Bio::T...::soap(3pm)

💖 NAME 💖

Bio::Tools::Run::AnalysisFactory::soap — a SOAP-based access to the list of analysis tools ✨

okay bestie, real talk: this whole page is about Bio::T...::soap(3pm) from the User Contributed Perl Documentation crew, and it's lowkey iconic for one very specific job. let's get into it 💅

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🌸 SYNOPSIS 🌸

bestie. do not use this object directly, fr fr. the move is to access it and use it through the Bio::Tools::Run::AnalysisFactory module:

use Bio::Tools::Run::AnalysisFactory;
my $list = Bio::Tools::Run::AnalysisFactory->new(-access => 'soap')
   ->available_analyses;
print join ("\n", @$list) . "\n";

that's it. that's the whole vibe. she does one thing and she ate 🔥

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🦋 DESCRIPTION 🦋

all the public methods are documented over in the interface module Bio::Factory::AnalysisI. that's where the lore lives, go read that one 💜

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🫶 FEEDBACK 🫶

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, your comments and suggestions matter so much. send them preferably to the Bioperl mailing list. your participation is much appreciated, no cap 🥹

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

🎀 Support

please direct usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. why? because there are so many experienced and responsive experts on there who can look at your problem and quickly address it — group chat energy, but make it bioinformatics 💅 please include a thorough description of the problem with code and data examples if at all possible, like give us the whole story bestie.

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution — tracking is the whole point, periodt. bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

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👑 AUTHOR 👑

Martin Senger (martin.senger@gmail.com) — we stan ✨

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💜 COPYRIGHT 💜

Copyright (c) 2003, Martin Senger and EMBL-EBI. All Rights Reserved.

this module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. so generous, so iconic 🎀

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💀 DISCLAIMER 💀

this software is provided "as is" without warranty of any kind. yeah. that kind of disclaimer. it's giving "we said what we said" 🙈

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🌈 SEE ALSO 🌈

• http://www.ebi.ac.uk/soaplab/Perl_Client.html

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🔥 BUGS AND LIMITATIONS 🔥

none known at the time of writing this. a flawless queen, allegedly 👑

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🧚 APPENDIX 🧚

the main documentation details are in Bio::Factory::AnalysisI.

⭐ _initialize

Usage   : my $factory = Bio::Tools::Run::AnalysisFactory->new(@args);
          (_initialize is internally called from the 'new()' method)
Returns : nothing interesting
Args    : This module recognises and uses following arguments:
            -location
            -httpproxy
            -soap
          Additionally, the main module Bio::Tools::Run::AnalysisFactory
          recognises also:
            -access

okay so what does she actually do? it populates the calling object with the given arguments, and then — for some attributes, and only if they are not yet populated — it assigns some default values. little fill-in-the-blanks moment, we love her for it 💖

this is an actual new() method (except for the real object creation and its blessing, which is done in the parent class Bio::Root::Root in method _create_object). the blessing happens elsewhere, she just handles the setup ✨

note bestie: this method is called always as an object method (never as a class method) — and the object who calls this method may already be partly initiated (from the Bio::Tools::Run::AnalysisFactory::new method). so if you need to do some tricks with the 'class invocation', you need to change the Bio::Tools::Run::AnalysisFactory new method, not this one. important. write that down 🫶

🍓 -location

a URL (also called an endpoint) defining where a Web Service functioning for this object is located.

default is http://www.ebi.ac.uk/soaplab/services (a service running at European Bioinformatics Institute on top of most of the EMBOSS analyses, and on top of few others). that default is doing a lot of heavy lifting ngl 💅

for example, if you run your own Web Service using Java(TM) Apache Axis toolkit, the location might be something like http://localhost:8080/axis/services.

🌸 -httpproxy

in addition to the location parameter, you may need to specify also a location/URL of an HTTP proxy server (if your site requires one). the expected format is http://server:port. there is no default value — you're on your own for this one, bestie 😭

🦋 -soap

defines your own SOAP::Lite object. useful if you need finer-grained access to many features and attributes of the wonderful Paul Kulchenko's module. go off, Paul 👑

💫 VERSION and Revision

Usage   : print $Bio::Tools::Run::AnalysisFactory::soap::VERSION;
          print $Bio::Tools::Run::AnalysisFactory::soap::Revision;

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and that's the whole page bestie 💖 this one shipped as part of perl v5.36.0, dated 2023-01-22 — genuinely vintage in internet years, and she still slays. mwah 🎀✨🫶