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

💖 Bio::SeqFeature::TypedSeqFeatureI 💖

okay bestie, so this is a page from the User Contributed Perl Documentation — you're looking at Bio::S...eatureI(3pm), and it's all about a strongly typed SeqFeature. sit down, hydrate, let's go 🫶

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✨ NAME ✨

Bio::SeqFeature::TypedSeqFeatureI — a strongly typed SeqFeature, no cap 💅

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🦋 SYNOPSIS 🦋

# get Sequence Features in some manner, eg
# from a Sequence object

foreach $sf ( $seq->get_SeqFeatures() ) {
    # all sequence features must have primary_tag() return a string
    $type_as_string = $sf->primary_tag();
    if( $sf->isa("Bio::SeqFeature::TypedSeqFeatureI") ) {
        $ot = $sf->ontology_term();
        print "Ontology identifier:",$ot->identifier(),
              " name:",$ot->name(),
              " Description:",$ot->description(),"\n";

    } else {
        print "Sequence Feature does not have an ontology type\n";
    }

}

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🌸 DESCRIPTION 🌸

So basically, this interface describes the extension of SeqFeatureI to being a strongly typed SeqFeature. it's giving glow-up, honestly ✨

Bio::SeqFeature::TypedSeqFeatureI extends the Bio::SeqFeatureI interface — meaning a TypedSeqFeatureI feature must also implement all of the Bio::SeqFeatureI interface too. no skipping, bestie, it's a package deal 🎀

It is suggested that the primary_tag() method of SeqFeatureI return the same as the ontology_term()->name() of the OntologyTypedI (ie, the "string" name of the ontology type is used as the primary tag), but this should not be assumed by client code, because there are scenarios where one would like to maintain the difference. iykyk 🙈

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated — fr fr, they want to hear from you 🥺

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. 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. like, give them the whole lore, not just the vibes 💀

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us 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 - Ewan Birney 👑

Email - please email the BioPerl mailing list above.

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🎀 APPENDIX 🎀

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — so if you see an underscore, mind your business, that's the backend 💅

⭐ ontology_term ⭐

Title   : ontology_term
Usage   : my $ot = $seqfeature->ontology_term()
Returns : a Bio::Ontology::TermI compliant object
Args    : none
Status  : public

This method returns the ontology term for a strongly typed sequence feature. that's it, that's the method, and it ate 🔥

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🧚 quick vibe check: every flag, argument, return value and link up there is exactly as the original says it. no invented lore, bestie, only certified facts.

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perl v5.32.1 🌈 2021-08-15 🌈 Bio::S...eatureI(3pm)

and that's the whole page, mwah 💋 ty for reading, go forth and type your features responsibly 🌸💖🦋