Class BlastLikeSAXParser
- All Implemented Interfaces:
XMLReader
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
- 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)
- 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:
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected int
protected String
protected ContentHandler
protected String
protected boolean
protected boolean
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Constructor Summary
ConstructorsConstructorDescriptionInitialises SAXParser, and sets default namespace prefix to "biojava". -
Method Summary
Modifier and TypeMethodDescriptionvoid
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.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.Do-nothing implementation of interface methodDo-nothing implementation of interface methodDo-nothing implementation of interface methodboolean
getFeature
(String poName) Do-nothing implementation of interface methodDescribegetNamespacePrefix
method here.boolean
Support SAX2 configuration of namespace support of parser.boolean
Support SAX2 configuration of namespace support of parser.getProperty
(String name) Do-nothing implementation of interface methodgetURIFromPrefix
(String poPrefix) Gets the URI for a namespace prefix, given that prefix, or null if the prefix is not recognised.void
Full implementation of interface method.void
parse
(InputSource poSource) parse
initiates the parsing operation.Given an unprefixed element name, returns a new element name with a namespace prefixvoid
setContentHandler
(ContentHandler poHandler) Allow an application to register a content event handler.void
setDTDHandler
(DTDHandler handler) Do-nothing implementation of interface methodvoid
setEntityResolver
(EntityResolver resolver) Do-nothing implementation of interface methodvoid
setErrorHandler
(ErrorHandler handler) Do-nothing implementation of interface methodvoid
setFeature
(String poName, boolean value) Handles support for ReasoningDomain and Namespace-prefixesvoid
Setting the mode to lazy means that, if the program is recognised, e.g.void
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 methodprotected void
startElement
(org.biojava.bio.program.sax.QName poQName, Attributes atts) Utility method to centralize sending of a SAX startElement message to document handler
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Field Details
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oHandler
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tNamespaces
protected boolean tNamespaces -
tNamespacePrefixes
protected boolean tNamespacePrefixes -
oNamespacePrefix
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oFullNamespacePrefix
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iState
protected int iState
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Constructor Details
-
BlastLikeSAXParser
public BlastLikeSAXParser()Initialises SAXParser, and sets default namespace prefix to "biojava".
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Method Details
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parse
parse
initiates the parsing operation.- Specified by:
parse
in interfaceXMLReader
- Parameters:
poSource
- anInputSource
.- Throws:
IOException
- if an error occurs.SAXException
- if an error occurs.
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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
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
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 interfaceXMLReader
- Parameters:
poHandler
- aContentHandler
The XML content handler- Throws:
NullPointerException
- If the handler argument is null
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getContentHandler
Return the content handler.- Specified by:
getContentHandler
in interfaceXMLReader
- Returns:
- a
ContentHandler
The current content handler, or null if none has been registered.
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parse
Full implementation of interface method.- Specified by:
parse
in interfaceXMLReader
- Throws:
IOException
SAXException
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getFeature
Do-nothing implementation of interface method- Specified by:
getFeature
in interfaceXMLReader
- Throws:
SAXNotRecognizedException
SAXNotSupportedException
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setFeature
public void setFeature(String poName, boolean value) throws SAXNotRecognizedException, SAXNotSupportedException Handles support for ReasoningDomain and Namespace-prefixes- Specified by:
setFeature
in interfaceXMLReader
- Throws:
SAXNotRecognizedException
SAXNotSupportedException
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getProperty
Do-nothing implementation of interface method- Specified by:
getProperty
in interfaceXMLReader
- Throws:
SAXNotRecognizedException
SAXNotSupportedException
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setProperty
public void setProperty(String name, Object value) throws SAXNotRecognizedException, SAXNotSupportedException Do-nothing implementation of interface method- Specified by:
setProperty
in interfaceXMLReader
- Throws:
SAXNotRecognizedException
SAXNotSupportedException
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setEntityResolver
Do-nothing implementation of interface method- Specified by:
setEntityResolver
in interfaceXMLReader
-
getEntityResolver
Do-nothing implementation of interface method- Specified by:
getEntityResolver
in interfaceXMLReader
-
setDTDHandler
Do-nothing implementation of interface method- Specified by:
setDTDHandler
in interfaceXMLReader
-
getDTDHandler
Do-nothing implementation of interface method- Specified by:
getDTDHandler
in interfaceXMLReader
-
setErrorHandler
Do-nothing implementation of interface method- Specified by:
setErrorHandler
in interfaceXMLReader
-
getErrorHandler
Do-nothing implementation of interface method- Specified by:
getErrorHandler
in interfaceXMLReader
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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
- aQName
valueatts
- anAttributes
value- Throws:
SAXException
- if an error occurs
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endElement
Utility method to centralize the sending of a SAX endElement message a document handler.- Parameters:
poQName
- -
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characters
Utility method to centralize the sending of a SAX characters message a document handler.- Parameters:
ch
- -start
- -length
- -
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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
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
- aString
representation of the namespace prefixpoURI
- aString
representation of the URI for the namespace prefix.
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getURIFromPrefix
Gets the URI for a namespace prefix, given that prefix, or null if the prefix is not recognised.- Parameters:
poPrefix
- aString
The namespace prefix.
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setNamespacePrefix
- Parameters:
poPrefix
- aString
value
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getNamespacePrefix
DescribegetNamespacePrefix
method here.- Returns:
- a
String
value
-
prefix
Given an unprefixed element name, returns a new element name with a namespace prefix- Returns:
- a
String
value
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getContentStream
Create a stream from an an InputSource, picking the correct stream according to order of precedance.- Parameters:
poSource
- anInputSource
value- Returns:
- a
BufferedReader
value
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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
- anint
value
-