| Bio::SearchIO::IteratedSearchResultEventBuilder(3pm) | User Contributed Perl Documentation | Bio::SearchIO::IteratedSearchResultEventBuilder(3pm) |
Bio::SearchIO::IteratedSearchResultEventBuilder - Event Handler for SearchIO events.
# Do not use this object directly, this object is part of the SearchIO # event based parsing system.
This object handles Search Events generated by the SearchIO classes and build appropriate Bio::Search::* objects from them.
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
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.
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/bioperl-live/issues
Email sac-at-bioperl.org
Parts of code based on SearchResultEventBuilder by Jason Stajich jason@bioperl.org
Sendu Bala, bix@sendu.me.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : my $obj = Bio::SearchIO::IteratedSearchResultEventBuilder->new();
Function: Builds a new Bio::SearchIO::IteratedSearchResultEventBuilder object
Returns : Bio::SearchIO::IteratedSearchResultEventBuilder
Args : -hsp_factory => Bio::Factory::ObjectFactoryI
-hit_factory => Bio::Factory::ObjectFactoryI
-result_factory => Bio::Factory::ObjectFactoryI
-iteration_factory => Bio::Factory::ObjectFactoryI
-inclusion_threshold => e-value threshold for inclusion in the
PSI-BLAST score matrix model (blastpgp)
-signif => float or scientific notation number to be used
as a P- or Expect value cutoff
-score => integer or scientific notation number to be used
as a blast score value cutoff
-bits => integer or scientific notation number to be used
as a bit score value cutoff
-hit_filter => reference to a function to be used for
filtering hits based on arbitrary criteria.
See Bio::SearchIO::SearchResultEventBuilder for more information
Title : will_handle
Usage : if( $handler->will_handle($event_type) ) { ... }
Function: Tests if this event builder knows how to process a specific event
Returns : boolean
Args : event type name
Title : start_result Usage : $handler->start_result($resulttype) Function: Begins a result event cycle Returns : none Args : Type of Report
Title : start_iteration Usage : $handler->start_iteration() Function: Starts an Iteration event cycle Returns : none Args : type of event and associated hashref
Title : end_iteration Usage : $handler->end_iteration() Function: Ends an Iteration event cycle Returns : Bio::Search::Iteration object Args : type of event and associated hashref
| 2020-10-28 | perl v5.30.3 |