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

R

rand - Variable in class uk.ac.man.entitytagger.networking.SimpleClientMatcher

random - Variable in class martin.common.r.RGraphics

random - Static variable in class martin.common.Selector

raw_type - Variable in class uk.ac.man.documentparser.dataholders.Document

rawContent - Variable in class uk.ac.man.documentparser.dataholders.Document

rawContent - Variable in class uk.ac.man.entitytagger.doc.TaggedDocument

rawMatches - Variable in class uk.ac.man.entitytagger.doc.TaggedDocument

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

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

RECONNECT_SLEEP_TIME - Variable in class martin.common.MyConnection

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

reduceIDs(Map<String, List<Mention>>) - Static method in class uk.ac.man.entitytagger.evaluate.Evaluate

refTags - Variable in class uk.ac.man.entitytagger.evaluate.EvaluateProblem

refTagsByDoc - Variable in class uk.ac.man.entitytagger.evaluate.EvaluateProblem

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

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

regexpify(String, String) - Static method in class uk.ac.man.entitytagger.entities.misc.OBOParser

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

RegexpMatcher(Map<String, Pattern>) - Constructor for class uk.ac.man.entitytagger.matching.matchers.RegexpMatcher

remove() - Method in class martin.common.ArrayIterator

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

remove() - Method in class martin.common.compthreads.IteratorBasedMaster

Does not do anything, as next() also removes elements from storage after returning them.

remove() - Method in class martin.common.SentenceSplitter

remove() - Method in class martin.common.StreamIterator

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

remove() - Method in class uk.ac.man.documentparser.input.BMCXML

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

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

remove() - Method in class uk.ac.man.documentparser.input.Directory

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

remove() - Method in class uk.ac.man.documentparser.input.IDIterator

remove() - Method in class uk.ac.man.documentparser.input.Medline

remove() - Method in class uk.ac.man.documentparser.input.MedlineIndex

remove() - Method in class uk.ac.man.documentparser.input.MedlinePMCIndex

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

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

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

remove() - Method in class uk.ac.man.documentparser.input.PMCAbstract

remove() - Method in class uk.ac.man.documentparser.input.PMCIndex

remove() - Method in class uk.ac.man.documentparser.input.TextFile

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

remove() - Method in class uk.ac.man.documentparser.input.util.DocumentBuffer

remove() - Method in class uk.ac.man.documentparser.input.util.Skipper

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

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

remove() - Method in class uk.ac.man.entitytagger.generate.GenerateAutomatons.ToAutomatonProblemIterator

not implemented

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

remove() - Method in class uk.ac.man.entitytagger.networking.SimpleServer

RemoveDuplicates - Class in uk.ac.man.documentparser.misc

RemoveDuplicates() - Constructor for class uk.ac.man.documentparser.misc.RemoveDuplicates

removeLineNumbers(List<Mention>) - Method in class uk.ac.man.entitytagger.matching.Postprocessor

removeSections(Section[], String) - Method in class uk.ac.man.documentparser.input.PMC

removeSections(Section[], String) - Method in class uk.ac.man.documentparser.input.PMC2

replicateChar(char, int) - Static method in class martin.common.Misc

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

report(E, int) - Method in class martin.common.compthreads.ArrayBasedMaster

Called by the worker threads as they complete.

report(E, int) - Method in class martin.common.compthreads.IteratorBasedMaster

report(E, int) - Method in class martin.common.compthreads.Master

reportProgress - Variable in class martin.common.compthreads.Master

reset() - Method in class martin.common.compthreads.IteratorBasedMaster

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

resolveEntity(String, String) - Method in class martin.common.xml.EntityResolver

Result - Class in uk.ac.man.entitytagger.evaluate

Result() - Constructor for class uk.ac.man.entitytagger.evaluate.Result

retrieved - Variable in class uk.ac.man.documentparser.input.util.DocumentBuffer

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

RGraphics - Class in martin.common.r

Utility class for producing R graphs from Java, utilizing a set of R scripts (in the martin.common.r.scripts folder)

RGraphics(File, File, File) - Constructor for class martin.common.r.RGraphics

root - Variable in class uk.ac.man.documentparser.input.OTMI

round(double, int) - Static method in class martin.common.Misc

rounds a double value to a given number of digits

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

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

RScriptPath - Variable in class martin.common.r.RGraphics

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

The method which is run as the master thread starts.

run() - Method in class martin.common.compthreads.IteratorBasedMaster

Runs the thread.

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

run() - Method in class martin.common.compthreads.Worker

runs the compute() function of the problem, and then reports back to the master object with the result.

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

run(DocumentIterator, File, boolean, int) - Static method in class uk.ac.man.documentparser.DocumentParser

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

run(Connection, String, PreparedStatement, int, Logger) - Static method in class uk.ac.man.documentparser.misc.MeshExtractor

run(Connection, Set<String>, String) - Static method in class uk.ac.man.documentparser.misc.RemoveDuplicates

run(Node, File, Matcher, Logger, Connection, String) - Static method in class uk.ac.man.entitytagger.entities.misc.CellLines

run(File, File, Set<String>, Logger) - Static method in class uk.ac.man.entitytagger.entities.misc.DrugBank

run(File[], File, File, File, Logger, PreparedStatement, String) - Static method in class uk.ac.man.entitytagger.entities.misc.OBOParser

run() - Method in class uk.ac.man.entitytagger.networking.AlibabaWorker

run2(Node, PreparedStatement, BufferedWriter, Matcher) - Static method in class uk.ac.man.entitytagger.entities.misc.CellLines

runDB(Matcher, DocumentIterator, int, String, int, Logger, Connection, boolean) - Static method in class uk.ac.man.entitytagger.matching.MatchOperations

runHTML(Matcher, DocumentIterator, int, File, int, Logger, TaggedDocument.Format, boolean, Function<Pair<String>>) - Static method in class uk.ac.man.entitytagger.matching.MatchOperations

runHTML(Matcher, DocumentIterator, int, File, int, Logger, TaggedDocument.Format) - Static method in class uk.ac.man.entitytagger.matching.MatchOperations

runHTML(Matcher, DocumentIterator, int, File, int, Logger, TaggedDocument.Format, boolean) - Static method in class uk.ac.man.entitytagger.matching.MatchOperations

runOutWithContext(Matcher, DocumentIterator, int, int, File, Logger, int, int) - Static method in class uk.ac.man.entitytagger.matching.MatchOperations

runPMID(String) - Method in class uk.ac.man.entitytagger.networking.AlibabaWorker

runScript(String, File, File) - Method in class martin.common.r.RGraphics

runScript(String, File, File, String) - Method in class martin.common.r.RGraphics

runSeparated(DocumentIterator, File, int, Logger) - Static method in class uk.ac.man.documentparser.DocumentParser

runText(String) - Method in class uk.ac.man.entitytagger.networking.AlibabaWorker

runToDir(Matcher, DocumentIterator, int, int, File, Logger) - Static method in class uk.ac.man.entitytagger.matching.MatchOperations

runToFile(Matcher, DocumentIterator, int, int, File, Logger) - Static method in class uk.ac.man.entitytagger.matching.MatchOperations