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

💖 Bio::S...Builder(3pm) 💖

okay bestie, so this page is straight out of User Contributed Perl Documentation — the manual name is Bio::S...Builder(3pm) and yes the name is literally abbreviated with dots like that, we don't make the rules 💅

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✨ NAME ✨

Bio::SearchIO::IteratedSearchResultEventBuilder — the Event Handler for SearchIO events. that's the whole vibe. it handles events. it builds stuff. icon.

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🌸 SYNOPSIS 🌸

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

no cap, do not come for this object directly. it's a backstage crew member, not the main character. it lives inside the SearchIO event-based parsing system, okay? respect the ecosystem 🫶

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🦋 DESCRIPTION 🦋

so here's the tea: this object catches the Search Events that the SearchIO classes throw out into the world, and then it builds the appropriate Bio::Search::* objects out of them. like a little factory fairy 🧚 turning events into objects. that's it. that's the job.

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🎀 FEEDBACK 🎀

💌 Mailing Lists 💌

user feedback is an integral part of the evolution of this and other Bioperl modules — literally, the modules grow because you talk to them. send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated. fr fr, they mean it 💖

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. yes, really, bestie — not the maintainer's DMs. there are many experienced and reponsive experts (that's their spelling, we're keeping it, character-for-character 💀) who will be able to look at the problem and quickly address it. and please include a thorough description of the problem with code and data examples if at all possible. give them the whole story, not just the cliffhanger 🙈

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system so they 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 - Steve Chervitz 👑

email: sac-at-bioperl.org

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🌈 CONTRIBUTORS 🌈

parts of the code are based on SearchResultEventBuilder by Jason Stajich — jason@bioperl.org

Sendu Bala, bix@sendu.me.uk

shoutout to the collaborators, we love a group project that actually ships ⭐

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⭐ APPENDIX ⭐

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk — underscore = backstage pass 🎟️)

🍓 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 — go read your sibling's docs, they have lore 📚

💜 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

it's a vibe check for events. does this builder know how to process this event type? boolean says yes or no, periodt ✨

🌸 SAX methods 🌸

🎀 start_result 🎀

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

returns none. it just kicks off the cycle and walks away like a legend 💅

🦋 start_iteration 🦋

Title   : start_iteration
Usage   : $handler->start_iteration()
Function: Starts an Iteration event cycle
Returns : none
Args    : type of event and associated hashref

starts an Iteration event cycle. also returns none. also iconic.

🔥 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

closes out the Iteration event cycle and hands you back a Bio::Search::Iteration object — the rare one that actually gives you something back 🫶

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💀 reminder bestie: don't instantiate this directly, it's part of the SearchIO event based parsing system. use it through the system, not against it.

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and that's the whole page, no skips, no cuts, every single detail intact 💖 this was perl v5.32.1, dated 2021-08-15, from the Bio::S...Builder(3pm) manual — mwah, slay, go build some objects 🌈💅🎀