Bio::T...odeNHX(3pm)

💖 Bio::Tree::NodeNHX — a Simple Tree Node with support for NHX tags 💖

okay bestie, pull up a chair, we're doing phylogenetic trees today 🌳✨ the module is Bio::Tree::NodeNHX, and yes the manpage header says Bio::T...odeNHX(3pm) because Unix is dramatic and truncates things, but we know her full name 💅

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🌸 NAME 🌸

Bio::Tree::NodeNHX — a Simple Tree Node with support for NHX tags 🦋

it's giving "small module, big tree energy" and honestly? iconic.

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✨ SYNOPSIS ✨

use Bio::Tree::NodeNHX;
my $nodeA = Bio::Tree::NodeNHX->new();
my $nodeL = Bio::Tree::NodeNHX->new();
my $nodeR = Bio::Tree::NodeNHX->new();

my $node = Bio::Tree::NodeNHX->new();
$node->add_Descendents($nodeL);
$node->add_Descendents($nodeR);

print "node is not a leaf \n" if( $node->is_leaf);

look at her go 🫶 three lil nodes, one parent node, two descendents attached, and then a check on is_leaf. (yes $nodeA is just vibing there unused, she's main character energy for no reason, we love her anyway 💀)

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🎀 DESCRIPTION 🎀

Makes a Tree Node with NHX tags, suitable for building a Tree. 🌈

and if you want the full list of functionality, go read Bio::Tree::Node — this one is her cute NHX-flavored sibling. no cap.

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💌 FEEDBACK 💌

🌷 Mailing Lists 🌷

User feedback is an integral part of the evolution of this and other Bioperl modules. fr fr. 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. the way that so 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. (like, give us the receipts, bestie 📎)

🐛 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 asking you to file the bug instead of suffering in silence 😭 do it for the plot.

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👑 AUTHOR - Aaron Mackey 👑

Email amackey@virginia.edu

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🌟 CONTRIBUTORS 🌟

The NHX (New Hampshire eXtended) format was created by Chris Zmasek, and is described at:

http://sourceforge.net/projects/forester-atv/

shoutout to Chris, absolute legend, ate and left no crumbs 🔥

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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 means "you probably shouldn't be calling me directly, bestie").

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🦋 new 🦋

• Title: new
• Usage: my $obj = Bio::Tree::NodeNHX->new();
• Function: Builds a new Bio::Tree::NodeNHX object
• Returns: Bio::Tree::NodeNHX
• Args:
  • -left => pointer to Left descendent (optional)
  • -right => pointer to Right descenent (optional)
  • -branch_length => branch length [integer] (optional)
  • -bootstrap => bootstrap value (string)
  • -description => description of node
  • -id => unique id for node
  • -nhx => hashref of NHX tags and values

(yes it literally says descenent in the original, we are preserving her exactly as she is, no edits, periodt 💅)

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🌸 nhx_tag 🌸

• Title: nhx_tag
• Usage: my $tag = $nodenhx->nhx_tag(%tags);
• Function: Set tag-value pairs for NHX nodes
• Returns: none
• Args: hashref to update the tags/value pairs

OR

with a scalar value update the bootstrap value by default

so like, hand her a hashref and she updates the tag/value pairs, or hand her a plain scalar and she'll update the bootstrap value by default. two moods, one method 🎀

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and that's the whole page, bestie!! you now know Bio::Tree::NodeNHX better than most people know their own wifi password. slay 💜

perl v5.32.1 — 2021-08-15 — Bio::T...odeNHX(3pm) 🎀 that's the version, the date, and the lil truncated title, mwah, bye 💖✨🦋🌸💅🫶