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

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GenerateAutomatons - Class in uk.ac.man.entitytagger.generate

Class providing functions used to generate automatons for efficient regular expression matching

GenerateAutomatons() - Constructor for class uk.ac.man.entitytagger.generate.GenerateAutomatons

GenerateAutomatons.ProcessProblem - Class in uk.ac.man.entitytagger.generate

Class used to join several automatons together and minimize the result (put into a class to enable concurrent computations)

GenerateAutomatons.ProcessProblem(ArrayList<Automaton>, boolean) - Constructor for class uk.ac.man.entitytagger.generate.GenerateAutomatons.ProcessProblem

GenerateAutomatons.ToAutomatonProblem - Class in uk.ac.man.entitytagger.generate

GenerateAutomatons.ToAutomatonProblem(DictionaryEntry, boolean) - Constructor for class uk.ac.man.entitytagger.generate.GenerateAutomatons.ToAutomatonProblem

GenerateAutomatons.ToAutomatonProblemIterator - Class in uk.ac.man.entitytagger.generate

GenerateAutomatons.ToAutomatonProblemIterator(ArrayList<DictionaryEntry>, boolean) - Constructor for class uk.ac.man.entitytagger.generate.GenerateAutomatons.ToAutomatonProblemIterator

GenerateDictionary - Class in uk.ac.man.entitytagger.entities.species

GenerateDictionary() - Constructor for class uk.ac.man.entitytagger.entities.species.GenerateDictionary

generateGenusDictionary(File, File[], boolean, Logger) - Static method in class uk.ac.man.entitytagger.entities.species.GenerateDictionary

GenerateMatchers - Class in uk.ac.man.entitytagger.generate

Main class for loading a species name dictionary and custom synonyms, and then calling other classes to generate regular expressions for species entries and convert them into automatons for efficient text matching.

GenerateMatchers() - Constructor for class uk.ac.man.entitytagger.generate.GenerateMatchers

generateSpeciesDictionary(File, File[], boolean, Logger, int) - Static method in class uk.ac.man.entitytagger.entities.species.GenerateDictionary

generateSpeciesNames(File, File[], boolean, Logger) - Static method in class uk.ac.man.entitytagger.entities.species.GenerateDictionary

get(String) - Method in class martin.common.ArgParser

get(String, String) - Method in class martin.common.ArgParser

get(K) - Method in class martin.common.CacheMap

get() - Method in class martin.common.SimpleClass

get(Node, String) - Method in class uk.ac.man.documentparser.input.Elsevier

get(Node, String[]) - Method in class uk.ac.man.documentparser.input.Elsevier

getA() - Method in class martin.common.ComparableTuple

getA() - Method in class martin.common.Tuple

getAbbrev() - Method in class uk.ac.man.documentparser.dataholders.Journal

getAbs() - Method in class uk.ac.man.documentparser.dataholders.Document

getAbs() - Method in class uk.ac.man.entitytagger.doc.TaggedDocument

getAcceptedName(String) - Static method in class uk.ac.man.entitytagger.entities.species.GenerateDictionary

getAllMatchedSpecies() - Method in class uk.ac.man.entitytagger.doc.TaggedDocument

getAllMatches() - Method in class uk.ac.man.entitytagger.doc.TaggedDocument

getAllMatches() - Method in class uk.ac.man.entitytagger.doc.TaggedSection

getArrayListSolutions() - Method in class martin.common.compthreads.ArrayBasedMaster

getArrayNodeList(String, Node) - Static method in class martin.common.xml.XPath

getAuthors() - Method in class uk.ac.man.documentparser.dataholders.Document

getAuthors(Element) - Method in class uk.ac.man.documentparser.input.BMC

getAuthors(Document) - Method in class uk.ac.man.documentparser.input.Elsevier

getAutomatons() - Method in class uk.ac.man.entitytagger.matching.matchers.AutomatonMatcher

getB() - Method in class martin.common.ComparableTuple

getB() - Method in class martin.common.Tuple

getBody() - Method in class uk.ac.man.documentparser.dataholders.Document

getBody(Document) - Method in class uk.ac.man.documentparser.input.Elsevier

getBody() - Method in class uk.ac.man.entitytagger.doc.TaggedDocument

getBoolean(String, boolean) - Method in class martin.common.ArgParser

getBoolean(String) - Method in class martin.common.ArgParser

getBooleanProperty(String) - Method in class martin.common.Properties

getBooleanProperty(String, boolean) - Method in class martin.common.Properties

getBooleans(String) - Method in class martin.common.ArgParser

getChars() - Method in class dk.brics.automaton.CustomAutomatonMatcher

getChildren() - Method in class uk.ac.man.entitytagger.doc.TaggedSection

getComment() - Method in class uk.ac.man.entitytagger.generate.DictionaryEntry

getComment() - Method in class uk.ac.man.entitytagger.Mention

getCommonNames(String) - Static method in class uk.ac.man.entitytagger.entities.species.CatalogueOfLife

getConn() - Method in class martin.common.MyConnection

getContent() - Method in class uk.ac.man.documentparser.dataholders.Section

getContent() - Method in class uk.ac.man.entitytagger.doc.TaggedDocument

getContentsRecursive() - Method in class uk.ac.man.documentparser.dataholders.Section

getDefaultConsoleHandler() - Static method in class martin.common.Loggers

getDefaultFileFormatter() - Static method in class martin.common.Loggers

getDefaultFileLogger(File) - Static method in class martin.common.Loggers

getDefaultFormatter() - Static method in class martin.common.Loggers

getDefaultHelpMessage() - Static method in class uk.ac.man.entitytagger.EntityTagger

getDefaultLogger(ArgParser) - Static method in class martin.common.Loggers

getDescription() - Method in class uk.ac.man.documentparser.dataholders.Document

getDescription() - Method in class uk.ac.man.entitytagger.Mention.IDPair

getDoc() - Method in class uk.ac.man.documentparser.input.DatabaseListIterator

getDocid() - Method in class uk.ac.man.entitytagger.Mention

getDocumentHelpMessage() - Static method in class uk.ac.man.documentparser.DocumentParser

getDocuments(ArgParser) - Static method in class uk.ac.man.documentparser.DocumentParser

getDocuments(ArgParser, Logger) - Static method in class uk.ac.man.documentparser.DocumentParser

getDocumentSelection(String[], int) - Static method in class uk.ac.man.entitytagger.evaluate.Evaluate

Randomly returns n document ids from an array of document ids.

getDocumentsToHash(ArgParser) - Static method in class uk.ac.man.documentparser.DocumentParser

getDouble(String) - Method in class martin.common.ArgParser

getDouble(String, double) - Method in class martin.common.ArgParser

getDoubleProperty(String) - Method in class martin.common.Properties

getDoubles(String) - Method in class martin.common.ArgParser

getDuration(long) - Static method in class martin.common.Misc

getEmail() - Method in class uk.ac.man.documentparser.dataholders.Author

getEnd() - Method in class uk.ac.man.entitytagger.Mention

getEnd() - Method in class uk.ac.man.entitytagger.Mention.SimpleMention

getExternalID() - Method in class uk.ac.man.documentparser.dataholders.Document

getFile(String) - Method in class martin.common.ArgParser

getFile(String, File) - Method in class martin.common.ArgParser

getFiles(String) - Method in class martin.common.ArgParser

getForenames() - Method in class uk.ac.man.documentparser.dataholders.Author

getFScore() - Method in class uk.ac.man.entitytagger.evaluate.Result

getHeader() - Static method in class uk.ac.man.entitytagger.evaluate.Result

getID() - Method in class uk.ac.man.documentparser.dataholders.Document

getID() - Method in class uk.ac.man.documentparser.dataholders.ExternalID

getId() - Method in class uk.ac.man.entitytagger.generate.DictionaryEntry

getId() - Method in class uk.ac.man.entitytagger.Mention.IDPair

getIDs(int) - Method in class dk.brics.automaton.CustomAutomatonMatcher

getIDs(MyConnection, File, Logger, int) - Static method in class uk.ac.man.documentparser.misc.MedlineFixer

getIds() - Method in class uk.ac.man.entitytagger.Mention

getIds() - Method in class uk.ac.man.entitytagger.Mention.SimpleMention

getIdsToString() - Method in class uk.ac.man.entitytagger.Mention

getIdsWithLineNumbers() - Method in class uk.ac.man.entitytagger.Mention

getIndices(String[]) - Static method in class martin.common.SQL

getInputStream(String) - Method in class martin.common.ArgParser

getInputStream(String, InputStream) - Method in class martin.common.ArgParser

getInputStreams(String) - Method in class martin.common.ArgParser

getInt(String) - Method in class martin.common.ArgParser

getInt(String, int) - Method in class martin.common.ArgParser

getIntegerProperty(String) - Method in class martin.common.Properties

getIntegerProperty(String, int) - Method in class martin.common.Properties

getIntegerProperty(String, double) - Method in class martin.common.Properties

getInts(String) - Method in class martin.common.ArgParser

getISSN() - Method in class uk.ac.man.documentparser.dataholders.Journal

getIssue() - Method in class uk.ac.man.documentparser.dataholders.Document

getJournal() - Method in class uk.ac.man.documentparser.dataholders.Document

getLength() - Method in class martin.common.xml.MyNodeList

getLength() - Method in class uk.ac.man.documentparser.dataholders.Section

getMatchEnd() - Method in class dk.brics.automaton.CustomAutomatonMatcher

getMatcher(ArgParser, Logger) - Static method in class uk.ac.man.entitytagger.EntityTagger

returns a entity recognition Matcher based on the input parameters in ap (provided by the user on the command-line or in a configuration file)

getMatcher(ArgParser, Logger, String) - Static method in class uk.ac.man.entitytagger.EntityTagger

returns a entity recognition Matcher based on the input parameters in ap (provided by the user on the command-line or in a configuration file)

getMatches() - Method in class uk.ac.man.entitytagger.doc.TaggedSection

getMatchIDs() - Method in class dk.brics.automaton.CustomAutomatonMatcher

getMatchIds(List<Pair<Integer>>, int, String) - Method in class uk.ac.man.entitytagger.matching.matchers.VariantDictionaryMatcher

Performs dictionary matching on the text, finding terms that start with the token 'token'.

getMatchStart() - Method in class dk.brics.automaton.CustomAutomatonMatcher

getMatchTags(Mention, TaggedDocument.Format, boolean) - Static method in class uk.ac.man.entitytagger.doc.TaggedDocument

getMentionsInRange(List<Mention>, int, int) - Static method in class uk.ac.man.entitytagger.Mention

getMeshTaxIDs(HashMap<String, Integer>) - Method in class uk.ac.man.documentparser.dataholders.Document

getMostProbableID() - Method in class uk.ac.man.entitytagger.Mention

getMostProbableIDWithIdLine() - Method in class uk.ac.man.entitytagger.Mention

getNext() - Method in class uk.ac.man.documentparser.input.util.Splitter

getNode(String, Node) - Static method in class martin.common.xml.XPath

getNodeList(String, Node) - Static method in class martin.common.xml.XPath

getOrCreate(K) - Method in class martin.common.CacheMap

getOriginal() - Method in class uk.ac.man.entitytagger.doc.TaggedDocument

getOriginal() - Method in class uk.ac.man.entitytagger.doc.TaggedSection

getPages() - Method in class uk.ac.man.documentparser.dataholders.Document

getParser(String[]) - Static method in class martin.common.ArgParser

getParser() - Static method in class martin.common.ArgParser

getPattern() - Method in class uk.ac.man.entitytagger.generate.DictionaryEntry

getPostprocessor(ArgParser, Logger, Map<String, String>) - Static method in class uk.ac.man.entitytagger.entities.misc.CellLinePostprocessor

getPostprocessor(ArgParser, Logger, Map<String, String>) - Static method in class uk.ac.man.entitytagger.EntityTagger

getPostprocessor(ArgParser, Logger, Map<String, String>, String) - Static method in class uk.ac.man.entitytagger.EntityTagger

getPrecision() - Method in class uk.ac.man.entitytagger.evaluate.Result

getProb() - Method in class uk.ac.man.entitytagger.Mention.IDPair

getProbabilities() - Method in class uk.ac.man.entitytagger.Mention

getRaw_type() - Method in class uk.ac.man.documentparser.dataholders.Document

getRawContent() - Method in class uk.ac.man.documentparser.dataholders.Document

getRawMatches() - Method in class uk.ac.man.entitytagger.doc.TaggedDocument

getRecall() - Method in class uk.ac.man.entitytagger.evaluate.Result

getRegexp() - Method in class uk.ac.man.entitytagger.generate.DictionaryEntry

getReportProgress() - Method in class martin.common.compthreads.Master

getRequired(String) - Method in class martin.common.ArgParser

gets(String) - Method in class martin.common.ArgParser

getSection(NodeList) - Method in class uk.ac.man.documentparser.input.BMC

getSection(Node) - Method in class uk.ac.man.documentparser.input.Elsevier

getSection(NodeList) - Method in class uk.ac.man.documentparser.input.PMC

getSection(NodeList) - Method in class uk.ac.man.documentparser.input.PMC2

getSectionCoordinates(String, String, int, int) - Static method in class martin.common.xml.Misc

getSectionCoordinates(String, String[]) - Static method in class martin.common.xml.Misc

getSerialVersionUID() - Static method in class uk.ac.man.documentparser.dataholders.Document

getSkipIDs(Connection, String) - Method in class uk.ac.man.documentparser.input.DatabaseIterator

getSnippets(NodeList) - Method in class uk.ac.man.documentparser.input.OTMI

getSolutions() - Method in class martin.common.compthreads.ArrayBasedMaster

This method will block until all problems have been processed and computed.

getSource() - Method in class uk.ac.man.documentparser.dataholders.ExternalID

getStart() - Method in class uk.ac.man.entitytagger.Mention

getStart() - Method in class uk.ac.man.entitytagger.Mention.SimpleMention

getStoredData() - Method in class uk.ac.man.entitytagger.matching.matchers.PrecomputedMatcher

getSubSections() - Method in class uk.ac.man.documentparser.dataholders.Section

getSurname() - Method in class uk.ac.man.documentparser.dataholders.Author

getTempFile() - Method in class martin.common.r.RGraphics

getText() - Method in class uk.ac.man.entitytagger.Mention

getText() - Method in class uk.ac.man.entitytagger.Mention.SimpleMention

getTitle() - Method in class uk.ac.man.documentparser.dataholders.Document

getTitle() - Method in class uk.ac.man.documentparser.dataholders.Journal

getTitle() - Method in class uk.ac.man.documentparser.dataholders.Section

getType() - Method in class uk.ac.man.documentparser.dataholders.Document

getValidChars(int) - Method in class dk.brics.automaton.CustomRunAutomaton

getValidDocs(Set<String>, Set<String>, Set<String>, Set<String>, HashMap<String, String>) - Static method in class uk.ac.man.entitytagger.evaluate.Evaluate

Function which given document id sets will return a set of IDs that are relevant for evaluation.

getVolume() - Method in class uk.ac.man.documentparser.dataholders.Document

getWordCounts(NodeList) - Method in class uk.ac.man.documentparser.input.OTMI

getX() - Method in class martin.common.Pair

getXml() - Method in class uk.ac.man.documentparser.dataholders.Document

getY() - Method in class martin.common.Pair

getYear() - Method in class uk.ac.man.documentparser.dataholders.Document

group() - Method in class dk.brics.automaton.CustomAutomatonMatcher

Returns the subsequence of the input found by the previous match.

group(int) - Method in class dk.brics.automaton.CustomAutomatonMatcher

Returns the subsequence of the input found by the specified capturing group during the previous match operation.

groupCount() - Method in class dk.brics.automaton.CustomAutomatonMatcher

Returns the number of capturing groups in the underlying automaton.

groups - Variable in class uk.ac.man.entitytagger.matching.matchers.ACIDMatcher

guessTypes(File, String) - Static method in class martin.common.SQL