Bio::SearchIO::IteratedSearchResultEventBuilder(3pm) User Contributed Perl Documentation Bio::SearchIO::IteratedSearchResultEventBuilder(3pm)
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:
https://redmine.open-bio.org/projects/bioperl/
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.
perl v5.14.2 2012-03-02 Bio::SearchIO::IteratedSearchResultEventBuilder(3pm)