Bio::C...FamilyI(3pm)

💖 NAME 💖

Bio::Cluster::FamilyI — it's the Family Interface, bestie. That's the whole name, that's the whole vibe. It's a Perl module (you clocked the (3pm), right? iykyk).

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✨ SYNOPSIS ✨

okay so real talk, you don't instantiate this one directly — you go look at whoever implements this interface for the deets. But here's the shape of it:

# see the implementations of this interface for details

my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
                           -members    =>[$seq1,$seq2]);
my @members = $cluster->get_members();
my @sub_members = $cluster->get_members(-species=>"homo sapiens");

like. she's giving interface. she's giving polymorphism. we stan a pluggable abstraction. 💅

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🦋 DESCRIPTION 🦋

This here interface is for a Family object — as in, an object representing a whole family of biological objects. Your squad of sequences. Your little found family of biomolecules. 🫶

A generic implementation for this may be found a Bio::Cluster::Family. (that's where the actual code lives, this one's just the contract, no cap)

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🌸 FEEDBACK 🌸

💌 Mailing Lists

User feedback is, like, an integral part of the evolution of this and other Bioperl modules — literally the whole glow-up depends on y'all. Send your comments and suggestions 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

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. The reason is that many experienced and responsive experts will be able to 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 — the more receipts you bring, the faster someone can help. 🙏

🐛 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

not me filing a bug report with zero repro steps… bestie PLEASE include the code and the data, the maintainers are begging 😭

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👑 AUTHOR - Shawn Hoon

Email shawnh@fugu-sg.org

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🎀 APPENDIX 🎀

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (yes, the underscore is the "do not touch, that's private, mind your business" flag 💀).

⭐ new

We don't mandate but encourage implementors to support at least the following named parameters upon object initialization. (translation: you can skip them, but don't be that person, okay?)

• -family_id — the name of the family
• -description — the consensus description of the family
• -annotation_score — the confidence by which the consensus description is representative of the family
• -members — the members belonging to the family
• -alignment — the multiple alignment of the members

⭐ family_id

• Title : family_id
• Usage : Bio::Cluster::FamilyI->family_id("znfp");
• Function: get/set for the family id
• Returns : the family id
• Args : the family id

⭐ family_score

• Title : family_score
• Usage : Bio::Cluster::FamilyI->family_score(95);
• Function: get/set for the score of algorithm used to generate the family if present
• Returns : the score
• Args : the score

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🌈 Methods inherited from Bio::ClusterI 🌈

⭐ display_id

• Title : display_id
• Usage :
• Function: Get the display name or identifier for the cluster
• Returns : a string
• Args :

⭐ get_members

• Title : get_members
• Usage : Bio::Cluster::FamilyI->get_members();
• Function: get the members of the family
• Returns : the array of members
• Args : the array of members

⭐ description

• Title : description
• Usage : Bio::Cluster::FamilyI->description("Zinc Finger Protein");
• Function: get/set for the description of the family
• Returns : the description
• Args : the description

⭐ size

• Title : size
• Usage : Bio::Cluster::FamilyI->size();
• Function: get/set for the description of the family
• Returns : size
• Args :

⭐ cluster_score

• Title : cluster_score
• Usage : $cluster ->cluster_score(100);
• Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster.
• Returns : a number

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and that's the whole page, bestie!! this one's from perl v5.34.0, dated 2022-03-27, and it's the User Contributed Perl Documentation for Bio::C...FamilyI (3pm). go forth and cluster your families. slay. 💅✨🧬