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

M

main(String[]) - Static method in class martin.common.CacheMap

main(String[]) - Static method in class martin.common.ExtractAbbrev

main(String[]) - Static method in class martin.common.SentenceSplitter

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

main(String[]) - Static method in class uk.ac.man.documentparser.DocumentParser

main(String[]) - Static method in class uk.ac.man.documentparser.misc.MedlineFixer

main(String[]) - Static method in class uk.ac.man.documentparser.misc.MedlineIndexer

main(String[]) - Static method in class uk.ac.man.documentparser.misc.MeshExtractor

main(String[]) - Static method in class uk.ac.man.documentparser.misc.RemoveDuplicates

main(String[]) - Static method in class uk.ac.man.entitytagger.entities.misc.CellLines

main(String[]) - Static method in class uk.ac.man.entitytagger.entities.misc.DrugBank

main(String[]) - Static method in class uk.ac.man.entitytagger.entities.misc.OBOParser

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

main(String[]) - Static method in class uk.ac.man.entitytagger.entities.species.ExtractMesh

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

main(String[]) - Static method in class uk.ac.man.entitytagger.EntityTagger

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

main(String[]) - Static method in class uk.ac.man.entitytagger.generate.AcronymAnalysis

main(String[]) - Static method in class uk.ac.man.entitytagger.generate.GenerateMatchers

main(String[]) - Static method in class uk.ac.man.entitytagger.networking.AlibabaServer

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

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

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

mapConvertIDs - Variable in class uk.ac.man.entitytagger.matching.matchers.MatchPostProcessor

martin.common - package martin.common

martin.common.compthreads - package martin.common.compthreads

martin.common.r - package martin.common.r

martin.common.xml - package martin.common.xml

Master<E> - Class in martin.common.compthreads

Master() - Constructor for class martin.common.compthreads.Master

master - Variable in class martin.common.compthreads.Worker

match(String, Matcher) - Static method in class uk.ac.man.entitytagger.entities.misc.CellLines

match(HashMap<String, HashMap<String, Integer>>, Matcher) - Static method in class uk.ac.man.entitytagger.generate.AcronymAnalysis

match(String, Document) - Method in class uk.ac.man.entitytagger.matching.Matcher

Search a given text for mentions

match(String) - Method in class uk.ac.man.entitytagger.matching.Matcher

match(String, String) - Method in class uk.ac.man.entitytagger.matching.Matcher

match(Document) - Method in class uk.ac.man.entitytagger.matching.Matcher

match(String, Document) - Method in class uk.ac.man.entitytagger.matching.matchers.ACIDMatcher

match(String, Document) - Method in class uk.ac.man.entitytagger.matching.matchers.AutomatonMatcher

Performs matching

match(String, Document) - Method in class uk.ac.man.entitytagger.matching.matchers.DuplicationMatcher

match(String, Document) - Method in class uk.ac.man.entitytagger.matching.matchers.IntersectionMatcher

match(String, Document) - Method in class uk.ac.man.entitytagger.matching.matchers.MatchPostProcessor

match(String, Document) - Method in class uk.ac.man.entitytagger.matching.matchers.PrecomputedMatcher

match(String, Document) - Method in class uk.ac.man.entitytagger.matching.matchers.RegexpMatcher

match(String, Document) - Method in class uk.ac.man.entitytagger.matching.matchers.SentenceMatcher

match(String, Document) - Method in class uk.ac.man.entitytagger.matching.matchers.TaxonGrabMatcher

match(String, Document) - Method in class uk.ac.man.entitytagger.matching.matchers.UnionMatcher

match(String, Document) - Method in class uk.ac.man.entitytagger.matching.matchers.VariantDictionaryMatcher

match(String, Document) - Method in class uk.ac.man.entitytagger.networking.SimpleClientMatcher

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

matchDocument(Document) - Method in class uk.ac.man.entitytagger.matching.matchers.IntersectionMatcher

matchDocument(Document) - Method in class uk.ac.man.entitytagger.matching.matchers.UnionMatcher

matchDocument(Matcher, Document) - Static method in class uk.ac.man.entitytagger.matching.MatchOperations

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

Matcher - Class in uk.ac.man.entitytagger.matching

Abstract class describing a matcher, and providing common methods for the available matchers

Matcher() - Constructor for class uk.ac.man.entitytagger.matching.Matcher

matcher - Variable in class uk.ac.man.entitytagger.matching.matchers.ConcurrentMatcher

matcher - Variable in class uk.ac.man.entitytagger.matching.matchers.ConcurrentMatcher.MatchProblem

matcher - Variable in class uk.ac.man.entitytagger.matching.matchers.DuplicationMatcher

matcher - Variable in class uk.ac.man.entitytagger.matching.matchers.MatchPostProcessor

matcher - Variable in class uk.ac.man.entitytagger.networking.AlibabaWorker

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

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

Matcher.Disambiguation - Enum in uk.ac.man.entitytagger.matching

OFF: No disambiguation is performed ON_EARLIER: Disambiguation is performed by looking at earlier contents in the document ON_WHOLE: Disambiguation is performed by looking in the whole document

Matcher.Disambiguation() - Constructor for enum uk.ac.man.entitytagger.matching.Matcher.Disambiguation

matchers - Variable in class uk.ac.man.entitytagger.matching.matchers.IntersectionMatcher

matchers - Variable in class uk.ac.man.entitytagger.matching.matchers.UnionMatcher

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

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

Helper method to check that the last match attempt was valid.

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

MatchOperations - Class in uk.ac.man.entitytagger.matching

MatchOperations() - Constructor for class uk.ac.man.entitytagger.matching.MatchOperations

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

MatchPostProcessor(Matcher, Matcher.Disambiguation, boolean, File, Postprocessor) - Constructor for class uk.ac.man.entitytagger.matching.matchers.MatchPostProcessor

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

maxSize - Variable in class martin.common.CacheMap

Medline - Class in uk.ac.man.documentparser.input

Medline(String) - Constructor for class uk.ac.man.documentparser.input.Medline

Medline(StringBuffer) - Constructor for class uk.ac.man.documentparser.input.Medline

Medline(File) - Constructor for class uk.ac.man.documentparser.input.Medline

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

medlineBaseDir - Variable in class uk.ac.man.documentparser.input.MedlineIndexFactory

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

medlineBaseDir - Variable in class uk.ac.man.documentparser.input.MedlinePMCIndexFactory

medlineBaseDir - Variable in class uk.ac.man.entitytagger.networking.AlibabaWorker

medlineDocs - Variable in class uk.ac.man.documentparser.input.PMCAbstract

MedlineFactory - Class in uk.ac.man.documentparser.input

MedlineFactory() - Constructor for class uk.ac.man.documentparser.input.MedlineFactory

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

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

MedlineIndex - Class in uk.ac.man.documentparser.input

MedlineIndex(File, File, Set<String>) - Constructor for class uk.ac.man.documentparser.input.MedlineIndex

MedlineIndex(File, File) - Constructor for class uk.ac.man.documentparser.input.MedlineIndex

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

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

MedlineIndexFactory - Class in uk.ac.man.documentparser.input

MedlineIndexFactory(File, Set<String>) - Constructor for class uk.ac.man.documentparser.input.MedlineIndexFactory

MedlineIndexFactory(File) - Constructor for class uk.ac.man.documentparser.input.MedlineIndexFactory

MedlinePMCIndex - Class in uk.ac.man.documentparser.input

MedlinePMCIndex(File, File, File, String[], int, Set<String>) - Constructor for class uk.ac.man.documentparser.input.MedlinePMCIndex

MedlinePMCIndexFactory - Class in uk.ac.man.documentparser.input

MedlinePMCIndexFactory(File, File, String[], Set<String>) - Constructor for class uk.ac.man.documentparser.input.MedlinePMCIndexFactory

MedlinePMCIndexFactory(File) - Constructor for class uk.ac.man.documentparser.input.MedlinePMCIndexFactory

Mention - Class in uk.ac.man.entitytagger

Class for representing a text match, containing the matched text, document coordinates and normalized IDs.

Mention(String[]) - Constructor for class uk.ac.man.entitytagger.Mention

Mention(String, int, int, String) - Constructor for class uk.ac.man.entitytagger.Mention

Mention(String[], int, int, String) - Constructor for class uk.ac.man.entitytagger.Mention

Mention.IDPair - Class in uk.ac.man.entitytagger

Mention.IDPair(String, Double, String) - Constructor for class uk.ac.man.entitytagger.Mention.IDPair

Mention.SimpleMention - Class in uk.ac.man.entitytagger

Mention.SimpleMention(String[], Double[], int, int, String, Map<String, String>) - Constructor for class uk.ac.man.entitytagger.Mention.SimpleMention

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

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

millisToString(long) - Static method in class martin.common.Loggers

minimize - Variable in class uk.ac.man.entitytagger.generate.GenerateAutomatons.ProcessProblem

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

minYearFilter - Variable in class uk.ac.man.documentparser.input.MedlinePMCIndexFactory

Misc - Class in martin.common

Misc() - Constructor for class martin.common.Misc

Misc - Class in martin.common.xml

Misc() - Constructor for class martin.common.xml.Misc

mode - Variable in class uk.ac.man.entitytagger.matching.matchers.MatchPostProcessor

mStats - Variable in class martin.common.ExtractAbbrev

mTestDefinitions - Variable in class martin.common.ExtractAbbrev

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

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

MyConnection - Class in martin.common

MyConnection(String, String, String, int, String, Logger) - Constructor for class martin.common.MyConnection

MyNodeList - Class in martin.common.xml

MyNodeList(List<Node>) - Constructor for class martin.common.xml.MyNodeList

MyNodeList(NodeList) - Constructor for class martin.common.xml.MyNodeList