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Bio-SearchIO-blastxml-1.70
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/ Bio::SearchIO::XML::PsiBlastHandler

NAME

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

VERSION

version 1.70

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.

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'

eventHandler

Title   : eventHandler
Usage   : $parser->eventHandler($handler)
Function: Get/Set event handler (XML::SAX::Base) instance
Returns : XML::SAX::Base
Args    : XML::SAX::Base implemntation (Optional)

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/Support.html    - 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/bio-searchio-blastxml/issues

AUTHORS

Jason Stajich <jason-at-bioperl.org>

Chris Fields <cjfields@cpan.org>

COPYRIGHT

This software is copyright (c) 2006-2018 by Jason Stajich.

This software is available under the same terms as the perl 5 programming language system itself.