org.biojava.bio.program.sax
Class FastaSearchSAXParser

java.lang.Object
  |
  +--org.biojava.bio.program.sax.AbstractNativeAppSAXParser
        |
        +--org.biojava.bio.program.sax.FastaSearchSAXParser

All Implemented Interfaces:

org.biojava.bio.program.sax.NamespaceConfigurationIF, SearchContentHandler, org.xml.sax.XMLReader

public class FastaSearchSAXParser

extends org.biojava.bio.program.sax.AbstractNativeAppSAXParser

implements SearchContentHandler

FastaSearchSAXParser is a SAX2 compliant parser for '-m 10' format output from the the Fasta search program (see the Fasta documentation for details of this format).

Versions of Fasta supported are as follows. Note that the compile time option -DM10_CONS should be used to allow correct reporting of the number of matches in HSPSummary elements

• 33t07
• 33t08 (current tests are against output from this version)

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.

Since:

1.2

Author:

Keith James

Field Summary

protected int	iState
protected java.lang.String	oFullNamespacePrefix
protected org.xml.sax.ContentHandler	oHandler
protected java.lang.String	oNamespacePrefix
protected boolean	tNamespacePrefixes
protected boolean	tNamespaces

Constructor Summary

FastaSearchSAXParser()
Creates a new FastaSearchSAXParser instance.

Method Summary

void	addHitProperty(java.lang.Object key, java.lang.Object value) The addHitProperty method adds a key/value pair containing some property of a particular hit.
void	addPrefixMapping(java.lang.String poPrefix, java.lang.String poURI) Adds a namespace prefix to URI mapping as (key,value) pairs.
void	addSearchProperty(java.lang.Object key, java.lang.Object value) The addSearchProperty method adds a key/value pair containing some property of the overall search result.
void	addSubHitProperty(java.lang.Object key, java.lang.Object value) The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.
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.
void	endHeader() The endHeader method indicates the end of a formatted header.
void	endHit() The endHit method indicates the end of a formatted hit.
void	endSearch() The endSearch method indicates the end of useful search information.
void	endSubHit() The endSubHit method indicates the end of a formatted subhit.
org.xml.sax.ContentHandler	getContentHandler() Return the content handler.
protected java.io.BufferedReader	getContentStream(org.xml.sax.InputSource poSource) Create a stream from an an InputSource, picking the correct stream according to order of precedance.
org.xml.sax.DTDHandler	getDTDHandler() Do-nothing implementation of interface method
org.xml.sax.EntityResolver	getEntityResolver() Do-nothing implementation of interface method
org.xml.sax.ErrorHandler	getErrorHandler() Do-nothing implementation of interface method
boolean	getFeature(java.lang.String poName) Do-nothing implementation of interface method
boolean	getMoreSearches() getMoreSearches returns the state of the SearchContentHandler with respect to further searches from its data source.
java.lang.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.
java.lang.Object	getProperty(java.lang.String name) Do-nothing implementation of interface method
java.lang.String	getURIFromPrefix(java.lang.String poPrefix) Gets the URI for a namespace prefix, given that prefix, or null if the prefix is not recognised.
void	parse(org.xml.sax.InputSource source) Do-nothing implementation of interface method
void	parse(java.lang.String poSystemId) Full implementation of interface method.
java.lang.String	prefix(java.lang.String poElementName) Given an unprefixed element name, returns a new element name with a namespace prefix
void	setContentHandler(org.xml.sax.ContentHandler poHandler) Allow an application to register a content event handler.
void	setDatabaseID(java.lang.String databaseID) setDatabaseID identifies the database searched by a name, ID or URN.
void	setDTDHandler(org.xml.sax.DTDHandler handler) Do-nothing implementation of interface method
void	setEntityResolver(org.xml.sax.EntityResolver resolver) Do-nothing implementation of interface method
void	setErrorHandler(org.xml.sax.ErrorHandler handler) Do-nothing implementation of interface method
void	setFeature(java.lang.String poName, boolean value) Handles support for Namespaces and Namespace-prefixes
void	setMoreSearches(boolean value) setMoreSearches sets the state of the SearchContentHandler's expectation of receiving more results.
void	setNamespacePrefix(java.lang.String poPrefix)
void	setProperty(java.lang.String name, java.lang.Object value) Do-nothing implementation of interface method
void	setQueryID(java.lang.String queryID) setQueryID identifies the query sequence by a name, ID or URN.
void	setQuerySeq(java.lang.String identifier) Deprecated. use setQueryID instead.
void	setSubjectDB(java.lang.String identifier) Deprecated. use setDatabaseID instead.
protected void	startElement(org.biojava.bio.program.sax.QName poQName, org.xml.sax.Attributes atts) Utility method to centralize sending of a SAX startElement message to document handler
void	startHeader() The startHeader method indicates the start of a formatted header.
void	startHit() The startHit method indicates the start of a formatted hit.
void	startSearch() The startSearch method indicates the start of useful search information.
void	startSubHit() The startSubHit method indicates the start of a formatted subhit.

Methods inherited from class java.lang.Object

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

Field Detail

oHandler

protected org.xml.sax.ContentHandler oHandler

tNamespaces

protected boolean tNamespaces

tNamespacePrefixes

protected boolean tNamespacePrefixes

oNamespacePrefix

protected java.lang.String oNamespacePrefix

oFullNamespacePrefix

protected java.lang.String oFullNamespacePrefix

iState

protected int iState

Constructor Detail

FastaSearchSAXParser

public FastaSearchSAXParser()

Creates a new FastaSearchSAXParser instance.

Method Detail

parse

public void parse(org.xml.sax.InputSource source)
           throws java.io.IOException,
                  org.xml.sax.SAXException

Description copied from class: org.biojava.bio.program.sax.AbstractNativeAppSAXParser

Do-nothing implementation of interface method

Specified by:

parse in interface org.xml.sax.XMLReader

Overrides:

parse in class org.biojava.bio.program.sax.AbstractNativeAppSAXParser

java.io.IOException

org.xml.sax.SAXException

getMoreSearches

public boolean getMoreSearches()

Description copied from interface: SearchContentHandler

getMoreSearches returns the state of the SearchContentHandler with respect to further searches from its data source. Used for handling streams of search results.

Specified by:

getMoreSearches in interface SearchContentHandler

Returns:

a boolean value.

setMoreSearches

public void setMoreSearches(boolean value)

Description copied from interface: SearchContentHandler

setMoreSearches sets the state of the SearchContentHandler's expectation of receiving more results. Used for handling streams of search results.

Specified by:

setMoreSearches in interface SearchContentHandler

Parameters:

value - a boolean value.

setQuerySeq

public void setQuerySeq(java.lang.String identifier)

Deprecated. use setQueryID instead.

setQuerySeq identifies the query sequence by a name, ID or URN.

Parameters:

identifier - a String which should be an unique identifer for the sequence.

setQueryID

public void setQueryID(java.lang.String queryID)

Description copied from interface: SearchContentHandler

setQueryID identifies the query sequence by a name, ID or URN.

Specified by:

setQueryID in interface SearchContentHandler

Parameters:

queryID - a String which should be an unique identifer for the sequence.

setSubjectDB

public void setSubjectDB(java.lang.String identifier)

Deprecated. use setDatabaseID instead.

setSubjectDB identifies the database searched by a name, ID or URN.

setDatabaseID

public void setDatabaseID(java.lang.String databaseID)

Description copied from interface: SearchContentHandler

setDatabaseID identifies the database searched by a name, ID or URN.

Specified by:

setDatabaseID in interface SearchContentHandler

Parameters:

databaseID - a String which should be an unique identifier for the database searched.

startSearch

public void startSearch()

Description copied from interface: SearchContentHandler

The startSearch method indicates the start of useful search information.

Specified by:

startSearch in interface SearchContentHandler

addSearchProperty

public void addSearchProperty(java.lang.Object key,
                              java.lang.Object value)

Description copied from interface: SearchContentHandler

The addSearchProperty method adds a key/value pair containing some property of the overall search result.

Specified by:

addSearchProperty in interface SearchContentHandler

Parameters:

key - an Object.

value - an Object.

endSearch

public void endSearch()

Description copied from interface: SearchContentHandler

The endSearch method indicates the end of useful search information.

Specified by:

endSearch in interface SearchContentHandler

startHeader

public void startHeader()

Description copied from interface: SearchContentHandler

The startHeader method indicates the start of a formatted header. This usually contains information relevant to the search as a whole.

Specified by:

startHeader in interface SearchContentHandler

endHeader

public void endHeader()

Description copied from interface: SearchContentHandler

The endHeader method indicates the end of a formatted header.

Specified by:

endHeader in interface SearchContentHandler

startHit

public void startHit()

Description copied from interface: SearchContentHandler

The startHit method indicates the start of a formatted hit. This could be a single line, or a block of lines.

Specified by:

startHit in interface SearchContentHandler

addHitProperty

public void addHitProperty(java.lang.Object key,
                           java.lang.Object value)

Description copied from interface: SearchContentHandler

The addHitProperty method adds a key/value pair containing some property of a particular hit.

Specified by:

addHitProperty in interface SearchContentHandler

Parameters:

key - an Object.

value - an Object.

endHit

public void endHit()

Description copied from interface: SearchContentHandler

The endHit method indicates the end of a formatted hit.

Specified by:

endHit in interface SearchContentHandler

startSubHit

public void startSubHit()

Description copied from interface: SearchContentHandler

The startSubHit method indicates the start of a formatted subhit. There may be zero or more of these per hit.

Specified by:

startSubHit in interface SearchContentHandler

addSubHitProperty

public void addSubHitProperty(java.lang.Object key,
                              java.lang.Object value)

Description copied from interface: SearchContentHandler

The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.

Specified by:

addSubHitProperty in interface SearchContentHandler

Parameters:

key - an Object.

value - an Object.

endSubHit

public void endSubHit()

Description copied from interface: SearchContentHandler

The endSubHit method indicates the end of a formatted subhit.

Specified by:

endSubHit in interface SearchContentHandler

setContentHandler

public void setContentHandler(org.xml.sax.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 org.xml.sax.XMLReader

Parameters:

poHandler - a ContentHandler The XML content handler

Throws:

java.lang.NullPointerException - If the handler argument is null

getContentHandler

public org.xml.sax.ContentHandler getContentHandler()

Return the content handler.

Specified by:

getContentHandler in interface org.xml.sax.XMLReader

Returns:

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

parse

public void parse(java.lang.String poSystemId)
           throws java.io.IOException,
                  org.xml.sax.SAXException

Full implementation of interface method.

Specified by:

parse in interface org.xml.sax.XMLReader

java.io.IOException

org.xml.sax.SAXException

getFeature

public boolean getFeature(java.lang.String poName)
                   throws org.xml.sax.SAXNotRecognizedException,
                          org.xml.sax.SAXNotSupportedException

Do-nothing implementation of interface method

Specified by:

getFeature in interface org.xml.sax.XMLReader

org.xml.sax.SAXNotRecognizedException

org.xml.sax.SAXNotSupportedException

setFeature

public void setFeature(java.lang.String poName,
                       boolean value)
                throws org.xml.sax.SAXNotRecognizedException,
                       org.xml.sax.SAXNotSupportedException

Handles support for Namespaces and Namespace-prefixes

Specified by:

setFeature in interface org.xml.sax.XMLReader

org.xml.sax.SAXNotRecognizedException

org.xml.sax.SAXNotSupportedException

getProperty

public java.lang.Object getProperty(java.lang.String name)
                             throws org.xml.sax.SAXNotRecognizedException,
                                    org.xml.sax.SAXNotSupportedException

Do-nothing implementation of interface method

Specified by:

getProperty in interface org.xml.sax.XMLReader

org.xml.sax.SAXNotRecognizedException

org.xml.sax.SAXNotSupportedException

setProperty

public void setProperty(java.lang.String name,
                        java.lang.Object value)
                 throws org.xml.sax.SAXNotRecognizedException,
                        org.xml.sax.SAXNotSupportedException

Do-nothing implementation of interface method

Specified by:

setProperty in interface org.xml.sax.XMLReader

org.xml.sax.SAXNotRecognizedException

org.xml.sax.SAXNotSupportedException

setEntityResolver

public void setEntityResolver(org.xml.sax.EntityResolver resolver)

Do-nothing implementation of interface method

Specified by:

setEntityResolver in interface org.xml.sax.XMLReader

getEntityResolver

public org.xml.sax.EntityResolver getEntityResolver()

Do-nothing implementation of interface method

Specified by:

getEntityResolver in interface org.xml.sax.XMLReader

setDTDHandler

public void setDTDHandler(org.xml.sax.DTDHandler handler)

Do-nothing implementation of interface method

Specified by:

setDTDHandler in interface org.xml.sax.XMLReader

getDTDHandler

public org.xml.sax.DTDHandler getDTDHandler()

Do-nothing implementation of interface method

Specified by:

getDTDHandler in interface org.xml.sax.XMLReader

setErrorHandler

public void setErrorHandler(org.xml.sax.ErrorHandler handler)

Do-nothing implementation of interface method

Specified by:

setErrorHandler in interface org.xml.sax.XMLReader

getErrorHandler

public org.xml.sax.ErrorHandler getErrorHandler()

Do-nothing implementation of interface method

Specified by:

getErrorHandler in interface org.xml.sax.XMLReader

startElement

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

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

Parameters:

poQName - a QName value

atts - an Attributes value

Throws:

org.xml.sax.SAXException - if an error occurs

endElement

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

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

Throws:

org.xml.sax.SAXException - thrown if

thrown - if

characters

protected void characters(char[] ch,
                          int start,
                          int length)
                   throws org.xml.sax.SAXException

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

Parameters:

start - -

length - -

Throws:

org.xml.sax.SAXException - thrown if

thrown - if

getNamespaces

public boolean getNamespaces()

Support SAX2 configuration of namespace support of parser.

Specified by:

getNamespaces in interface org.biojava.bio.program.sax.NamespaceConfigurationIF

getNamespacePrefixes

public boolean getNamespacePrefixes()

Support SAX2 configuration of namespace support of parser.

Specified by:

getNamespacePrefixes in interface org.biojava.bio.program.sax.NamespaceConfigurationIF

addPrefixMapping

public void addPrefixMapping(java.lang.String poPrefix,
                             java.lang.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 java.lang.String getURIFromPrefix(java.lang.String poPrefix)

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

Specified by:

getURIFromPrefix in interface org.biojava.bio.program.sax.NamespaceConfigurationIF

Parameters:

poPrefix - a String The namespace prefix.

setNamespacePrefix

public void setNamespacePrefix(java.lang.String poPrefix)

Parameters:

poPrefix - a String value

getNamespacePrefix

public java.lang.String getNamespacePrefix()

Describe getNamespacePrefix method here.

Returns:

a String value

prefix

public java.lang.String prefix(java.lang.String poElementName)

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

Returns:

a String value

getContentStream

protected java.io.BufferedReader getContentStream(org.xml.sax.InputSource poSource)

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

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