uk.ac.ebi.ep.mm.app
Class Uniprot2DiseaseParser

java.lang.Object
  uk.ac.ebi.ep.mm.app.Uniprot2DiseaseParser

All Implemented Interfaces:

MmParser

public class Uniprot2DiseaseParser
extends Object
implements MmParser

Class to parse the HTML file containing a table of equivalences from UniProt accessions to OMIM IDs and MeSH terms.

Author:

rafa

Constructor Summary

Uniprot2DiseaseParser()

Method Summary

static void	main(String[] args) Parses the HTML file and stores in the mega-map the xrefs from UniProt accessions to OMIM and MeSH terms, but only if the scores is equal or greater than minScore.
void	parse(String htmlFile) Parses a XML file and extracts interesting data into a mega-map.
void	setWriter(MegaMapper mm) 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

Uniprot2DiseaseParser

public Uniprot2DiseaseParser()

Method Detail

main

public static void main(String[] args)
                 throws Exception

Parses the HTML file and stores in the mega-map the xrefs from UniProt accessions to OMIM and MeSH terms, but only if the scores is equal or greater than minScore.

Parameters:

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

Throws:

Exception - in case of error while parsing.

parse

public void parse(String htmlFile)
           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:

htmlFile - an XML file.

Throws:

Exception

setWriter

public void setWriter(MegaMapper mm)

Description copied from interface: MmParser

Sets a writer to make the mega-map persistent.

Specified by:

setWriter in interface MmParser