Package org.biojava.bio.program.blast2html

Class Blast2HTMLHandler

  • All Implemented Interfaces:
    org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler
    public class Blast2HTMLHandler
extends org.xml.sax.helpers.DefaultHandler
    Takes a SAX event stream and a HTMLRenderer to produce a HTML Blast like program report. Primary author - Colin Hardman (CAT) Other authors - Tim Dilks (CAT) Simon Brocklehurst (CAT) Stuart Johnston (CAT) Lawerence Bower (CAT) Derek Crockford (CAT) Neil Benn (CAT) Copyright 2001 Cambridge Antibody Technology Group plc. This code released to the biojava project, May 2001 under the LGPL license.
    Version:
    1.0
    Author:
    Cambridge Antibody Technology Group plc, Greg Cox

    • Constructor Summary

      Constructors 
      Constructor Description
      Blast2HTMLHandler​(HTMLRenderer poRenderer)
      A content handler for rendering blast like outputs into HTML.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void characters​(char[] charBuffer, int start, int length)
      Describe characters method here.
      void endElement​(java.lang.String poNameSpace, java.lang.String poElementName, java.lang.String poQName)
      Called when the end of an element is reached.
      void startElement​(java.lang.String poNameSpace, java.lang.String poElementName, java.lang.String poQName, org.xml.sax.Attributes poAtts)
      This is called when an element is entered.

      • Methods inherited from class org.xml.sax.helpers.DefaultHandler

        endDocument, endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startDocument, startPrefixMapping, unparsedEntityDecl, warning

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • Blast2HTMLHandler

        public Blast2HTMLHandler​(HTMLRenderer poRenderer)
        A content handler for rendering blast like outputs into HTML.
        Parameters:
        poRenderer - HTMLRenderer - a configured HTMLRenderer.

    • Method Detail

      • startElement

        public void startElement​(java.lang.String poNameSpace,
                         java.lang.String poElementName,
                         java.lang.String poQName,
                         org.xml.sax.Attributes poAtts)
                  throws org.xml.sax.SAXException
        This is called when an element is entered. That is, the parser has met the first tag of the tag pair.
        Specified by:
        startElement in interface org.xml.sax.ContentHandler
        Overrides:
        startElement in class org.xml.sax.helpers.DefaultHandler
        Parameters:
        poNameSpace - String - the name space.
        poElementName - String - the local name of the tag.
        poQName - String - the fully qualified name with prefix
        poAtts - an Attributes - the tag attributes.
        Throws:
        org.xml.sax.SAXException - if an error occurs

      • endElement

        public void endElement​(java.lang.String poNameSpace,
                       java.lang.String poElementName,
                       java.lang.String poQName)
        Called when the end of an element is reached.
        Specified by:
        endElement in interface org.xml.sax.ContentHandler
        Overrides:
        endElement in class org.xml.sax.helpers.DefaultHandler
        Parameters:
        poNameSpace - a String - the name space.
        poElementName - a String - the local element name.
        poQName - a String value - the qualified element name.

      • characters

        public void characters​(char[] charBuffer,
                       int start,
                       int length)
        Describe characters method here.
        Specified by:
        characters in interface org.xml.sax.ContentHandler
        Overrides:
        characters in class org.xml.sax.helpers.DefaultHandler
        Parameters:
        charBuffer - - character array containing data.
        start - - the start position of relavent chars in passes array
        length - - the stop position of relavent chars in passes array