - Constructor for class test.TestMetaMapGui
 
text - Variable in class test.TestGUI
 
text - Variable in class test.TestMetaMapGui
 
toString() - Method in class examples.DirectMMO.EvImpl
 
toString() - Method in class examples.DirectMMO.MatchMapImpl
 
toString() - Method in class gov.nih.nlm.nls.metamap.PCMBase.EvImpl
 
toString() - Method in class gov.nih.nlm.nls.metamap.PCMBase.MatchMapImpl
 
toString() - Method in class gov.nih.nlm.nls.metamap.PhraseImpl
 
toString() - Method in class gov.nih.nlm.nls.metamap.PositionImpl
 
toString() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.AcronymsAbbrevsImpl
 
toString() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.NegationImpl.ConceptPairImpl
 
toString() - Method in class gov.nih.nlm.nls.metamap.ResultImpl
Implementation of toString method for Result.
toString() - Method in class gov.nih.nlm.nls.metamap.ResultImpl.UtteranceImpl
 
traverse(PBTerm) - Method in class examples.PrologBeansTermExample
 
traverse(PrintStream) - Method in interface gov.nih.nlm.nls.metamap.Result
Print machine output to stream.
traverse(PrintStream) - Method in class gov.nih.nlm.nls.metamap.ResultImpl
 
traverselist(PBTerm, int) - Method in class gov.nih.nlm.nls.metamap.AutoGen
 

U

unsetOptions(String) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Deprecated. 
unsetOptions(List<String>) - Method in interface gov.nih.nlm.nls.metamap.MetaMapApi
Deprecated. 
unsetOptions(String) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Deprecated. 
unsetOptions(List<String>) - Method in class gov.nih.nlm.nls.metamap.MetaMapApiImpl
Deprecated. 
Utils - Class in gov.nih.nlm.nls.metamap
Describe class Utils here.
Utils() - Constructor for class gov.nih.nlm.nls.metamap.Utils
 
Utterance - Interface in gov.nih.nlm.nls.metamap
Representation of MetaMap Utterance elements.
utteranceCount - Variable in class examples.CUIListExampleInstrumented
 
UtteranceImpl(PBTerm, int, ResultImpl) - Constructor for class gov.nih.nlm.nls.metamap.ResultImpl.UtteranceImpl
 
utteranceTerm - Variable in class gov.nih.nlm.nls.metamap.ResultImpl.UtteranceImpl
 

X

x - Variable in class gov.nih.nlm.nls.metamap.PositionImpl
 

Y

y - Variable in class gov.nih.nlm.nls.metamap.PositionImpl
 
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