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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
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