fcmodeler.pathbinder
Class MedCrawler

java.lang.Object
  edu.iastate.jtm.gui.DefaultMonitorable
      edu.iastate.jtm.EntityFinder
          fcmodeler.pathbinder.MedCrawler

All Implemented Interfaces:

Monitorable

public class MedCrawler
extends EntityFinder

Search Medline XML files against a dictionary.

Author:

Jing Ding fcmodeler.pathbinder MetNet

Nested Class Summary

Nested classes/interfaces inherited from class edu.iastate.jtm.EntityFinder

EntityFinder.Hit

Field Summary

Fields inherited from class edu.iastate.jtm.EntityFinder

globalDic, hits, localDic, peekDic, peekRegex, pluralDetector

Fields inherited from class edu.iastate.jtm.gui.DefaultMonitorable

message, monitorable, progress

Constructor Summary

MedCrawler()

MedCrawler(MySqlConnector db)
Creates a new instance of MedCrawler

Method Summary

void	batchScan(java.io.File[] medfiles)
void	batchScan(java.lang.String[] medfiles)
void	closeDatabaseConnection()
void	emptyTables()
int	getTotalAbsCount()
void	loadJournalFilter(java.io.File jrnFile)
static void	main(java.lang.String[] args)
void	scanCitation(java.lang.String title, java.lang.String abs)
void	scanFile(java.io.File medfile)
void	setRescanTitle(boolean r)
void	setSplitWithinParen(boolean s)
void	updateDuplicationChecker(int minPmid, int maxPmid)

Methods inherited from class edu.iastate.jtm.EntityFinder

findEntity, getEntitiesFound, getEntityCount, getGlobalDictionary, getHit, getHitsCount, getPluralDetector, getTaggedText, getTotalHitsCount, getTotalSenCount, loadGlobalDictionary, loadPeekDefinition, loadPluralDictionary, loadPluralDictionary, outputHits, setHitsThreshold, setMaxSentenceLength, setPeekNext, setRejectHits, setRejectLong, setVerbose

Methods inherited from class edu.iastate.jtm.gui.DefaultMonitorable

getMessage, getProgress, isDeterministic, isFinished, isMonitorable, isRunning, setMessage, setMonitorable, setProgress

Methods inherited from class java.lang.Object

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

Constructor Detail

MedCrawler

public MedCrawler(MySqlConnector db)
           throws org.xml.sax.SAXException

Creates a new instance of MedCrawler

Throws:

org.xml.sax.SAXException

java.sql.SQLException

MedCrawler

public MedCrawler()
           throws java.lang.Exception

Throws:

java.lang.Exception

Method Detail

updateDuplicationChecker

public void updateDuplicationChecker(int minPmid,
                                     int maxPmid)
                              throws java.sql.SQLException

Throws:

java.sql.SQLException

setRescanTitle

public void setRescanTitle(boolean r)

setSplitWithinParen

public void setSplitWithinParen(boolean s)

getTotalAbsCount

public int getTotalAbsCount()

closeDatabaseConnection

public void closeDatabaseConnection()
                             throws java.sql.SQLException

Throws:

java.sql.SQLException

scanCitation

public void scanCitation(java.lang.String title,
                         java.lang.String abs)

loadJournalFilter

public void loadJournalFilter(java.io.File jrnFile)
                       throws java.io.IOException

Throws:

java.io.IOException

scanFile

public void scanFile(java.io.File medfile)
              throws org.dom4j.DocumentException,
                     java.io.IOException,
                     java.sql.SQLException

Throws:

org.dom4j.DocumentException

java.io.IOException

java.sql.SQLException

batchScan

public void batchScan(java.lang.String[] medfiles)
               throws org.dom4j.DocumentException,
                      java.io.IOException,
                      java.sql.SQLException

Throws:

org.dom4j.DocumentException

java.io.IOException

java.sql.SQLException

batchScan

public void batchScan(java.io.File[] medfiles)
               throws org.dom4j.DocumentException,
                      java.io.IOException,
                      java.sql.SQLException

Throws:

org.dom4j.DocumentException

java.io.IOException

java.sql.SQLException

emptyTables

public void emptyTables()
                 throws java.sql.SQLException

Throws:

java.sql.SQLException

main

public static void main(java.lang.String[] args)

Parameters:

args - the command line arguments