EMBOSS...I::Conf(3pm)

🦋 EMBOSS::GUI::Conf — the manual page, but make it cute

okay bestie, gather round, because we're talking about EMBOSS::GUI::Conf — that's the EMBOSS::GUI::Conf Perl module, filed under User Contributed Perl Documentation, and it's literally the spot where your site-specific EMBOSS::GUI config lives. 💖

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✨ NAME ✨

EMBOSS::GUI::Conf — the repository for EMBOSS::GUI site-specific configuration. that's it. that's the whole vibe. 🎀

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👑 AUTHOR 👑

Luke McCarthy <lukem@gene.pbi.nrc.ca> — the icon who wrote this. give them their flowers. 🌸

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🌈 SYNOPSIS 🌈

here's how you actually use it, no cap:

use EMBOSS::GUI::Conf;

$conf = EMBOSS::GUI::Conf->new();

foreach $app ($conf->apps) {
      ($name, $doc) = @$app;
      if (!$conf->is_excluded($name)) {
              ...
      }
}

foreach $group ($conf->groups) {
      $group_name = shift @$group;
      if (!conf->is_excluded($group_name) {
              foreach $app (@$group) {
                      ($name, $doc) = @$app;
                      ...
              }
      }
}

(yes, we're looping over apps AND groups, checking if things are excluded, and doing stuff. main character behavior. ✨)

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💅 DESCRIPTION 💅

so EMBOSS::GUI::Conf contains the site-specific configuration information for EMBOSS::GUI. if you wanna know what variables you can actually set — go look at the source, bestie, it's all described in there. 📖

the public methods are described below, and yes we're going through every single one:

new()

returns a brand-new EMBOSS::GUI::Conf object. 🫶 what it does while it's at it:

• stores the EMBOSS::GUI::Conf package variables in the object hash
• makes sure the specified output path is writeable
• adds the EMBOSS binaries to the path

that's three (3) whole jobs. slay.

apps()

returns a list of the available EMBOSS applications. each element of the list is a reference to an array holding the name and description of an application. 🧚

groups()

returns a list of application groups. each element of the list is a reference to an array containing the name of the group, plus a list of applications belonging to that group — and each of those applications is itself a reference to an array, exactly like the ones described in apps() above. it's arrays inside arrays, iykyk. 🌀

⚠️ note: an individual application can appear in multiple groups. it's not cheating, it's just popular. 💅

is_excluded($subject)

returns true if the subject is being excluded from public display, and false otherwise.

$subject is the name of an application or application group as it appears in the output from wossname. don't rename it, don't freestyle it, use the exact name. 📌

databases()

returns a list of available databases. each element of the list is the name of a database, suitable for use in a USA. 🔥

matrices()

returns a list of available alignment scoring matrices. each element of the list is a reference to an array containing:

• the filename of the scoring matrix, suitable for use as the value of a matrix or matrixf argument
• a description of the matrix

codon_usage_tables()

returns a list of available codon usage tables. each element of the list is a reference to an array containing:

• the filename of the codon usage table, suitable for use as the value of a codon argument
• the name of the species from which it is derived

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💀 BUGS 💀

none that I know of. (iconic. flawless. no notes. ✨)

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🎀 COPYRIGHT 🎀

copyright (c) 2004 Luke McCarthy. all rights reserved. this program is free software. you may copy or redistribute it under the same terms as Perl itself. 🫶

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and that's the whole page, bestie!! this lil masterpiece comes to you from perl v5.38.2, dated 2024-02-25, and it lives in the User Contributed Perl Documentation corner of the world. go forth and configure your site. periodt. 💖🌸🦋💅