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

A

abstracts - Variable in class GENIAHandler
 
abstracts - Variable in class TQLHandler
 
action(String, String) - Method in class EvEx
This is the invoking method of the entire system.
addEvent(GEvent) - Method in class GAbstract
Adding an event to the array of events, and setting this abstract as parent for the GEvent.
addEvent(GEvent) - Method in class GSentence
Add a GEvent to this sentence.
addEvent(Event) - Method in class TQLAbstract
Method to add an Event to the list of events in this abstract.
addLine(String) - Method in class TQL
Add a TQL-statement to the list of lines.
addSentence(GSentence) - Method in class GAbstract
Adding asentence to the array of sentences and incrementing the counter.
addTerm(GTerm) - Method in class GSentence
Add a GTerm to this sentence.
addTQL(TQL) - Method in class TQLAbstract
Method to add a TQL to the list of TQL-statements in this abstract.
Anto - Class in <Unnamed>
An abstraction class for holding antonym definitions.
Anto() - Constructor for class Anto
Constructor for creating an Anto.
anto - Variable in class EvalE
 
anto - Variable in class Evaluator
 
anto - Variable in class EvEx
 
antofile - Variable in class Anto
 

B

block - Variable in class TQL
 
buildTerms() - Method in class GAbstract
Traverses the list of Terms in each Sentence, and adds key,value-pair to this abstracts hashtable.

C

cause - Variable in class EvalE.EvalEvent
 
cause - Variable in class Event
 
cause_adjectives - Variable in class Event
 
cause_extended - Variable in class Event
 
characters(char[], int, int) - Method in class EvalE.EvalTHandler
 
characters(char[], int, int) - Method in class GENIAHandler
The string between tags (usually empty) is processed by this method.
characters(char[], int, int) - Method in class OntologyParser
The string between tags (usually empty) is processed by this method.
characters(char[], int, int) - Method in class TQLHandler
The string between tags (usually empty) is processed by this method.
closeXML() - Method in class XMLWriter
Flush the writer and close the output files.
clues - Variable in class OntologyParser
 
countEvents() - Method in class GAbstract
Returns the size of this abstracts event array.
countEvents() - Method in class TQLAbstract
Method to count number of events in this abstact.
countSentences() - Method in class GAbstract
Returns the number of sentences in this abstract.
countTQLs() - Method in class TQLAbstract
Method to count number of logic statements in this abstact.
currClass - Variable in class OntologyParser
 

D

d - Variable in class Anto
 
d - Variable in class Syno
 
debug_eval - Variable in class Evaluator
 
debug_ge - Variable in class EvEx
 
debug_geh - Variable in class GENIAHandler
 
debug_op - Variable in class EvEx
 
debug_op - Variable in class OntologyParser
 
debug_op_2 - Variable in class OntologyParser
 
debug_tql - Variable in class EvEx
 
debug_tql - Variable in class TQL
 

E

echoEvaluation(GEvent, Event) - Method in class Evaluator
Simple method to echo the evaulation to stdout
emit(String) - Method in class EvalE.EvalTHandler
 
emit(String) - Method in class GENIAHandler
 
emit(String) - Method in class OntologyParser
 
emit(String) - Method in class TQLHandler
 
endDocument() - Method in class EvalE.EvalTHandler
 
endDocument() - Method in class GENIAHandler
Invoked when a document is finished parsed.
endDocument() - Method in class OntologyParser
XML-parsing function for end of parsing.\ It has no function but to inform the user of parser completion.
endDocument() - Method in class TQLHandler
Invoked when a document is finished parsed.
endElement(String, String, String) - Method in class EvalE.EvalTHandler
 
endElement(String, String, String) - Method in class GENIAHandler
This method completes the action of startElement, namely unsets references that has been set, and adding items to misc lists.
endElement(String, String, String) - Method in class OntologyParser
This method completes the action of startElement, namely unsets references that has been set, and adding items to misc lists.
endElement(String, String, String) - Method in class TQLHandler
This method completes the action of startElement, namely unsets references that has been set, and adding items to misc lists.
escapeRegEx(String) - Method in class TQL
for an abitary string, escape each character that could be misinterpreted in the context of regular expressions
eval() - Method in class EvalE
The method for performing evaluation of events.
eval() - Method in class Evaluator
Wrapper method to start evaluation.
evalAuto() - Method in class Evaluator
Method to evaluate the events in a given sentence.
EvalE - Class in <Unnamed>
Standalone class for evaluation for XML-formatted event files.
EvalE(String, String) - Constructor for class EvalE
The constructor of EvalE enables it to be invoked from another class if needed.
EvalE.EvalEvent - Class in <Unnamed>
Conatiner class to hold parsed events
EvalE.EvalEvent() - Constructor for class EvalE.EvalEvent
 
EvalE.EvalTHandler - Class in <Unnamed>
Internal class to parse the distilled xml event file.
EvalE.EvalTHandler(ArrayList) - Constructor for class EvalE.EvalTHandler
 
evaluation - Variable in class EvEx
 
Evaluator - Class in <Unnamed>
This class performs evaluations of the events affilated with a sentence.
Evaluator(GSentence, TQL, EvEx, Syno, Anto, XMLWriter) - Constructor for class Evaluator
Create a new evaluation for the sentence defined by GSentence and TQL.
Event - Class in <Unnamed>
Container class for holding events from GeneTUC.
Event(TQL, String, String, String) - Constructor for class Event
Create an event with all attributes.
Event(TQL, String, String) - Constructor for class Event
Create a incomplete event for later refinement.
Event(TQL, String) - Constructor for class Event
Create a incomplete event for later refinement.
Event(TQL) - Constructor for class Event
Create a incomplete event for later refinement.
Event() - Constructor for class Event
Create an empty event for filling "holes" in event arrays.
eventcounter - Variable in class TQL
 
events - Variable in class GSentence
 
events - Variable in class TQL
 
events - Variable in class TQLAbstract
 
EvEx - Class in <Unnamed>
Main class for the EvEx program.
EvEx() - Constructor for class EvEx
 
extractEvents() - Method in class TQL
initiate extraction of events accorting to rules specified in this funciton

F

file - Variable in class GENIAParser
 
file - Variable in class OntologyParser
 
file - Variable in class TQLParser
 
fileGoldFile - Variable in class EvEx
 
fileTestFile - Variable in class EvEx
 
findEvent() - Method in class TQL
initiate extraction of events according to rule
findNoun() - Method in class TQL
initiate extraction of events according to rule
findNREL(Event) - Method in class TQL
check if a sentence contains a noun relation, and possibly add into to already existing event (this method wraps for identifyNREL()
findVerb() - Method in class TQL
initiate extraction of events according to rule
floatDiv(float, float) - Method in class EvEx
Method for float division that returns 0 if dividend is 0.

G

g - Variable in class Evaluator
 
g_events - Variable in class Evaluator
 
g_total - Variable in class Evaluator
 
GAbstract - Class in <Unnamed>
Class to hold GEvents, GSentences, sentence counter and a hash table over terms.
GAbstract() - Constructor for class GAbstract
This class does not need anything to be instantiated.
gabstract - Variable in class GENIAHandler
 
ge - Variable in class GENIAHandler
 
genfile - Variable in class EvalE
 
genhandler - Variable in class EvalE
 
genia - Variable in class EvEx
 
GENIAHandler - Class in <Unnamed>
This class handles the content of XML in GOLD-files.
GENIAHandler() - Constructor for class GENIAHandler
This class does not need anything in particular to be instantiated.
GENIAParser - Class in <Unnamed>
This class invokes the parsing of a GOLD-document.
GENIAParser(File) - Constructor for class GENIAParser
 
genxml_file - Variable in class XMLWriter
 
genxml_fw - Variable in class XMLWriter
 
genxml_name - Variable in class EvEx
 
genxml_name - Variable in class XMLWriter
 
get(String) - Method in class GEvent
Gets an attribute value from this Event
getAbstracts() - Method in class GENIAHandler
Accessor method for getting the abstracts handled by this handler.
getAbstracts() - Method in class GENIAParser
Access method to get the abstracts parsed by this parser.
getAbstracts() - Method in class TQLHandler
Accessor method to get the abstracts that has been handled by this Handler.
getAbstracts() - Method in class TQLParser
Access method to get the abstracts parsed by this parser.
getCause() - Method in class Event
Gets the cause of this event.
getCause() - Method in class GEvent
Gets the cause of this Event
getEvents() - Method in class GAbstract
Returns this abstracts list of events.
getEvents() - Method in class GSentence
Get the events associated with this sentence.
getEvents() - Method in class TQL
Get an arraylist of the events in this TQL
getEvents() - Method in class TQLAbstract
Method to access the events in this abstract.
getEventTheme(String) - Method in class GAbstract
Get the theme of an event, given it's PMID.
getEventType(String) - Method in class GAbstract
Get the type of an event, given it's PMID.
getHandler() - Method in class GENIAParser
Access method to get the handler of this parser.
getHandler() - Method in class TQLParser
Access method to get the handler of this parser.
getID() - Method in class Event
Gets the numeric ID of this event
getLines() - Method in class TQL
Get an arraylist of all statements
getLitCause() - Method in class Event
Get-method for member variable return litCause
getLitTheme() - Method in class Event
Get-method for member variable return litTheme
getLitType() - Method in class Event
Get-method for member variable return litType
getNextEvID() - Method in class TQL
Get the next available event id number
getRealCause() - Method in class GEvent
Gets the real (resolved) of this Event
getRealTheme() - Method in class GEvent
Gets the real (resolved) theme of this Event
getRealType() - Method in class GEvent
Gets the real (resolved) type of this Event
getSentences() - Method in class GAbstract
Get the sentences in this abstract.
getTheme() - Method in class Event
Gets the theme of this event.
getTheme() - Method in class GEvent
Gets the theme of this Event
getTQL() - Method in class TQLAbstract
Method to access the logic statements in this abstract.
getType() - Method in class Event
Gets the type of this event.
getType() - Method in class GEvent
Gets the type of this Event
getTypeAhead(String, int) - Method in class Evaluator
Assisting method to determine how far ahead one have to skip to get to a given type in the golden array.
getXML() - Method in class Event
Method for returning an XML-representation of this event.
getXML() - Method in class GEvent
Gets the XML-representation of this Event for printing distilled
GEvent - Class in <Unnamed>
A container class for holding all data on events from the golden corpus.
GEvent() - Constructor for class GEvent
No data is needed to construct an GEvent
Gevents - Variable in class GAbstract
 
gparser - Variable in class EvEx
 
gs - Variable in class GENIAHandler
 
GSentence - Class in <Unnamed>
This class represents a sentence from GENIA golden corpus.
GSentence(GAbstract) - Constructor for class GSentence
To construct an GSentence, it has to belong to an abstract.
Gsentences - Variable in class GAbstract
 
GTerm - Class in <Unnamed>
Container class to hold information about GTerms, which are important expressions in GSentences.
GTerm(GSentence) - Constructor for class GTerm
To construct a term, it has to belong to a sentence.

H

handler - Variable in class GENIAParser
 
handler - Variable in class OntologyParser
 
handler - Variable in class TQLParser
 
hello() - Method in class Evaluator
Simple method for echoing an evaluation.
hello() - Method in class Event
Wrapper method for printEvent();
hello() - Method in class GAbstract
Method to echo the contents of this abstract to stdout.
hello() - Method in class GEvent
Method for echoing the content of this event to stdout.
hello() - Method in class GSentence
Wrapper for printEvents()
hello() - Method in class GTerm
Echo this Term to stdout.
hello() - Method in class TQL
A wrapper method for printEvents
ht - Variable in class Anto
 
ht - Variable in class GEvent
 
ht - Variable in class Syno
 
ht_lex - Variable in class GAbstract
 
ht_sem - Variable in class GAbstract
 

I

id - Variable in class Event
 
id - Variable in class GEvent
 
id - Variable in class GSentence
 
id - Variable in class GTerm
 
identifyAdjTheme(Event) - Method in class TQL
check if a sentence contains an adjective that could add data to an event
identifyAdjType(Event) - Method in class TQL
 
identifyEvent(String) - Method in class TQL
check if a sentence contains a event definition, and initiate further logic.
identifyITVerb(String) - Method in class TQL
check if a sentence contains an intrasitive verb, and possibly initiate event
identifyNoun(String) - Method in class TQL
check if a sentence contains a noun and initiate event logic.
identifyNREL(Event) - Method in class TQL
check if a sentence contains a noun relation, and possibly add into to already existing event
identifySREL(Event) - Method in class TQL
 
identifySREL2(Event, String) - Method in class TQL
 
identifyTransVerb(String) - Method in class TQL
check if a sentence contains a verb, and initiate event logic.
inBlock - Variable in class TQLHandler
 
input - Variable in class TQL
 
intDiv(int, int) - Method in class EvalE
 
intDiv(int, int) - Method in class EvEx
Simplifies division of two integers by returning the results in percent.
intervention(String, String) - Method in class EvalE
Intervention is a method for comparing two strings.
intervention(String, String) - Method in class Evaluator
Method to determine if two strings are "equal".
isAhead(String, int) - Method in class Evaluator
Assisting method to determine is an event type is ahead in the golden array of events.
isAnto(String, String) - Method in class Anto
Method to check if a word is an antonyme of another.
isBuzzAdjective(String) - Method in class OntologyParser
Wrapper method to mid-levelly check if an adjective has some significance.\ This method is tentative.
isBuzzNoun(String) - Method in class OntologyParser
Wrapper method to low-levelly check if a word has some significance.
isBuzzVerb(String) - Method in class OntologyParser
Wrapper method to low-levelly check if a word has some significance.
isBuzzWord(String) - Method in class OntologyParser
Wrapper method to mid-levelly check if a word has some significance.
isClueWord(String) - Method in class OntologyParser
Wrapper method to low-levelly check if a word has some significance.
isHit(String, String) - Method in class Evaluator
Wrapper method to ensure backward compatibility with evalManual(); Invokes intervention();
isInOntology(String) - Method in class OntologyParser
Wrapper method to high-levelly check if a word has some significance.
isOfClass(String, String) - Method in class OntologyParser
Checks if a word (noun, verb) is of a certain class in the ontology.
isSyno(String, String) - Method in class Syno
Method to check if a word is an synonyme of another.

L

lastTag - Variable in class GENIAHandler
 
lex - Variable in class GTerm
 
litCause - Variable in class Event
 
litTheme - Variable in class Event
 
litType - Variable in class Event
 

M

main(String[]) - Static method in class EvalE
Static method allowing invocation of this class from command line.
main(String[]) - Static method in class EvEx
Invoked when starting program from command line, e.g.\ common Java behaviour.
main(String[]) - Static method in class OntologyParser
An onologyparser may be started from the command line to verify the correctness of an ontology.\ Thus it has a main-method.
makeParser() - Method in class EvalE
Method to invoke parsing of the xml event files.
makeParser(String) - Method in class OntologyParser
Makes a parser, and invokes parsing if there is a defined ontology file.
manual - Variable in class EvEx
 
medlineid - Variable in class TQLAbstract
 

N

nouns - Variable in class TQL
 

O

onto - Variable in class OntologyParser
 
OntologyParser - Class in <Unnamed>
This class is assisting TQL in the extraction of events.
OntologyParser(String) - Constructor for class OntologyParser
An ontologyparser with a predefined ontology.
OntologyParser() - Constructor for class OntologyParser
An ontologyparser without a ontology (yet).
op - Variable in class EvEx
 
op - Variable in class TQL
 
op - Variable in class TQLHandler
 
op - Variable in class TQLParser
 

P

parent - Variable in class Evaluator
 
parent - Variable in class Event
 
parent - Variable in class GEvent
 
parent - Variable in class GSentence
 
parent - Variable in class GTerm
 
parent_abstract - Variable in class Event
 
parent_abstract - Variable in class TQL
 
parseGENIA(File) - Method in class GENIAParser
Creates a new parser, and starts this with the actual document.
parseTQL(File) - Method in class TQLParser
Creates a new parser, and starts this with the actual document.
perc(int, int) - Method in class EvalE
 
perc(int, int) - Method in class EvEx
Wrapper method for intDiv that return the answer enclosed in a string, appended ( %)
PMID - Variable in class GAbstract
 
printEvent() - Method in class Event
Echos this event to stdout.
printEvents() - Method in class GSentence
Echo the events of this sentence to stdour.
printEvents() - Method in class TQL
Echo the events in this TQL to stdout
printTerms() - Method in class GSentence
Echo the terms of this sentence to stdout.
prolog(String) - Method in class TQL
 

R

resolveReference(String) - Method in class GAbstract
Find the most likely resolve of a reference (term, event theme or semantic expression in prioritized sequence)
resolveSkolemns() - Method in class TQL
map all skolemns in this TQL to their appropriate class
resolveTermLex(String) - Method in class GAbstract
Tries to look up the lexical interpretation of a term code in this abstracts hashtable.
resolveTermPermanent() - Method in class GEvent
Method to resolve each attribute into the lexiacal representation, and store is as real_attribute.
rmH(String) - Method in class OntologyParser
This method removes a hash (#) occuring at the start of a string.

S

sem - Variable in class GTerm
 
sentence - Variable in class GEvent
 
sentence_counter - Variable in class GAbstract
 
sentence_number - Variable in class GSentence
 
sentencecounter - Variable in class GENIAHandler
 
set(String, String) - Method in class GEvent
Sets an attribute of this Event
setAbstract(TQLAbstract) - Method in class Event
Set-method for member variable
setAnto(String, String) - Method in class Anto
Method to define two words as antonymes.
setCause(String) - Method in class Event
Sets the cause of this event
setCause(String) - Method in class GEvent
Sets the cause of this Event
setID(String) - Method in class GEvent
Sets the identification string from corpus of this Event
setID(String) - Method in class GSentence
Set the ID of this sentence.
setID(String) - Method in class GTerm
Set the identificator of this term
setID(String) - Method in class TQLAbstract
Method to set the identification string of this abstract.
setlex(String) - Method in class GTerm
Set the lexical representation of this term
setLitCause(String) - Method in class Event
Set-method for member variable
setLitTheme(String) - Method in class Event
Set-method for member variable
setLitType(String) - Method in class Event
Set-method for member variable
setOntologyParser(OntologyParser) - Method in class TQLHandler
Method to set the ontologyparser this Handler should use.
setParent(GAbstract) - Method in class GEvent
Sets the of parent abstract this Event
setPMID(String) - Method in class GAbstract
Setting the unique medline identification number for this abstract.
setsem(String) - Method in class GTerm
Set the semantic representation of this term
setSyno(String, String) - Method in class Syno
Method to define two words as synonymes.
setTheme(String) - Method in class Event
Sets the theme of this event
setTheme(String) - Method in class GEvent
Sets the theme of this Event
setType(String) - Method in class Event
Sets the type of this event
setType(String) - Method in class GEvent
Sets the type of this Event
sk(String) - Method in class TQL
 
startDocument() - Method in class EvalE.EvalTHandler
 
startDocument() - Method in class GENIAHandler
Invoked when a document is about to be parsed.\ Does nothing.
startDocument() - Method in class OntologyParser
XML-parsing function for start of parsing, but it has no function.
startDocument() - Method in class TQLHandler
Invoked when a document is about to be parsed.\ Does nothing.
startElement(String, String, String, Attributes) - Method in class EvalE.EvalTHandler
 
startElement(String, String, String, Attributes) - Method in class GENIAHandler
Called when the parser find a new starting tag.
startElement(String, String, String, Attributes) - Method in class OntologyParser
Called when the parser find a new starting tag.
startElement(String, String, String, Attributes) - Method in class TQLHandler
Called when the parser find a new starting tag.
statements - Variable in class TQL
 
subclass - Variable in class OntologyParser
 
syno - Variable in class EvalE
 
syno - Variable in class Evaluator
 
syno - Variable in class EvEx
 
Syno - Class in <Unnamed>
An abstraction class for holding synonym definitions.
Syno() - Constructor for class Syno
Constructor for creating an Syno.
synofile - Variable in class Syno
 

T

t - Variable in class Evaluator
 
t - Variable in class TQLHandler
 
t_all_correct - Variable in class Evaluator
 
t_cause_correct - Variable in class Evaluator
 
t_cause_total - Variable in class Evaluator
 
t_events - Variable in class Evaluator
 
t_theme_correct - Variable in class Evaluator
 
t_theme_total - Variable in class Evaluator
 
t_total - Variable in class Evaluator
 
t_type_correct - Variable in class Evaluator
 
t_type_total - Variable in class Evaluator
 
terms - Variable in class GSentence
 
theme - Variable in class EvalE.EvalEvent
 
theme - Variable in class Event
 
theme_extended - Variable in class Event
 
tparser - Variable in class EvEx
 
TQL - Class in <Unnamed>
This class contains most of the logic for recognising events.
TQL(int, int, TQLAbstract, OntologyParser) - Constructor for class TQL
A TQL represents a block of TQL-statements, and the associated events.
tqlabs - Variable in class EvEx
 
TQLAbstract - Class in <Unnamed>
Container class to hold data on TEST-abstracts.
TQLAbstract() - Constructor for class TQLAbstract
An abstract can be constructed without any additional parameters.
tqlabstract - Variable in class TQLHandler
 
tqlfile - Variable in class EvalE
 
tqlhandler - Variable in class EvalE
 
TQLHandler - Class in <Unnamed>
This class handles the content of XML in TEST-files.
TQLHandler() - Constructor for class TQLHandler
A TQLHandler can be constructed without any particular parameters
TQLParser - Class in <Unnamed>
This class invokes the parsing of a TEST-document.
TQLParser(File, OntologyParser) - Constructor for class TQLParser
 
tqls - Variable in class TQLAbstract
 
tqlxml_file - Variable in class XMLWriter
 
tqlxml_fw - Variable in class XMLWriter
 
tqlxml_name - Variable in class EvEx
 
tqlxml_name - Variable in class XMLWriter
 
type - Variable in class EvalE.EvalEvent
 
type - Variable in class Event
 
type_extended - Variable in class Event
 

W

writeGENEvent(GEvent) - Method in class XMLWriter
Write a GENIA/GOLD-event to the output files.
writeTQLEvent(Event) - Method in class XMLWriter
Write a TQL/TEST-event to the output files.

X

XMLWriter - Class in <Unnamed>
This class takes care of writing distilled XML-events to the output-files given as parameters on the command line.
XMLWriter(String, String) - Constructor for class XMLWriter
To create this Writer, it needs pathname to one or both files to be written.
xw - Variable in class Evaluator
 

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