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

P

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

Pair<E> - Class in martin.common

Pair(E, E) - Constructor for class martin.common.Pair

parse(String) - Method in class uk.ac.man.documentparser.input.BMCFactory

parse(StringBuffer) - Method in class uk.ac.man.documentparser.input.BMCFactory

parse(File) - Method in class uk.ac.man.documentparser.input.BMCFactory

parse(String) - Method in class uk.ac.man.documentparser.input.BMCXMLFactory

parse(File) - Method in class uk.ac.man.documentparser.input.BMCXMLFactory

parse(StringBuffer) - Method in class uk.ac.man.documentparser.input.BMCXMLFactory

parse(String) - Method in class uk.ac.man.documentparser.input.ElsevierFactory

parse(File) - Method in class uk.ac.man.documentparser.input.ElsevierFactory

parse(StringBuffer) - Method in class uk.ac.man.documentparser.input.ElsevierFactory

parse(String) - Method in interface uk.ac.man.documentparser.input.InputFactory

parse(File) - Method in interface uk.ac.man.documentparser.input.InputFactory

parse(StringBuffer) - Method in interface uk.ac.man.documentparser.input.InputFactory

parse(StringBuffer) - Method in class uk.ac.man.documentparser.input.MedlineFactory

parse(String) - Method in class uk.ac.man.documentparser.input.MedlineFactory

parse(File) - Method in class uk.ac.man.documentparser.input.MedlineFactory

parse(StringBuffer) - Method in class uk.ac.man.documentparser.input.MedlineIndexFactory

parse(String) - Method in class uk.ac.man.documentparser.input.MedlineIndexFactory

parse(File) - Method in class uk.ac.man.documentparser.input.MedlineIndexFactory

parse(StringBuffer) - Method in class uk.ac.man.documentparser.input.MedlinePMCIndexFactory

parse(String) - Method in class uk.ac.man.documentparser.input.MedlinePMCIndexFactory

parse(File) - Method in class uk.ac.man.documentparser.input.MedlinePMCIndexFactory

parse(StringBuffer) - Method in class uk.ac.man.documentparser.input.OTMIFactory

parse(String) - Method in class uk.ac.man.documentparser.input.OTMIFactory

parse(File) - Method in class uk.ac.man.documentparser.input.OTMIFactory

parse(String) - Method in class uk.ac.man.documentparser.input.PMCFactory

parse(File) - Method in class uk.ac.man.documentparser.input.PMCFactory

parse(StringBuffer) - Method in class uk.ac.man.documentparser.input.PMCFactory

parse(StringBuffer) - Method in class uk.ac.man.documentparser.input.PMCIndexFactory

parse(String) - Method in class uk.ac.man.documentparser.input.PMCIndexFactory

parse(File) - Method in class uk.ac.man.documentparser.input.PMCIndexFactory

parse(StringBuffer) - Method in class uk.ac.man.documentparser.input.TextFileFactory

parse(String) - Method in class uk.ac.man.documentparser.input.TextFileFactory

parse(File) - Method in class uk.ac.man.documentparser.input.TextFileFactory

parser - Static variable in class martin.common.ArgParser

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

pass - Variable in class martin.common.MyConnection

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

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

performAcronymResolution(Document, String, List<Mention>) - Static method in class uk.ac.man.entitytagger.matching.Matcher

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

PMC(File, String[]) - Constructor for class uk.ac.man.documentparser.input.PMC

PMC(StringBuffer, String[]) - Constructor for class uk.ac.man.documentparser.input.PMC

PMC(String, String[], String, boolean, boolean, boolean, boolean) - Constructor for class uk.ac.man.documentparser.input.PMC

PMC2 - Class in uk.ac.man.documentparser.input

PMC2(File, String[]) - Constructor for class uk.ac.man.documentparser.input.PMC2

PMC2(StringBuffer, String[]) - Constructor for class uk.ac.man.documentparser.input.PMC2

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

PMCAbstract(DocumentIterator, DocumentIterator) - Constructor for class uk.ac.man.documentparser.input.PMCAbstract

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

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

pmcBaseDir - Variable in class uk.ac.man.documentparser.input.PMCIndex

pmcBaseDir - Variable in class uk.ac.man.documentparser.input.PMCIndexFactory

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

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

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

PMCFactory(String[]) - Constructor for class uk.ac.man.documentparser.input.PMCFactory

pmcID - Variable in class uk.ac.man.documentparser.input.PMC

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

PMCIndex(File, File, String[]) - Constructor for class uk.ac.man.documentparser.input.PMCIndex

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

PMCIndexFactory(File, String[]) - Constructor for class uk.ac.man.documentparser.input.PMCIndexFactory

populateRecursive(Set<String>, Set<String>, File[]) - Static method in class uk.ac.man.entitytagger.entities.misc.OBOParser

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

port - Variable in class martin.common.MyConnection

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

POST - Variable in class uk.ac.man.entitytagger.entities.misc.CellLinePostprocessor

postProcess(List<Mention>, String) - Method in class uk.ac.man.entitytagger.entities.misc.CellLinePostprocessor

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

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

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

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

Postprocessor(InputStream[], InputStream[], InputStream[], Map<String, String>, Logger) - Constructor for class uk.ac.man.entitytagger.matching.Postprocessor

PRE - Variable in class uk.ac.man.entitytagger.entities.misc.CellLinePostprocessor

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

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

PrecomputedMatcher(Connection, String) - Constructor for class uk.ac.man.entitytagger.matching.matchers.PrecomputedMatcher

PrecomputedMatcher(File, Set<String>, String) - Constructor for class uk.ac.man.entitytagger.matching.matchers.PrecomputedMatcher

prepareInsertStatements(Connection, boolean) - Static method in class uk.ac.man.documentparser.dataholders.Document

prepareInsertStatements(Connection, String, boolean) - Static method in class uk.ac.man.documentparser.dataholders.Document

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

printContents() - Method in class martin.common.ArgParser

Will print the contents to System.out (mainly for debugging purposes).

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

Function which will print a few statistics to System.out

printStats() - Static method in class martin.common.Stopwatch

printValues() - Method in class martin.common.ChiTester

priority - Variable in class martin.common.CacheMap

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

prob - Variable in class uk.ac.man.entitytagger.Mention.IDPair

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

Problem<E> - Interface in martin.common.compthreads

Implement this interface to allow easy parallelization of computational code.

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

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

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

process(File, File, File, String, boolean) - Static method in class uk.ac.man.entitytagger.entities.species.CatalogueOfLife

process(Map<String, List<Mention>>, Map<String, Map<String, List<Evaluate.Tag>>>, Map<String, List<Mention>>, Map<String, Map<String, List<Evaluate.Tag>>>, Map<String, String>, Set<String>, File, boolean, Set<String>, String) - Method in class uk.ac.man.entitytagger.evaluate.Evaluate

The main evaluation processing method

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

process(ArrayList<Automaton>, int, boolean, boolean, int, Logger) - Method in class uk.ac.man.entitytagger.generate.GenerateAutomatons

Function which will take a list of automatons and join them together in groups of size multiJoin (e.g.

Properties - Class in martin.common

Extended version of they java.util.Properties class.

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

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

put(K, V) - Method in class martin.common.CacheMap