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

💖 Bio::Tree::AnnotatableNode 💖

okay bestie, welcome to the Bio::Tree::AnnotatableNode page — it's a chunk of User Contributed Perl Documentation and honestly? it's giving tree-node-with-extras. it's the one where your node can also hold vibes (by which i mean annotations). let's go 🦋

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✨ NAME ✨

Bio::Tree::AnnotatableNode — a Tree Node with support for annotation 💅

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🌸 SYNOPSIS 🌸

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

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

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

# $node is-a Bio::AnnotatableI, hence:
my $ann_coll = $node->annotation();
# $ann_coll is-a Bio::AnnotationCollectionI, hence:
my @all_anns = $ann_coll->get_Annotations();
# do something with the annotation objects

no cap, that last part is the whole point — you grab the collection, you grab the annotations, you do whatever you want with the annotation objects ✨

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🎀 DESCRIPTION 🎀

it makes a Tree Node with Annotations, and it's suitable for building a Tree. if you want the full list of functionality, go look at Bio::Tree::Node — that's where the rest of the moves live 🫶

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🫶 FEEDBACK 🫶

Mailing Lists 💌

user feedback is, like, an integral part of the evolution of this and other Bioperl modules. so 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. why? because many experienced and reponsive experts will be able look at the problem and quickly address it 👑 and please include a thorough description of the problem with code and data examples if at all possible — the more detail the better, bestie.

Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system so we can 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 - Mira Han 👑

email mirhan@indiana.edu

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🧚 APPENDIX 🧚

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk) 💀

new ⭐

• Title — new
• Usage — my $obj = Bio::Tree::AnnotatableNode->new();
• Function — Builds a new Bio::Tree::AnnotatableNode object
• Returns — Bio::Tree::AnnotatableNode
• Args — -tostring => code reference to the tostring callback function (optional)

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Methods for implementing Bio::AnnotatableI 💜

annotation 🎀

• Title — annotation
• Usage — $ann = $node->annotation or $node->annotation($ann)
• Function — Gets or sets the annotation
• Returns — Bio::AnnotationCollectionI object
• Args — None or Bio::AnnotationCollectionI object

see Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information 👀

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Methods for implementing tag access through Annotation::SimpleValue 🍓

add_tag_value 🏷️

• Title — add_tag_value
• Usage — $node->add_tag_value($tag,$value)
• Function — Adds a tag value to a node
• Returns — number of values stored for this tag
• Args — $tag — tag name; $value — value to store for the tag

remove_tag ✂️

• Title — remove_tag
• Usage — $node->remove_tag($tag)
• Function — Remove the tag and all values for this tag
• Returns — boolean representing success (0 if tag does not exist)
• Args — $tag — tagname to remove

remove_all_tags 💥

• Title — remove_all_tags
• Usage — $node->remove_all_tags()
• Function — Removes all tags
• Returns — None
• Args — None

get_all_tags 📋

• Title — get_all_tags
• Usage — my @tags = $node->get_all_tags()
• Function — Gets all the tag names for this Node
• Returns — Array of tagnames
• Args — None

get_tag_values 🔍

• Title — get_tag_values
• Usage — my @values = $node->get_tag_value($tag)
• Function — Gets the values for given tag ($tag)
• Returns — Array of values or empty list if tag does not exist
• Args — $tag — tag name

has_tag ✅

• Title — has_tag
• Usage — $node->has_tag($tag)
• Function — Boolean test if tag exists in the Node
• Returns — Boolean
• Args — $tag — tagname

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Methods for implementing to_string 🪄

to_string_callback 🎯

• Title — to_string_callback
• Usage — $node->to_string_callback(\&func)
• Function — get/set callback for to_string
• Returns — code reference for the to_string callback function
• Args — \&func — code reference to be set as the callback function

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Methods for accessing Bio::Seq 🧬

sequence 🌸

• Title — sequence
• Usage — $ann = $node->sequence or $node->sequence($seq)
• Function — Gets or sets the sequence
• Returns — array reference of Bio::SeqI objects
• Args — None or Bio::SeqI object

see Bio::SeqI and Bio::Seq for more information 💖

has_sequence 🌟

• Title — has_sequence
• Usage — if( $node->has_sequence) { # do something }
• Function — tells if node has sequence attached
• Returns — Boolean for whether or not node has Bio::SeqI attached.
• Args — None

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and that's the whole page, bestie — you ate it UP 💅✨

this was served to you straight outta User Contributed Perl Documentation, perl v5.32.1, dated 2021-08-15. go build a tree that knows things, queen 👑🦋💜