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

S

s - Variable in class martin.common.SimpleClass

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

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

save(File, HashMap<String, DictionaryEntry>, Logger) - Static method in class uk.ac.man.entitytagger.entities.species.GenerateDictionary

saveNames(File, HashMap<String, List<String>>, HashMap<String, DictionaryEntry>, Logger) - Static method in class uk.ac.man.entitytagger.entities.species.GenerateDictionary

saveTempFile(List<Double>[], String[], File, boolean) - Method in class martin.common.r.RGraphics

saveTempFileBars(double[], String[], File) - Method in class martin.common.r.RGraphics

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

saveToDB(DocumentIterator, Connection, Logger, String, int, boolean) - Static method in class uk.ac.man.documentparser.DocumentParser

saveToFile(ArrayList<Mention>, File) - Static method in class uk.ac.man.entitytagger.Mention

Saves the list of matches to file, sorted by their start and end coordinates.

saveToStreamInBCFormat(BufferedWriter, List<Mention>, String, Map<String, String>) - Static method in class uk.ac.man.entitytagger.Mention

Saves a list of mentions to a stream, in BioCreative 2 format, suitable for evaluation.

saveToTextFile(File, boolean) - Method in class uk.ac.man.documentparser.dataholders.Document

saveVariantsToDB(PreparedStatement, Set<String>) - Method in class uk.ac.man.entitytagger.generate.DictionaryEntry

sb - Variable in class martin.common.InputStreamDumper

scanStrings - Variable in class martin.common.xml.EntityResolver

schema - Variable in class martin.common.MyConnection

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

Section - Class in uk.ac.man.documentparser.dataholders

Section(String, String, Section[]) - Constructor for class uk.ac.man.documentparser.dataholders.Section

select(E[], int) - Method in class martin.common.Selector

Selector<E extends java.lang.Comparable<E>> - Class in martin.common

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

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

sendMail(String[], String, String) - Method in class martin.common.Email

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

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

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

SentenceSplitter - Class in martin.common

SentenceSplitter(String) - Constructor for class martin.common.SentenceSplitter

SentenceSplitter(String, boolean) - Constructor for class martin.common.SentenceSplitter

serialVersionUID - Static variable in class dk.brics.automaton.CustomRunAutomaton

serialVersionUID - Static variable in class martin.common.Properties

serialVersionUID - Static variable in class uk.ac.man.documentparser.dataholders.Document

serialVersionUID - Static variable in class uk.ac.man.documentparser.dataholders.Section

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

set(PreparedStatement, int, Boolean) - Static method in class martin.common.SQL

set(PreparedStatement, int, Float) - Static method in class martin.common.SQL

set(PreparedStatement, int, Double) - Static method in class martin.common.SQL

set(PreparedStatement, int, Integer) - Static method in class martin.common.SQL

set(PreparedStatement, int, String) - Static method in class martin.common.SQL

setA(E) - Method in class martin.common.ComparableTuple

setA(E) - Method in class martin.common.Tuple

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

setB(T) - Method in class martin.common.ComparableTuple

setB(T) - Method in class martin.common.Tuple

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

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

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

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

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

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

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

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

setIds(String[]) - Method in class uk.ac.man.entitytagger.Mention

Will also clear the probabilities.

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

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

setMatch(int, int, ArrayList<String>) - Method in class dk.brics.automaton.CustomAutomatonMatcher

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

setMinYearFilter(int) - Method in class uk.ac.man.documentparser.input.MedlinePMCIndexFactory

setProbabilities(Double[]) - Method in class uk.ac.man.entitytagger.Mention

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

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

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

setReportProgress(boolean) - Method in class martin.common.compthreads.Master

Set whether the object should report once each computational process is finished.

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

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

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

setX(E) - Method in class martin.common.Pair

setY(E) - Method in class martin.common.Pair

SimpleClass<E> - Class in martin.common

SimpleClass(E, long) - Constructor for class martin.common.SimpleClass

SimpleClientMatcher - Class in uk.ac.man.entitytagger.networking

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

SimpleClientMatcher(String) - Constructor for class uk.ac.man.entitytagger.networking.SimpleClientMatcher

SimpleServer - Class in uk.ac.man.entitytagger.networking

SimpleServer(int, Matcher, boolean) - Constructor for class uk.ac.man.entitytagger.networking.SimpleServer

SimpleServerWorker - Class in uk.ac.man.entitytagger.networking

SimpleServerWorker(Socket, Matcher, Map<Integer, List<Mention>>, Semaphore) - Constructor for class uk.ac.man.entitytagger.networking.SimpleServerWorker

simplify(Map<String, String>) - Method in class uk.ac.man.entitytagger.Mention

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

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

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

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

size() - Method in class uk.ac.man.entitytagger.matching.matchers.RegexpMatcher

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

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

very rough estimate of the dictionary memory footprint, in bytes

size() - Method in class uk.ac.man.entitytagger.matching.matchers.VariantDictionaryMatcher

size() - Method in class uk.ac.man.entitytagger.networking.SimpleClientMatcher

Sizeable - Interface in martin.common

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

sizeof() - Method in interface martin.common.Sizeable

sizeof() - Method in class uk.ac.man.entitytagger.matching.matchers.VariantDictionaryMatcher

Gives a rough estimate of the memory consumption of this object.

sizes - Variable in class martin.common.CacheMap

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

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

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

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

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

skip() - Method in interface uk.ac.man.documentparser.input.DocumentIterator

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

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

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

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

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

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

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

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

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

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

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

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

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

skip - Variable in class uk.ac.man.documentparser.input.util.Skipper

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

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

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

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

Skipper(DocumentIterator, int) - Constructor for class uk.ac.man.documentparser.input.util.Skipper

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

solutions - Variable in class martin.common.compthreads.ArrayBasedMaster

solutions - Variable in class martin.common.compthreads.IteratorBasedMaster

solutionsem - Variable in class martin.common.compthreads.ArrayBasedMaster

solutionsem - Variable in class martin.common.compthreads.IteratorBasedMaster

solutionSemaphores - Variable in class martin.common.compthreads.IteratorBasedMaster

sort(List) - Static method in class martin.common.Misc

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

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

source - Variable in class uk.ac.man.documentparser.dataholders.ExternalID

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

Adaptor Class for splitting documents on x number of sentences

Splitter(DocumentIterator, int) - Constructor for class uk.ac.man.documentparser.input.util.Splitter

Create a documentiterator adaptor, which will return documents, with a maximum of "sentencesPerSplit" sentences Uses martin.common.SentenceSplitter.

SQL - Class in martin.common

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

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

Returns the offset of the first character matched.

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

Returns the offset of the first character matched of the specified capturing group.

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

Starts the stopwatch, storing the time when this function is called.

start - Variable in class uk.ac.man.entitytagger.evaluate.Evaluate.Tag

start - Variable in class uk.ac.man.entitytagger.Mention.SimpleMention

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

startNew(String) - Static method in class martin.common.Stopwatch

Starts the stopwatch, storing the time when this function is called.

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

Spawns a new thread for the master object and starts it.

startTime - Variable in class martin.common.Stopwatch

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

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

staticid - Static variable in class uk.ac.man.documentparser.input.PMC

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

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

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

Stops the Stopwatch, and adds the elapsed time to a global sum for the label specified on construction.

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

Stopwatch - Class in martin.common

Class useful for profiling the time usage of java software.

Stopwatch(String) - Constructor for class martin.common.Stopwatch

Returns a running Stopwatch object.

storageLimitSem - Variable in class martin.common.compthreads.IteratorBasedMaster

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

Will store the automatons in the automaton matcher to a file

storeArray(File, ArrayList<Automaton>, boolean) - Static method in class uk.ac.man.entitytagger.generate.GenerateAutomatons

storeRArray(ArrayList<Automaton>, boolean, boolean, File, Logger) - Static method in class uk.ac.man.entitytagger.generate.GenerateAutomatons

storeVariants(File, PreparedStatement, List<Automaton>, Logger, int) - Static method in class uk.ac.man.entitytagger.generate.GenerateAutomatons

stream - Variable in class martin.common.InputStreamDumper

stream - Variable in class martin.common.StreamIterator

StreamIterator - Class in martin.common

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

StreamIterator(File, boolean) - Constructor for class martin.common.StreamIterator

StreamIterator(InputStream, boolean) - Constructor for class martin.common.StreamIterator

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

sums - Static variable in class martin.common.Stopwatch

surname - Variable in class uk.ac.man.documentparser.dataholders.Author