relations

Class SenSimplifier

java.lang.Object

relations.SenSimplifier

public class SenSimplifier
extends Object

Author:

Chinh

Field Summary

Fields

Modifier and Type	Field and Description
Map<String,List<String>>	equiList
Map<String,String>	equimap
int	er_count Check whether this sentence qualify for extracting event
static Map<String,Integer>	hashType
static Map<String,String>	modifiers
static Map<String,String>	none_rel
int	nr_event
static Set<String>	prepmap
static String[]	preps
Map<String,KeyData>	sharedDic
Set<String>	simpleDic
static String[]	trigger_type

Constructor Summary

Constructors

Constructor and Description
SenSimplifier()
SenSimplifier(DBUtils dbs)

Method Summary

Methods

Modifier and Type	Method and Description
String[]	abs2Sen(String txt, String br) Deprecated.
String[]	brLine(String txt, String br) 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.
void	closeDB()
SentenceSplitter.BioSemSentence[]	doSentenceSplitting(String txt, String br)
void	doSimplify() Deprecated.
String[]	doSimplifySentenceWise(SentenceSplitter.BioSemSentence[] originalSentences, List<TData> proList)
int	findProIndex(List<TData> plist, int pos)
int	getOffset(int idx, int[] subpos)
int	getPIndex(String pname)
List<String>	getProteins(String s)
int	getSenIndex(int start, int[] subpos)
void	loadDict(DBUtils dbs) Load dictionary from default database DB: DB source to load dictionary
List<String[]>	loadEquiv(String pmid)
List<EData>	loadEvent(String pmid)
Map<String,Rules>[]	loadPatterns(DBUtils db) Load pattern from database
List<String>	loadPMIDs() Load abstract ID from database
List<TData>	loadProtein(String pmid)
Map<String,RuleSet>	loadRuleSet(DBUtils db)
String	loadSentence(String pmid)
void	loadSimpleDic()
void	loadSimpleDic(Map<String,KeyData> map)
String	loadSimplified(String pmid) Deprecated.
List<TData>	loadTrigger(String pmid)
static void	main(String[] args)
void	setDB(DBUtils dbs) Set default database
void	setModifier() These data learn form Modifier Learner; It would be nicer to automatically set these modifiers.
void	setSimpleDic(Set<String> map)
void	testSpliter()
String	trim(String txt)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

simpleDic

public Set<String> simpleDic

er_count

public int er_count

Check whether this sentence qualify for extracting event

nr_event

public final int nr_event

See Also:

Constant Field Values

preps

public static final String[] preps

prepmap

public static final Set<String> prepmap

modifiers

public static final Map<String,String> modifiers

equimap

public Map<String,String> equimap

none_rel

public static final Map<String,String> none_rel

trigger_type

public static final String[] trigger_type

hashType

public static final Map<String,Integer> hashType

sharedDic

public Map<String,KeyData> sharedDic

equiList

public Map<String,List<String>> equiList

Constructor Detail

SenSimplifier

public SenSimplifier(DBUtils dbs)

SenSimplifier

public SenSimplifier()

Method Detail

setDB

public void setDB(DBUtils dbs)

Set default database

Parameters:

dbs -

loadPatterns

public Map<String,Rules>[] loadPatterns(DBUtils db)

Load pattern from database

Parameters:

db - : DB source to load pattern (training DB)

loadRuleSet

public Map<String,RuleSet> loadRuleSet(DBUtils db)

loadSimpleDic

public void loadSimpleDic(Map<String,KeyData> map)

loadSimpleDic

public void loadSimpleDic()

setSimpleDic

public void setSimpleDic(Set<String> map)

loadDict

public final void loadDict(DBUtils dbs)

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

setModifier

public void setModifier()

These data learn form Modifier Learner; It would be nicer to automatically set these modifiers. However, due to their complexity, for now, semi-automatic approach is applied i.e. we need to check muanually for each trigger.

loadProtein

public List<TData> loadProtein(String pmid)

getPIndex

public int getPIndex(String pname)

getProteins

public List<String> getProteins(String s)

findProIndex

public int findProIndex(List<TData> plist,
               int pos)

loadTrigger

public List<TData> loadTrigger(String pmid)

loadEvent

public List<EData> loadEvent(String pmid)

loadPMIDs

public List<String> loadPMIDs()

Load abstract ID from database

loadSimplified

@Deprecated
public String loadSimplified(String pmid)

Deprecated.

loadSentence

public String loadSentence(String pmid)

trim

public String trim(String txt)

loadEquiv

public List<String[]> loadEquiv(String pmid)

testSpliter

public void testSpliter()

brLine

public String[] brLine(String txt,
              String br)

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.

Parameters:

txt -

br -

Returns:

abs2Sen

@Deprecated
public String[] abs2Sen(String txt,
                          String br)

Deprecated.

doSentenceSplitting

public SentenceSplitter.BioSemSentence[] doSentenceSplitting(String txt,
                                                    String br)

getSenIndex

public int getSenIndex(int start,
              int[] subpos)

getOffset

public int getOffset(int idx,
            int[] subpos)

doSimplifySentenceWise

public String[] doSimplifySentenceWise(SentenceSplitter.BioSemSentence[] originalSentences,
                              List<TData> proList)

doSimplify

@Deprecated
public void doSimplify()

Deprecated.

closeDB

public void closeDB()

main

public static void main(String[] args)