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

💖 Bio::Search::Result::hmmer3Result 💖

okay bestie, gather round, because we're looking at Bio::S...3Result — that's the perl manual page for Bio::Search::Result::hmmer3Result, a module in the User Contributed Perl Documentation collection. she's giving "template that got committed before anyone filled her in" and honestly? iconic behaviour. let's read her anyway 💅

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✨ NAME ✨

Bio::Search::Result::hmmer3Result — the description of the object. and yes, the official description literally says "DESCRIPTION of Object". no notes. we love a placeholder queen 🎀

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🌸 SYNOPSIS 🌸

okay so the synopsis says, and I quote, "Give standard usage here". that's it. that's the whole synopsis. she's manifesting her own documentation rn 🦋

bestie if you're looking for the actual usage, scroll down to APPENDIX — that's where the real methods live 💖

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🫶 DESCRIPTION 🫶

"Describe the object here."

periodt. that's the entire description. she said figure it out yourself and honestly, respect 💀

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💌 FEEDBACK 💌

🌈 Mailing Lists 🌈

User feedback is, like, an integral part of the evolution of this module and all the other Bioperl modules. so if you have comments or suggestions, send them — 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 🧚

okay this part is important, bestie, so listen up: please send your usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

...and not straight to the module maintainer. there are so many experienced and responsive experts on that list who can look at your problem and address it quickly. and please — if at all possible — include a thorough description of the problem with code and data examples. give them the whole lore, not just the vibe 🙏

🐛 Reporting Bugs 🐛

found a bug? report it to the Bioperl bug tracking system so the team can keep track of bugs and how they get resolved. bug reports can be submitted via the web here:

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

do it for the plot 🦋

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👑 AUTHOR - Thomas Sharpton 👑

Email: thomas.sharpton@gmail.com

(and then the page says "Describe contact details here." — she's still workshopping it, we support her 💜)

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🎀 CONTRIBUTORS 🎀

the page says: "Additional contributors names and emails here". so... the contributor list is currently a mood board. when they show up, they'll be listed here ✨

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💅 APPENDIX 💅

okay this is the good part!! the rest of the documentation details each of the object methods. and heads up — internal methods are usually preceded with a _, so if you see an underscore, that's an inside-job method, iykyk.

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🌸 new

• Title — new
• Usage — my $obj = new Bio::Search::Result::hmmer3Result.pm();
• Function — Builds a new Bio::Search::Result::hmmer3Result.pm object
• Returns — an instance of Bio::Search::Result::hmmer3Result.pm
• Args — -hmm_name => string, name of hmm file and -sequence_file => name of the sequence file

it's giving "birth". you hand her the name of the hmm file and the name of the sequence file, and she hands you back a whole object. slay 🫶

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🦋 hmm_name

• Title — hmm_name
• Usage — $obj->hmm_name($newval)
• Function — Get/Set the value of hmm_name
• Returns — value of hmm_name
• Args — newvalue (optional)

getter and setter in one, main character energy. pass a newvalue to set it, pass nothing to just read it 💅

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🎀 sequence_file

• Title — sequence_file
• Usage — $obj->sequence_file($newval)
• Function — Get/Set the value of sequence_file
• Returns — value of sequence_file
• Args — newvalue (optional)

same deal, same energy — optional newvalue, get or set, no cap 🌸

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🔥 next_model

• Title — next_model
• Usage — my $domain = $result->next_model
• Function — Returns the next domain — this is an alias for next_hit
• Returns — L<Bio::Search::Hit::HitI> object
• Args — none

okay important detail: she calls it a domain in the usage and the function line, but the function is literally an alias for next_hit. so it's the same thing wearing a different outfit 💖 no args, she just gives you the next Bio::Search::Hit::HitI object.

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💜 models

• Title — models
• Usage — my @domains = $result->models;
• Function — Returns the list of HMM models seen — this is an alias for hits()
• Returns — Array of L<Bio::Search::Hit::HitI> objects
• Args — none

she returns the whole list of HMM models, as an array of Bio::Search::Hit::HitI objects. and again — alias alert — this is hits(). same girly, plural edition 🎀

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🌈 rewind

• Title — rewind
• Usage — $result->rewind;
• Function — Allow one to reset the Hit iteration to the beginning. Since this is an in-memory implementation
• Returns — none
• Args — none

you know when you finish the list and you wanna start over? that's her. she resets the Hit iteration back to the beginning. and the reason she can do that so casually is because this is an in-memory implementation — no disk drama, just vibes ✨

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💀 tiny disclaimer bestie: the NAME, SYNOPSIS and DESCRIPTION sections of this page are genuinely, canonically placeholders. I'm not making that up, I'm reporting it. everything else above is exactly what she says.

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and that's the page!! she was written by Thomas Sharpton, she ships with perl v5.30.0, and she was dated 2019-10-29. thanks for coming to my ted talk, go read the actual methods, mwah 💖🎀🦋🌸💅