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

🎀 Bio::Annotation::SimpleValue 🎀

okay bestie, welcome to the manual page for Bio::Annotation::SimpleValue(3pm) — it lives in the User Contributed Perl Documentation corner of the Perl universe, and it's genuinely one of the most chill little modules you'll ever meet. let's get into it 💅

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✨ NAME ✨

Bio::Annotation::SimpleValue — a simple scalar. that's it. that's the whole vibe. one value, holding space, being iconic 🫶

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🌸 SYNOPSIS 🌸

look, here's the whole thing in action, no cap:

use Bio::Annotation::SimpleValue;
use Bio::Annotation::Collection;

my $col = Bio::Annotation::Collection->new();
my $sv = Bio::Annotation::SimpleValue->new(-value => 'someval');
$col->add_Annotation('tagname', $sv);

see? you make a collection, you make a simple value, you tuck it in. that's the group chat. 💖

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🦋 DESCRIPTION 🦋

Scalar value annotation object. lowkey does exactly what it says on the tin and honestly? we love a self-aware queen. 👑

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💌 FEEDBACK 💌

Mailing Lists

okay so user feedback is, like, an integral part of the evolution of this and other Bioperl modules — literally the whole thing grows because people speak up. so if you've got comments or suggestions, send them preferably to one of the Bioperl mailing lists. your participation is much appreciated, fr fr. 🥹

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

pleaseee direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

...and not straight to the module maintainer, bestie. the whole point is that lots of experienced and reponsive experts can look at your problem and quickly address it. and if it's at all possible, include a thorough description of the problem with code and data examples — the more context, the faster the slay. ✨

Reporting Bugs

found a bug? report it 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 — Ewan Birney 👑

Email: birney@ebi.ac.uk

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🌈 APPENDIX 🌈

the rest of the documentation details each of the object methods. internal methods are usually preceded with an _ (iykyk — underscore means don't touch unless you know what you're doing 🙈).

new

• Title: new
• Usage: my $sv = Bio::Annotation::SimpleValue->new();
• Function: Instantiate a new SimpleValue object
• Returns: Bio::Annotation::SimpleValue object
• Args:
  • -value => $value to initialize the object data field [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 SimpleValue 💅

value

• Title: value
• Usage: $obj->value($newval)
• Function: Get/Set the value for simplevalue
• Returns: value of value
• Args: newvalue (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!! 🥳 this was perl v5.32.1, dated 2021-08-15, and it's the Bio::Annotation::SimpleValue(3pm) manpage — go forth and annotate your scalars, you absolute main character 💖✨🎀