PdbSAXParser (BioJava-1.5-beta API)
Keywords: org.biojava.bio.program.sax.PdbSAXParser class

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## org.biojava.bio.program.sax
Class PdbSAXParser

    java.lang.Object
      org.biojava.bio.program.sax.PdbSAXParser

All Implemented Interfaces:
  XMLReader

    public class PdbSAXParser

extends 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. All Rights Reserved.

Primary author -

- Simon Brocklehurst (CAT)

Other authors -

- 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
`protected int` | `iState`
`protected String` | `oFullNamespacePrefix`
`protected ContentHandler` | `oHandler`
`protected String` | `oNamespacePrefix`
`protected boolean` | `tNamespacePrefixes`
`protected boolean` | `tNamespaces`

Constructor Summary
`PdbSAXParser()` Sets namespace prefix to "biojava"

Method Summary
`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)` Describe 'parse' method here.
`void` | `parse(String poURI)` 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` | `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

### PdbSAXParser

    public PdbSAXParser()

  Sets namespace prefix to "biojava"

Method Detail

### parse

    public void parse(String poURI)
               throws IOException,
                      SAXException

  Full implementation of interface method.

  Specified by:
    `parse` in interface `XMLReader`
  Throws:
    `IOException`
    `SAXException`

### parse

    public void parse(InputSource poSource)
               throws IOException,
                      SAXException

  Describe 'parse' method here.

  Specified by:
    `parse` in interface `XMLReader`
  Parameters:
    `poSource` - -
  Throws:
    `IOException`
    `SAXException`

### 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.

### 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

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