Christopher Fields > BioPerl > Bio::SearchIO::IteratedSearchResultEventBuilder

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Module Version: 1.006924   Source  

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
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