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Manual Reference Pages  -  BIO::SEARCHIO::XML::BLASTHANDLER (3)

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NAME

Bio::SearchIO::XML::BlastHandler - XML Handler for NCBI Blast XML parsing.

CONTENTS

SYNOPSIS



  # This is not to be used directly.



DESCRIPTION

This is the XML handler for BLAST XML parsing. Currently it passes elements off to the event handler, which is ultimately responsible for Bio::Search object generation.

This was recently split off from the original code for Bio::SearchIO::blastxml primarily for maintenance purposes.

DEPENDENCIES

In addition to parts of the Bio:: hierarchy, this module uses:



 XML::SAX::Base



which comes with the XML::SAX distribution.

FEEDBACK

    Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.



  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists



    Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

    Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:



  https://github.com/bioperl/bioperl-live/issues



AUTHOR - Jason Stajich, Chris Fields

Email jason-at-bioperl.org Email cjfields-at-uiuc dot edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

    SAX methods

    start_document



 Title   : start_document
 Usage   : $parser->start_document;
 Function: SAX method to indicate starting to parse a new document
 Returns : none
 Args    : none



    end_document



 Title   : end_document
 Usage   : $parser->end_document;
 Function: SAX method to indicate finishing parsing a new document
 Returns : Bio::Search::Result::ResultI object
 Args    : none



    start_element



 Title   : start_element
 Usage   : $parser->start_element($data)
 Function: SAX method to indicate starting a new element
 Returns : none
 Args    : hash ref for data



    end_element



 Title   : end_element
 Usage   : $parser->end_element($data)
 Function: Signals finishing an element
 Returns : Bio::Search object dpending on what type of element
 Args    : hash ref for data



    characters



 Title   : characters
 Usage   : $parser->characters($data)
 Function: Signals new characters to be processed
 Returns : characters read
 Args    : hash ref with the key Data



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perl v5.20.3 BIO::SEARCHIO::XML::BLASTHANDLER (3) 2016-04-05

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