TFBS::PatternI(3pm)

🌸 TFBS::PatternI 💖

okay bestie, welcome to the manual page for TFBS::PatternI (that's the 3pm one, the Perl module doc, not a command — very important, don't @ me) ✨

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👑 NAME

TFBS::PatternI — the interface definition for all the pattern objects. Right now it's giving matrices and word (consensus and regular expressions) 🎀

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💅 DESCRIPTION

So, TFBS::PatternI is a draft class that's supposed to hold the general interface for matrix and other (future ✨) pattern objects.

But here's the tea 🫖 — it is not defined and not used yet, because the author needs to ponder over certain unresolved issues in general pattern definition. Classic main character behaviour, honestly.

User feedback is more than welcome — like literally please, the author wants it 🙈.

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🦋 FEEDBACK

Please send bug reports and other comments to the author. That's it, that's the vibe. 📬

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👑 AUTHOR - Boris Lenhard

Boris Lenhard <Boris.Lenhard@cgb.ki.se> — the icon, the legend 🌟

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📖 APPENDIX

The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore. iykyk 💫

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⭐ ID

• Title: ID
• Usage:

my $ID = $icm->ID()
$pfm->ID('M00119');

• Function: Get/set on the ID of the pattern (unique in a DB or a set) 🔥
• Returns: pattern ID (a string)
• Args: none for get, string for set

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⭐ name

• Title: name
• Usage:

my $name = $pwm->name()
$pfm->name('PPARgamma');

• Function: Get/set on the name of the pattern 🏷️
• Returns: pattern name (a string)
• Args: none for get, string for set

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⭐ class

• Title: class
• Usage:

my $class = $pwm->class()
$pfm->class('forkhead');

• Function: Get/set on the structural class of the pattern 🧬
• Returns: class name (a string)
• Args: none for get, string for set

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⭐ tag

• Title: tag
• Usage:

my $acc = $pwm->tag('acc')
$pfm->tag(source => "Gibbs");

• Function: Get/set on the structural class of the pattern
• Returns: tag value (a scalar/reference)
• Args: tag name (string) for get, tag name (string) and value (any scalar/reference) for set 🎀

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⭐ all_tags

• Title: all_tags
• Usage:

my %tag = $pfm->all_tags();

• Function: get a hash of all tags for a matrix
• Returns: a hash of all tag values keyed by tag name
• Args: none 💖

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⭐ delete_tag

• Title: delete_tag
• Usage:

$pfm->delete_tag('score');

• Function: get a hash of all tags for a matrix
• Returns: nothing (yeah, it said "nothing", and it meant it 💀)
• Args: a string (tag name)

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k that's the whole page, bestie. go forth and build those pattern objects ✨🫶

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this was TFBS::PatternI(3pm), from perl v5.42.3, dated 2026-08-21 — slayed, no cap, periodt 💅🌈