A B C D E F G H I J L M N O P R S T U V W _

A

AbstractBaseDictionary - Class in org.apache.ctakes.dictionary.lookup

AbstractBaseDictionary() - Constructor for class org.apache.ctakes.dictionary.lookup.AbstractBaseDictionary

AbstractBaseMetaDataHit - Class in org.apache.ctakes.dictionary.lookup

Base impl for a MetaDataHit implementation.

AbstractBaseMetaDataHit() - Constructor for class org.apache.ctakes.dictionary.lookup.AbstractBaseMetaDataHit

addCacheEntry(String) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine

Adds an entry to the dictionary lookup cache.

addCollectionFilter(CollectionFilter) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine

Adds a Collection filter to the engine.

addField(String, String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRow

addPostLookupFilter(PostLookupFilter) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine

Adds a Post-lookup filter to the engine.

addPreLookupFilter(PreLookupFilter) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine

Adds a Pre-lookup filter to the engine.

addRow(StringTableRow) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTable

addStringAttribute(String, String) - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter

Adds an attribute that may be used for filtering.

addStringAttribute(String, String) - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation

Adds an attribute that may be used for filtering.

addStringAttribute(String, String) - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter

AND_RELATION - Static variable in class org.apache.ctakes.dictionary.lookup.filter.PostLookupFilterGroupImpl

applyFilter(Collection<MetaDataHit>) - Method in interface org.apache.ctakes.dictionary.lookup.filter.CollectionFilter

Prunes the Collection of MetaDataHit objects that meet the filter implementation's match criteria.

applyFilter(Collection<MetaDataHit>) - Method in class org.apache.ctakes.dictionary.lookup.filter.TruncateCollectionFilterImpl

Implementation

AssertionCuePhraseConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae

Implementation that takes Rxnorm dictionary lookup hits and stores only the ones that are also present in the Orange Book.

AssertionCuePhraseConsumerImpl(UimaContext, Properties, int) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl

AssertionCuePhraseConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl

B

BaseDictionaryImpl - Class in org.apache.ctakes.dictionary.lookup

Deprecated. Use AbstractBaseDictionary

BaseDictionaryImpl() - Constructor for class org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl

Deprecated.

BaseLookupConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae

Provides some base functionality for subclasses.

BaseLookupConsumerImpl() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl

BaseLookupConsumerImpl.LookupHitKey - Class in org.apache.ctakes.dictionary.lookup.ae

Using a String as a HashMap Key can be slow as the hashCode is computed per character with each call - ditto for equals

BaseMetaDataHitImpl - Class in org.apache.ctakes.dictionary.lookup

Deprecated. please use AbstractBaseMetaDataHit

BaseMetaDataHitImpl() - Constructor for class org.apache.ctakes.dictionary.lookup.BaseMetaDataHitImpl

Deprecated.

binaryLookup(String) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine

Determines whether the input text is contained by the Dictionary.

build(Reader, String, String, boolean) - Static method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableFactory

Reads from a character stream.

build(Reader, String, String, FieldConstraint, boolean) - Static method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableFactory

Reads from a character stream.

build(Reader, String, String[], boolean) - Static method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableFactory

Reads from a character stream.

build(Reader, String, String[], FieldConstraint, boolean) - Static method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableFactory

Reads from a character stream.

C

close() - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl

CollectionFilter - Interface in org.apache.ctakes.dictionary.lookup.filter

Filters a Collection of MetaDataHit objects.

collectionProcessComplete() - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator

Close db connections in UmlsToSnomedDbConsumerImpl

compare(MetaDataHit, MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.MetaDataHitComparator

Implementation

compare(LookupToken, LookupToken) - Method in enum org.apache.ctakes.dictionary.lookup.vo.LookupTokenComparator

consumeHits(JCas, Iterator) - Method in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl

consumeHits(JCas, Iterator) - Method in class org.apache.ctakes.dictionary.lookup.ae.DebugConsumerImpl

consumeHits(JCas, Iterator<LookupHit>) - Method in interface org.apache.ctakes.dictionary.lookup.ae.LookupConsumer

Consumes the hits produced by the LookupAnnotator.

consumeHits(JCas, Iterator<LookupHit>) - Method in class org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl

Consumes the hits produced by the LookupAnnotator.

consumeHits(JCas, Iterator<LookupHit>) - Method in class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl

Consumes the hits produced by the LookupAnnotator.

consumeHits(JCas, Iterator<LookupHit>) - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl

Consumes the hits produced by the LookupAnnotator.

contains(String) - Method in class org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl

Deprecated.

contains(String) - Method in interface org.apache.ctakes.dictionary.lookup.Dictionary

Determines whether the Dictionary contains the specified input text.

contains(MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.filter.MetaDataPostLookupFilterImpl

contains(MetaDataHit) - Method in interface org.apache.ctakes.dictionary.lookup.filter.PostLookupFilter

contains(MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.filter.PostLookupFilterGroupImpl

contains(String) - Method in interface org.apache.ctakes.dictionary.lookup.filter.PreLookupFilter

contains(MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl

contains(String) - Method in class org.apache.ctakes.dictionary.lookup.filter.StringPreLookupFilterImpl

contains(String) - Method in class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl

Determines whether the Dictionary contains the specified input text.

contains(String) - Method in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl

Determines whether the Dictionary contains the specified input text.

contains(String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableDictionaryImpl

Determines whether the Dictionary contains the specified input text.

CreateAssertionLuceneIndexFromDelimitedFile - Class in org.apache.ctakes.dictionary.assertion

Driver for populating a Lucene Index with assertion cue phrases, so that the tokenization of the dictionary entries matches the tokenization that will be done to clinical text during pipeline processing.

CreateAssertionLuceneIndexFromDelimitedFile(TokenizerPTB) - Constructor for class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

Constructor

createLookupHitMap(Iterator<LookupHit>) - Static method in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl

CTX_KEY_WINDOW_ANNOTATIONS - Static variable in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl

Key value for context map.

CUE_PHRASE_CATEGORY_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

CUE_PHRASE_CATEGORY_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl

CUE_PHRASE_FAMILY_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

CUE_PHRASE_FAMILY_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl

CUE_PHRASE_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

CUE_PHRASE_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl

CUE_PHRASE_FIRST_WORD_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

CUE_PHRASE_FIRST_WORD_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl

D

DebugConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae

LookupConsumer implementation that outputs debug info to the log about each LookupHit.

DebugConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.DebugConsumerImpl

Dictionary - Interface in org.apache.ctakes.dictionary.lookup

DictionaryEngine - Class in org.apache.ctakes.dictionary.lookup

The engine adds additional functionality to executing a dictionary.

DictionaryEngine(Dictionary, boolean) - Constructor for class org.apache.ctakes.dictionary.lookup.DictionaryEngine

DictionaryException - Exception in org.apache.ctakes.dictionary.lookup

DictionaryException(Throwable) - Constructor for exception org.apache.ctakes.dictionary.lookup.DictionaryException

DictionaryLookupAnnotator - Class in org.apache.ctakes.dictionary.lookup.ae

UIMA annotator that identified entities based on lookup.

DictionaryLookupAnnotator() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator

DirectLookupInitializerImpl - Class in org.apache.ctakes.dictionary.lookup.ae

DirectLookupInitializerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl

DirectPassThroughImpl - Class in org.apache.ctakes.dictionary.lookup.algorithms

Each individual LookupToken is referenced against a Dictionary.

DirectPassThroughImpl(DictionaryEngine, PhraseBuilder) - Constructor for class org.apache.ctakes.dictionary.lookup.algorithms.DirectPassThroughImpl

Constructor

E

EQ_OP - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst

EQ_OP - Static variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl

equals(MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.AbstractBaseMetaDataHit

Two MetaDataHits are equal if their Meta field name/value pairs are equal.

equals(Object) - Method in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl.LookupHitKey

equals(MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.BaseMetaDataHitImpl

Deprecated. Two MetaDataHits are equal if their Meta field name/value pairs are equal.

equals(MetaDataHit) - Method in interface org.apache.ctakes.dictionary.lookup.MetaDataHit

equals(Object) - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupHit

Override default equals method.

F

FieldConstraint - Interface in org.apache.ctakes.dictionary.lookup.strtable

Defines when a row should NOT be added to a StringTable object.

FieldConstraintImpl - Class in org.apache.ctakes.dictionary.lookup.strtable

FieldConstraintImpl(String, int, String, Class) - Constructor for class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl

FilterException - Exception in org.apache.ctakes.dictionary.lookup.filter

FilterException(Throwable) - Constructor for exception org.apache.ctakes.dictionary.lookup.filter.FilterException

FirstTokenPermLookupInitializerImpl - Class in org.apache.ctakes.dictionary.lookup.ae

FirstTokenPermLookupInitializerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl

FirstTokenPermutationImpl - Class in org.apache.ctakes.dictionary.lookup.algorithms

OVERVIEW: Each LookupToken is fed into a "first token" Dictionary.

FirstTokenPermutationImpl(DictionaryEngine, PhraseBuilder, String[], int) - Constructor for class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl

Constructor

FLOAT_TYPE - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst

G

GenericMetaDataHitImpl - Class in org.apache.ctakes.dictionary.lookup

GenericMetaDataHitImpl(Map<String, String>) - Constructor for class org.apache.ctakes.dictionary.lookup.GenericMetaDataHitImpl

getAllRows() - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTable

getContextMap(JCas, int, int) - Method in class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl

returns an empty map Gets context for the specified window.

getContextMap(JCas, int, int) - Method in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl

Gets context for the specified window.

getContextMap(JCas, int, int) - Method in interface org.apache.ctakes.dictionary.lookup.ae.LookupInitializer

Gets context for the specified window.

getDictMetaDataHit() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupHit

getEndOffset() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter

Gets the end offset.

getEndOffset() - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation

Gets the end offset.

getEndOffset() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter

getEndOffset() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupHit

getEntries(String) - Method in class org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl

Deprecated.

getEntries(String) - Method in interface org.apache.ctakes.dictionary.lookup.Dictionary

Gets any meta data entries associated with the specified input text.

getEntries(String) - Method in class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl

Gets any meta data entries associated with the specified input text.

getEntries(String) - Method in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl

Gets any meta data entries associated with the specified input text.

getEntries(String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableDictionaryImpl

Gets any meta data entries associated with the specified input text.

getFieldValue(String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRow

getInstance() - Static method in enum org.apache.ctakes.dictionary.lookup.vo.LookupTokenComparator

getLength() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter

Gets the length of this annotation based on offsets.

getLength() - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation

Gets the length of this annotation based on offsets.

getLength() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter

getLinearPermutations(List<Integer>) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.PermutationUtil

Gets a collection of lists, each list represents a single permutation.

getLookupAlgorithm(DictionaryEngine) - Method in class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl

Gets the LookupAlgorithm to be used to perform the lookup operations.

getLookupAlgorithm(DictionaryEngine) - Method in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl

Gets the LookupAlgorithm to be used to perform the lookup operations.

getLookupAlgorithm(DictionaryEngine) - Method in interface org.apache.ctakes.dictionary.lookup.ae.LookupInitializer

Gets the LookupAlgorithm to be used to perform the lookup operations.

getLookupAlgorithm() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupSpec

getLookupConsumer() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupSpec

getLookupInitializer() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupSpec

getLookupTokenIterator(JCas) - Method in class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl

Gets an iteration of tokens that represent the finest grain used for a lookup operation.

getLookupTokenIterator(JCas) - Method in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl

Gets an iteration of tokens that represent the finest grain used for a lookup operation.

getLookupTokenIterator(JCas) - Method in interface org.apache.ctakes.dictionary.lookup.ae.LookupInitializer

Gets an iteration of tokens that represent the finest grain used for a lookup operation.

getLookupWindowIterator(JCas) - Method in class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl

Gets an iteration of windows.

getLookupWindowIterator(JCas) - Method in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl

Gets an iteration of windows.

getLookupWindowIterator(JCas) - Method in interface org.apache.ctakes.dictionary.lookup.ae.LookupInitializer

Gets an iteration of windows.

getMaxSizeList() - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities

Get the maximum list size to be returned from a lucene index

getMetaFieldNames() - Method in class org.apache.ctakes.dictionary.lookup.AbstractBaseDictionary

TODO - get rid of the using class iterators and use Collection foreach

getMetaFieldNames() - Method in class org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl

Deprecated.

getMetaFieldNames() - Method in class org.apache.ctakes.dictionary.lookup.GenericMetaDataHitImpl

getMetaFieldNames() - Method in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDocumentMetaDataHitImpl

getMetaFieldNames() - Method in interface org.apache.ctakes.dictionary.lookup.MetaDataHit

getMetaFieldNames() - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRowMetaDataHitImpl

getMetaFieldValue(String) - Method in class org.apache.ctakes.dictionary.lookup.GenericMetaDataHitImpl

getMetaFieldValue(String) - Method in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDocumentMetaDataHitImpl

getMetaFieldValue(String) - Method in interface org.apache.ctakes.dictionary.lookup.MetaDataHit

getMetaFieldValue(String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRowMetaDataHitImpl

getMetaFieldValues() - Method in class org.apache.ctakes.dictionary.lookup.GenericMetaDataHitImpl

getMetaFieldValues() - Method in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDocumentMetaDataHitImpl

getMetaFieldValues() - Method in interface org.apache.ctakes.dictionary.lookup.MetaDataHit

getMetaFieldValues() - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRowMetaDataHitImpl

getNames() - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRow

getPermutationList(int) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.PermutationUtil

Gets all permutations for the given level and all sub-levels.

getPhrases(List) - Method in interface org.apache.ctakes.dictionary.lookup.phrasebuilder.PhraseBuilder

Given a list of LookupTokens, one or more phrases are built.

getPhrases(List) - Method in class org.apache.ctakes.dictionary.lookup.phrasebuilder.VariantPhraseBuilderImpl

getRows(String, String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTable

getSnomedCodes(String) - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl

Searches for the Snomed codes that are synonyms of the UMLS concept with CUI umlsCode

getSnomedCodes(String) - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl

Queries the given UMLS CUI against the DB.

getSnomedCodes(String) - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl

Find all Snomed codes that map to the given UMLS code (CUI), by looking in a lucene index

getSortedLookupTokens(JCas, Annotation) - Method in class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl

Gets a list of tokens that we promise to return in sorted order that are constrained by the input annotation.

getSortedLookupTokens(JCas, Annotation) - Method in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl

Gets a list of tokens that we promise to return in sorted order that are constrained by the input annotation.

getSortedLookupTokens(JCas, Annotation) - Method in interface org.apache.ctakes.dictionary.lookup.ae.LookupInitializer

Gets a list of tokens that we promise to return in sorted order that are constrained by the input annotation.

getStartOffset() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter

Gets the start offset.

getStartOffset() - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation

Gets the start offset.

getStartOffset() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter

getStartOffset() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupHit

getStringAttribute(String) - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter

Gets an attribute.

getStringAttribute(String) - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation

Gets an attribute.

getStringAttribute(String) - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter

getText() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter

Gets the text.

getText() - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation

Gets the text.

getText() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter

getUniqueKey() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupHit

Generates a unique key based on this objects values.

getUsage() - Static method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

getValues() - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRow

GT_OP - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst

GT_OP - Static variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl

GTEQ_OP - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst

GTEQ_OP - Static variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl

H

hashCode() - Method in class org.apache.ctakes.dictionary.lookup.AbstractBaseMetaDataHit

hashCode() - Method in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl.LookupHitKey

hashCode() - Method in class org.apache.ctakes.dictionary.lookup.BaseMetaDataHitImpl

Deprecated.

hashCode() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupHit

I

initialize(UimaContext) - Method in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator

initialize(UimaContext) - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator

initialize(UimaContext) - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedUmlsDictionaryLookupAnnotator

initialize(UimaContext) - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator

INTEGER_TYPE - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst

isConstrained(String, String) - Method in interface org.apache.ctakes.dictionary.lookup.strtable.FieldConstraint

isConstrained(String, String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl

isValidUMLSUser(String, String, String, String) - Static method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedUmlsDictionaryLookupAnnotator

isValidUMLSUser(String, String, String, String) - Static method in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator

J

JdbcDictionaryImpl - Class in org.apache.ctakes.dictionary.lookup.jdbc

JdbcDictionaryImpl(Connection, String, String) - Constructor for class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl

L

load(String) - Static method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

Loads text from a file.

loadHyphMap(String) - Static method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

Loads hyphenated words and a frequency value for each, from a file.

lookup(List<LookupToken>, Map<String, List<LookupAnnotation>>) - Method in class org.apache.ctakes.dictionary.lookup.algorithms.DirectPassThroughImpl

Lookup the given text specified via LookupToken objects.

lookup(List<LookupToken>, Map<String, List<LookupAnnotation>>) - Method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl

Lookup the given text specified via LookupToken objects.

lookup(List<LookupToken>, Map<String, List<LookupAnnotation>>) - Method in interface org.apache.ctakes.dictionary.lookup.algorithms.LookupAlgorithm

Lookup the given text specified via LookupToken objects.

LookupAlgorithm - Interface in org.apache.ctakes.dictionary.lookup.algorithms

Generic interface to specific lookup algorithm implementations.

LookupAnnotation - Interface in org.apache.ctakes.dictionary.lookup.vo

Value object that models a text annotation.

LookupAnnotationToJCasAdapter - Class in org.apache.ctakes.dictionary.lookup.ae

LookupAnnotationToJCasAdapter(Annotation) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter

LookupAnnotationToTokAdapter - Class in org.apache.ctakes.dictionary.lookup.vo

LookupAnnotationToTokAdapter(Token) - Constructor for class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter

LookupConsumer - Interface in org.apache.ctakes.dictionary.lookup.ae

Defines how to consume the lookup hits produced by the LookupAnnotator.

LookupHit - Class in org.apache.ctakes.dictionary.lookup.vo

Represents a single hit found by a lookup algorithm.

LookupHit(MetaDataHit, int, int) - Constructor for class org.apache.ctakes.dictionary.lookup.vo.LookupHit

LookupInitializer - Interface in org.apache.ctakes.dictionary.lookup.ae

Defines how to initialize the LookupAnnotator.

LookupParseUtilities - Class in org.apache.ctakes.dictionary.lookup.ae

LookupParseUtilities() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities

LookupParseUtilitiesRefactor - Class in org.apache.ctakes.dictionary.lookup.ae

LookupSpec - Class in org.apache.ctakes.dictionary.lookup.ae

A container for three related classes used to lookup terms in a dictionary and process hits found.

LookupSpec(LookupAlgorithm, LookupInitializer, LookupConsumer) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.LookupSpec

LookupToken - Interface in org.apache.ctakes.dictionary.lookup.vo

This object represents the SMALLEST span of text that could potentially be a lookup hit.

LookupTokenComparator - Enum in org.apache.ctakes.dictionary.lookup.vo

Comparator that sorts LookupToken objects by their start and end offsets.

LT_KEY_USE_FOR_LOOKUP - Static variable in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl

Key value for LookupToken attribute.

LT_OP - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst

LT_OP - Static variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl

LTEQ_OP - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst

LTEQ_OP - Static variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl

LuceneDictionaryImpl - Class in org.apache.ctakes.dictionary.lookup.lucene

LuceneDictionaryImpl(IndexSearcher, String) - Constructor for class org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl

Constructor

LuceneDictionaryImpl(IndexSearcher, String, int) - Constructor for class org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl

Constructor

LuceneDocumentMetaDataHitImpl - Class in org.apache.ctakes.dictionary.lookup.lucene

LuceneDocumentMetaDataHitImpl(Document) - Constructor for class org.apache.ctakes.dictionary.lookup.lucene.LuceneDocumentMetaDataHitImpl

M

main(String[]) - Static method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

MetaDataHit - Interface in org.apache.ctakes.dictionary.lookup

MetaDataHitComparator - Class in org.apache.ctakes.dictionary.lookup

Allows two MetaDataHit objects to be compared based on a specific metadata value that they both contain.

MetaDataHitComparator(String, int, boolean) - Constructor for class org.apache.ctakes.dictionary.lookup.MetaDataHitComparator

Constructor

MetaDataHitConst - Interface in org.apache.ctakes.dictionary.lookup

MetaDataPostLookupFilterImpl - Class in org.apache.ctakes.dictionary.lookup.filter

MetaDataPostLookupFilterImpl(DictionaryEngine, String[], boolean) - Constructor for class org.apache.ctakes.dictionary.lookup.filter.MetaDataPostLookupFilterImpl

metaLookup(String) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine

Gets a collection of MetaDataHits from the Dictionary based on the input text.

N

NamedEntityLookupConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae

NamedEntityLookupConsumerImpl(UimaContext, Properties, int) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl

NamedEntityLookupConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl

O

OR_RELATION - Static variable in class org.apache.ctakes.dictionary.lookup.filter.PostLookupFilterGroupImpl

OrangeBookFilterConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae

Implementation that takes Rxnorm dictionary lookup hits and stores only the ones that are also present in the Orange Book.

OrangeBookFilterConsumerImpl(UimaContext, Properties, int) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl

OrangeBookFilterConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl

org.apache.ctakes.dictionary.assertion - package org.apache.ctakes.dictionary.assertion

org.apache.ctakes.dictionary.lookup - package org.apache.ctakes.dictionary.lookup

org.apache.ctakes.dictionary.lookup.ae - package org.apache.ctakes.dictionary.lookup.ae

org.apache.ctakes.dictionary.lookup.algorithms - package org.apache.ctakes.dictionary.lookup.algorithms

org.apache.ctakes.dictionary.lookup.filter - package org.apache.ctakes.dictionary.lookup.filter

org.apache.ctakes.dictionary.lookup.jdbc - package org.apache.ctakes.dictionary.lookup.jdbc

org.apache.ctakes.dictionary.lookup.lucene - package org.apache.ctakes.dictionary.lookup.lucene

org.apache.ctakes.dictionary.lookup.phrasebuilder - package org.apache.ctakes.dictionary.lookup.phrasebuilder

org.apache.ctakes.dictionary.lookup.strtable - package org.apache.ctakes.dictionary.lookup.strtable

org.apache.ctakes.dictionary.lookup.vo - package org.apache.ctakes.dictionary.lookup.vo

organizeByOffset(Iterator<LookupHit>) - Static method in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl

Organizes the LookupHit objects by begin and end offsets.

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parseDescriptor(File, UimaContext, int) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities

parseDescriptor(File, UimaContext) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities

parseDescriptor(File, UimaContext, int) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilitiesRefactor

parseDescriptor(File, UimaContext) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilitiesRefactor

PermutationUtil - Class in org.apache.ctakes.dictionary.lookup.algorithms

PermutationUtil() - Constructor for class org.apache.ctakes.dictionary.lookup.algorithms.PermutationUtil

PhraseBuilder - Interface in org.apache.ctakes.dictionary.lookup.phrasebuilder

Interface for building phrases from LookupToken objects.

PostLookupFilter - Interface in org.apache.ctakes.dictionary.lookup.filter

PostLookupFilterGroupImpl - Class in org.apache.ctakes.dictionary.lookup.filter

Groups multiple PostLookupFilter objects together and applies boolean logic to them.

PostLookupFilterGroupImpl(PostLookupFilter[], int, boolean) - Constructor for class org.apache.ctakes.dictionary.lookup.filter.PostLookupFilterGroupImpl

Constructor

PreLookupFilter - Interface in org.apache.ctakes.dictionary.lookup.filter

printResults(String, List) - Static method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

Prints out the tokenized results, for debug use.

process(JCas) - Method in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator

Entry point for processing.

process(JCas) - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator

Entry point for processing.

props - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl

R

retainMetaData(String) - Method in class org.apache.ctakes.dictionary.lookup.AbstractBaseDictionary

Tells the Dictionary to retain specific bits of metadata for each entry in the Dictionary.

retainMetaData(String) - Method in class org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl

Deprecated.

retainMetaData(String) - Method in interface org.apache.ctakes.dictionary.lookup.Dictionary

Tells the Dictionary to retain specific bits of metadata for each entry in the Dictionary.

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setMaxSizeList(int) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities

Set the maximum list size to be returned from a lucene index

setValue(String) - Method in class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl

SetValuePostLookupFilterImpl - Class in org.apache.ctakes.dictionary.lookup.filter

A filter that uses a value to filter against a MetaDataHit.

SetValuePostLookupFilterImpl(String, int, int, boolean) - Constructor for class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl

STRING_TYPE - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst

StringPreLookupFilterImpl - Class in org.apache.ctakes.dictionary.lookup.filter

StringPreLookupFilterImpl(Set<String>) - Constructor for class org.apache.ctakes.dictionary.lookup.filter.StringPreLookupFilterImpl

StringTable - Class in org.apache.ctakes.dictionary.lookup.strtable

StringTable(String[]) - Constructor for class org.apache.ctakes.dictionary.lookup.strtable.StringTable

StringTableDictionaryImpl - Class in org.apache.ctakes.dictionary.lookup.strtable

StringTableDictionaryImpl(StringTable, String) - Constructor for class org.apache.ctakes.dictionary.lookup.strtable.StringTableDictionaryImpl

StringTableFactory - Class in org.apache.ctakes.dictionary.lookup.strtable

StringTableFactory() - Constructor for class org.apache.ctakes.dictionary.lookup.strtable.StringTableFactory

StringTableRow - Class in org.apache.ctakes.dictionary.lookup.strtable

StringTableRow() - Constructor for class org.apache.ctakes.dictionary.lookup.strtable.StringTableRow

StringTableRowMetaDataHitImpl - Class in org.apache.ctakes.dictionary.lookup.strtable

StringTableRowMetaDataHitImpl(StringTableRow) - Constructor for class org.apache.ctakes.dictionary.lookup.strtable.StringTableRowMetaDataHitImpl

T

ThreadedDictionaryLookupAnnotator - Class in org.apache.ctakes.dictionary.lookup.ae

Date: 12/18/12

ThreadedDictionaryLookupAnnotator() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator

ThreadedUmlsDictionaryLookupAnnotator - Class in org.apache.ctakes.dictionary.lookup.ae

UIMA annotator that identified entities based on lookup.

ThreadedUmlsDictionaryLookupAnnotator() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.ThreadedUmlsDictionaryLookupAnnotator

TruncateCollectionFilterImpl - Class in org.apache.ctakes.dictionary.lookup.filter

Truncates objects in the collection.

TruncateCollectionFilterImpl(Comparator, int) - Constructor for class org.apache.ctakes.dictionary.lookup.filter.TruncateCollectionFilterImpl

Constructor

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UmlsDictionaryLookupAnnotator - Class in org.apache.ctakes.dictionary.lookup.ae

UIMA annotator that identified entities based on lookup.

UmlsDictionaryLookupAnnotator() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator

UmlsToSnomedConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae

Implementation that takes UMLS dictionary lookup hits and stores as NamedEntity objects only the ones that have a SNOMED synonym.

UmlsToSnomedConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl

UmlsToSnomedDbConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae

Implementation that takes UMLS dictionary lookup hits and stores as NamedEntity objects only the ones that have a SNOMED synonym, by looking in a database for SNOMED codes that map to the identified CUI.

UmlsToSnomedDbConsumerImpl(UimaContext, Properties, int) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl

UmlsToSnomedDbConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl

UmlsToSnomedLuceneConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae

Implementation that takes UMLS dictionary lookup hits and stores as NamedEntity objects only the ones that have a SNOMED synonym, by looking in a lucene index for SNOMED codes that map to the identified CUI.

UmlsToSnomedLuceneConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl

UmlsToSnomedLuceneConsumerImpl(UimaContext, Properties, int) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl

V

valueOf(String) - Static method in enum org.apache.ctakes.dictionary.lookup.vo.LookupTokenComparator

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.apache.ctakes.dictionary.lookup.vo.LookupTokenComparator

Returns an array containing the constants of this enum type, in the order they are declared.

VariantPhraseBuilderImpl - Class in org.apache.ctakes.dictionary.lookup.phrasebuilder

Builds phrases based on various variants of a LookupToken.

VariantPhraseBuilderImpl(String[], boolean) - Constructor for class org.apache.ctakes.dictionary.lookup.phrasebuilder.VariantPhraseBuilderImpl

Constructor

W

writeToFile(String) - Method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

writeToFormatLucene(String, String, String) - Method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

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__end - Variable in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl.LookupHitKey

__start - Variable in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl.LookupHitKey

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