Bio::SearchIO::XML::PsiBlastHandler - XML Handler for NCBI Blast PSIBLAST XML parsing.
# This is not to be used directly.
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.
In addition to parts of the Bio:: hierarchy, this module uses:
which comes with the XML::SAX distribution.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : start_document Usage : $parser->start_document; Function: SAX method to indicate starting to parse a new document Returns : none Args : none
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
Title : start_element Usage : $parser->start_element($data) Function: SAX method to indicate starting a new element Returns : none Args : hash ref for data
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
Title : characters Usage : $parser->characters($data) Function: Signals new characters to be processed Returns : characters read Args : hash ref with the key 'Data'
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)
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Please direct usage questions or support issues to the mailing list: email@example.com
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.
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:
Jason Stajich <jason-at-bioperl.org>
Chris Fields <firstname.lastname@example.org>
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.