uk.ac.ebi.ep.mm.app
Class EbeyeSaxParser

java.lang.Object
  org.xml.sax.helpers.DefaultHandler
      uk.ac.ebi.ep.mm.app.EbeyeSaxParser

All Implemented Interfaces:

ContentHandler, DTDHandler, EntityResolver, ErrorHandler, MmParser

public class EbeyeSaxParser
extends org.xml.sax.helpers.DefaultHandler
implements MmParser

Parser for EB-Eye XML files to populate a mega-map. Currently, this implementation has been used with ChEBI and ChEMBL-target files (ChEMBL target is the only one for this database which links compounds with protein IDs).

Author:

rafa

Constructor Summary

EbeyeSaxParser()

Method Summary

void	characters(char[] ch, int start, int length)
void	endElement(String uri, String localName, String qName)
protected String	getCurrentXpath()
static void	main(String... args) Parses a EB-Eye XML file and indexes/stores the entry IDs, accessions and xrefs into a mega-map.
void	parse(String xmlFile) Parses a XML file and extracts interesting data into a mega-map.
void	setWriter(MegaMapper writer) Sets a writer to make the mega-map persistent.
void	startElement(String uri, String localName, String qName, Attributes attributes)

Methods inherited from class org.xml.sax.helpers.DefaultHandler

endDocument, endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startDocument, startPrefixMapping, unparsedEntityDecl, warning

Methods inherited from class java.lang.Object

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

Constructor Detail

EbeyeSaxParser

public EbeyeSaxParser()

Method Detail

main

public static void main(String... args)
                 throws Exception

Parses a EB-Eye XML file and indexes/stores the entry IDs, accessions and xrefs into a mega-map.

Parameters:

args - see CliOptionsParser.getCommandLine(String...)

Throws:

Exception - in case of error while parsing.

parse

public void parse(String xmlFile)
           throws Exception

Description copied from interface: MmParser

Parses a XML file and extracts interesting data into a mega-map.

Specified by:

parse in interface MmParser

Parameters:

xmlFile - an XML file.

Throws:

Exception

startElement

public void startElement(String uri,
                         String localName,
                         String qName,
                         Attributes attributes)
                  throws SAXException

Specified by:

startElement in interface ContentHandler

Overrides:

startElement in class org.xml.sax.helpers.DefaultHandler

Throws:

SAXException

characters

public void characters(char[] ch,
                       int start,
                       int length)
                throws SAXException

Specified by:

characters in interface ContentHandler

Overrides:

characters in class org.xml.sax.helpers.DefaultHandler

Throws:

SAXException

endElement

public void endElement(String uri,
                       String localName,
                       String qName)
                throws SAXException

Specified by:

endElement in interface ContentHandler

Overrides:

endElement in class org.xml.sax.helpers.DefaultHandler

Throws:

SAXException

setWriter

public void setWriter(MegaMapper writer)

Description copied from interface: MmParser

Sets a writer to make the mega-map persistent.

Specified by:

setWriter in interface MmParser

getCurrentXpath

protected String getCurrentXpath()