Package org.biojava.bio.program.sax
Class PdbSAXParser
- java.lang.Object
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- org.biojava.bio.program.sax.PdbSAXParser
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- All Implemented Interfaces:
org.xml.sax.XMLReader
public class PdbSAXParser extends java.lang.Object
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
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Field Summary
Fields Modifier and Type Field Description 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
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Constructor Summary
Constructors Constructor Description PdbSAXParser()
Sets namespace prefix to "biojava"
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addPrefixMapping(java.lang.String poPrefix, java.lang.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.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 methodorg.xml.sax.EntityResolver
getEntityResolver()
Do-nothing implementation of interface methodorg.xml.sax.ErrorHandler
getErrorHandler()
Do-nothing implementation of interface methodboolean
getFeature(java.lang.String poName)
Do-nothing implementation of interface methodjava.lang.String
getNamespacePrefix()
DescribegetNamespacePrefix
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 methodjava.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(java.lang.String poURI)
Full implementation of interface method.void
parse(org.xml.sax.InputSource poSource)
Describe 'parse' method here.java.lang.String
prefix(java.lang.String poElementName)
Given an unprefixed element name, returns a new element name with a namespace prefixvoid
setContentHandler(org.xml.sax.ContentHandler poHandler)
Allow an application to register a content event handler.void
setDTDHandler(org.xml.sax.DTDHandler handler)
Do-nothing implementation of interface methodvoid
setEntityResolver(org.xml.sax.EntityResolver resolver)
Do-nothing implementation of interface methodvoid
setErrorHandler(org.xml.sax.ErrorHandler handler)
Do-nothing implementation of interface methodvoid
setFeature(java.lang.String poName, boolean value)
Handles support for ReasoningDomain and Namespace-prefixesvoid
setNamespacePrefix(java.lang.String poPrefix)
void
setProperty(java.lang.String name, java.lang.Object value)
Do-nothing implementation of interface methodprotected 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
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Field Detail
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oHandler
protected org.xml.sax.ContentHandler oHandler
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tNamespaces
protected boolean tNamespaces
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tNamespacePrefixes
protected boolean tNamespacePrefixes
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oNamespacePrefix
protected java.lang.String oNamespacePrefix
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oFullNamespacePrefix
protected java.lang.String oFullNamespacePrefix
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iState
protected int iState
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Constructor Detail
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PdbSAXParser
public PdbSAXParser()
Sets namespace prefix to "biojava"
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Method Detail
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parse
public void parse(java.lang.String poURI) throws java.io.IOException, org.xml.sax.SAXException
Full implementation of interface method.- Specified by:
parse
in interfaceorg.xml.sax.XMLReader
- Throws:
java.io.IOException
org.xml.sax.SAXException
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parse
public void parse(org.xml.sax.InputSource poSource) throws java.io.IOException, org.xml.sax.SAXException
Describe 'parse' method here.- Specified by:
parse
in interfaceorg.xml.sax.XMLReader
- Parameters:
poSource
- -- Throws:
java.io.IOException
org.xml.sax.SAXException
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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 interfaceorg.xml.sax.XMLReader
- Parameters:
poHandler
- aContentHandler
The XML content handler- Throws:
java.lang.NullPointerException
- If the handler argument is null
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getContentHandler
public org.xml.sax.ContentHandler getContentHandler()
Return the content handler.- Specified by:
getContentHandler
in interfaceorg.xml.sax.XMLReader
- Returns:
- a
ContentHandler
The current content handler, or null if none has been registered.
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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 interfaceorg.xml.sax.XMLReader
- Throws:
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException
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setFeature
public void setFeature(java.lang.String poName, boolean value) throws org.xml.sax.SAXNotRecognizedException, org.xml.sax.SAXNotSupportedException
Handles support for ReasoningDomain and Namespace-prefixes- Specified by:
setFeature
in interfaceorg.xml.sax.XMLReader
- Throws:
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException
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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 interfaceorg.xml.sax.XMLReader
- Throws:
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException
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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 interfaceorg.xml.sax.XMLReader
- Throws:
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException
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setEntityResolver
public void setEntityResolver(org.xml.sax.EntityResolver resolver)
Do-nothing implementation of interface method- Specified by:
setEntityResolver
in interfaceorg.xml.sax.XMLReader
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getEntityResolver
public org.xml.sax.EntityResolver getEntityResolver()
Do-nothing implementation of interface method- Specified by:
getEntityResolver
in interfaceorg.xml.sax.XMLReader
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setDTDHandler
public void setDTDHandler(org.xml.sax.DTDHandler handler)
Do-nothing implementation of interface method- Specified by:
setDTDHandler
in interfaceorg.xml.sax.XMLReader
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getDTDHandler
public org.xml.sax.DTDHandler getDTDHandler()
Do-nothing implementation of interface method- Specified by:
getDTDHandler
in interfaceorg.xml.sax.XMLReader
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setErrorHandler
public void setErrorHandler(org.xml.sax.ErrorHandler handler)
Do-nothing implementation of interface method- Specified by:
setErrorHandler
in interfaceorg.xml.sax.XMLReader
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getErrorHandler
public org.xml.sax.ErrorHandler getErrorHandler()
Do-nothing implementation of interface method- Specified by:
getErrorHandler
in interfaceorg.xml.sax.XMLReader
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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
- aQName
valueatts
- anAttributes
value- Throws:
org.xml.sax.SAXException
- if an error occurs
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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.- Parameters:
poQName
- -- Throws:
org.xml.sax.SAXException
- thrown ifthrown
- if
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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:
ch
- -start
- -length
- -- Throws:
org.xml.sax.SAXException
- thrown ifthrown
- if
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getNamespaces
public boolean getNamespaces()
Support SAX2 configuration of namespace support of parser.
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getNamespacePrefixes
public boolean getNamespacePrefixes()
Support SAX2 configuration of namespace support of parser.
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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
- aString
representation of the namespace prefixpoURI
- aString
representation of the URI for the namespace prefix.
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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.- Parameters:
poPrefix
- aString
The namespace prefix.
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setNamespacePrefix
public void setNamespacePrefix(java.lang.String poPrefix)
- Parameters:
poPrefix
- aString
value
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getNamespacePrefix
public java.lang.String getNamespacePrefix()
DescribegetNamespacePrefix
method here.- Returns:
- a
String
value
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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
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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.- 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
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