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

💖 Bio::SearchIO::FastHitEventBuilder 💖

okay so bestie, welcome to the docs for Bio::SearchIO::FastHitEventBuilder, straight out of the User Contributed Perl Documentation collection. she's a 3pm girlie, she lives with all the other Perl module pages, and she is so much faster than her sibling. let's get into it 🫶

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✨ NAME ✨

Bio::SearchIO::FastHitEventBuilder — Event Handler for SearchIO events. that's it. that's the whole name. iconic.

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🦋 SYNOPSIS 🦋

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

# to use the FastHitEventBuilder do this

use Bio::SearchIO::FastHitEventBuilder;

my $searchio = Bio::SearchIO->new(-format => $format, -file => $file);

$searchio->attach_EventHandler(Bio::SearchIO::FastHitEventBuilder->new());

while( my $r = $searchio->next_result ) {
 while( my $h = $r->next_hit ) {
  # note that Hits will NOT have HSPs
 }
}

⚠️ do NOT use this object directly, bestie. she is part of the SearchIO event based parsing system. she's not a solo act, she's in a group project and she's carrying it.

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🌸 DESCRIPTION 🌸

so this object handles Search Events that the SearchIO classes generate, and she builds the appropriate Bio::Search::* objects out of them. that's her whole job and she does it beautifully.

she's made for lightweight parsers — the ones that only want Hits and genuinely cannot be bothered with the overhead of HSPs. like, why are we doing all that. she is a lot faster than the standard parser event handler, but of course you are getting less information and less objects out. it's giving trade-off, it's giving ✨ sacrifice ✨. you knew what you signed up for 💅

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💌 FEEDBACK 💌

📧 Mailing Lists 📧

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

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. like, no DMs please 🙈. 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 — receipts, bestie, bring receipts 📎

🐛 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 — yes the -at- is on purpose, we're being polite to the spambots 💖

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🎀 APPENDIX 🎀

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — that underscore is the "do not perceive me" marker 🫥

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🌟 new 🌟

Title   : new
Usage   : my $obj = Bio::SearchIO::FastHitEventBuilder->new();
Function: Builds a new Bio::SearchIO::FastHitEventBuilder object
Returns : Bio::SearchIO::FastHitEventBuilder
Args    : -hit_factory    => Bio::Factory::ObjectFactoryI
          -result_factory => Bio::Factory::ObjectFactoryI

she's born ✨ two args, both factories. see Bio::Factory::ObjectFactoryI for more information.

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🌟 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

basically the vibe check. she tests if this event builder knows how to process a specific event, and hands you back a boolean. true = she got this, false = not her department 💅

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🌟 SAX methods 🌟

🌈 start_result 🌈

Title   : start_result
Usage   : $handler->start_result($resulttype)
Function: Begins a result event cycle
Returns : none
Args    : Type of Report

the opening ceremony of a result event cycle. returns none, because she's mysterious like that.

🌈 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

finishes a result handler cycle and hands you a Bio::Search::Result::ResultI. (yes the Returns : is squished onto the Function: line in the original, we don't gatekeep run-on formatting here 😭 she's doing her best)

🌈 start_hit 🌈

Title   : start_hit
Usage   : $handler->start_hit()
Function: Starts a Hit event cycle
Returns : none
Args    : type of event and associated hashref

starts a Hit event cycle. returns none. the beginning of something beautiful 💜

🌈 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

ends a Hit event cycle and returns a Bio::Search::Hit::HitI object. closing the loop, slay.

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🌟 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

register a specific factory for an object type class. returns none. 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 or undef if none registered
Args    : name of factory class to retrieve

retrieves the associated factory for the requested 'TYPE', and gives you a Bio::Factory::ObjectFactoryI — or undef if none registered 😭 (not me getting undef back). see Bio::Factory::ObjectFactoryI for more information.

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🌟 inclusion_threshold 🌟

see Bio::SearchIO::blast::inclusion_threshold. that's the whole section. she said "go read the other one" and honestly? valid, respect the cross-reference 💅

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🫶 one last thing bestie: this page ships with perl v5.32.1, dated 2021-08-15, and it's Bio::S...uilder(3pm) — yeah the title got truncated in the header, but you and I both know who she really is 💖✨