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
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AUTHOR - Jason Stajich
Email jason-at-bioperl.orgCONTRIBUTORS
Sendu Bala, [email protected]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.