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

💖 Bio::Seq::SeqFactory 💖

okay bestie, so this page is from Bio::Seq::SeqFactory, which lives in the User Contributed Perl Documentation section of the manual (that's the 3pm vibe, iykyk). And like… it's giving factory energy. Let's get into it 🫶

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✨ NAME ✨

Bio::Seq::SeqFactory — instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory 💅

no cap, that's literally the whole job. a lil factory that spits out sequence objects.

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🌸 SYNOPSIS 🌸

use Bio::Seq::SeqFactory;
my $factory = Bio::Seq::SeqFactory->new();
my $primaryseq = $factory->create( -seq => 'WYRAVLC',
                                   -id  => 'name'     );

# Create Bio::Seq instead of Bio::PrimarySeq objects:
my $factory = Bio::Seq::SeqFactory->new( -type => 'Bio::Seq' );

see how easy that was?? copy, paste, slay. ✨

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🦋 DESCRIPTION 🦋

so this object will build Bio::PrimarySeqI and Bio::SeqI objects generically. that's it. that's the whole vibe. it's a factory. it makes seqs. main character energy fr fr.

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📬 FEEDBACK 📬

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules. so send your comments and suggestions, preferably to the Bioperl mailing list. your participation is much appreciated 🥺

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. lowkey there are so many experienced and reponsive experts who 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 🙏

🐛 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@bioperl.org — iconic, we stan 💜

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🎀 APPENDIX 🎀

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (noted, bestie, noted).

🌟 new

Title   : new
Usage   : my $obj = Bio::Seq::SeqFactory->new();
Function: Builds a new Bio::Seq::SeqFactory object
Returns : Bio::Seq::SeqFactory
Args    : -type => string, name of a PrimarySeqI derived class
                   This is optional. Default=Bio::PrimarySeq.

so yeah, -type is optional — if you don't pass it, you get Bio::PrimarySeq by default. cute.

🌈 create

Title   : create
Usage   : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name');
Function: Instantiates new Bio::SeqI (or one of its child classes)
          This object allows us to genericize the instantiation of sequence
          objects.
Returns : Bio::PrimarySeq object (default)
          The return type is configurable using new(-type =>"...").
Args    : initialization parameters specific to the type of sequence
          object we want.  Typically
          -seq        => $str,
          -display_id => $name

this is the moment the factory actually does its thing. the return type is configurable using new(-type =>"..."), so you're never stuck with the default if you don't want it 💅

⭐ type

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

getter/setter situation. pass a new value and it sets, don't pass one and it just tells you the value of type. classic ✨

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⚠️ heads up bestie: that Function: line under type is literally empty in the original. not me forgetting it — it's just like that. we respect the source 😭

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and that's the whole page!! no notes, ate and left no crumbs 🍓🧚

perl v5.32.1 · 2021-08-15 — mwah, that's the version and date this lil doc was generated, so if you're reading this from the future, hi, hope the seqs are sequencing 💖