A B C D E F G H I K L M N O P R S T U V W
All Classes All Packages

A

abs2Sen(String, String) - Method in class relations.SenSimplifier

Deprecated.

add(int) - Method in class relations.Counter

addChunk(BasicChunk) - Method in class relations.BasicChunk

addChunk(Chunk) - Method in class relations.BasicChunk

addPattern(int, String, String, boolean, boolean, boolean, String, String, boolean, boolean, int, int, boolean, boolean, String, String, boolean) - Method in class relations.Rules

Regulatory events

addPattern(int, String, String, boolean, boolean, boolean, String, String, boolean, boolean, int, int, String, boolean) - Method in class relations.Rules

Binding events

addPattern(int, String, String, boolean, String, boolean, int, String, boolean) - Method in class relations.Rules

For simple events

addPro(Word) - Method in class relations.BasicChunk

addPro(Word) - Method in class relations.Chunk

Add protein

addToMap(KeyData) - Method in class relations.KeyData

Add shared/mix trigger to map

addTrg(Word) - Method in class relations.BasicChunk

addTrigger(Word) - Method in class relations.Chunk

Add trigger

addVerb(Chunk) - Method in class relations.VerbChunk

addWord(String) - Method in class relations.Chunk

allMap - Variable in class relations.ChunkAnalyzer

analyze(String) - Method in class relations.SenAnalyzer

Main method to analyze text

analyzeChunk(List<Chunk>, String[], String[]) - Method in class relations.ChunkAnalyzer

Analyzing chunks to form NP, VP...

application - package application

applyScore() - Method in class relations.RuleSet

appoList - Static variable in class relations.BasicChunk

appoMap - Static variable in class relations.BasicChunk

appoMap - Variable in class relations.ChunkAnalyzer

B

BasicChunk - Class in relations

BasicChunk() - Constructor for class relations.BasicChunk

begin - Variable in class relations.Chunk

begin - Variable in class utils.SentenceSplitter.BioSemSentence

belongTO(Word, Word) - Method in class relations.BasicChunk

belongTO(Word, Word) - Method in class relations.VerbChunk

For simple events/ or binding without theme2

belongTO(Word, Word, Word) - Method in class relations.BasicChunk

belongTO(Word, Word, Word) - Method in class relations.VerbChunk

beMap - Variable in class relations.ChunkAnalyzer

BioSemApplication - Class in application

BioSemApplication() - Constructor for class application.BioSemApplication

BioSemException - Exception in utils

BioSemException(Exception) - Constructor for exception utils.BioSemException

BioSemSentence() - Constructor for class utils.SentenceSplitter.BioSemSentence

BioSemSentence(String, int, int) - Constructor for class utils.SentenceSplitter.BioSemSentence

breakMap - Variable in class relations.ChunkAnalyzer

brLine(String, String) - Method in class relations.SenSimplifier

Used to split the text after the title which often does not end with a full stop, this posing an issue for the sentence splitter.

C

cause - Variable in class relations.Chunk

cause - Variable in class relations.Word

ccList - Static variable in class relations.BasicChunk

ccList - Static variable in class relations.EventExtraction

ccMap - Static variable in class relations.BasicChunk

ccMap - Variable in class relations.ChunkAnalyzer

ccSet - Static variable in class relations.EventExtraction

checkTable(String) - Method in class utils.DBUtils

Check if a table already exists

child - Variable in class relations.TriggerLearner.TriggerData

childMap - Variable in class relations.RuleData

Chunk - Class in relations

Chunk(String) - Constructor for class relations.Chunk

chunk_type - Variable in class relations.Word

ChunkAnalyzer - Class in relations

Define all operations on Chunk such as forming NP, VP, PP, AP

ChunkAnalyzer() - Constructor for class relations.ChunkAnalyzer

cleanChunk(List<Chunk>, String[], String[]) - Method in class relations.ChunkAnalyzer

clearList() - Method in class relations.TriggerLearner

close() - Method in class corpora.DataSaver

closeDB() - Method in class relations.SenAnalyzer

Close database [never called]

closeDB() - Method in class relations.SenSimplifier

closeDB() - Method in class utils.DBUtils

combined - Variable in class relations.Word

combiningRules(Map<String, Rules>[]) - Method in class relations.RuleLearner

comparePatterns() - Method in class relations.Eval

compareTo(Object) - Method in class relations.Counter

compareTo(Object) - Method in class relations.KeyData

compareTo(Object) - Method in class relations.PData

compareTo(Object) - Method in class relations.RuleData

compareTo(Object) - Method in class relations.TData

compareTo(Object) - Method in class relations.Word

compound - Variable in class relations.Word

con - Variable in class utils.DBUtils

contains(Word) - Method in class relations.Chunk

containsKey(Word) - Method in class relations.BasicChunk

corpora - package corpora

count - Variable in class relations.Counter

count_chunk - Variable in class relations.ChunkAnalyzer

countChunks(Word, Word) - Method in class relations.BasicChunk

Counter - Class in relations

Counter() - Constructor for class relations.Counter

Counter(int) - Constructor for class relations.Counter

countLevel() - Method in class relations.Eval

createRule(List<RuleData>) - Method in class relations.RuleSets

Split of pattern into defined group

createTriggers() - Method in class relations.TriggerLearner

Creating trigger list from training data

cscore - Variable in class relations.KeyData

curr_text - Variable in class relations.ChunkAnalyzer

D

DataLoader - Class in corpora

DataLoader() - Constructor for class corpora.DataLoader

DataSaver - Class in corpora

DataSaver(DBUtils) - Constructor for class corpora.DataSaver

DBUtils - Class in utils

DBUtils() - Constructor for class utils.DBUtils

DBUtils(String, String) - Constructor for class utils.DBUtils

DBUtils(String, String, String) - Constructor for class utils.DBUtils

detectTrg(String) - Method in class relations.SenAnalyzer

DictEval() - Method in class relations.Eval

Evaluating dictionary

doSentenceSplitting(String, String) - Method in class relations.SenSimplifier

doSimplify() - Method in class relations.SenSimplifier

Deprecated.

doSimplifySentenceWise(SentenceSplitter.BioSemSentence[], List<TData>) - Method in class relations.SenSimplifier

dropTable(String) - Method in class utils.DBUtils

E

EData - Class in relations

EData(String, String, String, String, String, String, String) - Constructor for class relations.EData

end - Variable in class relations.Chunk

end - Variable in class utils.SentenceSplitter.BioSemSentence

equiList - Variable in class relations.SenSimplifier

equimap - Variable in class relations.SenSimplifier

er_count - Variable in class relations.SenSimplifier

Check whether this sentence qualify for extracting event

escore - Variable in class relations.KeyData

Eval - Class in relations

Eval() - Constructor for class relations.Eval

Main class for extracting event from text

Eval(SenSimplifier) - Constructor for class relations.Eval

evalReg() - Method in class relations.Eval

evalSimple() - Method in class relations.Eval

evaluateTrg(BasicChunk, List<Word>, List<Word>, String[], List<Word>) - Method in class relations.EventExtraction

Evaluating candidate triggers whether they can form events

EventExtraction - Class in relations

EventExtraction(DBUtils, DBUtils) - Constructor for class relations.EventExtraction

Extract event from the given data

evt_type - Variable in class relations.PData

evtMap - Variable in class relations.Eval

execUpdate(String) - Method in class utils.DBUtils

extractBindNP(Word, BasicChunk, List<Word>) - Method in class relations.EventExtraction

12.10.2011 Extracting binding events

extractBindVP(Word, VerbChunk, List<Word>) - Method in class relations.EventExtraction

extracted - Variable in class relations.BasicChunk

extracted - Variable in class relations.RuleData

extractEvents(String) - Method in class relations.EventExtraction

Extracting events from abstract/paragraph.

extractNP(int, BasicChunk, List<Word>) - Method in class relations.EventExtraction

extractNP(BasicChunk, List<Word>) - Method in class relations.EventExtraction

extractRegNP(Word, BasicChunk, List<Word>) - Method in class relations.EventExtraction

extractRegVP(Word, VerbChunk, List<Word>) - Method in class relations.EventExtraction

extractSentence(int) - Method in class relations.EventExtraction

extractSimpleNP(Word, BasicChunk, List<Word>) - Method in class relations.EventExtraction

Extracting simple event from BasicChunk with a given trigger (+type)

extractSimpleVP(Word, VerbChunk, List<Word>) - Method in class relations.EventExtraction

Find pros for binding event which has pattern as: Pro1 - Trg - Pro2

extractVP(VerbChunk, List<Word>, List<Word>) - Method in class relations.EventExtraction

extraMap - Variable in class relations.ChunkAnalyzer

F

findCausePro(BasicChunk, Word) - Method in class relations.EventExtraction

Get Pro as cause for : PRO-xx TG PRO/EVENT

findCoordinator(List<Chunk>) - Method in class relations.BasicChunk

findEquiv(String) - Method in class relations.SenAnalyzer

DO NOT USE! This method is not correct due to some changes.

findFrontPro(BasicChunk, Word, int) - Method in class relations.EventExtraction

12.10.2011 Find pro in front of tg for noun phrase/subject patterns: PRO - TG

findObject(int, List<Chunk>, int) - Method in class relations.ChunkAnalyzer

findPos(int[], Word[]) - Method in class relations.Eval

findPreviousNP(BasicChunk) - Method in class relations.ChunkAnalyzer

For 'which' and 'that' relative clause

findPro(BasicChunk, int, int) - Method in class relations.EventExtraction

Find pro after a given position (for use with tg- prep1 - prep2) Only looks for pro after prep2

findPro(BasicChunk, Word, String, int) - Method in class relations.EventExtraction

11.10.2011.

findProIndex(List<TData>, int) - Method in class relations.SenSimplifier

findRegPro(BasicChunk, Word, int, int) - Method in class relations.EventExtraction

Find pro after a given position (for use with tg- prep1 - prep2) Only looks for pro after prep2

findSubject(int, List<Chunk>, int) - Method in class relations.ChunkAnalyzer

findTrigger(int[], List<Word>) - Method in class relations.SenAnalyzer

findTrigger(Word, Word) - Method in class relations.BasicChunk

fullword - Variable in class relations.Word

G

generateKeyData() - Method in class relations.TriggerLearner

genia_tag - Variable in class parser.Parser

getBehindScore() - Method in class relations.RuleSets

Score of event having theme behind TG ; for simple event only; TODO: for other events need to take into account group 6

getBy_Through(Word, Word, String[]) - Method in class relations.BasicChunk

getCause() - Method in class relations.EData

getCauseScore() - Method in class relations.RuleSet

Ratio of event has cause

getCauseScore() - Method in class relations.RuleSets

Get score of an event having cause/theme2.

getChunk(int) - Method in class relations.BasicChunk

getChunkPos(int) - Method in class relations.BasicChunk

getConnection() - Method in class utils.DBUtils

Unused

getDb_root() - Method in class application.BioSemApplication

getDefault() - Method in class relations.KeyData

Get default event type (ignoring modifiers) In this case, use the highest frequency as default type

getDestination() - Method in class application.BioSemApplication

getEv2Score() - Method in class relations.RuleSet

Ratio of event as cause

getEvalRules(String) - Method in class relations.Rules

Get list of patterns

getEvtCause(int) - Method in class relations.RuleSets

Get score of an event having cause as an event

getEvtScore() - Method in class relations.RuleSet

Ratio of event as theme

getEvtScore(int) - Method in class relations.RuleSets

Get score of an event having theme as an event

getExtractedEvents() - Method in class relations.EventExtraction

Available after EventExtraction.Test() or EventExtraction.Test(String) has been run.

getExtractedTriggers() - Method in class relations.EventExtraction

Available after EventExtraction.Test() or EventExtraction.Test(String) has been run.

getFreq() - Method in class relations.RuleSet

Count frequency of this rule, should not use alone, use getScore instead.

getFrontScore() - Method in class relations.RuleSets

Score of event having theme infront of TG

getInchunkCause() - Method in class relations.RuleSets

getInChunkEvtScore() - Method in class relations.RuleSets

getInChunkPro(BasicChunk, Word) - Method in class relations.EventExtraction

11.10.2011.

getInChunkPro(Word, String[]) - Method in class relations.Chunk

Get in_chunk pro for a given tg

getInput_root() - Method in class application.BioSemApplication

getKey() - Method in class relations.RuleData

getKeyData(String) - Method in class relations.KeyData

get KeyData for shared and mixed trigger

getKeyInfo() - Method in class relations.RuleData

getLevel(int) - Method in class relations.EData

getMap() - Method in class relations.KeyData

get list of shared /mix trigger -> which has the same key

getMod(int, int, List<Word>) - Method in class relations.EventExtraction

Get modifier for trigger in order to determine trigger type

getMod(BasicChunk, Word, List<Word>) - Method in class relations.EventExtraction

Get modifier for trigger in order to determine trigger type

getMod(BasicChunk, Word, List<Word>, List<Word>) - Method in class relations.EventExtraction

Get modifier for trigger in order to determine trigger type

getMod(Chunk, Chunk, List<Word>) - Method in class relations.EventExtraction

Get modifier for trigger in order to determine trigger type

getModifier(String[]) - Method in class relations.SenAnalyzer

Get list of prepositions of a sentence

getModus() - Method in class application.BioSemApplication

getOffset(int, int[]) - Method in class relations.SenSimplifier

getPdata1() - Method in class relations.PData

getPdata2() - Method in class relations.PData

getPIndex(String) - Method in class relations.SenSimplifier

getPrep(Word, Word) - Method in class relations.BasicChunk

getPrep(Word, Word, BasicChunk) - Method in class relations.RuleLearner

getPrep2(Word, Word, BasicChunk) - Method in class relations.RuleLearner

getPrepFront(Word, Word, BasicChunk) - Method in class relations.RuleLearner

getPreps(String[]) - Method in class relations.SenAnalyzer

Get list of prepositions of a sentence

getPro() - Method in class relations.BasicChunk

getPro() - Method in class relations.EData

Get protein closest to the trigger in order to map trigger location into sentence and vice vesa

getPro(String[]) - Method in class relations.Chunk

12.10.2011 Get pro list in form TG_PRO for strict case (no other trigger in between)

getPro(Word, String[]) - Method in class relations.Chunk

Get pros (same chunk with trg) that follow the given trigger for pattern: TG - PR This method is used in case there is no prep or trg has JJ/VBx form in noun chunk

getPro1() - Method in class relations.PData

getPro2() - Method in class relations.PData

getProCause(int) - Method in class relations.RuleSets

Get score of an event having cause as an pro

getProFront() - Method in class relations.Chunk

12.10.2011 Get pro list for strict case (no other trigger in between)

getProScore(int) - Method in class relations.RuleSets

Get score of an event having theme as an pro

getProtein() - Method in class relations.PData

getProteins(String) - Method in class relations.SenSimplifier

getScore() - Method in class relations.RuleSet

Confident score for this rule, if this value is low, skip this rule

getSenIndex(int, int[]) - Method in class relations.SenSimplifier

getSet() - Method in class application.BioSemApplication

getSubKey() - Method in class relations.RuleData

getT1Score() - Method in class relations.RuleSet

For binding only; this value is used to determine whether to use pro in front of TG as theme/ or use t2 score

getT2Score() - Method in class relations.RuleSet

Theme 2 score

getText() - Method in class relations.Chunk

getText() - Method in class relations.PData

getTrigger() - Method in class relations.EData

getTrigger() - Method in class relations.PData

getTxt() - Method in class relations.EData

getTxt(int) - Method in class relations.EData

getType() - Method in class relations.Chunk

getType() - Method in class relations.EData

getType(List<Word>) - Method in class relations.KeyData

Determine event type based on a given list of modifiers

getValue() - Method in class relations.Counter

getValues() - Method in class relations.Chunk

getVerbChunkType(Chunk) - Method in class relations.ChunkAnalyzer

Determine verb chunk type: passive/active/gerund

getWriteID() - Method in class relations.PData

groupRules(Map<String, Rules>[]) - Method in class relations.EventExtraction

H

hashType - Static variable in class relations.SenSimplifier

I

id - Variable in class parser.Parser

inc() - Method in class relations.Counter

inchunk - Variable in class relations.Word

inChunk() - Method in class relations.RuleSets

Check whether this pattern has inchunk form

inChunk(Word, Word) - Method in class relations.BasicChunk

inChunk(Word, Word) - Method in class relations.Chunk

Check TG and Pro in the same chunk, for use with learning rules

inChunk(Word, Word, String[]) - Method in class relations.Chunk

Check TG and Pro in the same chunk, for use with learning rules

inchunkScore() - Method in class relations.RuleSet

Percentage of event has in chunk form, if this value is low, then skip in-chunk event

inChunkTG(Word, Word) - Method in class relations.BasicChunk

Two tg in the same chunk ; for learning rule only

inChunkTG(Word, Word) - Method in class relations.Chunk

Check two trg in the same chunk, without any pro in between of them

inChunkTrg(Word, String[]) - Method in class relations.BasicChunk

Check whether a given trigger is in_chunk form

init - Variable in class relations.BasicChunk

init - Variable in class relations.KeyData

init() - Method in class relations.EventExtraction

init() - Method in class relations.SenAnalyzer

Loading dictionaries

init(Map<String, TData>, Map<String, TData>, Map<String, EData>) - Method in class relations.EData

initAbstract(String) - Method in class relations.Eval

Load all data (protein, trigger, event) belong to this abtract/paragraph Split abstract/paragraph into sentences

initAbstract(String) - Method in class relations.SenAnalyzer

initData(String) - Method in class relations.SenAnalyzer

Workflow: 1.

initData(String, String) - Method in class relations.KeyData

initEventData(String) - Method in class relations.TriggerLearner

initMap() - Method in class relations.Rules

initParser() - Method in class parser.Parser

initSentence(String) - Method in class relations.EventExtraction

is_a_Map - Variable in class relations.ChunkAnalyzer

is_a_phrase(Chunk) - Method in class relations.ChunkAnalyzer

is_inChunk(Word, String[]) - Method in class relations.Chunk

Check whether a trg has in_chunk form

is_merged - Variable in class relations.BasicChunk

is_merged - Variable in class relations.Chunk

is_passive(Chunk) - Method in class relations.ChunkAnalyzer

isEmpty() - Method in class relations.BasicChunk

Check whether this basic chunk is empty.

isQualify() - Method in class relations.BasicChunk

isQualify() - Method in class relations.Chunk

isQualify() - Method in class relations.VerbChunk

isSameChunk(Word, Word) - Method in class relations.BasicChunk

Check whether in the same chunk but not in_chunk form

isSameRole(Word, Word, String[]) - Method in class relations.BasicChunk

Check whether two trigger has the same role (i.e have the same arguments)

isSameRole(Word, Word, String[]) - Method in class relations.Chunk

isSkipped() - Method in class relations.RuleSets

Check whether to skip this pattern

isSkipped(int) - Method in class relations.RuleSets

Check whether to skip this pattern

K

KeyData - Class in relations

KeyData(String, String, int, int, int) - Constructor for class relations.KeyData

keytype - Variable in class relations.Word

L

LearnData() - Method in class relations.RuleLearner

loadData(String, boolean) - Method in class corpora.DataLoader

loadDict(DBUtils) - Method in class relations.SenSimplifier

Load dictionary from default database DB: DB source to load dictionary

loadEquiv(String) - Method in class relations.SenSimplifier

loadEvent(String) - Method in class relations.SenSimplifier

loadPatterns(DBUtils) - Method in class relations.SenSimplifier

Load pattern from database

loadPMIDs() - Method in class relations.SenSimplifier

Load abstract ID from database

loadProtein(String) - Method in class relations.SenSimplifier

loadRuleSet(DBUtils) - Method in class relations.SenSimplifier

loadSentence(String) - Method in class relations.SenSimplifier

loadSimpleDic() - Method in class relations.SenSimplifier

loadSimpleDic(Map<String, KeyData>) - Method in class relations.SenSimplifier

loadSimplified(String) - Method in class relations.SenSimplifier

Deprecated.

loadTrigger(String) - Method in class relations.SenSimplifier

loc - Variable in class relations.Word

locs - Variable in class relations.Word

M

main(String[]) - Static method in class application.BioSemApplication

main(String[]) - Static method in class corpora.DataLoader

main(String[]) - Static method in class parser.Parser

main(String[]) - Static method in class relations.ChunkAnalyzer

main(String[]) - Static method in class relations.Eval

main(String[]) - Static method in class relations.EventExtraction

main(String[]) - Static method in class relations.RuleLearner

main(String[]) - Static method in class relations.SenAnalyzer

main(String[]) - Static method in class relations.SenSimplifier

main(String[]) - Static method in class relations.TriggerLearner

main(String[]) - Static method in class utils.SentenceSplitter

mapToStr(Map<String, Set<String>>) - Method in class relations.RuleLearner

mapToString(Set<String>) - Method in class relations.RuleData

merge() - Method in class relations.VerbChunk

Merge this verb chunk to create BasicChunk

merge(Chunk) - Method in class relations.Chunk

Merge two chunks: appending a chunk to the current chunk

mergeNP() - Method in class relations.BasicChunk

modifiers - Static variable in class relations.SenSimplifier

N

none_rel - Static variable in class relations.SenSimplifier

none_rel - Static variable in class relations.TriggerLearner

nr_event - Variable in class relations.SenSimplifier

O

old_txt - Variable in class parser.Parser

openDB() - Method in class utils.DBUtils

openDB(String) - Method in class utils.DBUtils

P

parent - Variable in class relations.TriggerLearner.TriggerData

parentMap - Variable in class relations.RuleData

parse(String[]) - Method in class parser.Parser

Shallow parser: generating chunks (NP,VP, PP) from untokenized text

parse(String[], String[]) - Method in class parser.Parser

parser - package parser

Parser - Class in parser

Parser() - Constructor for class parser.Parser

PData - Class in relations

PData(Word, Object, Object, String) - Constructor for class relations.PData

PData(Word, Object, String) - Constructor for class relations.PData

PID - Variable in class relations.PData

pos - Variable in class relations.Word

pos_tag - Variable in class relations.Word

POSTag(String[]) - Method in class parser.Parser

Tag a list of tokens with POS

preparedData() - Method in class relations.TriggerLearner

Read raw data from tables, generate statistical values

prepList - Static variable in class relations.EventExtraction

prepmap - Static variable in class relations.RuleLearner

prepmap - Static variable in class relations.SenSimplifier

prepMap - Variable in class relations.ChunkAnalyzer

preps - Static variable in class relations.RuleLearner

preps - Static variable in class relations.SenSimplifier

prepSet - Static variable in class relations.EventExtraction

prepWord - Variable in class relations.TriggerLearner

print() - Method in class relations.VerbChunk

print_chunk - Variable in class relations.ChunkAnalyzer

printAllSentence(int) - Method in class relations.Eval

printChunk() - Method in class relations.BasicChunk

printChunk(String) - Method in class parser.Parser

printChunk(List<Chunk>) - Method in class parser.Parser

printChunk(List<Chunk>) - Method in class relations.ChunkAnalyzer

print chunks contain marker word

printChunk(List<Chunk>) - Method in class relations.SenAnalyzer

printChunkList() - Method in class relations.EventExtraction

printCompoundEvent(int) - Method in class relations.Eval

printCompoundTrigger(TData, List<Word>) - Method in class relations.Eval

printEventbyType(int, String) - Method in class relations.Eval

printEvents(String) - Method in class relations.Eval

printEventType(int) - Method in class relations.Eval

printFile(String, String) - Method in class relations.Eval

printInChunks() - Method in class relations.SenAnalyzer

printInfo() - Method in class relations.Rules

processSentence(String, String[], int) - Method in class relations.SenAnalyzer

proCount() - Method in class relations.BasicChunk

proIDMap - Variable in class relations.SenAnalyzer

proMap - Variable in class relations.Eval

pros - Variable in class relations.Chunk

proWord - Variable in class relations.TriggerLearner

R

relations - package relations

relWords - Variable in class relations.TriggerLearner

removePro(int) - Method in class relations.Chunk

removePRO(Word) - Method in class relations.Chunk

removeTrg(Word) - Method in class relations.BasicChunk

removeTRG(Word) - Method in class relations.Chunk

required - Variable in class relations.KeyData

rs - Variable in class utils.DBUtils

RuleData - Class in relations

RuleData() - Constructor for class relations.RuleData

RuleData(int, String, String, boolean, boolean, boolean, String, String, boolean, boolean, int, int, boolean, boolean, String, String) - Constructor for class relations.RuleData

RuleData(int, String, String, boolean, boolean, boolean, String, String, boolean, boolean, int, int, String) - Constructor for class relations.RuleData

RuleData(int, String, String, boolean, String, boolean, int, String) - Constructor for class relations.RuleData

RuleLearner - Class in relations

RuleLearner() - Constructor for class relations.RuleLearner

RuleLearner(DBUtils, DBUtils) - Constructor for class relations.RuleLearner

Rules - Class in relations

Rules(int, String) - Constructor for class relations.Rules

RuleSet - Class in relations

RuleSet() - Constructor for class relations.RuleSet

RuleSets - Class in relations

Dec 12, 2011

RuleSets() - Constructor for class relations.RuleSets

group0 : in-chunk -> PRO-TG | POS: NN/JJ group1 : in-chunk + cause/theme2: PRO-TG PRO/EVT |POS: NN/JJ group2 : TG prep PRO/EVT (theme) | POS: NN/JJ/VB (active) group3 : TG prep PRO/EVT prep PRO/EVT |POS: NN/JJ/VB group4 : PRO/EVT (theme) TG | POS: NN/VB (passive)(binding) group5 : PRO/EVT (theme) (prep) TG (prep) PRO/EVT (cause) | POS: NN/VB(passive) group6 : PRO/EVT (cause) (prep) TG (prep) PRO/EVT (theme) | POS: NN/VB(active) group7 : PRO - PRO - TG For NP chunk -> POS: NNx/JJ/VBx With NNx -> possible group: G0,G1,G2,G3,G4,G5,G6,G7 -->Reg: G0,G1,G2(has prep or dist=0),G3, can skip G4,G6 -->Binding:G0,G1,G2(has prep or dist=0),G3, can skip G4, no G6 -->Simple:G0, G2 With JJ -> Possible group: G0,G1,G2, skip the other group With VBx -> Possible group: G2,G4,G5,G6 -->Reg: G2, G3(by), G5 (by); can skip G4,G0,G1 For VP chunk -> POS:JJ/VBx Possible group (Reg event): G2,G6 (active); G4,G5 (passive) ; For binding, no distinction between passive and active For simple event: G2 and G4

S

saveAbstract(String, String) - Method in class corpora.DataSaver

saveEquiv(String, String, String) - Method in class corpora.DataSaver

Store modified values

saveEvent(String, String, String, String, String, String, String) - Method in class corpora.DataSaver

saveModify(String, String, String, String) - Method in class corpora.DataSaver

Store modified values

saveProtein(String, String, int, int, String) - Method in class corpora.DataSaver

saveTrigger(String, String, String, int, int, String) - Method in class corpora.DataSaver

Store trigger into Trigger table

score - Variable in class relations.KeyData

SenAnalyzer - Class in relations

SenAnalyzer(SenSimplifier) - Constructor for class relations.SenAnalyzer

For creating new dictionary only

SenAnalyzer(DBUtils, DBUtils) - Constructor for class relations.SenAnalyzer

Use given database

senid - Variable in class parser.Parser

SenSimplifier - Class in relations

SenSimplifier() - Constructor for class relations.SenSimplifier

SenSimplifier(DBUtils) - Constructor for class relations.SenSimplifier

SentenceSplitter - Class in utils

SentenceSplitter() - Constructor for class utils.SentenceSplitter

SentenceSplitter.BioSemSentence - Class in utils

set2String(Set<String>) - Method in class relations.KeyData

Convert a map into string separeted by commar.

setChildTrigger(String) - Method in class relations.RuleData

setDb(DBUtils) - Method in class relations.EventExtraction

setDB(DBUtils) - Method in class relations.SenAnalyzer

Set default database

setDB(DBUtils) - Method in class relations.SenSimplifier

Set default database

setModifier() - Method in class relations.SenSimplifier

These data learn form Modifier Learner; It would be nicer to automatically set these modifiers.

setModifiers(String[]) - Method in class relations.KeyData

Set modifers for this trigger

setParentTrigger(String) - Method in class relations.RuleData

setPID(String) - Method in class relations.PData

setSimpleDic(Set<String>) - Method in class relations.SenSimplifier

setToStr(Set<String>) - Method in class relations.RuleLearner

sharedDic - Variable in class relations.SenSimplifier

shutdownDB() - Method in class utils.DBUtils

simpleDic - Variable in class relations.SenSimplifier

skip - Variable in class relations.PData

skipMap - Variable in class relations.ChunkAnalyzer

skipPhrase(List<Chunk>, int, int) - Method in class relations.ChunkAnalyzer

First step: remove

splitData(List<TData>) - Method in class relations.Eval

Split list of Data (Trigger/Protein) based on number of sentences

splitData(List<TData>, int[]) - Method in class relations.SenAnalyzer

Split list of Data (Trigger/Protein) based on number of sentences

spliter(String) - Static method in class utils.SentenceSplitter

splitEvents(List<EData>) - Method in class relations.Eval

Spliting event per sentence

splitEvents(List<EData>) - Method in class relations.SenAnalyzer

splitTrg(List<Word>) - Method in class relations.Eval

splitTrg(List<Word>, int[]) - Method in class relations.SenAnalyzer

splitWord(String) - Method in class parser.Parser

Split text into tokens

stmt - Variable in class utils.DBUtils

storePatterns(Map<String, Rules>[], DBUtils) - Method in class relations.RuleLearner

storeRuleSet(Map<String, RuleSet>, DBUtils) - Method in class relations.RuleLearner

T

t2score - Variable in class relations.KeyData

TData - Class in relations

test() - Method in class relations.Eval

Test() - Method in class relations.EventExtraction

Test(String) - Method in class relations.EventExtraction

testAll() - Method in class relations.SenAnalyzer

testChunks() - Method in class relations.SenAnalyzer

testParser(String) - Method in class parser.Parser

testSentence() - Method in class relations.SenAnalyzer

testSpliter() - Method in class relations.SenSimplifier

text - Variable in class utils.SentenceSplitter.BioSemSentence

TID - Variable in class relations.Word

toString() - Method in class relations.BasicChunk

Operation: 1.

toString() - Method in class relations.Chunk

toString() - Method in class relations.EData

toString() - Method in class relations.PData

toString() - Method in class relations.Rules

toString() - Method in class relations.Word

total - Variable in class parser.Parser

trgCount() - Method in class relations.BasicChunk

trgIDMap - Variable in class relations.Eval

trig_ID - Variable in class relations.PData

trigger_type - Static variable in class relations.SenSimplifier

trigger_type - Static variable in class relations.TriggerLearner

Map between absolute position into related position of a given trigger with abstract/sentence

TriggerData(String, String) - Constructor for class relations.TriggerLearner.TriggerData

TriggerLearner - Class in relations

TriggerLearner(DBUtils, DBUtils) - Constructor for class relations.TriggerLearner

TriggerLearner.TriggerData - Class in relations

trigs - Variable in class relations.Chunk

trim(String) - Method in class relations.SenSimplifier

txt - Variable in class relations.Chunk

Txt2Db(String, String, boolean) - Method in class corpora.DataLoader

Txt2Db(String, String, List<String>) - Method in class corpora.DataLoader

Creates a database for event extraction as an programmatic API-call where all values are given directly rather then reading the values from files.

type - Variable in class relations.BasicChunk

type - Variable in class relations.Chunk

type - Variable in class relations.Word

U

used - Variable in class relations.Word

utils - package utils

V

VerbChunk - Class in relations

VerbChunk() - Constructor for class relations.VerbChunk

W

word - Variable in class relations.Word

Word - Class in relations

Word(String, int, int) - Constructor for class relations.Word

wordSpliter(String) - Static method in class utils.SentenceSplitter

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