Provided by: libbio-perl-perl_1.6.901-2_all bug

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://redmine.open-bio.org/projects/bioperl/

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

   end_result
        Title   : end_result
        Usage   : my @results = $parser->end_result
        Function: Finishes a result handler cycle
        Returns : A Bio::Search::Result::ResultI
        Args    : none

   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

   max_significance
        Usage     : $obj->max_significance();
        Purpose   : Set/Get the P or Expect value used as significance screening cutoff.
                    This is the value of the -signif parameter supplied to new().
                    Hits with P or E-value above this are skipped.
        Returns   : Scientific notation number with this format: 1.0e-05.
        Argument  : Number (sci notation, float, integer) (when setting)
        Throws    : Bio::Root::BadParameter exception if the supplied argument is
                  : not a valid number.
        Comments  : Screening of significant hits uses the data provided on the
                  : description line. For NCBI BLAST1 and WU-BLAST, this data
                  : is P-value. for NCBI BLAST2 it is an Expect value.

   signif
       Synonym for max_significance()

   min_score
        Usage     : $obj->min_score();
        Purpose   : Gets the Blast score used as screening cutoff.
                    This is the value of the -score parameter supplied to new().
                    Hits with scores below this are skipped.
        Returns   : Integer (or undef if not set)
        Argument  : Integer (when setting)
        Throws    : Bio::Root::BadParameter exception if the supplied argument is
                  : not a valid number.
        Comments  : Screening of significant hits uses the data provided on the
                  : description line.

   min_bits
        Usage     : $obj->min_bits();
        Purpose   : Gets the Blast bit score used as screening cutoff.
                    This is the value of the -bits parameter supplied to new().
                    Hits with bits score below this are skipped.
        Returns   : Integer (or undef if not set)
        Argument  : Integer (when setting)
        Throws    : Bio::Root::BadParameter exception if the supplied argument is
                  : not a valid number.
        Comments  : Screening of significant hits uses the data provided on the
                  : description line.

   hit_filter
        Usage     : $obj->hit_filter();
        Purpose   : Set/Get a function reference used for filtering out hits.
                    This is the value of the -hit_filter parameter supplied to new().
                    Hits that fail to pass the filter are skipped.
        Returns   : Function ref (or undef if not set)
        Argument  : Function ref (when setting)
        Throws    : Bio::Root::BadParameter exception if the supplied argument is
                  : not a function reference.

   inclusion_threshold
       See Bio::SearchIO::blast::inclusion_threshold.

perl v5.14.2                                2Bio::SearchIO::IteratedSearchResultEventBuilder(3pm)