TFBS::...PairSet(3pm)

💖 TFBS::SitePairSet 💖

okay bestie, so this is the manual page for TFBS::...PairSet(3pm) from the User Contributed Perl Documentation collection — aka the whole TFBS perl module fam. And it's literally about a set of TFBS::SitePair objects. That's the vibe. Let's get into it 🦋

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✨ NAME ✨

TFBS::SitePairSet — a set of TFBS::SitePair objects. that's it, that's the name, slay 💅

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🎀 SYNOPSIS 🎀

my $site_pair_set = TFBS::SitePairSet->new(@list_of_site_pair_objects);

# add a TFBS::SitePair object to set:

$site_pair_set->add_site_pair($site_pair_obj);

# append another TFBS::SitePairSet contents:

$site_pair_set->add_site_pair_set($site_pair_obj);

# create an iterator:

my $it = $site_pair_set->Iterator(-sort_by => 'start');

like. the whole thing in four little moves. iconique ✨

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🌸 DESCRIPTION 🌸

TFBS::SitePairSet is an aggregate class — meaning it's the container, the girl who holds everybody's stuff — and it's packed with a whole collection of TFBS::SitePair objects. 💖

you can make one from scratch and fill it up with TFBS::Site::Pair objects. it's also what comes back at you when you call the search_aln() method on TFBS::PatternI subclasses (think TFBS::Matrix::PWM, bestie 👑).

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🫶 FEEDBACK 🫶

found a bug? got thoughts? send your bug reports and other comments to the author, fr fr. they wanna hear it. 😭

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👑 AUTHOR - Boris Lenhard 👑

Boris Lenhard <Boris.Lenhard@cgb.ki.se>

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🌈 APPENDIX 🌈

the rest of this doc breaks down every single object method, one by one. and psst — internal methods are marked with an underscore up front. iykyk 🙈

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⭐ size

• Title : size
• Usage : my $size = $sitepairset->size()
• Function: returns a number of TFBS::SitePair objects contained in the set
• Returns : a scalar (integer)
• Args : none

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⭐ add_site_pair

• Title : add_site_pair
• Usage : $sitepairset->add_site_pair($site_pair_object) $sitepairset->add_site_pair(@list_of_site_pair_objects)
• Function: adds TFBS::SitePair objects to an existing TFBS::SitePairSet object
• Returns : $sitepairset object (usually ignored)
• Args : A list of TFBS::SitePair objects to add

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⭐ add_site_pair_set

• Title : add_site_pair_set
• Usage : $sitepairset->add_site_pair_set($site_pair_set_object) $sitepairset->add_site_pair(@list_of_site_pair_set_objects)
• Function: adds the contents of other TFBS::SitePairSet objects to an existing TFBS::SitePairSet object
• Returns : $sitepairset object (usually ignored)
• Args : A list of TFBS::SitePairSet objects whose contents should be added to $sitepairset

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⭐ Iterator

• Title : Iterator
• Usage :

my $it = $sitepairset->Iterator(-sort_by=>'start');
while (my $site_pair = $it->next()) { #...

• Function: Returns an iterator object, used to iterate thorugh elements (TFBS::SitePair objects)
• Returns : a TFBS::_Iterator object
• Args :

-sort_by # optional - currently it accepts
         #   (default sort order in parenthetse)
         #    'name' (pattern name, alphabetically)
         #    'ID' (pattern/matrix ID, alphabetically)
         #    'start' (site start in sequence,
         #             numerically,increasing order)
         #    'end' (site end in sequence,
         #           numerically, increasing order)
         #    'score' (1st site in pair,
         #             numerically, decreasing order)
-reverse # optional - reverses the default sorting order if true

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⭐ set1 / set2

• Title : set1 / set2
• Usage :

my $siteset1 = $sitepairset->set1();
: my $siteset2 = $sitepairset->set2()

• Function: Returns individual TFBS::SiteSet objects, from the site set pair
• Returns : A TFBS::SiteSet object
• Args : none

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⭐ GFF

• Title : GFF
• Usage :

print $site->GFF();
: print $site->GFF($gff_formatter)

• Function: returns a "standard" multiline GFF string
• Returns : a string (multiline, newline terminated)
• Args : a $gff_formatter function reference (optional)

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and that's the whole page bestie!! no cap, you now know TFBS::SitePairSet better than it knows itself 💜

this one was cooked up with perl v5.42.3, dated 2026-08-21 — that's the TFBS::...PairSet(3pm) energy right there. go forth and pair your sites, queen 🎀🦋💅