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

C

c - Variable in class martin.common.SentenceSplitter

cache - Variable in class uk.ac.man.entitytagger.networking.SimpleServer

cache - Variable in class uk.ac.man.entitytagger.networking.SimpleServerWorker

CacheMap<K,V extends Sizeable> - Class in martin.common

CacheMap(long) - Constructor for class martin.common.CacheMap

CacheMap(long, Function<V>, Logger) - Constructor for class martin.common.CacheMap

cacheSem - Variable in class uk.ac.man.entitytagger.networking.SimpleServer

cacheSem - Variable in class uk.ac.man.entitytagger.networking.SimpleServerWorker

cancel() - Method in class martin.common.Stopwatch

Stops the stopwatch, without adding the elapsed time to the global data store.

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

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

CellLinePostprocessor - Class in uk.ac.man.entitytagger.entities.misc

CellLinePostprocessor(File[], File[], File[], Logger, Map<String, String>) - Constructor for class uk.ac.man.entitytagger.entities.misc.CellLinePostprocessor

CellLines - Class in uk.ac.man.entitytagger.entities.misc

This class will, given a CLKB CellLine database .owl file, parse its contents and output a tab-delimited regular expression file suitable for import by the automaton generating software.

CellLines() - Constructor for class uk.ac.man.entitytagger.entities.misc.CellLines

chars - Variable in class dk.brics.automaton.CustomAutomatonMatcher

check(String, List<Mention>) - Method in class uk.ac.man.entitytagger.networking.AlibabaWorker

children - Variable in class uk.ac.man.entitytagger.doc.TaggedSection

ChiTester - Class in martin.common

ChiTester(File) - Constructor for class martin.common.ChiTester

citations - Variable in class uk.ac.man.documentparser.input.Medline

clean(String) - Method in class uk.ac.man.documentparser.input.util.CleanUnicode

CleanUnicode - Class in uk.ac.man.documentparser.input.util

CleanUnicode(DocumentIterator) - Constructor for class uk.ac.man.documentparser.input.util.CleanUnicode

clear() - Method in class martin.common.CacheMap

clear(Map<String, List<String>>, String, Set<String>) - Static method in class uk.ac.man.entitytagger.entities.misc.OBOParser

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

closeAll() - Method in class martin.common.InputStreamDumper

COL_WEBSERVICE_URL - Static variable in class uk.ac.man.entitytagger.entities.species.GenerateDictionary

Catalogue of Life web service used to perform species lookups in order to determine the accepted names for species where latin names have been deprecated.

combineMatches(List<Mention>) - Static method in class uk.ac.man.entitytagger.matching.Matcher

comment - Variable in class uk.ac.man.entitytagger.generate.DictionaryEntry

comment(List<Mention>, Map<String, String>) - Method in class uk.ac.man.entitytagger.matching.Postprocessor

comment - Variable in class uk.ac.man.entitytagger.Mention

COMMENT_SEPARATOR - Static variable in class uk.ac.man.entitytagger.Mention

comments - Variable in class uk.ac.man.entitytagger.matching.Postprocessor

ComparableTuple<E extends java.lang.Comparable<E>,T extends java.lang.Comparable<T>> - Class in martin.common

Tuple class implementing the Comparable interface.

ComparableTuple(E, T) - Constructor for class martin.common.ComparableTuple

compareTo(ComparableTuple<E, T>) - Method in class martin.common.ComparableTuple

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

compute() - Method in interface martin.common.compthreads.Problem

This is the method called by the master threads, and should contain the code that should be computed concurrently.

compute(File, String, Set<String>) - Static method in class uk.ac.man.documentparser.misc.MedlineIndexer

compute() - Method in class uk.ac.man.entitytagger.evaluate.EvaluateProblem

compute() - Method in class uk.ac.man.entitytagger.generate.ConvertToVariantsProblemIterator.ConvertToVariantsProblem

compute() - Method in class uk.ac.man.entitytagger.generate.GenerateAutomatons.ProcessProblem

compute() - Method in class uk.ac.man.entitytagger.generate.GenerateAutomatons.ToAutomatonProblem

compute() - Method in class uk.ac.man.entitytagger.matching.matchers.ConcurrentMatcher.MatchProblem

compute() - Method in class uk.ac.man.entitytagger.networking.SimpleServerWorker

ConcurrentMatcher - Class in uk.ac.man.entitytagger.matching.matchers

Class for facilitating concurrent text matching.

ConcurrentMatcher(Matcher, DocumentIterator) - Constructor for class uk.ac.man.entitytagger.matching.matchers.ConcurrentMatcher

Create an object which will do matching using a single matcher over a number of documents.

ConcurrentMatcher.MatchProblem - Class in uk.ac.man.entitytagger.matching.matchers

ConcurrentMatcher.MatchProblem(Matcher, Document) - Constructor for class uk.ac.man.entitytagger.matching.matchers.ConcurrentMatcher.MatchProblem

configureLogger(Logger, ArgParser) - Static method in class martin.common.Loggers

conn - Variable in class martin.common.MyConnection

conn - Variable in class uk.ac.man.documentparser.input.DatabaseIterator

conn - Variable in class uk.ac.man.documentparser.input.DatabaseListIterator

conn - Variable in class uk.ac.man.entitytagger.matching.matchers.PrecomputedMatcher

conn - Variable in class uk.ac.man.entitytagger.matching.matchers.VariantDictionaryMatcher

SQL database connection and table names, from which dictionaries should be loaded initially

connectMySQL(ArgParser, Logger, String) - Static method in class martin.common.SQL

Creates a connection to a MySQL database, using arguments held by the ArgParser.

connectMySQL2(ArgParser, Logger, String) - Static method in class martin.common.SQL

Creates a connection to a MySQL database, using arguments held by the ArgParser.

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

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

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

content - Variable in class uk.ac.man.documentparser.dataholders.Section

contents - Variable in class uk.ac.man.documentparser.input.Directory

convAuthors(String) - Method in class uk.ac.man.documentparser.input.DatabaseIterator

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

convert(Map<String, List<Mention>>) - Method in class uk.ac.man.entitytagger.evaluate.Evaluate

convertIDs(List<Mention>, Map<String, String>) - Method in class uk.ac.man.entitytagger.matching.matchers.MatchPostProcessor

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

convertToVariants(HashMap<String, DictionaryEntry>, File, PreparedStatement, int, Logger, int) - Static method in class uk.ac.man.entitytagger.generate.GenerateMatchers

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

ConvertToVariantsProblemIterator(HashMap<String, DictionaryEntry>) - Constructor for class uk.ac.man.entitytagger.generate.ConvertToVariantsProblemIterator

ConvertToVariantsProblemIterator.ConvertToVariantsProblem - Class in uk.ac.man.entitytagger.generate

ConvertToVariantsProblemIterator.ConvertToVariantsProblem(DictionaryEntry) - Constructor for class uk.ac.man.entitytagger.generate.ConvertToVariantsProblemIterator.ConvertToVariantsProblem

convSource(String) - Method in class uk.ac.man.documentparser.input.DatabaseIterator

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

convTextRawType(String) - Method in class uk.ac.man.documentparser.input.DatabaseIterator

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

convType(String) - Method in class uk.ac.man.documentparser.input.DatabaseIterator

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

createTable(Connection, String, String[], String[], boolean) - Static method in class martin.common.SQL

createTable(Connection, String) - Static method in class uk.ac.man.documentparser.misc.MeshExtractor

currentFile - Variable in class uk.ac.man.documentparser.input.MedlineIndex

currentFile - Variable in class uk.ac.man.documentparser.input.MedlinePMCIndex

currentFileIterator - Variable in class uk.ac.man.documentparser.input.Directory

currentFilePassed - Variable in class uk.ac.man.documentparser.input.MedlineIndex

currentFilePassed - Variable in class uk.ac.man.documentparser.input.MedlinePMCIndex

currentFileStream - Variable in class uk.ac.man.documentparser.input.MedlineIndex

currentFileStream - Variable in class uk.ac.man.documentparser.input.MedlinePMCIndex

currentIDs - Variable in class uk.ac.man.documentparser.input.util.Splitter

currentItem - Variable in class uk.ac.man.entitytagger.generate.GenerateAutomatons.ToAutomatonProblemIterator

currentLine - Variable in class uk.ac.man.documentparser.input.MedlineIndex

currentLine - Variable in class uk.ac.man.documentparser.input.MedlinePMCIndex

currentSize - Variable in class martin.common.CacheMap

currentSubDirectory - Variable in class uk.ac.man.documentparser.input.Directory

currentTexts - Variable in class uk.ac.man.documentparser.input.util.Splitter

CustomAutomatonMatcher - Class in dk.brics.automaton

A tool that performs match operations on a given character sequence using a compiled automaton.

CustomAutomatonMatcher(CharSequence, CustomRunAutomaton) - Constructor for class dk.brics.automaton.CustomAutomatonMatcher

CustomRunAutomaton - Class in dk.brics.automaton

Finite-state automaton with fast run operation.

CustomRunAutomaton(Automaton, boolean) - Constructor for class dk.brics.automaton.CustomRunAutomaton

Constructs a new RunAutomaton from a deterministic Automaton.