Class FastaSequenceSAXParser

  • All Implemented Interfaces:

    public class FastaSequenceSAXParser
    extends Object
    A SAX2 parser for dealing with multiple sequences in FASTA format. For example:

    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)
    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

      • FastaSequenceSAXParser

        public FastaSequenceSAXParser()
        Initialises internal state Sets namespace prefix to "biojava"
    • 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
        poHandler - a ContentHandler The XML content handler
        NullPointerException - If the handler argument is null
      • getContentHandler

        public ContentHandler getContentHandler()
        Return the content handler.
        Specified by:
        getContentHandler in interface XMLReader
        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​( poQName,
                                    Attributes atts)
                             throws SAXException
        Utility method to centralize sending of a SAX startElement message to document handler
        poQName - a QName value
        atts - an Attributes value
        SAXException - if an error occurs
      • endElement

        protected void endElement​( poQName)
                           throws SAXException
        Utility method to centralize the sending of a SAX endElement message a document handler.
        poQName - -
        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.
        ch - -
        start - -
        length - -
        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.
        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.
        poPrefix - a String The namespace prefix.
      • setNamespacePrefix

        public void setNamespacePrefix​(String poPrefix)
        poPrefix - a String value
      • getNamespacePrefix

        public String getNamespacePrefix()
        Describe getNamespacePrefix method here.
        a String value
      • prefix

        public String prefix​(String poElementName)
        Given an unprefixed element name, returns a new element name with a namespace prefix
        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.
        poSource - an InputSource value
        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.
        piState - an int value