Bio::SearchIO::IteratedSearchResultEventBuilder.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::SearchIO::IteratedSearchResultEventBuilder - 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:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Steve Chervitz

Email sac-at-bioperl.org

CONTRIBUTORS

Parts of code based on SearchResultEventBuilder by Jason Stajich jason@bioperl.org

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::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

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.