++ed by:
YUSRIDEB GENEHACK ILUX PROCH MAJENSEN

11 PAUSE users
14 non-PAUSE users.

Christopher Fields
and 1 contributors

NAME

Bio::SearchIO::XML::PsiBlastHandler - XML Handler for NCBI Blast PSIBLAST XML parsing.

SYNOPSIS

  # This is not to be used directly.

DESCRIPTION

This is the XML handler for BLAST PSIBLAST 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

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'