Bio::ClusterI(3pm)

💖 Bio::ClusterI — Cluster Interface 💖

okay bestie, welcome to Bio::ClusterI(3pm), from the User Contributed Perl Documentation collection. yes it's a 3pm page, yes it's a real one, and yes it's lowkey the blueprint for every cluster of bioperl objects you're ever gonna meet. sit down, grab a strawberry 🍓, we're doing interfaces.

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✨ SYNOPSIS ✨

# 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");

so like. you build a cluster with a description and some members, you grab all the members, and if you're feeling ✨picky✨ you grab some of the members with criteria. that's the whole vibe check right there. 💅

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🌸 DESCRIPTION 🌸

This interface is the basic structure for a cluster of bioperl objects. fr fr, that's its whole job — be the shape of a cluster.

and here's the tea: it is up to the implementer to check arguments and initialize whatever new object the implementing class is designed for. so Bio::ClusterI itself is not out here doing the work, it's just the icon, the blueprint, the main character energy that every implementing class has to live up to. 👑

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📬 FEEDBACK 📬

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. (translation: they literally want to hear from you, bestie.) 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. (yes, slide into the group chat, not the DMs. 🙈) 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.

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 - 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 _ (iykyk, underscore = private business, don't touch 🫣).

Implementation Specific Functions

These functions are the ones that a specific implementation must define. no skipping, no "I'll do it later", periodt. 💀

new

We don't mandate but encourage implementors to support at least the following named parameters upon object initialization. (so it's a soft launch, not a hard requirement ✨)

• -display_id — the display ID or name for the cluster
• -description — the consensus description or name of the cluster
• -members — the array of objects belonging to the family

display_id

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

grab the display name or identifier for the cluster and it hands you back a string. that's it, that's the function. 🌈

description

Title   : description
Usage   : Bio::ClusterI->description("POLYUBIQUITIN")
Function: get/set for the consensus description of the cluster
Returns : the description string
Args    : Optional the description string

get/set for the consensus description of the cluster — pass in the description string if you want to set it (it's optional!), and it returns the description string. a classic little get/set moment. 💜

size

Title   : size
Usage   : Bio::ClusterI->size();
Function: get/set for the size of the family,
          calculated from the number of members
Returns : the size of the family
Args    :

get/set for the size of the family, and bestie, it's calculated from the number of members. it returns the size of the family. math, but make it bioperl. 🧚

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

get/set for cluster_score, which represent the score in which the clustering algorithm assigns to this cluster. returns a number. it's giving algorithmic judgement, honestly. 🔥

get_members

Title   : get_members
Usage   : Bio::ClusterI->get_members(($seq1, $seq2));
Function: retrieve the members of the family by some criteria, for
          example :
          $cluster->get_members(-species => 'homo sapiens');

          Will return all members if no criteria are provided.

Returns : the array of members
Args    :

retrieve the members of the family by some criteria, for example:

$cluster->get_members(-species => 'homo sapiens');

and the crucial bit — Will return all members if no criteria are provided. so no criteria = no filter = everybody's invited to the party. 🎉

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ok that's the whole page, no cap. Bio::ClusterI is an interface, it's chill, it's iconic, and now you know it. 💅

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and finally, the receipts bestie: this was perl v5.34.0, dated 2022-03-27, and it's Bio::ClusterI(3pm). mwah. 💖✨🎀🦋🌸