A

addToFSArray(FSArray, TOP, JCas) - Static method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.UimaUtil

Adds a single feature structure to the input FSArray.

addToStringArray(StringArray, String, JCas) - Static method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.UimaUtil

Adds a single String to the input StringArray.

Americanize - Class in edu.ucdenver.ccp.nlp.biolemmatizer

Takes a String and returns an Americanized version of it based on a list of British-to-American spellings and some rules.

Americanize() - Constructor for class edu.ucdenver.ccp.nlp.biolemmatizer.Americanize

Constructor to load the British-to-American spelling mapping file

americanize(String) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.Americanize

Convert the spelling of a word from British to American English.

americanizedLemma() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizerCmdOpts

 

B

BioLemmatizer - Class in edu.ucdenver.ccp.nlp.biolemmatizer

BioLemmatizer: Lemmatize a word in biomedical texts and return its lemma; the part of speech (POS) of the word is optional.

BioLemmatizer() - Constructor for class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

Default constructor loads the lexicon from the classpath

BioLemmatizer(File) - Constructor for class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

Constructor to initialize the class fields

BioLemmatizer_AE - Class in edu.ucdenver.ccp.nlp.biolemmatizer.uima

This annotator processes tokens in the CAS and inserts corresponding lemmas.

BioLemmatizer_AE() - Constructor for class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

 

BioLemmatizerCmdOpts - Class in edu.ucdenver.ccp.nlp.biolemmatizer

Command-line options for the BioLemmatizer

BioLemmatizerCmdOpts() - Constructor for class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizerCmdOpts

 

C

createAnalysisEngineDescription(TypeSystemDescription, Class<? extends Annotation>, String, Class<? extends AnnotationDataExtractor>, Class<? extends LemmaDecorator>) - Static method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

Initializes an AnalysisEngine that will determine lemmas for tokens that are present in the CAS

createAnalysisEngineDescription(TypeSystemDescription, String, Class<? extends PartOfSpeechDecorator>, Class<? extends AnnotationDataExtractor>, Class<? extends LemmaDecorator>) - Static method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

 

createAnalysisEngineDescription(TypeSystemDescription, Class<? extends Annotation>) - Static method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

 

createAnalysisEngineDescription(TypeSystemDescription, Class<? extends Annotation>, String) - Static method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

 

D

decorateAnnotation(Annotation, String, Lemma) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.DefaultLemmaDecorator

 

DefaultLemmaDecorator - Class in edu.ucdenver.ccp.nlp.biolemmatizer.uima

This simple implementation of the LemmaDecorator interface adds a new LemmaAnnotation to the CAS for each token annotation processed.

DefaultLemmaDecorator() - Constructor for class edu.ucdenver.ccp.nlp.biolemmatizer.uima.DefaultLemmaDecorator

 

E

edu.ucdenver.ccp.nlp.biolemmatizer - package edu.ucdenver.ccp.nlp.biolemmatizer

 

edu.ucdenver.ccp.nlp.biolemmatizer.uima - package edu.ucdenver.ccp.nlp.biolemmatizer.uima

 

equals(Object) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.LemmataEntry.Lemma

 

extractAttribute(Annotation, String) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.DefaultLemmaDecorator

 

extractLemmas(Annotation) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.DefaultLemmaDecorator

 

G

getAnnotationToDecorate(Annotation, AnnotationDataExtractor) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.DefaultLemmaDecorator

In the case of the DefaultLemmaDecorator, the annotation to decorate is a LemmaAnnotation with the same span as the token that was used to process the lemma.

getInputFile() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizerCmdOpts

 

getInputStr() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizerCmdOpts

 

getInputStrPos() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizerCmdOpts

 

getLemma() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.LemmataEntry.Lemma

 

getLemmas() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.LemmataEntry

 

getLexiconFile() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizerCmdOpts

 

getOutputFile() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizerCmdOpts

 

getPos() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.LemmataEntry.Lemma

 

getTagSetName() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.LemmataEntry.Lemma

 

H

hashCode() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.LemmataEntry.Lemma

 

I

initialize(UimaContext) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

Initializes the BioLemmatizer that will be used by the process(JCas) method

insertLemma(Annotation, Lemma) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.DefaultLemmaDecorator

Inserts information representing the input Lemma into the input Annotation which is assumed to be of type LemmaAnnotation in this instance.

invokeNoArgsConstructor(String) - Static method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

Returns an instantiation of the class specified by the input String.

J

join(String[], String) - Static method in class edu.ucdenver.ccp.nlp.biolemmatizer.Americanize

static method to concatenate String items with a specified delimiter

L

lemmasAndCategories - Variable in class edu.ucdenver.ccp.nlp.biolemmatizer.LemmataEntry

Map to store lemmata info.

lemmaSeparator - Static variable in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

Lemma separator character

lemmaSeparator - Static variable in class edu.ucdenver.ccp.nlp.biolemmatizer.LemmataEntry

Lemma separator character

lemmasToString() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.LemmataEntry

Represent lemmas of different POS tags; separated by lemmaSeparator

LemmataEntry - Class in edu.ucdenver.ccp.nlp.biolemmatizer

LemmataEntry: store POS tags and corresponding lemmas for one lemmata entry

LemmataEntry(Map<String, String>, POSEntry) - Constructor for class edu.ucdenver.ccp.nlp.biolemmatizer.LemmataEntry

Construtor to initialize the class field

LemmataEntry.Lemma - Class in edu.ucdenver.ccp.nlp.biolemmatizer

Simple utility class to store a single lemma/pos combination

LemmataEntry.Lemma(String, String, String) - Constructor for class edu.ucdenver.ccp.nlp.biolemmatizer.LemmataEntry.Lemma

 

lemmatizeByLexicon(String, String) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

Lemmatize a string with POS tag using Lexicon only

lemmatizeByLexiconAndRules(String, String) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

Lemmatize a string with POS tag using both lexicon lookup and lemmatization rules This is the preferred method as it gives the best lemmatization performance

lemmatizeByRules(String, String) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

Lemmatize a string with POS tag using lemmatization rules only

lemmatizer - Variable in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

BioLemmatizer

M

main(String[]) - Static method in class edu.ucdenver.ccp.nlp.biolemmatizer.Americanize

Americanize and print the command line arguments.

main(String[]) - Static method in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

Input arguments are parsed into a BioLemmatizerCmdOpts object.

mappingFileName - Static variable in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

the Part-Of-Speech mapping file

mappingMajorClasstoPennPOS - Variable in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

Hierachical mapping file from major class to Penn Treebank POS

mappingPennPOStoNUPOS - Variable in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

Hierachical mapping file from PennPOS to NUPOS

N

newAnnotation(JCas, String, Span) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.DefaultLemmaDecorator

 

O

outputLemmaOnly() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizerCmdOpts

 

P

PARAM_ANNOTATION_DATA_EXTRACTOR_CLASS - Static variable in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

Parameter name used in the UIMA descriptor file for the annotation data extractor implementation to use

PARAM_LEMMA_DECORATOR_CLASS - Static variable in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

Parameter name used in the UIMA descriptor file for the LemmaDecorator implementation to use

PARAM_POS_DECORATOR_CLASS - Static variable in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

Parameter name used in the UIMA descriptor file for the PartOfSpeechDecorator implementation to use

PARAM_TOKEN_GET_POS_METHOD_NAME - Static variable in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

Parameter name used in the UIMA descriptor file for the name of the method that returns a part-of-speech (as a String) from the token annotation

PARAM_TOKEN_TYPE_NAME - Static variable in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

Parameter name used in the UIMA descriptor file for the token type

partOfSpeechTags - Variable in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

NUPOS tags

posEntry - Variable in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

POSEntry object to retrieve POS tag information

process(JCas) - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.uima.BioLemmatizer_AE

This process(JCas) method cycles through all annotations in the CAS.

S

spellingTokenizer - Variable in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

Extract individual word parts from a contracted word.

T

toString() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.LemmataEntry

Override toString() method to represent lemma and POS info in a concatenated triplet; Different lemmas are separated by lemmaSeparator

U

UimaUtil - Class in edu.ucdenver.ccp.nlp.biolemmatizer.uima

This class contains a few simple utility methods related to UIMA

UimaUtil() - Constructor for class edu.ucdenver.ccp.nlp.biolemmatizer.uima.UimaUtil

 

useInteractiveMode() - Method in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizerCmdOpts

 

W

wordLexicon - Variable in class edu.ucdenver.ccp.nlp.biolemmatizer.BioLemmatizer

Word lexicon for lemma lookup