Bio::B...linexml(3pm)

📦 version 1.70, in debian trixie, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 Bio::Biblio::IO::medlinexml — bestie's guide 💖

okay so real talk, this is a page from the User Contributed Perl Documentation, section 3pm, and the module is Bio::Biblio::IO::medlinexml (yes the header truncates it to Bio::B...linexml, the terminal is just being dramatic and short on space 💅). It's a converter of XML files with MEDLINE citations, and I am obsessed with how much it does while looking this chill.

✨ NAME ✨

Bio::Biblio::IO::medlinexml — a converter of XML files with MEDLINE citations 🦋

🌸 VERSION 🌸

version 1.70 — she's serving, she's current, periodt.

🎀 SYNOPSIS 🎀

bestie, do not use this object directly. like, at all. the whole vibe is that you access it and use it through the Bio::Biblio::IO module instead. iykyk 🫶
use Bio::Biblio::IO;
my $io = Bio::Biblio::IO->new(-format => 'medlinexml');

💜 DESCRIPTION 💜

so what does this icon actually do? she reads bibliographic citations in XML/MEDLINE format and converts them into Bio::Biblio::RefI objects. it's giving translator, it's giving glow-up for your data. ✨

she's an implementation of methods defined in Bio::Biblio::IO.

and the main documentation details? those live in Bio::Biblio::IO, so go read her big sister's page too, no cap. 📚

🌈 METHODS 🌈

🧚 next_bibref

that's it. that's the whole method list for this section. she's lowkey mysterious, highkey essential.

⭐ FUNCTIONS ⭐

  • handle_doc_start
  • handle_doc_end
  • handle_char
  • handle_start
  • handle_end

these are the handler squad, all five of them, doing their little jobs. 👑

🔥 INTERNAL METHODS 🔥

these are the behind-the-scenes besties. very backstage, very "not for you to touch" energy.
  • _initialize
  • _parse
  • _process_citation — what to do when we have the whole $citation ready. like, she's fully prepped, she's ready, she's about to be processed. 💅
  • _add_element — add $element into an array named $key to the top object at @ObjectStack; if $element is empty, take it from @PCDataStack. cute little stack situation, we love to see it.
  • _data2obj — remove top of @PCDataStack and put it into top object at @ObjectStack under name $key. pop, drop, slay. 🍓
  • _obj2obj — remove top of @ObjectStack and put it into now-top at @ObjectStack under name $key. yes bestie, the stack shuffles itself, it's a whole choreography.
  • _eq_hash_elem — check if a $key exists in a ref-hash $rh and if it is equal to $value. equality check, no cap.
  • _debug_object_stack — --- only for debugging. like, strictly for the debugging girlies. 🐛

💌 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, fr fr. 🙏

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

🫂 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.

(and yes, that's "reponsive" exactly as written, i am not fixing her typo, she's iconic as she is 😭💖)

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

✍️ Authors

Martin Senger <senger@ebi.ac.uk> — the mastermind, the moment, the main character. 🌟

this software is Copyright (c) by 2002 European Bioinformatics Institute and released under the license of the same terms as the perl 5 programming language system itself.

bestie reminder: every flag, every stack operation, every email address and URL above is exactly what the page says. i added sparkle, not fiction. 💯

and that's the whole page, babe ✨ this was Bio::B...linexml(3pm) from the User Contributed Perl Documentation, generated by perl v5.36.0 on 2023-02-14 — valentine's day, because of course the cutest manpage dropped on the cutest day 💖🎀🌸 mwah, go convert some citations, you got this 🫶

📦 where this page comes from