Package org.biojava.bio.program.sax
Class PdbSAXParser
java.lang.Object
org.biojava.bio.program.sax.PdbSAXParser
- All Implemented Interfaces:
XMLReader
A SAX2 parser for dealing with native PDB files. That is,
this class allows native PDB format files to be processed
as if they were in PdbXML format, but without an interconversion
step. That is, events are generated that call methods
on an XML document handler.
Note this code is experimental, and may change without notice.
Copyright © 2000 - 2002 Cambridge Antibody Technology.
Primary author -
- Simon Brocklehurst (CAT)
- Neil Benn (CAT)
- Derek Crockford (CAT)
- Tim Dilks (CAT)
- Colin Hardman (CAT)
- Stuart Johnston (CAT)
- Version:
- 0.8
- Author:
- Cambridge Antibody Technology (CAT), Greg Cox
-
Field Summary
FieldsModifier and TypeFieldDescriptionprotected int
protected String
protected ContentHandler
protected String
protected boolean
protected boolean
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Constructor Summary
Constructors -
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) Describe 'parse' method here.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
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
-
oFullNamespacePrefix
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iState
protected int iState
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Constructor Details
-
PdbSAXParser
public PdbSAXParser()Sets namespace prefix to "biojava"
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Method Details
-
parse
Full implementation of interface method.- Specified by:
parse
in interfaceXMLReader
- Throws:
IOException
SAXException
-
parse
Describe 'parse' method here.- Specified by:
parse
in interfaceXMLReader
- Parameters:
poSource
- -- Throws:
IOException
SAXException
-
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.
-
getFeature
Do-nothing implementation of interface method- Specified by:
getFeature
in interfaceXMLReader
- 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 interfaceXMLReader
- Throws:
SAXNotRecognizedException
SAXNotSupportedException
-
getProperty
Do-nothing implementation of interface method- Specified by:
getProperty
in interfaceXMLReader
- Throws:
SAXNotRecognizedException
SAXNotSupportedException
-
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
-
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.
-
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
-
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
-