Bio::G...generic(3pm)

💖 Bio::G...generic — the "generic" glyph 💖

okay bestie, pull up a chair, because this is the User Contributed Perl Documentation page for Bio::Graphics::Glyph::generic, and honestly? she's the blueprint. the default. the moment. periodt.

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✨ NAME ✨

Bio::Graphics::Glyph::generic — The "generic" glyph 👑

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🎀 SYNOPSIS 🎀

See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

that's it, that's the synopsis, go read your faves 💅

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🦋 DESCRIPTION 🦋

So basically this glyph is identical to the "box" glyph, with one iconic little twist: it will draw the subparts of features that contain subfeatures. 👯‍♀️

But — and hear me out — the subparts are not connected. like, no lines linking them, no bridge, nothing. if that's the energy you want, go use the "segments" glyph instead, she does the connecting. 🔗

and the tea? "Generic" is the default glyph used when not otherwise specified. no cap. she's the fallback, the understudy who's actually the main character. 🌟

🌸 METHODS 🌸

okay so this module overrides the maxdepth() method so it returns 0 unless the -maxdepth option is provided explicitly. 💀

this is a big deal, bestie: it means any module that inherits from generic will need to override maxdepth() again in order to draw subfeatures. so in general, if you're implementing multi-segmented feature glyphs, you should inherit from Bio::Graphics::Glyph::segments instead — that one allows for one level of descent. 🙏

in addition, the following new methods are implemented:

• labelfont(), descfont(), labelwidth(), descriptionwidth() — return the font, width for the label or description. 🖋️
• label() — return the glyph label text (printed above the glyph). ⬆️
• description() — return the glyph description text (printed below the glyph). ⬇️
• draw_translation() — draw the protein translation of the feature (assumes that the feature is attached to a DNA sequence). 🧬
• draw_sequence() — draw the sequence of the feature (either DNA or protein). 🧪

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💅 OPTIONS 💅

the following options are standard among all Glyphs. see Bio::Graphics::Glyph for a full explanation. iykyk ✨

• -fgcolor — Foreground color. default: black 🖤
• -bgcolor — Background color. default: turquoise 💎
• -fillcolor — Synonym for -bgcolor. (yes girl, same thing, two names, we love an alias) 🪞
• -linewidth — Line width. default: 1 📏
• -height — Height of glyph. default: 10 📐
• -font — Default font. default: gdSmallFont 🔤
• -label_font — Font used for label. default: gdSmallFont 🏷️
• -desc_font — Font used for description. default: gdSmallFont 📝
• -connector — Connector type. default: 0 (false) 🔌
• -connector_color — Connector color. default: black 🖤
• -pad_top — Top padding. default: 0 ⬆️
• -pad_bottom — Bottom padding. default: 0 ⬇️
• -label — Whether to draw a label. default: 0 (false) 🏷️
• -label_position — Where to draw the label. default: "top" (default) or "left" 🧭
• -description — Whether to draw a description. default: 0 (false) 📝
• -strand_arrow — Whether to indicate strandedness. default: 0 (false) ➡️
• -hilite — Highlight color. default: undef (no color) 🖍️
• -draw_dna — If true, draw the dna residues when magnification level allows. default: 0 (false) 🧬
• -canonical_strand — If true, draw the dna residues as they appear on the plus strand even if the feature is on the minus strand. default: 0 (false) ➕

-pad_top and -pad_bottom allow you to insert some blank space between the glyph's boundary and its contents. this is useful if you are changing the glyph's height dynamically based on its feature's score. 📊 (padding = self-care for your glyphs, fr fr 🫶)

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😭 BUGS 😭

Please report them.

that's the whole section. yes really. please report them. we are begging. 🙈

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🌈 SEE ALSO 🌈

go off, read the whole squad:

Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse, Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments, Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle, Bio::Graphics::Glyph::xyplot, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD ✨

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👑 AUTHOR 👑

Allen Day <day@cshl.org>, Lincoln Stein <lincoln.stein@gmail.com> — icons, legends, the moment. 🫶

Copyright (c) 2001 Cold Spring Harbor Laboratory Copyright (c) 2010 Ontario Institute for Cancer Research

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. 📄

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and that's the whole page, bestie!! this beauty shipped with perl v5.30.0, dated 2019-11-25, and it lives under User Contributed Perl Documentation. slay, stay generic, and remember: no subparts were connected in the making of this glyph. 💖✨🎀🦋