Index (JCoRe Banner 2.3.0 API)

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

A

AbbreviationPair(String, String) - Constructor for class banner.postprocessing.ExtractAbbrev.AbbreviationPair
actionPerformed(ActionEvent) - Method in class banner.annotation.BEAT
add(String, EntityType) - Method in class banner.tagging.dictionary.DictionaryTagger: Adds a single entry to the dictionary.
add(String, Collection<EntityType>) - Method in class banner.tagging.dictionary.DictionaryTagger
add(List<String>, Collection<EntityType>) - Method in class banner.tagging.dictionary.DictionaryTagger
add(K[], V) - Method in class banner.util.Index
add(K, V) - Method in class banner.util.Index
add(double, E) - Method in class banner.util.RankedList
add(List<K>, V) - Method in class banner.util.Trie
add(E) - Method in class banner.util.UnmodifiableArraySet
addAll(Collection<? extends E>) - Method in class banner.util.UnmodifiableArraySet
addAlternateMentions(Sentence, HashMap<String, LinkedList<Dataset.Tag>>) - Method in class banner.eval.dataset.BC2GMDataset
addEntity(Entity) - Method in class banner.normalization.Gazetteer
addEntity(Entity) - Method in class banner.normalization.IndexedMentionIdentifier
addEntity(Entity) - Method in interface banner.normalization.MentionIdentifier
addId(String) - Method in class banner.eval.dataset.Dataset.Tag
addMention(Mention) - Method in class banner.types.Sentence: Adds a Mention to this Sentence, ignoring any potential overlap with existing Mentions.
addMentions(List<String>, double) - Method in class banner.types.Sentence
addName(EntityName) - Method in class banner.types.Entity
addPostProcessor(PostProcessor) - Method in class banner.postprocessing.SequentialPostProcessor
addToken(Token) - Method in class banner.types.Sentence: Adds a Token to this Sentence.
addValue(Collection<E>, V) - Method in class banner.util.IndexedMetricSetSimilarity
Annotation - Class in banner.annotation
Annotation(int, int, String, String, String) - Constructor for class banner.annotation.Annotation
AZDCDataset - Class in banner.eval.dataset
AZDCDataset(Tokenizer) - Constructor for class banner.eval.dataset.AZDCDataset
AZDCDataset() - Constructor for class banner.eval.dataset.AZDCDataset

B

BANNER - Class in banner.eval
BANNER() - Constructor for class banner.eval.BANNER
banner.annotation - package banner.annotation
banner.eval - package banner.eval
banner.eval.dataset - package banner.eval.dataset
banner.eval.uima - package banner.eval.uima
BANNER.MatchCriteria - Enum in banner.eval
banner.normalization - package banner.normalization
BANNER.Performance - Class in banner.eval
BANNER.PerformanceData - Class in banner.eval
banner.postprocessing - package banner.postprocessing
banner.tagging - package banner.tagging
banner.tagging.dictionary - package banner.tagging.dictionary
banner.tagging.pipe - package banner.tagging.pipe
banner.tokenization - package banner.tokenization
banner.types - package banner.types
banner.util - package banner.util
BANNERAnnotator - Class in de.julielab.jcore.ae.banner
BANNERAnnotator() - Constructor for class de.julielab.jcore.ae.banner.BANNERAnnotator
BANNERWrapper - Class in banner.eval.uima
BANNERWrapper() - Constructor for class banner.eval.uima.BANNERWrapper
BC2GMDataset - Class in banner.eval.dataset
BC2GMDataset(Tokenizer) - Constructor for class banner.eval.dataset.BC2GMDataset
BC2GMDataset() - Constructor for class banner.eval.dataset.BC2GMDataset
BEAT - Class in banner.annotation
BEAT(String, String, String, String, String) - Constructor for class banner.annotation.BEAT
BestMatchDisambiguator - Class in banner.normalization
BestMatchDisambiguator(double) - Constructor for class banner.normalization.BestMatchDisambiguator

C

caretUpdate(CaretEvent) - Method in class banner.annotation.BEAT
ChemicalSuffix - Class in banner.tagging.pipe
ChemicalSuffix(String) - Constructor for class banner.tagging.pipe.ChemicalSuffix
clear() - Method in class banner.util.RankedList
clear() - Method in class banner.util.UnmodifiableArraySet
CollectionsRand - Class in banner.util
compareTo(Annotation) - Method in class banner.annotation.Annotation
compareTo(Mention) - Method in class banner.types.Mention
compareTo(Token) - Method in class banner.types.Token
Concept - Class in banner.annotation
Concept(String, String, String) - Constructor for class banner.annotation.Concept
ConceptName - Class in banner.annotation
ConceptName(String, String) - Constructor for class banner.annotation.ConceptName
configure(HierarchicalConfiguration, Tokenizer) - Method in class banner.tagging.dictionary.DictionaryTagger
contains(Dataset.Tag) - Method in class banner.eval.dataset.Dataset.Tag
contains(int) - Method in class banner.types.Mention
contains(int) - Method in class banner.types.Token
contains(Object) - Method in class banner.util.UnmodifiableArraySet
containsAll(Collection<?>) - Method in class banner.util.UnmodifiableArraySet
convert(TagFormat) - Method in enum banner.tagging.TagPosition
copy(Mention) - Method in class banner.types.EntityIdentification
copy(Sentence) - Method in class banner.types.Mention
copy(boolean, boolean) - Method in class banner.types.Sentence
countWhitespace(int) - Method in class banner.types.Sentence
createFromTokens(String, List<Token>) - Static method in class banner.types.EntityName
CRFTagger - Class in banner.tagging
CRFTagger(CRF, FeatureSet, int) - Constructor for class banner.tagging.CRFTagger

D

Dataset - Class in banner.eval.dataset
Dataset() - Constructor for class banner.eval.dataset.Dataset
Dataset.Tag - Class in banner.eval.dataset
de.julielab.jcore.ae.banner - package de.julielab.jcore.ae.banner
de.julielab.jcore.banner.dataset - package de.julielab.jcore.banner.dataset
defaultInitialMapCapacity - Static variable in class banner.util.Index
defaultMapLoadFactor - Static variable in class banner.util.Index
describe(String) - Method in class banner.tagging.CRFTagger
DictionaryTagger - Class in banner.tagging.dictionary: This class represents a very simple dictionary-based tagger.
DictionaryTagger() - Constructor for class banner.tagging.dictionary.DictionaryTagger: Creates a new DictionaryTagger
disambiguate(Mention) - Method in class banner.normalization.BestMatchDisambiguator
disambiguateMentions(Sentence) - Method in class banner.normalization.BestMatchDisambiguator
disambiguateMentions(Sentence) - Method in interface banner.normalization.MentionDisambiguator

E

end - Variable in class banner.eval.dataset.Dataset.Tag
entities - Variable in class banner.tagging.dictionary.DictionaryTagger
Entity - Class in banner.types
Entity(String, EntityType) - Constructor for class banner.types.Entity
EntityIdentification - Class in banner.types
EntityIdentification(Mention) - Constructor for class banner.types.EntityIdentification
EntityName - Class in banner.types
EntityName(Entity, String, List<String>) - Constructor for class banner.types.EntityName
EntityType - Class in banner.types: Instances of this class represent the type of a Mention.
equals(Object) - Method in class banner.postprocessing.ExtractAbbrev.AbbreviationPair
equals(Object) - Method in class banner.types.Entity
equals(Object) - Method in class banner.types.EntityType
equals(Object) - Method in class banner.types.Mention
equals(Object) - Method in class banner.types.Sentence
equals(Object) - Method in class banner.types.Token
eval10Fold(HierarchicalConfiguration, Double) - Static method in class banner.eval.BANNER
eval5by2(HierarchicalConfiguration, Double) - Static method in class banner.eval.BANNER
ExtractAbbrev - Class in banner.postprocessing: This class was adapted from the BioText ExtractAbbrev.java software by Ariel S.
ExtractAbbrev() - Constructor for class banner.postprocessing.ExtractAbbrev
ExtractAbbrev.AbbreviationPair - Class in banner.postprocessing
extractAbbrPairs(String) - Method in class banner.postprocessing.ExtractAbbrev

F

FeatureSet - Class in banner.tagging
FeatureSet(TagFormat, Lemmatiser, Tagger, Tagger, String, Set<Mention.MentionType>, Sentence.OverlapOption, Sentence.OverlapOption) - Constructor for class banner.tagging.FeatureSet
find(E) - Method in class banner.util.RankedList
FlattenPostProcessor - Class in banner.postprocessing
FlattenPostProcessor(FlattenPostProcessor.FlattenType) - Constructor for class banner.postprocessing.FlattenPostProcessor
FlattenPostProcessor.FlattenType - Enum in banner.postprocessing

G

Gazetteer - Class in banner.normalization: A Gazetteer allows read in a list of Entitys and their associated EntityNames from a file.
Gazetteer() - Constructor for class banner.normalization.Gazetteer
Gazetteer.EntityFilter - Interface in banner.normalization
getAlternateTags(BufferedReader, String) - Method in class banner.eval.dataset.BC2GMDataset
getAncestors() - Method in class banner.types.EntityType
getAnnotations(String) - Method in class banner.eval.uima.BANNERWrapper
getBestEntities() - Method in class banner.types.EntityIdentification
getBestValue() - Method in class banner.types.EntityIdentification
getChild(K) - Method in class banner.util.Trie
getConceptId() - Method in class banner.annotation.Annotation
getConceptId() - Method in class banner.annotation.ConceptName
getDataset(HierarchicalConfiguration) - Static method in class banner.eval.BANNER
getDescription() - Method in class banner.annotation.Concept
getDictionary(HierarchicalConfiguration) - Static method in class banner.eval.BANNER
getDocumentId() - Method in class banner.types.Sentence
getElements() - Method in class banner.types.EntityName
getEnd() - Method in class banner.annotation.Annotation
getEnd() - Method in class banner.types.Mention
getEnd() - Method in class banner.types.Token
getEnd(boolean) - Method in class banner.types.Token
getEndChar() - Method in class banner.types.Mention
getEndChar(boolean) - Method in class banner.types.Mention
getEntities() - Method in class banner.normalization.Gazetteer
getEntity(String) - Method in class banner.normalization.Gazetteer
getEntity() - Method in class banner.types.EntityName
getEntityType() - Method in class banner.types.Entity
getEntityType() - Method in class banner.types.Mention
getFeatureNames() - Method in class banner.tagging.CRFTagger
getFeatureRepresentation(Sentence) - Method in class banner.tagging.CRFTagger
getFile(String) - Method in class banner.eval.uima.BANNERWrapper
getFile(String) - Method in class banner.eval.uima.Util
getFMeasure() - Method in class banner.eval.BANNER.PerformanceData
getId() - Method in class banner.annotation.Concept
getId() - Method in class banner.annotation.Text
getId() - Method in class banner.types.Entity
getIdentification(Mention) - Method in class banner.types.Sentence
getIds() - Method in class banner.eval.dataset.Dataset.Tag
getInstance(Sentence) - Method in class banner.tagging.CRFTagger
getLemmatiser(HierarchicalConfiguration) - Static method in class banner.eval.BANNER
getLongForm() - Method in class banner.postprocessing.ExtractAbbrev.AbbreviationPair
getMaxWeights() - Method in class banner.tagging.CRFTagger
getMention() - Method in class banner.types.EntityIdentification
getMentions() - Method in class banner.types.Sentence
getMentions(Mention.MentionType) - Method in class banner.types.Sentence
getMentions(Token, Set<Mention.MentionType>) - Method in class banner.types.Sentence
getMentionType() - Method in class banner.types.Mention
getMinWeights() - Method in class banner.tagging.CRFTagger
getName() - Method in class banner.annotation.ConceptName
getName() - Method in class banner.types.EntityName
getNames() - Method in class banner.types.Entity
getNames() - Method in class banner.types.EntityIdentification
getObject(int) - Method in class banner.util.RankedList
getOrder() - Method in class banner.tagging.CRFTagger
getOverall() - Method in class banner.eval.BANNER.Performance
getParent() - Method in class banner.types.EntityType
getPerMention() - Method in class banner.eval.BANNER.Performance
getPerText() - Method in class banner.eval.BANNER.Performance
getPipe() - Method in class banner.tagging.FeatureSet
getPositionText(TagFormat, Mention, int) - Static method in enum banner.tagging.TagPosition
getPosTagger(HierarchicalConfiguration) - Static method in class banner.eval.BANNER
getPostion(Mention, int) - Static method in enum banner.tagging.TagPosition
getPostProcessor(HierarchicalConfiguration) - Static method in class banner.eval.BANNER
getPrecision() - Method in class banner.eval.BANNER.PerformanceData
getProbability() - Method in class banner.types.Mention
getRecall() - Method in class banner.eval.BANNER.PerformanceData
getSemanticType() - Method in class banner.annotation.Annotation
getSentence(String, String, String, Tokenizer, HashMap<String, LinkedList<Dataset.Tag>>, Map<String, Set<String>>, Map<String, Set<String>>) - Method in class banner.eval.dataset.AZDCDataset
getSentence(String, String, Tokenizer, HashMap<String, LinkedList<Dataset.Tag>>) - Method in class banner.eval.dataset.BC2GMDataset
getSentence() - Method in class banner.types.Mention
getSentence() - Method in class banner.types.Token
getSentenceId() - Method in class banner.types.Sentence
getSentences() - Method in class banner.eval.dataset.Dataset
getShortForm() - Method in class banner.postprocessing.ExtractAbbrev.AbbreviationPair
getSimFindFilename(HierarchicalConfiguration) - Static method in class banner.eval.BANNER
getStart() - Method in class banner.annotation.Annotation
getStart() - Method in class banner.types.Mention
getStart() - Method in class banner.types.Token
getStart(boolean) - Method in class banner.types.Token
getStartChar() - Method in class banner.types.Mention
getStartChar(boolean) - Method in class banner.types.Mention
getStream(String) - Method in class banner.eval.uima.BANNERWrapper
getStream(String) - Method in class banner.eval.uima.Util
getTagList(Sequence<Object>) - Static method in class banner.tagging.CRFTagger
getTags(BufferedReader) - Method in class banner.eval.dataset.AZDCDataset
getTags(BufferedReader, String) - Method in class banner.eval.dataset.BC2GMDataset
getText() - Method in class banner.annotation.Text
getText() - Method in class banner.types.EntityType
getText() - Method in class banner.types.Mention
getText() - Method in class banner.types.Sentence
getText(int, int) - Method in class banner.types.Sentence
getText() - Method in class banner.types.Token
getTextId() - Method in class banner.annotation.Annotation
getTokenCountMention() - Method in class banner.eval.dataset.Dataset
getTokenCountTotal() - Method in class banner.eval.dataset.Dataset
getTokenIndex(List<Token>, int) - Static method in class banner.eval.dataset.BC2GMDataset
getTokenIndex(int, boolean) - Method in class banner.types.Sentence
getTokenizer(HierarchicalConfiguration) - Static method in class banner.eval.BANNER
getTokenizer() - Method in class banner.tagging.dictionary.DictionaryTagger
getTokenLabels(TagFormat, Set<Mention.MentionType>, Sentence.OverlapOption, Sentence.OverlapOption) - Method in class banner.types.Sentence
getTokens(String) - Method in class banner.tokenization.SimpleTokenizer
getTokens(String) - Method in interface banner.tokenization.Tokenizer
getTokens() - Method in class banner.types.Mention
getTokens() - Method in class banner.types.Sentence
getTrainingText(Sentence, TagFormat, Set<Mention.MentionType>, Sentence.OverlapOption, Sentence.OverlapOption) - Static method in class banner.eval.BANNER
getType() - Method in class banner.annotation.Concept
getType(String) - Static method in class banner.types.EntityType
getType(String, EntityType) - Static method in class banner.types.EntityType
getTypeCounts() - Method in class banner.eval.dataset.Dataset
getTypes() - Static method in class banner.types.EntityType
getValue(EntityName) - Method in class banner.types.EntityIdentification
getValue(int) - Method in class banner.util.RankedList
getValue() - Method in class banner.util.Trie
getValue(List<K>) - Method in class banner.util.Trie
getViewMap(EntityType) - Static method in class banner.types.EntityType

H

handle(Sentence, Set<Mention>) - Method in enum banner.postprocessing.FlattenPostProcessor.FlattenType
hashCode() - Method in class banner.postprocessing.ExtractAbbrev.AbbreviationPair
hashCode() - Method in class banner.types.Entity
hashCode() - Method in class banner.types.EntityType
hashCode() - Method in class banner.types.Mention
hashCode() - Method in class banner.types.Sentence
hashCode() - Method in class banner.types.Token

I

identifyMentions(Sentence) - Method in class banner.normalization.IndexedMentionIdentifier
identifyMentions(Sentence) - Method in interface banner.normalization.MentionIdentifier
ids - Variable in class banner.eval.dataset.Dataset.Tag
include(Entity) - Method in interface banner.normalization.Gazetteer.EntityFilter
Index<K,V> - Class in banner.util
Index() - Constructor for class banner.util.Index
Index(int) - Constructor for class banner.util.Index
Index(int, float) - Constructor for class banner.util.Index
IndexedMentionIdentifier - Class in banner.normalization
IndexedMentionIdentifier(SetSimilarityMetric, int) - Constructor for class banner.normalization.IndexedMentionIdentifier
IndexedMetricSetSimilarity<E,V> - Class in banner.util
IndexedMetricSetSimilarity(SetSimilarityMetric, int) - Constructor for class banner.util.IndexedMetricSetSimilarity
indexMatch(Collection<E>) - Method in class banner.util.IndexedMetricSetSimilarity
initialize(String, String) - Method in class banner.eval.uima.BANNERWrapper
initialize(UimaContext) - Method in class de.julielab.jcore.ae.banner.BANNERAnnotator
initializeModel(String, String) - Method in class banner.eval.uima.BANNERWrapper
initialSetCapacity - Static variable in class banner.util.Index
initialSetLoadFactor - Static variable in class banner.util.Index
isComplete() - Method in class banner.annotation.Text
isDropEndParentheticals() - Method in class banner.tagging.dictionary.DictionaryTagger
isEmpty() - Method in class banner.util.UnmodifiableArraySet
isEnd(String) - Static method in class banner.postprocessing.ParenthesisPostProcessor
isFilterContainedMentions() - Method in class banner.tagging.dictionary.DictionaryTagger
isGenerate2PartVariations() - Method in class banner.tagging.dictionary.DictionaryTagger
isIndependent(Collection<E>, Collection<E>) - Static method in class banner.util.CollectionsRand
isNormalizeDigits() - Method in class banner.tagging.dictionary.DictionaryTagger
isNormalizeMixedCase() - Method in class banner.tagging.dictionary.DictionaryTagger
isStart(String) - Static method in class banner.postprocessing.ParenthesisPostProcessor
isSubset(Collection<E>, Collection<E>) - Static method in class banner.util.CollectionsRand
iterator() - Method in class banner.util.UnmodifiableArraySet

J

JCoReEntityDataset - Class in de.julielab.jcore.banner.dataset
JCoReEntityDataset(Tokenizer) - Constructor for class de.julielab.jcore.banner.dataset.JCoReEntityDataset
JCoReEntityDataset() - Constructor for class de.julielab.jcore.banner.dataset.JCoReEntityDataset

K

keySet() - Method in class banner.util.Index

L

LChar - Class in banner.tagging.pipe: This class is used by the CRFTagger as the base for the feature set.
LChar(String) - Constructor for class banner.tagging.pipe.LChar
LemmaPOS - Class in banner.tagging.pipe: This class is used by the CRFTagger as the base for the feature set.
LemmaPOS(Lemmatiser, Tagger) - Constructor for class banner.tagging.pipe.LemmaPOS
length() - Method in class banner.types.Mention
length() - Method in class banner.types.Token
load(HierarchicalConfiguration) - Method in class banner.eval.dataset.AZDCDataset
load(HierarchicalConfiguration) - Method in class banner.eval.dataset.BC2GMDataset
load(String, String, String, String) - Method in class banner.eval.dataset.BC2GMDataset
load(HierarchicalConfiguration) - Method in class banner.eval.dataset.Dataset
load(Tokenizer, EntityType, String) - Method in class banner.normalization.Gazetteer
load(Tokenizer, String) - Method in class banner.normalization.Gazetteer
load(Tokenizer, String, Gazetteer.EntityFilter) - Method in class banner.normalization.Gazetteer
load(InputStream, Lemmatiser, Tagger, Tagger) - Static method in class banner.tagging.CRFTagger: Loads a CRFTagger from the specified file.
load(HierarchicalConfiguration) - Method in class banner.tagging.dictionary.DictionaryTagger
load(HierarchicalConfiguration) - Method in class banner.tagging.dictionary.UMLSMetathesaurusDictionaryTagger
load(File, Lemmatiser, Tagger, Tagger, int, boolean) - Static method in class banner.tagging.NBestCRFTagger
load(HierarchicalConfiguration) - Method in class de.julielab.jcore.banner.dataset.JCoReEntityDataset
load(File, File) - Method in class de.julielab.jcore.banner.dataset.JCoReEntityDataset
loadAnnotations(String, Map<String, Text>, Map<String, Concept>, Map<String, List<Annotation>>) - Static method in class banner.annotation.Annotation
loadConceptNames(String, Map<String, Concept>, Map<String, List<ConceptName>>) - Static method in class banner.annotation.ConceptName
loadConcepts(String, Map<String, Concept>) - Static method in class banner.annotation.Concept
loadTexts(String, String, List<String>, Map<String, Text>) - Static method in class banner.annotation.Text
LocalAbbreviationPostProcessor - Class in banner.postprocessing
LocalAbbreviationPostProcessor() - Constructor for class banner.postprocessing.LocalAbbreviationPostProcessor
logInput(Set<Sentence>, HierarchicalConfiguration) - Static method in class banner.eval.BANNER
lookup(K) - Method in class banner.util.Index
LowerCaseTokenText - Class in banner.tagging.pipe
LowerCaseTokenText(String, Pattern) - Constructor for class banner.tagging.pipe.LowerCaseTokenText
LowerCaseTokenText(String) - Constructor for class banner.tagging.pipe.LowerCaseTokenText

M

main(String[]) - Static method in class banner.annotation.BEAT
main(String[]) - Static method in class banner.eval.BANNER
main(String[]) - Static method in class banner.eval.uima.BANNERWrapper
main(String[]) - Static method in class banner.postprocessing.ExtractAbbrev
maxSize() - Method in class banner.util.RankedList
Mention - Class in banner.types: Instances of this class represent the mention of an entity within a Sentence.
Mention(Sentence, int, int, EntityType, Mention.MentionType) - Constructor for class banner.types.Mention
Mention(Sentence, int, int, EntityType, Mention.MentionType, Double) - Constructor for class banner.types.Mention
Mention.MentionType - Enum in banner.types
MentionDisambiguator - Interface in banner.normalization: Instances of this class make the final determination of which Entity a Mention refers.
MentionIdentifier - Interface in banner.normalization: Instances of this class are responsible for determining a set of candidate Entity objects for each Mention.
MentionTypeHint - Class in banner.tagging.pipe: Taken from GNormPlus code: Wei, C.
MentionTypeHint(String) - Constructor for class banner.tagging.pipe.MentionTypeHint
model - Variable in class banner.tagging.CRFTagger

N

NBestCRFTagger - Class in banner.tagging
NBestCRFTagger(CRF, FeatureSet, int, int, boolean) - Constructor for class banner.tagging.NBestCRFTagger
notInclude - Variable in class banner.tagging.dictionary.DictionaryTagger
numKeys() - Method in class banner.util.Index

O

OneSensePerDiscoursePostProcessor - Class in banner.postprocessing
OneSensePerDiscoursePostProcessor() - Constructor for class banner.postprocessing.OneSensePerDiscoursePostProcessor
OneSensePerDocument - Class in banner.postprocessing
OneSensePerDocument(Tokenizer, boolean) - Constructor for class banner.postprocessing.OneSensePerDocument
outputMentions(Sentence, PrintWriter, boolean, boolean) - Static method in class banner.eval.BANNER
overlaps(Dataset.Tag) - Method in class banner.eval.dataset.Dataset.Tag
overlaps(Mention) - Method in class banner.types.Mention: Determines whether this Mention overlaps the specified Mention

P

pack() - Method in class banner.util.Index
PARAM_CONFIG_FILE - Static variable in class de.julielab.jcore.ae.banner.BANNERAnnotator
PARAM_TYPE_MAPPING - Static variable in class de.julielab.jcore.ae.banner.BANNERAnnotator
ParenthesisPostProcessor - Class in banner.postprocessing: This class removes Mentions which contain a mismatched parenthesis ("(" or ")"), square bracket ("[" or "]") or curly bracket ("{" or "}").
ParenthesisPostProcessor() - Constructor for class banner.postprocessing.ParenthesisPostProcessor: Creates a new instance of ParenthesisPostProcessor
Performance(BANNER.MatchCriteria) - Constructor for class banner.eval.BANNER.Performance
PerformanceData() - Constructor for class banner.eval.BANNER.PerformanceData
pipe(Instance) - Method in class banner.tagging.pipe.ChemicalSuffix
pipe(Instance) - Method in class banner.tagging.pipe.LChar
pipe(Instance) - Method in class banner.tagging.pipe.LemmaPOS
pipe(Instance) - Method in class banner.tagging.pipe.LowerCaseTokenText
pipe(Instance) - Method in class banner.tagging.pipe.MentionTypeHint
pipe(Instance) - Method in class banner.tagging.pipe.Pretagger
pipe(Instance) - Method in class banner.tagging.pipe.ProteinSymbols
pipe(Instance) - Method in class banner.tagging.pipe.RChar
pipe(Instance) - Method in class banner.tagging.pipe.Sentence2TokenSequence
pipe(Instance) - Method in class banner.tagging.pipe.SimFind
pipe(Instance) - Method in class banner.tagging.pipe.TokenLength
pipe(Instance) - Method in class banner.tagging.pipe.TokenNumberClass
pipe(Instance) - Method in class banner.tagging.pipe.TokenWeight
pipe(Instance) - Method in class banner.tagging.pipe.TokenWordClass
postProcess(Sentence) - Method in class banner.postprocessing.FlattenPostProcessor
postProcess(Sentence) - Method in class banner.postprocessing.LocalAbbreviationPostProcessor
postProcess(Sentence) - Method in class banner.postprocessing.OneSensePerDiscoursePostProcessor
postProcess(Sentence) - Method in class banner.postprocessing.ParenthesisPostProcessor: Removes Mentions which contain a mismatched parenthesis ("(" or ")"), square bracket ("[" or "]") or curly bracket ("{" or "}").
postProcess(Sentence) - Method in interface banner.postprocessing.PostProcessor
postProcess(Sentence) - Method in class banner.postprocessing.SequentialPostProcessor
postProcess(Sentence) - Method in class banner.postprocessing.ThresholdMentionProbabilityPostProcessor
PostProcessor - Interface in banner.postprocessing: Instances of PostProcessor take Sentences which have been tagged and modify the set of Mentions according to some criteria.
Pretagger - Class in banner.tagging.pipe: This class is used by the CRFTagger as the base for the feature set.
Pretagger(String, Tagger) - Constructor for class banner.tagging.pipe.Pretagger
print() - Method in class banner.eval.BANNER.Performance
print() - Method in class banner.eval.BANNER.PerformanceData
printStats() - Method in class banner.util.Index
process(Tagger, Tokenizer, PostProcessor, Sentence) - Static method in class banner.eval.BANNER
process(List<Sentence>) - Method in class banner.postprocessing.OneSensePerDocument
process(String) - Method in class banner.tagging.dictionary.DictionaryTagger
process(JCas) - Method in class de.julielab.jcore.ae.banner.BANNERAnnotator
ProteinSymbols - Class in banner.tagging.pipe: Taken from GNormPlus code: Wei, C.
ProteinSymbols(String) - Constructor for class banner.tagging.pipe.ProteinSymbols

R

randomSplit(Collection<E>, int) - Static method in class banner.util.CollectionsRand
randomSubset(Collection<E>, int) - Static method in class banner.util.CollectionsRand
randomSubset(Collection<E>, double) - Static method in class banner.util.CollectionsRand
RankedList<E> - Class in banner.util
RankedList(int) - Constructor for class banner.util.RankedList
RChar - Class in banner.tagging.pipe: This class is used by the CRFTagger as the base for the feature set.
RChar(String) - Constructor for class banner.tagging.pipe.RChar
remove(Object) - Method in class banner.util.UnmodifiableArraySet
removeAll(Collection<?>) - Method in class banner.util.UnmodifiableArraySet
removeMention(Mention) - Method in class banner.types.Sentence
retainAll(Collection<?>) - Method in class banner.util.UnmodifiableArraySet

S

saveAnnotations(String, Map<String, Text>, Map<String, List<Annotation>>) - Static method in class banner.annotation.Annotation
saveTextCompletion(String, Map<String, Text>) - Static method in class banner.annotation.Text
Sentence - Class in banner.types: This class represents a single sentence, and provides for the text to be tokenized and for mentions.
Sentence(String, String, String) - Constructor for class banner.types.Sentence: Creates a new Sentence with the specified tag and text
Sentence.OverlapOption - Enum in banner.types
Sentence2TokenSequence - Class in banner.tagging.pipe: This class is used by the CRFTagger as the base for the feature set.
Sentence2TokenSequence(TagFormat, Set<Mention.MentionType>, Sentence.OverlapOption, Sentence.OverlapOption) - Constructor for class banner.tagging.pipe.Sentence2TokenSequence
sentences - Variable in class banner.eval.dataset.Dataset
SequentialPostProcessor - Class in banner.postprocessing
SequentialPostProcessor() - Constructor for class banner.postprocessing.SequentialPostProcessor
set(EntityName, double) - Method in class banner.types.EntityIdentification
setComplete(boolean) - Method in class banner.annotation.Text
setConceptId(String) - Method in class banner.annotation.Annotation
setDropEndParentheticals(boolean) - Method in class banner.tagging.dictionary.DictionaryTagger
setFilterContainedMentions(boolean) - Method in class banner.tagging.dictionary.DictionaryTagger
setGenerate2PartVariations(boolean) - Method in class banner.tagging.dictionary.DictionaryTagger
setIdentification(Mention, EntityIdentification) - Method in class banner.types.Sentence
setLemmatiser(Lemmatiser) - Method in class banner.tagging.FeatureSet
setLemmatiser(Lemmatiser) - Method in class banner.tagging.pipe.LemmaPOS
setNormalizeDigits(boolean) - Method in class banner.tagging.dictionary.DictionaryTagger
setNormalizeMixedCase(boolean) - Method in class banner.tagging.dictionary.DictionaryTagger
setPosTagger(Tagger) - Method in class banner.tagging.FeatureSet
setPosTagger(Tagger) - Method in class banner.tagging.pipe.LemmaPOS
setPreTagger(Tagger) - Method in class banner.tagging.FeatureSet
setPreTagger(Tagger) - Method in class banner.tagging.pipe.Pretagger
setProbability(Double) - Method in class banner.types.Mention
setSemanticType(String) - Method in class banner.annotation.Annotation
SetSimilarityMetric - Enum in banner.util
setTokenizer(Tokenizer) - Method in class banner.eval.dataset.Dataset
setTokenizer(Tokenizer) - Method in class banner.tagging.dictionary.DictionaryTagger
setTokenWeights(Map<String, Double>) - Method in class banner.tagging.pipe.TokenWeight
setValue(V) - Method in class banner.util.Trie
SimFind - Class in banner.tagging.pipe: This class is used by the CRFTagger as the base for the distributional semantics features.
SimFind(String) - Constructor for class banner.tagging.pipe.SimFind
simFindStoreProteins - Variable in class banner.tagging.pipe.SimFind
similarity(int, int, int) - Method in enum banner.util.SetSimilarityMetric
similarityInternal(int, int, int) - Method in enum banner.util.SetSimilarityMetric
SimpleTokenizer - Class in banner.tokenization: Tokens ouput by this tokenizer consist of a contiguous block of alphanumeric characters or a single punctuation mark.
SimpleTokenizer() - Constructor for class banner.tokenization.SimpleTokenizer
size() - Method in class banner.tagging.dictionary.DictionaryTagger
size() - Method in class banner.util.RankedList
size() - Method in class banner.util.Trie: Returns the number of mappings in this Trie
size() - Method in class banner.util.UnmodifiableArraySet
split(int) - Method in class banner.eval.dataset.AZDCDataset
split(int) - Method in class banner.eval.dataset.BC2GMDataset
split(int) - Method in class banner.eval.dataset.Dataset
split(int) - Method in class de.julielab.jcore.banner.dataset.JCoReEntityDataset
start - Variable in class banner.eval.dataset.Dataset.Tag
suppress(String) - Method in class banner.tagging.dictionary.DictionaryTagger

T

Tag(EntityType, int, int) - Constructor for class banner.eval.dataset.Dataset.Tag
tag(Sentence) - Method in class banner.tagging.CRFTagger
tag(Sentence) - Method in class banner.tagging.dictionary.DictionaryTagger
tag(Sentence) - Method in class banner.tagging.NBestCRFTagger
tag(Sentence) - Method in interface banner.tagging.Tagger: Add Mentions to the Sentence.
TagFormat - Enum in banner.tagging
Tagger - Interface in banner.tagging: Taggers add Mentions to a Sentence which has been tokenized.
TagPosition - Enum in banner.tagging
test(HierarchicalConfiguration) - Static method in class banner.eval.BANNER
test(Dataset, Tagger, HierarchicalConfiguration) - Static method in class banner.eval.BANNER
test(Dataset, Tagger, HierarchicalConfiguration, String) - Static method in class banner.eval.BANNER
testDict(HierarchicalConfiguration) - Static method in class banner.eval.BANNER
Text - Class in banner.annotation
Text(String, String, boolean) - Constructor for class banner.annotation.Text
ThresholdMentionProbabilityPostProcessor - Class in banner.postprocessing
ThresholdMentionProbabilityPostProcessor(double) - Constructor for class banner.postprocessing.ThresholdMentionProbabilityPostProcessor
toArray() - Method in class banner.util.UnmodifiableArraySet
toArray(T[]) - Method in class banner.util.UnmodifiableArraySet
Token - Class in banner.types: Represents a single token of text.
Token(Sentence, int, int) - Constructor for class banner.types.Token: The token is from character start to character end - 1
tokenize(Sentence) - Method in class banner.tokenization.SimpleTokenizer
tokenize(Sentence) - Method in interface banner.tokenization.Tokenizer: Tokenizes the given Sentence
tokenizer - Variable in class banner.eval.dataset.Dataset
Tokenizer - Interface in banner.tokenization: Tokenizers take the text of a sentence and turn it into a Sentence object.
TokenLength - Class in banner.tagging.pipe
TokenLength(String, Pattern) - Constructor for class banner.tagging.pipe.TokenLength
TokenLength(String) - Constructor for class banner.tagging.pipe.TokenLength
TokenNumberClass - Class in banner.tagging.pipe
TokenNumberClass(String, Pattern, boolean) - Constructor for class banner.tagging.pipe.TokenNumberClass
TokenNumberClass(String, boolean) - Constructor for class banner.tagging.pipe.TokenNumberClass
TokenWeight - Class in banner.tagging.pipe: This class is used by the CRFTagger as the base for the feature set.
TokenWeight(Map<String, Double>) - Constructor for class banner.tagging.pipe.TokenWeight
TokenWordClass - Class in banner.tagging.pipe
TokenWordClass(String, Pattern, boolean) - Constructor for class banner.tagging.pipe.TokenWordClass
TokenWordClass(String, boolean) - Constructor for class banner.tagging.pipe.TokenWordClass
toString() - Method in class banner.postprocessing.ExtractAbbrev.AbbreviationPair
toString() - Method in class banner.types.Entity
toString() - Method in class banner.types.EntityName
toString() - Method in class banner.types.EntityType
toString() - Method in class banner.types.Mention
toString() - Method in class banner.types.Token
train(HierarchicalConfiguration, Double) - Static method in class banner.eval.BANNER
train(Set<Sentence>, int, TagFormat, FeatureSet) - Static method in class banner.tagging.CRFTagger: Trains and returns a CRFTagger on the specified Sentence s.
transform(String) - Method in class banner.tagging.dictionary.DictionaryTagger
transform(E) - Method in class banner.util.IndexedMetricSetSimilarity: All elements are transformed prior to use for storage or lookup.
Trie<K,V> - Class in banner.util: A Trie (also known as a prefix tree) essentially maps from a list of objects (keys) to a value.
Trie() - Constructor for class banner.util.Trie
Trie(V) - Constructor for class banner.util.Trie
type - Variable in class banner.eval.dataset.Dataset.Tag

U

UMLSMetathesaurusDictionaryTagger - Class in banner.tagging.dictionary
UMLSMetathesaurusDictionaryTagger() - Constructor for class banner.tagging.dictionary.UMLSMetathesaurusDictionaryTagger
UnmodifiableArraySet<E> - Class in banner.util
UnmodifiableArraySet(Set<? extends E>) - Constructor for class banner.util.UnmodifiableArraySet
update(Sentence, Sentence) - Method in class banner.eval.BANNER.Performance
Util - Class in banner.eval.uima
Util() - Constructor for class banner.eval.uima.Util

V

valueOf(String) - Static method in enum banner.eval.BANNER.MatchCriteria: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum banner.postprocessing.FlattenPostProcessor.FlattenType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum banner.tagging.TagFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum banner.tagging.TagPosition: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum banner.types.Mention.MentionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum banner.types.Sentence.OverlapOption: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum banner.util.SetSimilarityMetric: Returns the enum constant of this type with the specified name.
values() - Static method in enum banner.eval.BANNER.MatchCriteria: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum banner.postprocessing.FlattenPostProcessor.FlattenType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum banner.tagging.TagFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum banner.tagging.TagPosition: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum banner.types.Mention.MentionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum banner.types.Sentence.OverlapOption: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum banner.util.SetSimilarityMetric: Returns an array containing the constants of this enum type, in the order they are declared.

W

write(String) - Method in class banner.normalization.Gazetteer: A gazetteer is written as two parts, one contains the Type, ID and EntityNames and the second contains the entity relationships
write(File) - Method in class banner.tagging.CRFTagger: Serializes and writes this CRFTagger to the specified file

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