Package org.biojava.bio.program.sax

Class ClustalWAlignmentSAXParser

  • All Implemented Interfaces:
    XMLReader
    public class ClustalWAlignmentSAXParser
extends Object
    A SAX2 parser for dealing with a multiple sequence alignment as produced by ClustalW outputing .aln format. For example, 
      K1C0_XENLA/125-441      DKVHALETANTELERKIKEWYEKQRPGSSSGDGAKDYSKYYT
  K1C4_XENLA/81-396       EKVRALEAANADLELKIREWYEKQK-GSGIGAGSKDFSKYFE
  K1C5_XENLA/73-384       DRVRSLEQANHELELKIREYLDKK-----AAVGSLDYSGYYN
  keratin15               DKVRALEEANADLEVKIHDWYQKQTP----ASPECDYSQYFK

  K1C0_XENLA/125-441      -----AKFLLQNDNARLAADDFKMKFEN--------------
  K1C4_XENLA/81-396       -----SRVVLQIDNAKLAADDFRLKFEN--------------
  K1C5_XENLA/73-384       -----TRLVLSIDNAKLAADDFKIKYES--------------
  keratin15               -----SRVILEIDNARLAADDFRLKYEN--------------

    Please note, this parser reads the whole alignment in to core memory and thus does not scale to work with very large alignments on low-end hardware.

    Please also note that this class has not been tested with many version of CLUSTAL W. Copyright © 2000,2001 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), Greg Cox

    • Field Detail

      • tNamespaces

        protected boolean tNamespaces

      • tNamespacePrefixes

        protected boolean tNamespacePrefixes

      • oNamespacePrefix

        protected String oNamespacePrefix

      • oFullNamespacePrefix

        protected String oFullNamespacePrefix

      • iState

        protected int iState

    • Constructor Detail

    • Method Detail

      • 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.

      • setDTDHandler

        public void setDTDHandler​(DTDHandler handler)
        Do-nothing implementation of interface method
        Specified by:
        setDTDHandler 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