/ 
BioPerl-1.007000
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SearchIO::IteratedSearchResultEventBuilder

NAME

Bio::SearchIO::IteratedSearchResultEventBuilder - Event Handler for SearchIO events.

SYNOPSIS

# Do not use this object directly, this object is part of the SearchIO # event based parsing system.

DESCRIPTION

This object handles Search Events generated by the SearchIO classes and build appropriate Bio::Search::* objects from them.

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

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/bioperl-live/issues

AUTHOR - Steve Chervitz

Email sac-at-bioperl.org

CONTRIBUTORS

Parts of code based on SearchResultEventBuilder by Jason Stajich jason@bioperl.org

Sendu Bala, bix@sendu.me.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

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

will_handle

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

SAX methods

start_result

Title   : start_result
Usage   : $handler->start_result($resulttype)
Function: Begins a result event cycle
Returns : none
Args    : Type of Report

start_iteration

Title   : start_iteration
Usage   : $handler->start_iteration()
Function: Starts an Iteration event cycle
Returns : none
Args    : type of event and associated hashref

end_iteration

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