Ace::S...:Homol(3pm)

💖 Ace::Sequence::Homol 💖

okay bestie, gather round, because this is Ace::S...:Homol(3pm) — the Temporary Sequence Homology Class — straight out of the User Contributed Perl Documentation. she's little. she's temporary. she's doing her best. let's go 🦋

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✨ NAME ✨

Ace::Sequence::Homol — Temporary Sequence Homology Class</p>. yes the class itself is telling you it's temporary, she's honest like that 💅

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🎀 SYNOPSIS 🎀

here's the whole vibe in code form, no notes:

# Get all similarity features from an Ace::Sequence
@homol = $seq->features('Similarity');

# sort by score
@sorted = sort { $a->score <=> $b->score } @homol;

# the last one has the highest score
$best = $sorted[$#sorted];

# fetch its associated Ace::Sequence::Homol
$homol = $best->target;

# print out the sequence name, DNA, start and end
print $homol->name,' ',$homol->start,'-',$homol->end,"\n";
print $homol->asDNA;

see how $best->target just hands you the whole Ace::Sequence::Homol? iconic of her ✨

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💜 DESCRIPTION 💜

so Ace::Sequence::Homol is a subclass of Ace::Object — not Ace::Sequence, okay, don't get it twisted — and she's specialized for returning information about a DNA or protein homology.

and girl. she is a temporary placeholder. like, literally, that's her whole deal. she's standing in for a more sophisticated homology class that will (eventually, someday) include support for alignments. so enjoy her while she's here 🫶

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🌸 OBJECT CREATION 🌸

fr fr, you will not ordinarily create an Ace::Sequence::Homol object directly. do not try to be the main character here.

instead, these objects get created for you in response to an info() or group() method call on a similarity feature inside an Ace::Sequence::Feature object. the object just appears. manifesting ✨

if you truly insist on creating an Ace::Sequence::Homol object directly — like, you're built different — then pretty please go consult the source code for the new() method. that's the lore. 📖

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👑 OBJECT METHODS 👑

most methods are inherited from Ace::Object. but the following methods are also supported, bestie:

• start()

$start = $homol->start;

returns the start of the area that is similar to the Ace::Sequence::Feature from which this homology was derived. coordinates are relative to the target homology. ⭐

• end()

$end = $homol->end;

returns the end of the area that is similar to the Ace::Sequence::Feature from which this homology was derived. coordinates are relative to the target homology. (yes, same caveat as start(), they're a matching set 💞)

• asString()

$label = $homol->asString;

returns a human-readable identifier describing the nature of the feature. the format is:

$name/$start-$end

for example:

HUMGEN13/1-67

and the cute part? this method is also called automatically when the object is treated in a string context. she just shows up. no cap 🌈

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🦋 SEE ALSO 🦋

go read these too, iykyk:

• Ace
• Ace::Object
• Ace::Sequence
• Ace::Sequence::FeatureList
• Ace::Sequence::Feature
• GFF

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💌 AUTHOR 💌

Lincoln Stein <lstein@w3.org> — with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr> 🫶

Copyright (c) 1999, Lincoln D. Stein

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. ⚠️

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and that's the whole page, bestie 💖 this was perl v5.42.3, dated 2026-08-19, from the User Contributed Perl Documentation. stay hydrated, read your SEE ALSOs, and remember: she's temporary, but she ate. 💅✨🎀