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.

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email sac@bioperl.org Parts of code based on SearchResultEventBuilder by Jason Stajich jason@bioperl.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::SearchIO::IteratedSearchResultEventBuilder(); 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.