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BioPerl-1.7.8
River stage two • 60 direct dependents • 64 total dependents
/ Bio::SearchIO::SearchResultEventBuilder

NAME

Bio::SearchIO::SearchResultEventBuilder - 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://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

CONTRIBUTORS

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::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.