Bio::SearchIO::SearchResultEventBuilder(3pm)

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new

 Title   : new
 Usage   : my $obj = Bio::SearchIO::SearchResultEventBuilder->new();
 Function: Builds a new Bio::SearchIO::SearchResultEventBuilder object
 Returns : Bio::SearchIO::SearchResultEventBuilder
 Args    : -hsp_factory    => Bio::Factory::ObjectFactoryI
           -hit_factory    => Bio::Factory::ObjectFactoryI
           -result_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::Factory::ObjectFactoryI 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_hsp

 Title   : start_hsp
 Usage   : $handler->start_hsp($name,$data)
 Function: Begins processing a HSP event
 Returns : none
 Args    : type of element
           associated data (hashref)

end_hsp

 Title   : end_hsp
 Usage   : $handler->end_hsp()
 Function: Finish processing a HSP event
 Returns : none
 Args    : type of event and associated hashref

start_hit

 Title   : start_hit
 Usage   : $handler->start_hit()
 Function: Starts a Hit event cycle
 Returns : none
 Args    : type of event and associated hashref

end_hit

 Title   : end_hit
 Usage   : $handler->end_hit()
 Function: Ends a Hit event cycle
 Returns : Bio::Search::Hit::HitI object
 Args    : type of event and associated hashref

Factory methods

register_factory

 Title   : register_factory
 Usage   : $handler->register_factory('TYPE',$factory);
 Function: Register a specific factory for a object type class
 Returns : none
 Args    : string representing the class and
           Bio::Factory::ObjectFactoryI

See Bio::Factory::ObjectFactoryI for more information

factory

 Title   : factory
 Usage   : my $f = $handler->factory('TYPE');
 Function: Retrieves the associated factory for requested 'TYPE'
 Returns : a Bio::Factory::ObjectFactoryI
 Throws  : Bio::Root::BadParameter if none registered for the supplied type
 Args    : name of factory class to retrieve

See Bio::Factory::ObjectFactoryI for more information

inclusion_threshold

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

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 at HIT level 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 at HIT level 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 at HIT level 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 at HIT level 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.