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.