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.\" ========================================================================
.\"
.IX Title "Bio::SearchIO::SearchResultEventBuilder 3pm"
.TH Bio::SearchIO::SearchResultEventBuilder 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::SearchIO::SearchResultEventBuilder \- Event Handler for SearchIO events.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
# Do not use this object directly, this object is part of the SearchIO
# event based parsing system.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object handles Search Events generated by the SearchIO classes
and build appropriate Bio::Search::* objects from them.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason\-at\-bioperl.org
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Sendu Bala, bix@sendu.me.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 10
\& 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.
.Ve
.PP
See Bio::Factory::ObjectFactoryI for more information
.SS "will_handle"
.IX Subsection "will_handle"
.Vb 5
\& 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
.Ve
.SS "\s-1SAX\s0 methods"
.IX Subsection "SAX methods"
.SS "start_result"
.IX Subsection "start_result"
.Vb 5
\& Title   : start_result
\& Usage   : $handler\->start_result($resulttype)
\& Function: Begins a result event cycle
\& Returns : none
\& Args    : Type of Report
.Ve
.SS "end_result"
.IX Subsection "end_result"
.Vb 5
\& Title   : end_result
\& Usage   : my @results = $parser\->end_result
\& Function: Finishes a result handler cycle
\& Returns : A Bio::Search::Result::ResultI
\& Args    : none
.Ve
.SS "start_hsp"
.IX Subsection "start_hsp"
.Vb 6
\& Title   : start_hsp
\& Usage   : $handler\->start_hsp($name,$data)
\& Function: Begins processing a HSP event
\& Returns : none
\& Args    : type of element
\&           associated data (hashref)
.Ve
.SS "end_hsp"
.IX Subsection "end_hsp"
.Vb 5
\& Title   : end_hsp
\& Usage   : $handler\->end_hsp()
\& Function: Finish processing a HSP event
\& Returns : none
\& Args    : type of event and associated hashref
.Ve
.SS "start_hit"
.IX Subsection "start_hit"
.Vb 5
\& Title   : start_hit
\& Usage   : $handler\->start_hit()
\& Function: Starts a Hit event cycle
\& Returns : none
\& Args    : type of event and associated hashref
.Ve
.SS "end_hit"
.IX Subsection "end_hit"
.Vb 5
\& 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
.Ve
.SS "Factory methods"
.IX Subsection "Factory methods"
.SS "register_factory"
.IX Subsection "register_factory"
.Vb 6
\& Title   : register_factory
\& Usage   : $handler\->register_factory(\*(AqTYPE\*(Aq,$factory);
\& Function: Register a specific factory for a object type class
\& Returns : none
\& Args    : string representing the class and
\&           Bio::Factory::ObjectFactoryI
.Ve
.PP
See Bio::Factory::ObjectFactoryI for more information
.SS "factory"
.IX Subsection "factory"
.Vb 6
\& Title   : factory
\& Usage   : my $f = $handler\->factory(\*(AqTYPE\*(Aq);
\& Function: Retrieves the associated factory for requested \*(AqTYPE\*(Aq
\& Returns : a Bio::Factory::ObjectFactoryI
\& Throws  : Bio::Root::BadParameter if none registered for the supplied type
\& Args    : name of factory class to retrieve
.Ve
.PP
See Bio::Factory::ObjectFactoryI for more information
.SS "inclusion_threshold"
.IX Subsection "inclusion_threshold"
See Bio::SearchIO::blast::inclusion_threshold.
.SS "max_significance"
.IX Subsection "max_significance"
.Vb 11
\& 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.
.Ve
.SS "signif"
.IX Subsection "signif"
Synonym for \fBmax_significance()\fR
.SS "min_score"
.IX Subsection "min_score"
.Vb 10
\& 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.
.Ve
.SS "min_bits"
.IX Subsection "min_bits"
.Vb 10
\& 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.
.Ve
.SS "hit_filter"
.IX Subsection "hit_filter"
.Vb 8
\& 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.
.Ve