/ 
bioperl-1.5.2_004-RCd
/ Bio::SearchIO::IteratedSearchResultEventBuilder

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

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 = 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.