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

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.