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

💖 Bio::Annotation::Target 💖

okay bestie, welcome to the manual page for Bio::Annotation::Target — that's a Perl module from the BioPerl crew (this copy lives in the User Contributed Perl Documentation section, section 3pm, iykyk) 🫶

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✨ NAME ✨

Bio::Annotation::Target — it's giving "object that represents a target". And by target we mean a similarity hit, like when one object goes "omg I match something over in this other database" 👀

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🌸 SYNOPSIS 🌸

ok so you can build one the constructor way:

$target1 = Bio::Annotation::Target->new(-target_id  => 'F321966.1',
                                       -start      => 1,
                                       -end        => 200,
                                       -strand     => 1,   # or -1
                                      );

or, alternatively, the build-it-up-yourself way:

$target2 = Bio::Annotation::Target->new();
$target2->target_id('Q75IM5');
$target2->start(7);
# ... etc ...

and here's the part where it gets main character energy: Target is-a Bio::AnnotationI object, so you can drop it into annotation collections — like the one chillin' on features or seqs 💅

$feat->annotation->add_Annotation('Target', $target2);

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🦋 DESCRIPTION 🦋

So basically: this gives you an object that represents a target (aka a similarity hit) going from one object to something in another database. And the cute part? It does not prescribe what's in that other database. It's like, unbothered. It's not gonna tell you what the other database is doing with its life. It just represents the hit. periodt ✨

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👑 AUTHOR - Scott Cain 👑

Scott Cain — cain@cshl.org

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🎀 APPENDIX 🎀

The rest of this doc goes into detail on each of the object methods. Heads up: internal methods usually get an underscore _ in front of them, so if you see one, that's why 🧚

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🌈 AnnotationI implementing functions 🌈

as_text

• Title: as_text
• Usage:
• Function:
• Example:
• Returns:
• Args:

ngl bestie this one's just an empty shell in the docs, no cap. All vibes, no details 💀

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

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 Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already.

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

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💜 Specific accessors for Targets 💜

target_id

Usage

$obj->target_id()        #get existing value
$obj->target_id($newval) #set new value

Function

Returns

value of target_id (a scalar)

Arguments

new value of target_id (to set)

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okay that's the whole page bestie, you ate that 🍓

signing off with the deets: this is perl v5.32.1, dated 2021-08-15, and the page itself is Bio::Annotation::Target(3pm) — love u, go annotate something iconic 💖✨🌸