org.biojava.bio.program.sax

Class BlastLikeSAXParser

java.lang.Object

org.biojava.bio.program.sax.BlastLikeSAXParser

All Implemented Interfaces:

XMLReader

public class BlastLikeSAXParser
extends Object

A facade class allowing for direct SAX2-like parsing of the native output from Blast-like bioinformatics software. Because the parser is SAX2 compliant, application writers can simply pass XML ContentHandlers to the parser in order to receive notifcation of SAX2 events.

The SAX2 events produced are as if the input to the parser was an XML file validating against the biojava BlastLikeDataSetCollection DTD. There is no requirement for an intermediate conversion of native output to XML format. An application of the parsing framework, however, is to create XML format files from native output files.

The biojava Blast-like parsing framework is designed to uses minimal memory,so that in principle, extremely large native outputs can be parsed and XML ContentHandlers can listen only for small amounts of information.

The framework currently supports parsing of native output from the following bioinformatics programs. Please note that if you are using different versions of NCBI or WU Blast to those listed below, it is worth considering trying setting the parsing mode to Lazy, which means parsing will be attempted if the program is recognised, regardless of version.

• NCBI Blast version 2.0.11
• NCBI Blast version 2.2.2
• NCBI Blast version 2.2.3
• WU-Blast version 2.0a19mp-washu
• HMMER 2.1.1 hmmsearch

Planned addition support

• Support for HMMER hmmpfam almost there but not fully tested

Notes to SAX driver writers

The framework that this parser is built on is designed to be extensible with support for both different pieces of software (i.e. not just software that produces Blast-like output), and multiple versions of programs.

This class inherits from the org.biojava.bio.program.sax.AbstractNativeAppSAXParser abstract base class. The abstract base class is a good place to start looking if you want to write new native application SAX2 parsers. This and releated classes have only package-level visibility. Typically, application writers are expected to provide a facade class in this package (similar to the current class) to allow users access to functionality.

NB Support for InputSource is not complete due to the fact that URLs are not resolved and cannot, therefore, be used as an InputSource. System pathnames, ByteStreams and CharacterStreams, however, are all supported.

Copyright © 2000 Cambridge Antibody Technology.

Primary author -

• Simon Brocklehurst (CAT)

Other authors -

• Tim Dilks (CAT)
• Colin Hardman (CAT)
• Stuart Johnston (CAT)
• Mathieu Wiepert (Mayo Foundation)
• Travis Banks

Version:

1.0

Author:

Cambridge Antibody Technology (CAT), Travis Banks

See Also:

BlastLikeToXMLConverter

Field Summary

Fields

Modifier and Type	Field and Description
protected int	iState
protected String	oFullNamespacePrefix
protected ContentHandler	oHandler
protected String	oNamespacePrefix
protected boolean	tNamespacePrefixes
protected boolean	tNamespaces

Constructor Summary

Constructors

Constructor and Description
BlastLikeSAXParser() Initialises SAXParser, and sets default namespace prefix to "biojava".

Method Summary

Methods

Modifier and Type	Method and Description
void	addPrefixMapping(String poPrefix, String poURI) Adds a namespace prefix to URI mapping as (key,value) pairs.
protected void	changeState(int piState) Centralise chaining of iState field to help with debugging.
protected void	characters(char[] ch, int start, int length) Utility method to centralize the sending of a SAX characters message a document handler.
protected void	endElement(org.biojava.bio.program.sax.QName poQName) Utility method to centralize the sending of a SAX endElement message a document handler.
ContentHandler	getContentHandler() Return the content handler.
protected BufferedReader	getContentStream(InputSource poSource) Create a stream from an an InputSource, picking the correct stream according to order of precedance.
DTDHandler	getDTDHandler() Do-nothing implementation of interface method
EntityResolver	getEntityResolver() Do-nothing implementation of interface method
ErrorHandler	getErrorHandler() Do-nothing implementation of interface method
boolean	getFeature(String poName) Do-nothing implementation of interface method
String	getNamespacePrefix() Describe getNamespacePrefix method here.
boolean	getNamespacePrefixes() Support SAX2 configuration of namespace support of parser.
boolean	getNamespaces() Support SAX2 configuration of namespace support of parser.
Object	getProperty(String name) Do-nothing implementation of interface method
String	getURIFromPrefix(String poPrefix) Gets the URI for a namespace prefix, given that prefix, or null if the prefix is not recognised.
void	parse(InputSource poSource) parse initiates the parsing operation.
void	parse(String poSystemId) Full implementation of interface method.
String	prefix(String poElementName) Given an unprefixed element name, returns a new element name with a namespace prefix
void	setContentHandler(ContentHandler poHandler) Allow an application to register a content event handler.
void	setDTDHandler(DTDHandler handler) Do-nothing implementation of interface method
void	setEntityResolver(EntityResolver resolver) Do-nothing implementation of interface method
void	setErrorHandler(ErrorHandler handler) Do-nothing implementation of interface method
void	setFeature(String poName, boolean value) Handles support for ReasoningDomain and Namespace-prefixes
void	setModeLazy() Setting the mode to lazy means that, if the program is recognised, e.g.
void	setModeStrict() This is the default, parsing will be attempted only if both the program e.g.
void	setNamespacePrefix(String poPrefix)
void	setProperty(String name, Object value) Do-nothing implementation of interface method
protected void	startElement(org.biojava.bio.program.sax.QName poQName, Attributes atts) Utility method to centralize sending of a SAX startElement message to document handler

Methods inherited from class java.lang.Object

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

Field Detail

oHandler

protected ContentHandler oHandler

tNamespaces

protected boolean tNamespaces

tNamespacePrefixes

protected boolean tNamespacePrefixes

oNamespacePrefix

protected String oNamespacePrefix

oFullNamespacePrefix

protected String oFullNamespacePrefix

iState

protected int iState

Constructor Detail

BlastLikeSAXParser

public BlastLikeSAXParser()

Initialises SAXParser, and sets default namespace prefix to "biojava".

Method Detail

parse

public void parse(InputSource poSource)
           throws IOException,
                  SAXException

parse initiates the parsing operation.

Specified by:

parse in interface XMLReader

Parameters:

poSource - an InputSource.

Throws:

IOException - if an error occurs.

SAXException - if an error occurs.

setModeStrict

public void setModeStrict()

This is the default, parsing will be attempted only if both the program e.g. NCBI BlastP, and a particular version are recognised as bsing supported.

setModeLazy

public void setModeLazy()

Setting the mode to lazy means that, if the program is recognised, e.g. WU-TBlastX, then parsing will be attempted even if the particular version is not recognised. Using this option is more likely to result in erroneous parsing than if the strict mode is used.

setContentHandler

public void setContentHandler(ContentHandler poHandler)

Allow an application to register a content event handler. If the application does not register a content handler, all content events reported by the SAX parser will be silently ignored.

Applications may register a new or different handler in the middle of a parse, and the SAX parser must begin using the new handler immediately.

Specified by:

setContentHandler in interface XMLReader

Parameters:

poHandler - a ContentHandler The XML content handler

Throws:

NullPointerException - If the handler argument is null

getContentHandler

public ContentHandler getContentHandler()

Return the content handler.

Specified by:

getContentHandler in interface XMLReader

Returns:

a ContentHandler The current content handler, or null if none has been registered.

parse

public void parse(String poSystemId)
           throws IOException,
                  SAXException

Full implementation of interface method.

Specified by:

parse in interface XMLReader

Throws:

IOException

SAXException

getFeature

public boolean getFeature(String poName)
                   throws SAXNotRecognizedException,
                          SAXNotSupportedException

Do-nothing implementation of interface method

Specified by:

getFeature in interface XMLReader

Throws:

SAXNotRecognizedException

SAXNotSupportedException

setFeature

public void setFeature(String poName,
              boolean value)
                throws SAXNotRecognizedException,
                       SAXNotSupportedException

Handles support for ReasoningDomain and Namespace-prefixes

Specified by:

setFeature in interface XMLReader

Throws:

SAXNotRecognizedException

SAXNotSupportedException

getProperty

public Object getProperty(String name)
                   throws SAXNotRecognizedException,
                          SAXNotSupportedException

Do-nothing implementation of interface method

Specified by:

getProperty in interface XMLReader

Throws:

SAXNotRecognizedException

SAXNotSupportedException

setProperty

public void setProperty(String name,
               Object value)
                 throws SAXNotRecognizedException,
                        SAXNotSupportedException

Do-nothing implementation of interface method

Specified by:

setProperty in interface XMLReader

Throws:

SAXNotRecognizedException

SAXNotSupportedException

setEntityResolver

public void setEntityResolver(EntityResolver resolver)

Do-nothing implementation of interface method

Specified by:

setEntityResolver in interface XMLReader

getEntityResolver

public EntityResolver getEntityResolver()

Do-nothing implementation of interface method

Specified by:

getEntityResolver in interface XMLReader

setDTDHandler

public void setDTDHandler(DTDHandler handler)

Do-nothing implementation of interface method

Specified by:

setDTDHandler in interface XMLReader

getDTDHandler

public DTDHandler getDTDHandler()

Do-nothing implementation of interface method

Specified by:

getDTDHandler in interface XMLReader

setErrorHandler

public void setErrorHandler(ErrorHandler handler)

Do-nothing implementation of interface method

Specified by:

setErrorHandler in interface XMLReader

getErrorHandler

public ErrorHandler getErrorHandler()

Do-nothing implementation of interface method

Specified by:

getErrorHandler in interface XMLReader

startElement

protected void startElement(org.biojava.bio.program.sax.QName poQName,
                Attributes atts)
                     throws SAXException

Utility method to centralize sending of a SAX startElement message to document handler

Parameters:

poQName - a QName value

atts - an Attributes value

Throws:

SAXException - if an error occurs

endElement

protected void endElement(org.biojava.bio.program.sax.QName poQName)
                   throws SAXException

Utility method to centralize the sending of a SAX endElement message a document handler.

Parameters:

poQName - -

Throws:

SAXException - thrown if

thrown - if

characters

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

Utility method to centralize the sending of a SAX characters message a document handler.

Parameters:

ch - -

start - -

length - -

Throws:

SAXException - thrown if

thrown - if

getNamespaces

public boolean getNamespaces()

Support SAX2 configuration of namespace support of parser.

getNamespacePrefixes

public boolean getNamespacePrefixes()

Support SAX2 configuration of namespace support of parser.

addPrefixMapping

public void addPrefixMapping(String poPrefix,
                    String poURI)

Adds a namespace prefix to URI mapping as (key,value) pairs. This mapping can be looked up later to get URIs on request using the getURIFromPrefix method.

Parameters:

poPrefix - a String representation of the namespace prefix

poURI - a String representation of the URI for the namespace prefix.

getURIFromPrefix

public String getURIFromPrefix(String poPrefix)

Gets the URI for a namespace prefix, given that prefix, or null if the prefix is not recognised.

Parameters:

poPrefix - a String The namespace prefix.

setNamespacePrefix

public void setNamespacePrefix(String poPrefix)

Parameters:

poPrefix - a String value

getNamespacePrefix

public String getNamespacePrefix()

Describe getNamespacePrefix method here.

Returns:

a String value

prefix

public String prefix(String poElementName)

Given an unprefixed element name, returns a new element name with a namespace prefix

Returns:

a String value

getContentStream

protected BufferedReader getContentStream(InputSource poSource)

Create a stream from an an InputSource, picking the correct stream according to order of precedance.

Parameters:

poSource - an InputSource value

Returns:

a BufferedReader value

changeState

protected void changeState(int piState)

Centralise chaining of iState field to help with debugging. E.g. printing out value etc. All changes to iState should be made through this method.

Parameters:

piState - an int value