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

💖 NAME 💖

Bio::Tools::Run::Phylo::Phylip::Base — bestie, this is the base object for the Phylip modules, no cap. It's the little foundation everyone else stands on 🫶

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✨ SYNOPSIS ✨

# Do not use directly # This module is for setting basic data sets for the Phylip wrapper # modules

okay so real talk: do NOT use this one directly 🙈 it's literally just here to set up the basic data sets for all the Phylip wrapper modules. it's the backstage crew, not the main character.

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🌸 DESCRIPTION 🌸

This module is just a base object for Bioperl Phylip wrappers. that's it, that's the whole job 💅

🚨 IMPORTANT PHYLIP VERSION ISSUES 🚨

By default we assume you have Phylip 3.6 installed. If you've got Phylip 3.5 instead, you need to set the environment variable PHYLIPVERSION. fr fr, don't skip this one or things get weird 😭

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🦋 FEEDBACK 🦋

💌 Mailing Lists 💌

User feedback is an integral part of the evolution of this and other Bioperl modules — like, the whole glow-up depends on y'all 🫶. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated, bestie.

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 — the more detail the better, give them the whole lore 📖✨

🐛 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:

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

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👑 AUTHOR - Jason Stajich 👑

Email jason-at-bioperl.org — shoutout to the icon who made this 💜

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📚 APPENDIX 📚

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (iykyk 🔥)

🎀 new

Title   : new
Usage   : my $obj = Bio::Tools::Run::Phylo::Phylip::Base->new();
Function: Builds a new Bio::Tools::Run::Phylo::Phylip::Base object
Returns : an instance of Bio::Tools::Run::Phylo::Phylip::Base
Args    :

• new — builds a brand new Bio::Tools::Run::Phylo::Phylip::Base object, and hands you back an instance of it. Args? none listed, it just vibes ✨

🎀 outfile

Title   : outfile
Usage   : $obj->outfile($newval)
Function: Get/Set default PHYLIP outfile name ('outfile' usually)
          Changing this is only necessary when you have compiled
          PHYLIP to use a different filename for the default 'outfile'
          This will not change the default output filename by
          PHYLIP
Returns : value of outfile
Args    : newvalue (optional)

• outfile — get/set the default PHYLIP outfile name (usually 'outfile'). You only need to change this if you compiled PHYLIP to use a different filename for the default 'outfile'.
• ⚠️ heads up: this will not change the default output filename by PHYLIP itself. it's giving "cosmetic only", okay? don't come for me 😭
• Returns the value of outfile, and takes a new value as an optional arg.

🎀 treefile

Title   : treefile
Usage   : $obj->treefile($newval)
Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
Returns : value of treefile
Args    : newvalue (optional)

• treefile — get/set the default PHYLIP treefile name (usually 'treefile', slay 🌳). Returns the value of treefile, arg is a new value, optional.

🎀 fontfile

Title   : fontfile
Usage   : $obj->fontfile($newval)
Function: Get/Set the fontfile
Returns : value of fontfile (a scalar)
Args    : on set, new value (a scalar or undef, optional)

• fontfile — get/set the fontfile. Returns the value of fontfile (a scalar), and on set takes a new value — a scalar or undef, your call, optional 💅

🎀 plotfile

Title   : plotfile
Usage   : $obj->plotfile($newval)
Function: Get/Set the plotfile
Returns : value of plotfile (a scalar)
Args    : on set, new value (a scalar or undef, optional)

• plotfile — get/set the plotfile. Returns the value of plotfile (a scalar), and on set takes a new value — a scalar or undef, optional ✨

🎀 version

Title   : version
Usage   : $obj->version($newval)
Function: Get/Set the version
Returns : value of version (a scalar)
Args    : on set, new value (a scalar or undef, optional)

• version — get/set the version. Returns the value of version (a scalar), and on set takes a new value — a scalar or undef, optional 🎀

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and that's the whole page, bestie! 🫶 this was perl v5.36.0, dated 2023-01-22, from the Bio::T...::Base(3pm) era of the docs. go forth and Phylip responsibly 💖✨