Bio::C...apperI(3pm)

💖 Bio::C...apperI — User Contributed Perl Documentation 💖

okay bestie, gather round, because today we're talking about Bio::Coordinate::MapperI — an interface that describes coordinate mappers. Yes it's giving very "abstract parent class, do not touch," but hear me out because it's actually iconic. ✨

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🌸 VERSION 🌸

version 1.007001

she's got a version number and she's proud of it 💅

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✨ SYNOPSIS ✨

  # not to be used directly

that's it. that's the synopsis. and honestly? the way she said "not to be used directly" with zero further explanation... main character energy fr fr.

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🦋 DESCRIPTION 🦋

MapperI defines the methods for classes that are capable of mapping locations between coordinate systems. It's an interface, so like — she's the blueprint, not the building. Other classes come along and actually do the mapping. iykyk 🌈

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🎀 METHODS 🎀

💜 in

• Title: in
• Usage: $obj->in('peptide');
• Function: Set and read the input coordinate system.
• Example: (empty — she left it blank, and that's valid)
• Returns: value of input system
• Args: new value (optional), Bio::LocationI

set it or read it, your call — the new value is optional so you can just peek at what's already there 👀

💜 out

• Title: out
• Usage: $obj->out('peptide');
• Function: Set and read the output coordinate system.
• Example: (empty)
• Returns: value of output system
• Args: new value (optional), Bio::LocationI

same vibe as in, but for where you're going instead of where you came from. the glow-up direction, if you will. 💫

💜 swap

• Title: swap
• Usage: $obj->swap;
• Function: Swap the direction of mapping: input <-> output)
• Example: (empty)
• Returns: 1
• Args: (none)

flip it and reverse it 🔄 input becomes output, output becomes input, no cap.

💜 test

• Title: test
• Usage: $obj->test;
• Function: test that both components are of same length
• Example: (empty)
• Returns: ( 1 | undef )
• Args: (none)

vibe check on your components — are they the same length? 1 if yes, undef if not. simple as. ⭐

💜 map

• Title: map
• Usage: $newpos = $obj->map($loc);
• Function: Map the location from the input coordinate system to a new value in the output coordinate system.
• Example: (empty)
• Returns: new value in the output coordiante system
• Args: Bio::LocationI

the whole point of the operation honestly — hand her a location, she hands you back the same spot translated into the output coordinate system. (yes, "coordiante" — we're preserving the typo, it's part of her charm 🙈)

💜 return_match

• Title: return_match
• Usage: $obj->return_match(1);
• Function: A flag to turn on the simplified mode of returning only one joined Match object or undef
• Example: (empty)
• Returns: boolean
• Args: boolean (optional)

turn this flag on and she stops being extra — instead of a whole pile of stuff, you get one joined Match object, or undef. simplified mode is the self-care mode. 🫶

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🌈 FEEDBACK 🌈

💌 Mailing lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

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

bestie, the maintainers literally want to hear from you. it's giving community. it's giving collaborative open source. ✨

💌 Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

tl;dr: don't DM the maintainer, post to the list, because a whole crowd of very experienced and responsive experts can look at it and fix it fast. and PLEASE bring code and data examples, the more thorough the better — context is everything. 💀

💌 Reporting bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/%%7Bdist%7D

yes, that's the URL exactly as written. don't touch it, don't "fix" it, just vibe with it. 🐛

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👑 AUTHOR 👑

Heikki Lehvaslaiho <heikki@bioperl.org>

shoutout to Heikki, the actual author of this whole thing 👑

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🌸 COPYRIGHT 🌸

This software is copyright (c) by Heikki Lehvaslaiho.

This software is available under the same terms as the perl 5 programming language system itself.

so basically — same licensing energy as perl 5 itself. no weird custom drama. we love a clean license. 💅

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and that's the whole page, bestie! this doc came to you from the perl v5.32.0 toolchain, dated 2020-11-24, and it lives in the Bio::C...apperI(3pm) manpage. take care of her, she's a whole interface. 🦋✨💖