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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Parts of code based on SearchResultEventBuilder by Jason Stajich jason@bioperl.org
Sendu Bala, bix@sendu.me.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
Title : start_result Usage : $handler->start_result($resulttype) Function: Begins a result event cycle Returns : none Args : Type of Report
Title : end_result Usage : my @results = $parser->end_result Function: Finishes a result handler cycle Returns : A Bio::Search::Result::ResultI Args : none
Title : start_iteration Usage : $handler->start_iteration() Function: Starts an Iteration event cycle Returns : none Args : type of event and associated hashref
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
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.
Synonym for max_significance()
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.
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.
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.
See Bio::SearchIO::blast::inclusion_threshold.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.