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

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

All Implemented Interfaces:

ContentHandler, DTDHandler, EntityResolver, ErrorHandler, MmParser

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

UniProt XML parser which takes into account only primary accessions, entry names (IDs), organisms, EC numbers and PDB codes, and indexes/stores them in a mega-map.
Only enzymes - i.e. entries with an EC number assigned - are considered.

Author:

rafa

Field Summary

protected List<String>	accessions
protected StringBuilder	currentChars The text value of the current element being parsed.
protected List<String>	ecs
protected List<String>	entryNames
protected boolean	isAccession
protected boolean	isDbRef
protected boolean	isEntry
protected boolean	isEntryName
protected boolean	isOrgComName
protected boolean	isOrgSciName
protected boolean	isProperty
protected boolean	isProtRecName
protected String	orgComName
protected String	orgSciName
protected List<String>	pdbCodes
protected String	protRecName

Constructor Summary

UniprotSaxParser()

Method Summary

void	characters(char[] ch, int start, int length)
void	endDocument()
void	endElement(String uri, String localName, String qName) Stores interesting data into the index.
protected String	getCurrentXpath()
static void	main(String... args) Parses a UniProt XML file and indexes/stores the UniProt accessions, IDs and organisms into a mega-map.
void	parse(String uniprotXml) Parses a UniProt XML file and indexes/stores the UniProt accessions, IDs and organisms into a lucene index. This method is not thread safe.
void	setWriter(MegaMapper mmWriter) Sets a writer to make the mega-map persistent.
void	startDocument()
void	startElement(String uri, String localName, String qName, Attributes attributes)

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

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

Methods inherited from class java.lang.Object

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

Field Detail

currentChars

protected StringBuilder currentChars

The text value of the current element being parsed.

isEntry

protected boolean isEntry

isAccession

protected boolean isAccession

isEntryName

protected boolean isEntryName

isOrgSciName

protected boolean isOrgSciName

isOrgComName

protected boolean isOrgComName

isDbRef

protected boolean isDbRef

isProperty

protected boolean isProperty

isProtRecName

protected boolean isProtRecName

accessions

protected List<String> accessions

entryNames

protected List<String> entryNames

orgSciName

protected String orgSciName

orgComName

protected String orgComName

ecs

protected List<String> ecs

pdbCodes

protected List<String> pdbCodes

protRecName

protected String protRecName

Constructor Detail

UniprotSaxParser

public UniprotSaxParser()

Method Detail

main

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

Parses a UniProt XML file and indexes/stores the UniProt accessions, IDs and organisms into a mega-map.

Parameters:

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

Throws:

Exception - in case of error while parsing.

setWriter

public void setWriter(MegaMapper mmWriter)

Description copied from interface: MmParser

Sets a writer to make the mega-map persistent.

Specified by:

setWriter in interface MmParser

parse

public void parse(String uniprotXml)
           throws Exception

Parses a UniProt XML file and indexes/stores the UniProt accessions, IDs and organisms into a lucene index.
This method is not thread safe.

Specified by:

parse in interface MmParser

Parameters:

uniprotXml - the XML file to parse

Throws:

FileNotFoundException - if the UniProt XML file is not found or not readable.

SAXException - if no default XMLReader can be found or instantiated, or exception during parsing.

IOException - if the lucene index cannot be opened/created, or from the parser.

Exception

startDocument

public void startDocument()
                   throws SAXException

Specified by:

startDocument in interface ContentHandler

Overrides:

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

Throws:

SAXException

endDocument

public void endDocument()
                 throws SAXException

Specified by:

endDocument in interface ContentHandler

Overrides:

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

Throws:

SAXException

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

Stores interesting data into the index.

Specified by:

endElement in interface ContentHandler

Overrides:

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

Throws:

SAXException

getCurrentXpath

protected String getCurrentXpath()