Bio::S...mer3Hit(3pm)

✨ NAME ✨

Bio::Search::Hit::hmmer3Hit — it's literally the object, bestie. The full title on the tin is Bio::S...mer3Hit(3pm) from the User Contributed Perl Documentation, and the description is... well. It's "DESCRIPTION of Object". That's the whole thing. No notes. 💅

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🌸 SYNOPSIS 🌸

Okay so the synopsis here is literally:</purgle>

Give standard usage here

That's it. That's the synopsis. We move. 🦋

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🎀 DESCRIPTION 🎀

And the description? It says:

Describe the object here

Iconic placeholder behavior, honestly. It's giving "I'll finish my homework later" and I respect it. 😭

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💖 FEEDBACK 💖

💌 Mailing Lists

Bestie, feedback is the integral part of the evolution of this module and every other Bioperl module out there. Send your comments and suggestions — preferably to the Bioperl mailing list — because your participation is much appreciated. Fr fr. 🫶

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

🫂 Support

Usage questions and support issues go to the mailing list:

bioperl-l@bioperl.org

...and not straight to the module maintainer, okay? Because there are so many experienced and responsive experts on that list who will clock your problem and address it quickly. Just please, for the love of everything, include a thorough description of the problem — with code and data examples if at all possible. Details = slay. ✨

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of them and their resolution. Bug reports can be submitted via the web right here:

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

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👑 AUTHOR - Thomas Sharpton 👑

Email: thomas.sharpton@gmail.com

And then it says "Describe contact details here." Which is, again, a placeholder living its best life. Not me pointing it out. 🙈

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🌈 CONTRIBUTORS 🌈

Additional contributors names and emails here

Yeah bestie, that's the entire contributors section. It's giving mystery. 🔥

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🧚 APPENDIX 🧚

Okay so the rest of the documentation details each of the object methods. And heads up: internal methods are usually preceded with a _ — iykyk. 💅

⭐ new

Title   : new
Usage   : my $obj = Bio::Search::Hit::HMMERHit->new();
Function: Builds a new Bio::Search::Hit::HMMERHit object
Returns : Bio::Search::Hit::HMMERHit
Args    :

Plus the Bio::Search::Hit::GenericHit inherited params, which are:

-name         => Name of Hit (required)
-description  => Description (optional)
-accession    => Accession number (optional)
-length       => Length of the Hit (optional)
-score        => Raw Score for the Hit (optional)
-significance => Significance value for the Hit (optional)
-algorithm    => Algorithm used (BLASTP, FASTX, etc...)
-hsps         => Array ref of HSPs for this Hit.

Note that -name is required, bestie — the rest are optional. Don't come for me when it complains. 🫶

🌸 next_domain

Title   : next_domain
Usage   : my $domain = $hit->next_domain();
Function: An alias for L<next_hsp()>, this will return the next HSP
Returns : L<Bio::Search::HSP::HSPI> object
Args    : none

It's an alias for next_hsp(), it hands you the next HSP, and it takes no args. Simple, clean, iconic. ✨

🦋 domains

Title   : domains
Usage   : my @domains = $hit->domains();
Function: An alias for L<hsps()>, this will return the full list of hsps
Returns : array of L<Bio::Search::HSP::HSPI> objects
Args    : none

Alias for hsps() — you get the full list of hsps back as an array of L<Bio::Search::HSP::HSPI> objects. No args needed. Ate. 🔥

💜 bits

Usage     : $hit_object->bits();
Purpose   : Gets the bit score of the best HSP for the current hit.
Example   : $bits = $hit_object->bits();
Returns   : Integer or undef if bit score is not set
Argument  : n/a

See Also: score()

Heads up: this returns an Integer — or undef if the bit score is not set. Don't be surprised, bestie. 💀

🎀 iteration

Title   : iteration
Usage   : $obj->iteration($newval)
Function: PSI-BLAST iteration
Returns : value of iteration
Args    : newvalue (optional)

It's the PSI-BLAST iteration. Returns the value of iteration, and newvalue is optional. That's the whole vibe. 💅

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And that's the whole page, bestie! This was perl v5.30.0, dated 2019-10-29, straight from the User Contributed Perl Documentation — the Bio::S...mer3Hit(3pm) original. Slay, mwah. 💖✨🎀