Index (chemicalTagger 1.5.0 API)

A C E F G I L M N O P R S T U W X
All Classes All Packages

A

addToTokenList(Token) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Adds token to wordTokenList.
AnalysePatents - Class in uk.ac.cam.ch.wwmm.chemicaltagger.modelParser: First steps at creating a corpus for the ChemicalTagger model parser.
AnalysePatents() - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.modelParser.AnalysePatents
ASTtoXML - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Converts ANTLR ASTTrees into XML Documents.
ASTtoXML() - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.ASTtoXML: Default constructor method.
ASTtoXML(String[], String[]) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.ASTtoXML

C

ChemicalTaggerTokeniser - Interface in uk.ac.cam.ch.wwmm.chemicaltagger: An interface for tokenisers.
ChemistryModelParser - Class in uk.ac.cam.ch.wwmm.chemicaltagger.modelParser: Runs the ChemicalParser model against text.
ChemistryModelParser() - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.modelParser.ChemistryModelParser
ChemistryPOSTagger - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Converts string input into tokenised and tagged text.
ChemistryPOSTagger(ChemicalTaggerTokeniser, List<Tagger>) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistryPOSTagger: Custom constructor for setting up non-standard ChemicalTagger operations.
ChemistryPOSTagger(ChemicalTaggerTokeniser, OscarTagger, RegexTagger, OpenNLPTagger) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistryPOSTagger: Deprecated.
ChemistrySentenceParser - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Passes tagged sentences to the ANTLR grammar.
ChemistrySentenceParser(InputStream) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistrySentenceParser: Constructor method for inputStream objects.
ChemistrySentenceParser(String) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistrySentenceParser: Constructor method for String objects.
ChemistrySentenceParser(POSContainer) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistrySentenceParser: Constructor method for POSContainer objects.
cleanHTMLText(String) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Cleans up text from html characters.
combineTaggers() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Combines the output of all the taggers.
containsNumber(String) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Checks if a string contains a number.
convert(Document) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.XMLtoAST: Converts AST Trees to XML Document.
convert(Parse) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.modelParser.ParseTreetoXML: Converts Parse Trees to XML Document.
convert(Tree) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ASTtoXML: Overloading Method that converts astTree to XML Document with ActionPhrases Included.
convert(Tree, boolean) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ASTtoXML: Converts AST Trees to XML Document.
convert(Tree, boolean, HashMap<String, String>) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ASTtoXML: Converts astTree to XML Document.
correctCombinedTagsList() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.PostProcessTags: Corrects known tagging problems in the tags in combinedtagsList.
correctCombinedTagsList(List<String>) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.PostProcessTags: Corrects known tagging problems in the tags in combinedtagsList.
createPosTagListFromStringArray(String[]) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.OpenNLPTagger: Creates the posTagList from the openNLP string Array format.
CreateTreeBank - Class in uk.ac.cam.ch.wwmm.chemicaltagger.modelParser: Creates a Treebank from the rule-based ChemicalTagger output
CreateTreeBank() - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.modelParser.CreateTreeBank

E

ExtractFromXML - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Extracts text from XML Patents.

F

Formatter - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Preprocesses text before it gets passed to tokenisation and tagging classes.

G

generateOscarTokenSequence(List<Token>, String) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.OscarTagger: Generates an OSCAR TokenSequence from a list of tokens
getActionMap() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.PostProcessTrees: Getter method for actionMap.
getCombinedTagsList() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Getter method for CombinedTagsList.
getContent(InputStream, String) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.ExtractFromXML: Returns the content of a searchTag from an XML File.
getContent(String) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.modelParser.CreateTreeBank: Extracts the content from the patent files.
getCTTokeniser() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistryPOSTagger: Getter method for ChemicalTaggerTokeniser.
getDefaultInstance() - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistryPOSTagger: Gets the default ChemistryPOSTagger instance - recommended for standard ChemicalTagger processing.
getExperimentalParagraphs(String) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.modelParser.AnalysePatents
getIgnoredTags() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.OpenNLPTagger
getIgnoredTags() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.OscarTagger
getIgnoredTags() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.RegexTagger
getIgnoredTags() - Method in interface uk.ac.cam.ch.wwmm.chemicaltagger.Tagger
getInputStream(Class<?>, String) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Returns the content of the resource as an inputstream.
getInputText() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Getter method for InputText.
getInstance() - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.OpenNLPTagger: Returns an OpenNLPTagger singleton.
getName() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.Rule: Getter method for name.
getNextTerminalElement(Element) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Gets the next terminal element.
getNodes(Element, ParserRuleContext) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.XMLtoAST: A recursive function that goes through the leaves of the tree to create XML nodes.
getNodes(Parse, Element) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.modelParser.ParseTreetoXML: A recursive function that goes through the leaves of the tree to create XML nodes.
getNodes(Tree, Element) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ASTtoXML: A recursive function that goes through the leaves of the tree to create XML nodes.
getOpenNLPTagger() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistryPOSTagger: Getter method for OpenNLPTagger.
getOscarTagger() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistryPOSTagger: Getter method for OscarTagger.
getParseTree() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.SentenceParser: Getter method for parseTree.
getPathAsInputStream(String) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Returns the content of the resource as an inputstream.
getPattern() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.Rule: Getter method for pattern.
getPreviousSiblingOrParentsSibling(Element) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Gets the previous sibling if one exists or the previous sibling of the first parent element with previous siblings
getPreviousTerminalElement(Element) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Gets the previous terminal element.
getPrioritiseOscar() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Getter method for prioritiseOscar.
getRegexTagger() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistryPOSTagger: Getter method for RegexTagger.
getRules() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.RegexTagger: Getter method for rules.
getSentenceList() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.XMLtoAST
getSpectrumElementList() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Getter method for SpectrumList.
getStringTree() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.XMLtoAST
getStringValue(Element, String) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.ExtractFromXML: Parses an XML files and saves the output into DocumentContainer.
getTaggedTokenInStream() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.SentenceParser: Getter method for taggedTokenInputStream.
getTagger() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.OpenNLPTagger: Getter method for posTagger.
getTaggersOrderedInDescendingPriority() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistryPOSTagger: Getter method for taggersOrderedInDescendingPriority.
getTagListContainer() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer
getTokenTagTupleAsString() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Gets the output of the string and tag as: "TAG TOKEN".
getWordTokenList() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Getter method for WordTokenList.

I

initializeRules() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.RegexTagger: Initialises the rules for the regular expression tagger.

L

loadDefaultActionMap() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.PostProcessTrees: Loads default ActionMap for ChemicalTagger.
loadsTagsFromFile(Class<?>) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Loads the tags from the .tokens file generated by Antlr.

M

main(String[]) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.modelParser.AnalysePatents: Main class.
main(String[]) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.modelParser.CreateTreeBank: Main class.
makeNCName(String) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Replaces all non-XML characters with _ .
makeXMLDocument() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistrySentenceParser
makeXMLDocument() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.SentenceParser: Creates an XML document from the parseTree.
makeXMLDocument(boolean) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistrySentenceParser

N

normaliseText(String) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Formatter: Normalises sentences e.g.

O

OpenNLPTagger - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Runs the OpenNLP tagger .
oscar - Variable in class uk.ac.cam.ch.wwmm.chemicaltagger.OscarTagger
OscarTagger - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Runs the OSCAR tagger .
OscarTagger(Oscar) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.OscarTagger: Default constructor method.
OscarTokeniser - Class in uk.ac.cam.ch.wwmm.chemicaltagger
OscarTokeniser() - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.OscarTokeniser: Public Constructor method.

P

parseSentence(String) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.modelParser.ChemistryModelParser
parseTags() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistrySentenceParser
parseTags() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.SentenceParser: Passes an inputstream to ANTLR and produces a parse tree.
ParseTreetoXML - Class in uk.ac.cam.ch.wwmm.chemicaltagger.modelParser: Converts OpenNLP Parse Trees into XML Documents.
ParseTreetoXML() - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.modelParser.ParseTreetoXML: Default constructor method.
POSContainer - Class in uk.ac.cam.ch.wwmm.chemicaltagger: A container class that stores the grammatical structure of the text .
POSContainer() - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Default constructor method.
PostProcessTags - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Corrects Mistagged tokens.
PostProcessTags(POSContainer) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.PostProcessTags: Corrects Mistagged tokens within the given POSContainer
PostProcessTrees - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Passes tagged sentences to the ANTLR grammar.
PostProcessTrees() - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.PostProcessTrees: Default Constructor method.
printPrettyXML(Document) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistrySentenceParser
process(Document) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.PostProcessTrees: Adds action phrases and roles to documents.

R

readSentence(String) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Loads a "sentence" file consisting of a single line of text.
recombineTokens(POSContainer) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.RecombineTokens: Indexes the tokens that need combining and then calls combineTokens.
RecombineTokens - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Combines tokens that have been erroneously split
RegexTagger - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Runs the regular expression tagger .
RegexTagger() - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.RegexTagger: Public Constructor.
RegexTagger(String) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.RegexTagger: Public Constructor.
RegexTagger(List<String>) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.RegexTagger: Public Constructor.
registerTagList(List<String>) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Adds tagLists to the tagListContainer
Rule - Class in uk.ac.cam.ch.wwmm.chemicaltagger: The Rule class .
Rule(String, String) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.Rule: Public Constructor method.
Rule(String, String, boolean) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.Rule: Public Constructor method.
run() - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.SentenceParser: Runs the thread.
runChemicalTagger(String) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Overloading method for running chemicalTagger Sets runSpectraTagger to false by default.
runChemicalTagger(String, boolean) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Convenience method for running chemicalTagger Includes a flag for setting spectraTagger.
runTagger(List<Token>, String) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.OpenNLPTagger: Runs the OpenNLP POS tagger against a list of tokens and returns a list of tags
runTagger(List<Token>, String) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.OscarTagger: Runs OSCAR over a list of tokens and returns a list of tags
runTagger(List<Token>, String) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.RegexTagger: Runs the regular expression tagger against a list of tokens and returns a list of tags
runTagger(List<Token>, String) - Method in interface uk.ac.cam.ch.wwmm.chemicaltagger.Tagger: Runs the tagger against the tokens and returns the tags as a list
runTagger(POSContainer) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.SpectraTagger: Tags the NMR Spectra in a chemistry text.
runTaggers(String) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistryPOSTagger: Overloading method for runTaggers passing the default flag for useSpectraTagger to ChemistryPOSTagger.runTaggers(String, boolean) .
runTaggers(String, boolean) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.ChemistryPOSTagger: Normalises the inputSentence Optionally removes spectra Then tokenises the input and runs the taggers over the tokens

S

SentenceParser - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Passes tagged sentences to the ANTLR grammar.
SentenceParser(InputStream) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.SentenceParser: Constructor method for inputStream objects.
SentenceParser(String) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.SentenceParser: Constructor method for String objects.
SentenceParser(POSContainer) - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.SentenceParser: Constructor method for POSContainer objects.
setActionMap(HashMap<String, String>) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.PostProcessTrees: Getter method for actionMap.
setCombinedTagsList(List<String>) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Setter method for CombinedTagsList.
setInputText(String) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Setter method for InputText.
setParseTree(ParseTree) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.SentenceParser: Setter method for parseTree.
setPrioritiseOscar(boolean) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Setter method for prioritiseOscar.
setRules(List<Rule>) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.RegexTagger: Setter method for rules.
setSpectrumList(List<Element>) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Setter method for SpectrumList.
setTaggedTokenInStream(InputStream) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.SentenceParser: Setter method for taggedTokenInputStream.
setWordTokenList(List<Token>) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.POSContainer: Setter method for WordTokenList.
SpectraTagger - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Runs the oscar SpectraTagger to pull out the NMR Spectra.
subTokeniseTokens(List<Token>) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Formatter: Returns the list of tokens with tokens divided into further tokens in cases where this improves tagging e.g.

T

tag(String[]) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.OpenNLPTagger
Tagger - Interface in uk.ac.cam.ch.wwmm.chemicaltagger: An interface for a tagger.
tokenise(String) - Method in interface uk.ac.cam.ch.wwmm.chemicaltagger.ChemicalTaggerTokeniser: Tokeniser method.
tokenise(String) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.OscarTokeniser: Tokenises input text using the OSCAR4 tokeniser.
tokenise(String) - Method in class uk.ac.cam.ch.wwmm.chemicaltagger.WhiteSpaceTokeniser: Tokenises a String on white space.
tokensToSpaceDelimitedStr(List<Token>) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Concatenates token surfaces adding a space between them

U

uk.ac.cam.ch.wwmm.chemicaltagger - package uk.ac.cam.ch.wwmm.chemicaltagger
uk.ac.cam.ch.wwmm.chemicaltagger.modelParser - package uk.ac.cam.ch.wwmm.chemicaltagger.modelParser
Utils - Class in uk.ac.cam.ch.wwmm.chemicaltagger: A Utils class.

W

WhiteSpaceTokeniser - Class in uk.ac.cam.ch.wwmm.chemicaltagger: A whitespace tokeniser to be used as a substitute to the OSCAR tokeniser.
WhiteSpaceTokeniser() - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.WhiteSpaceTokeniser: Default constructor method.
writeListToFile(List<String>, String) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Writes items of a list to a file.
writeXMLToFile(Document, String) - Static method in class uk.ac.cam.ch.wwmm.chemicaltagger.Utils: Writes out an XML document to a file.

X

XMLtoAST - Class in uk.ac.cam.ch.wwmm.chemicaltagger: Converts ANTLR ASTTrees into XML Documents.
XMLtoAST() - Constructor for class uk.ac.cam.ch.wwmm.chemicaltagger.XMLtoAST

A C E F G I L M N O P R S T U W X
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