Bio::S...Builder(3pm)

💖 Bio::S...Builder(3pm) 💖

okay bestie, welcome to the Bio::S...Builder(3pm) page from the User Contributed Perl Documentation — yes the title is literally truncated like that, we don't make the rules, we just vibe with them 💅

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✨ NAME ✨

Bio::SearchIO::SearchResultEventBuilder — Event Handler for SearchIO events. that's it, that's the whole name, and it's kind of a mouthful ngl but we move 🦋

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✨ SYNOPSIS ✨

# Do not use this object directly, this object is part of the SearchIO #
event based parsing system.

like, do not touch it directly fr fr. it lives inside the SearchIO event parsing system and it's doing its little job in there 🙈

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✨ DESCRIPTION ✨

so basically this object handles the Search Events that the SearchIO classes generate, and it builds the appropriate Bio::Search::* objects out of them 🎀

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✨ FEEDBACK ✨

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, your thoughts genuinely matter here 🫶 send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated no cap.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🌸 Support

please direct usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

...rather than to the module maintainer directly. because so many experienced and reponsive experts will be able look at the problem and quickly address it 👑 (that "reponsive" is not a typo, that's just how the original spells it, iykyk 💀)

please include a thorough description of the problem with code and data examples if at all possible. the more deets the better, bestie ✨

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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✨ AUTHOR - Jason Stajich ✨

Email jason-at-bioperl.org 📧

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✨ CONTRIBUTORS ✨

Sendu Bala, bix@sendu.me.uk 💜

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✨ APPENDIX ✨

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (classic move, we love an underscore moment 🌈)

🧚 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.

⚠️ quick reminder bestie: those Bio::Root::BadParameter throws are real — if you feed these setters something that isn't a valid number (or, for hit_filter, something that isn't a function ref), it will throw. no cap. 😭

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and that's the whole page!! 🌈 this was generated by perl v5.32.1 on 2021-08-15, and it's literally titled Bio::S...Builder(3pm) — stay iconic, go build some objects 💅✨🦋