Bio::SearchIO::XML::BlastHandler.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

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:
   http://bugzilla.open-bio.org/
 
 

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'