edu.iastate.jtm.jmed
Class MedlineParser

java.lang.Object
  edu.iastate.jtm.jmed.StreamXMLParser
      edu.iastate.jtm.jmed.MedlineParser

public class MedlineParser
extends StreamXMLParser

Extract citation info from Medline/PubMed XML files.

Author:

Jing Ding

Field Summary

Fields inherited from class edu.iastate.jtm.jmed.StreamXMLParser

unit

Constructor Summary

MedlineParser()
Creates a new blank instance of MedlineParser in default MEDLINE mode.

MedlineParser(boolean pubmode)

MedlineParser(org.dom4j.io.SAXReader xp)
Creates a new blank instance of MedlineParser in default MEDLINE mode.

MedlineParser(org.dom4j.io.SAXReader xp, boolean pubmode)

Method Summary

void	extractPlainText(java.io.File infile, java.io.File outDir) Extract plain text abstracts from an XML file into a directory.
void	extractPlainText(java.io.File infile, java.lang.String outDir, int size) Extract plain text abstracts from an XML file into multiple directories.
void	extractPlainText(java.io.InputStream instream, java.io.File outDir) Extract plain text abstracts from an input stream into a directory.
void	extractPlainText(java.io.InputStream instream, java.lang.String outDir, int size) Extract plain text abstracts from an input stream into multiple directories.
void	extractPmids(java.io.File output) Extract all PMIDs to a single file.
void	extractPmids(java.lang.String prefix, int size) Extract all PMIDs to multiple files.
boolean	isPubMode()
static void	main(java.lang.String[] args) For test.
protected boolean	open(boolean parseHeader)
void	setAutoAdjustMode(boolean auto)
void	setPubMode(boolean mode)
void	splitXml(java.io.File infile, java.lang.String prefix, int size, boolean compress) Split a large XML file into small ones.
void	splitXml(java.io.InputStream instream, java.lang.String prefix, int size, boolean compress) Split a large XML stream into small files.

Methods inherited from class edu.iastate.jtm.jmed.StreamXMLParser

close, copyUnit, getHeader, getRootName, getSingleField, getUnit, getUnitCount, nextUnit, nextUnit, open, open, open, open, open, open, setIgnoreXmlError, setOutputPlain, setRefillZone, setRootMatcher, setSaxParser, setUnitMatcher, setVerbose

Methods inherited from class java.lang.Object

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

Constructor Detail

MedlineParser

public MedlineParser(boolean pubmode)
              throws org.xml.sax.SAXException

Throws:

org.xml.sax.SAXException

MedlineParser

public MedlineParser()
              throws org.xml.sax.SAXException

Creates a new blank instance of MedlineParser in default MEDLINE mode.

Throws:

org.xml.sax.SAXException

MedlineParser

public MedlineParser(org.dom4j.io.SAXReader xp,
                     boolean pubmode)
              throws org.xml.sax.SAXException

Throws:

org.xml.sax.SAXException

MedlineParser

public MedlineParser(org.dom4j.io.SAXReader xp)
              throws org.xml.sax.SAXException

Creates a new blank instance of MedlineParser in default MEDLINE mode.

Throws:

org.xml.sax.SAXException

Method Detail

open

protected boolean open(boolean parseHeader)
                throws java.io.IOException

Overrides:

open in class StreamXMLParser

Throws:

java.io.IOException

setAutoAdjustMode

public void setAutoAdjustMode(boolean auto)

setPubMode

public void setPubMode(boolean mode)

isPubMode

public boolean isPubMode()

extractPmids

public void extractPmids(java.io.File output)
                  throws org.dom4j.DocumentException,
                         java.io.IOException

Extract all PMIDs to a single file.

Parameters:

output - the output file.

Throws:

org.dom4j.DocumentException

java.io.IOException

extractPmids

public void extractPmids(java.lang.String prefix,
                         int size)
                  throws org.dom4j.DocumentException,
                         java.io.IOException

Extract all PMIDs to multiple files.

Parameters:

prefix - prefix of output filenames.

size - number of PMIDs in each file.

Throws:

org.dom4j.DocumentException

java.io.IOException

extractPlainText

public void extractPlainText(java.io.File infile,
                             java.io.File outDir)
                      throws org.dom4j.DocumentException,
                             java.io.IOException

Extract plain text abstracts from an XML file into a directory.

Parameters:

infile - input XML file

outDir - output directory

Throws:

org.dom4j.DocumentException

java.io.IOException

extractPlainText

public void extractPlainText(java.io.File infile,
                             java.lang.String outDir,
                             int size)
                      throws org.dom4j.DocumentException,
                             java.io.IOException

Extract plain text abstracts from an XML file into multiple directories.

Parameters:

infile - input XML file

outDir - prefix of output directories

size - number of abstracts per directory

Throws:

org.dom4j.DocumentException

java.io.IOException

extractPlainText

public void extractPlainText(java.io.InputStream instream,
                             java.io.File outDir)
                      throws org.dom4j.DocumentException,
                             java.io.IOException

Extract plain text abstracts from an input stream into a directory.

Parameters:

instream - input stream

outDir - output directory

Throws:

org.dom4j.DocumentException

java.io.IOException

extractPlainText

public void extractPlainText(java.io.InputStream instream,
                             java.lang.String outDir,
                             int size)
                      throws org.dom4j.DocumentException,
                             java.io.IOException

Extract plain text abstracts from an input stream into multiple directories.

Parameters:

instream - input stream

outDir - prefix of output directories

size - number of abstracts per directory

Throws:

org.dom4j.DocumentException

java.io.IOException

splitXml

public void splitXml(java.io.File infile,
                     java.lang.String prefix,
                     int size,
                     boolean compress)
              throws org.dom4j.DocumentException,
                     java.io.IOException

Split a large XML file into small ones.

Parameters:

infile - input XML file

prefix - prefix of output XML files

size - number of abstracts in each output file

Throws:

org.dom4j.DocumentException

java.io.IOException

splitXml

public void splitXml(java.io.InputStream instream,
                     java.lang.String prefix,
                     int size,
                     boolean compress)
              throws org.dom4j.DocumentException,
                     java.io.IOException

Split a large XML stream into small files.

Parameters:

instream - input stream

prefix - prefix of output XML files

size - number of abstracts in each output file

Throws:

org.dom4j.DocumentException

java.io.IOException

main

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

For test.

Parameters:

args - the command line arguments