Bio::SearchIO::XML::BlastHandler - XML Handler for NCBI Blast XML parsing.
# This is not to be used directly.
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.
In addition to parts of the Bio:: hierarchy, this module uses:
XML::SAX::Base
which comes with the XML::SAX distribution.
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
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/
Email jason-at-bioperl.org Email cjfields-at-uiuc dot edu
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'
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.