Package org.biojava.bio.program.sax

Class SequenceAlignmentSAXParser

java.lang.Object
org.biojava.bio.program.sax.SequenceAlignmentSAXParser
All Implemented Interfaces:
XMLReader
public class SequenceAlignmentSAXParser extends Object
A SAX2 parser for dealing with a sequence alignments. The format of any given alignment is automatically detected (e.g. ClustalW, Needle). Supported alignment formats are:
  • ClustalW
  • Needle
Copyright © 2000-2002 Cambridge Antibody Technology.

Primary author -

  • Simon Brocklehurst (CAT)
Other authors -
  • Neil Benn (CAT)
  • Lawrence Bower (CAT)
  • Derek Crockford (CAT)
  • Tim Dilks (CAT)
  • Colin Hardman (CAT)
  • Stuart Johnston (CAT)
Version:
1.0
Author:
Cambridge Antibody Technology (CAT)

  • Field Details

    • 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 Details

  • Method Details

    • 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.

    • parse

      public void parse(String poSystemId) throws IOException, SAXException
      Full implementation of interface method.
      Specified by:
      parse in interface XMLReader
      Throws:
      IOException
      SAXException

    • 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