Bio::A...elation(3pm)

✨ Bio::Annotation::Relation 💖

okay bestie, so this is the manual page for Bio::Annotation::Relation — yeah, your terminal is doing that thing where it squishes the name into Bio::A...elation(3pm) and honestly it's giving "we ran out of room on the label" 💀. Don't worry, it's the same page. It's part of the Bioperl docs (User Contributed Perl Documentation, if you're keeping score).

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🌸 NAME 🌸

Bio::Annotation::Relation — Relationship (pairwise) with other objects SeqI and NodeI;

literally just: this thing models a relationship between your annotation and some other object. pairwise. two. iconic.

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✨ SYNOPSIS ✨

use Bio::Annotation::Relation;
use Bio::Annotation::Collection;

my $col = Bio::Annotation::Collection->new();
my $sv = Bio::Annotation::Relation->new(-type => "paralogy" -to => "someSeqI");
$col->add_Annotation('tagname', $sv);

(yes, that's exactly how it's written in the original, no I did not "fix" it, we keep it verbatim bestie 🫶)

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🦋 DESCRIPTION 🦋

Scalar value annotation object.

That's it. That's the whole vibe. A scalar value annotation object. ✨

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💜 FEEDBACK 💜

🌈 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. (fr fr, they want to hear from you 🥹)

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. 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.

no cap: don't DM the maintainer, post to the list — there are actual experts there who'll clock your problem fast. And pls include code + data examples, the more detail the better 💅

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track 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: if you see a method starting with _, that's an internal one — not your main character, leave it be 🙈

⭐ new

• Title: new
• Usage: my $sv = Bio::Annotation::Relation->new();
• Function: Instantiate a new Relation object
• Returns: Bio::Annotation::Relation object
• Args:

-type    => $type of relation [optional]
-to     => $obj which $self is in relation to [optional]
-tagname  => $tag to initialize the tagname [optional]
-tag_term => ontology term representation of the tag [optional]

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🧚 AnnotationI implementing functions

💫 as_text

• Title: as_text
• Usage: my $text = $obj->as_text
• Function: return the string "Value: $v" where $v is the value
• Returns: string
• Args: none

💫 display_text

• Title: display_text
• Usage: my $str = $ann->display_text();
• Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation.

One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned

• Example:
• Returns: a string
• Args: [optional] callback

💫 hash_tree

• Title: hash_tree
• Usage: my $hashtree = $value->hash_tree
• Function: For supporting the AnnotationI interface just returns the value as a hashref with the key 'value' pointing to the value
• Returns: hashrf
• Args: none

💫 tagname

• Title: tagname
• Usage: $obj->tagname($newval)
• Function: Get/set the tagname for this annotation value.

Setting this is optional. If set, it obviates the need to provide a tag to AnnotationCollection when adding this object.

• Example:
• Returns: value of tagname (a scalar)
• Args: new value (a scalar, optional)

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🌈 Specific accessors for Relation

🍓 type

• Title: type
• Usage: $obj->type($newval)
• Function: Get/Set the type
• Returns: type of relation
• Args: newtype (optional)

🍓 to

• Title: to
• Usage: $obj->to($newval)
• Function: Get/Set the object which $self is in relation to
• Returns: the object which the relation applies to
• Args: new target object (optional)

🍓 confidence

• Title: confidence
• Usage: $self->confidence($newval)
• Function: Gives the confidence value.
• Example:
• Returns: value of confidence
• Args: newvalue (optional)

🍓 confidence_type

• Title: confidence_type
• Usage: $self->confidence_type($newtype)
• Function: Gives the confidence type.
• Example:
• Returns: type of confidence
• Args: newtype (optional)

🍓 tag_term

• Title: tag_term
• Usage: $obj->tag_term($newval)
• Function: Get/set the L<Bio::Ontology::TermI> object representing the tag name.

This is so you can specifically relate the tag of this annotation to an entry in an ontology. You may want to do this to associate an identifier with the tag, or a particular category, such that you can better match the tag against a controlled vocabulary.

This accessor will return undef if it has never been set before in order to allow this annotation to stay light-weight if an ontology term representation of the tag is not needed. Once it is set to a valid value, tagname() will actually delegate to the name() of this term.

• Example:
• Returns: a L<Bio::Ontology::TermI> compliant object, or undef
• Args: on set, new value (a L<Bio::Ontology::TermI> compliant object or undef, optional)

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

this was perl v5.32.1, dated 2021-08-15 — shoutout to the Bio::A...elation(3pm) page for existing, mwah 🫶💖