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

java.lang.Object
  uk.ac.ebi.ep.mm.app.EbeyeParser

All Implemented Interfaces:

MmParser

Deprecated. use EbeyeSaxParser instead, this one requires lots of memory for big files.

public class EbeyeParser
extends Object
implements MmParser

Indexer for EB-Eye XML files, which parses them and indexes/stores database identifiers corresponding to UniProt accessions already existing in the index.
Currently, ChEBI and ChEMBL (target) are supported. PDBeChem is not, as it does not seem to provide xrefs to UniProt in its EB-Eye XML file.

Author:

rafa

Constructor Summary

EbeyeParser()
Deprecated.

Method Summary

static void	main(String... args) Deprecated. Parses a EB-Eye XML file and indexes/stores the database identifiers corresponding to UniProt accessions.
void	parse(String xmlFile) Deprecated. Parses a XML file and extracts interesting data into a mega-map.
void	setWriter(MegaMapper writer) Deprecated. Sets a writer to make the mega-map persistent.

Methods inherited from class java.lang.Object

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

Constructor Detail

EbeyeParser

public EbeyeParser()

Deprecated.

Method Detail

main

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

Deprecated.

Parses a EB-Eye XML file and indexes/stores the database identifiers corresponding to UniProt accessions.

Parameters:

args -

• -xmlFile: the XML file to parse
• -indexDir: the directory for the lucene index. If it does not exist, a new one is created.

Throws:

Exception

parse

public void parse(String xmlFile)
           throws Exception

Deprecated.

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

setWriter

public void setWriter(MegaMapper writer)

Deprecated.

Description copied from interface: MmParser

Sets a writer to make the mega-map persistent.

Specified by:

setWriter in interface MmParser