org.biojava.bio.program.sax.blastxml

Class BlastXMLParser

java.lang.Object

org.biojava.utils.stax.StAXContentHandlerBase

org.biojava.bio.program.sax.blastxml.BlastXMLParser

All Implemented Interfaces:

StAXContentHandler

public class BlastXMLParser
extends StAXContentHandlerBase

This class parses NCBI Blast XML output.

It has two modes:- i) single output document mode: this takes a document containing a single BlastOutput element and parses it. This is generated when a single query is searched against a sequence database.

ii) multiple query document mode: unfortunately, NCBI BLAST concatenates the results of multiple searches in one file. This leads to an ill-formed document that violates every XML format known to the human race and other nearby civilisations. This parser will take a bowdlerised version of this output that is wrapped in a blast_aggregate element.

The massaged form is generated by stripping the XML element and DOCTYPE elements and wrapping all the classes in a single blast_aggregate element. In Linux, this can be done with:-

 #!/bin/sh
 # Converts a Blast XML output to something vaguely well-formed
 # for parsing.
 # Use: blast_aggregate  

 # strips all <?xml> and <!DOCTYPE> tags
 # encapsulates the multiple <BlastOutput> elements into <blast_aggregator>

 sed '/>?xml/d' $1 | sed '/<!DOCTYPE/d' | sed '1i\
 <blast_aggregate>
 $a\
 </blast_aggregate>' > $2

Author:

David Huen

Field Summary

Fields

Modifier and Type	Field and Description
org.biojava.bio.program.sax.blastxml.StAXFeatureHandler	staxenv Nesting class that provides callback interfaces to nested class

Constructor Summary

Constructors

Constructor and Description
BlastXMLParser()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	addHandler(ElementRecognizer rec, org.biojava.bio.program.sax.blastxml.StAXHandlerFactory handler) Adds a feature to the Handler attribute of the StAXFeatureHandler object
void	endElement(String nsURI, String localName, String qName, StAXContentHandler handler) Handles basic exit processing.
void	endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) Element specific exit handler Subclass to do anything useful.
ContentHandler	getListener() get the SeqIOListener for this parser
void	setContentHandler(ContentHandler listener) sets the ContentHandler for this object
void	startElement(String nsURI, String localName, String qName, Attributes attrs, DelegationManager dm) we override the superclass startElement method so we can determine the the start tag type and use it to set up delegation for the superclass.

Methods inherited from class org.biojava.utils.stax.StAXContentHandlerBase

characters, endPrefixMapping, endTree, ignorableWhitespace, processingInstruction, setDocumentLocator, skippedEntity, startPrefixMapping, startTree

Methods inherited from class java.lang.Object

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

Field Detail

staxenv

public org.biojava.bio.program.sax.blastxml.StAXFeatureHandler staxenv

Nesting class that provides callback interfaces to nested class

Constructor Detail

BlastXMLParser

public BlastXMLParser()

Method Detail

setContentHandler

public void setContentHandler(ContentHandler listener)

sets the ContentHandler for this object

startElement

public void startElement(String nsURI,
                String localName,
                String qName,
                Attributes attrs,
                DelegationManager dm)
                  throws SAXException

we override the superclass startElement method so we can determine the the start tag type and use it to set up delegation for the superclass.

Specified by:

startElement in interface StAXContentHandler

Parameters:

nsURI - Description of the Parameter

localName - Description of the Parameter

qName - Description of the Parameter

attrs - Description of the Parameter

dm - Description of the Parameter

Throws:

SAXException - Description of the Exception

endElementHandler

public void endElementHandler(String nsURI,
                     String localName,
                     String qName,
                     StAXContentHandler handler)
                       throws SAXException

Element specific exit handler Subclass to do anything useful.

Parameters:

nsURI - Description of the Parameter

localName - Description of the Parameter

qName - Description of the Parameter

handler - Description of the Parameter

Throws:

SAXException - Description of the Exception

addHandler

protected void addHandler(ElementRecognizer rec,
              org.biojava.bio.program.sax.blastxml.StAXHandlerFactory handler)

Adds a feature to the Handler attribute of the StAXFeatureHandler object

Parameters:

rec - The feature to be added to the Handler attribute

handler - The feature to be added to the Handler attribute

getListener

public ContentHandler getListener()

get the SeqIOListener for this parser

endElement

public void endElement(String nsURI,
              String localName,
              String qName,
              StAXContentHandler handler)
                throws SAXException

Handles basic exit processing.

Specified by:

endElement in interface StAXContentHandler

Overrides:

endElement in class StAXContentHandlerBase

Parameters:

nsURI - Description of the Parameter

localName - Description of the Parameter

qName - Description of the Parameter

handler - Description of the Parameter

Throws:

SAXException - Description of the Exception