Bio::M...:Mlagan(3pm)

🌸 Bio::M...:Mlagan 💅

okay bestie, gather round, because this is the Bio::Matrix::Mlagan page from the User Contributed Perl Documentation and it's literally a whole vibe. it's a generic matrix, but make it mlagan. let's get into it 🫶

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✨ NAME ✨

Bio::Matrix::Mlagan — A generic matrix with mlagan fields 🧬

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🌈 SYNOPSIS 🌈

# See L<Bio::Matrix::Generic> for most methods.
# These are relevant for mlagan IO:
$matrix->gap_open(-400);
$matrix->gap_continue(-25);

like yes, Bio::Matrix::Generic is doing most of the heavy lifting (go read it, iykyk), but these two are the ones that actually matter for mlagan IO. 💖

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🦋 DESCRIPTION 🦋

so this whole thing is built on top of Bio::Matrix::Generic, and the one glow-up it brings is that it stores gap_open and gap_continue as data members, which is what lets it do mlagan IO — peep Bio::Matrix::IO::mlagan if you wanna see that in action. and bestie, important detail: those two values live 'outside' the matrix itself. they're not cells, they're just... hanging out next to it. periodt.

it also keeps the structure on a strict 6x6 matrix. no growing, no shrinking, no chaos. the row & column names are always, and only:

• 'A'
• 'C'
• 'G'
• 'T'
• '.'
• 'N'

that's the whole roster, no substitutions 💀

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💌 FEEDBACK 💌

🌷 Mailing Lists 🌷

user feedback is like, an integral part of the evolution of this and other Bioperl modules. so send your comments and suggestions, preferably to the Bioperl mailing list. your participation is so 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

and not straight to the module maintainer, okay? there are so many experienced and responsive experts on there who will look at your problem and address it fast. 🙌 and if you can, include a thorough description of the problem with code and data examples. the more detail, the better, no cap.

🐛 Reporting Bugs 🐛

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

https://github.com/bioperl/bioperl-live/issues

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👑 AUTHOR - Sendu Bala 👑

Email bix@sendu.me.uk ✨

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🎀 APPENDIX 🎀

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk, that underscore means it's for the backend, not for you bestie).

💫 new

Title   : new
Usage   : my $obj = Bio::Matrix::Generic->new();
Function: Builds a new Bio::Matrix::Generic object
Returns : an instance of Bio::Matrix::Generic
Args    : -values            => arrayref of arrayrefs of data initialization
          -matrix_id         => id of the matrix
          -matrix_name       => name of the matrix
          -matrix_init_value => default value to initialize empty cells
          -gap_open          => gap open penalty (int)
          -gap_continue      => gap continue penalty (int)

          NB: -rownames and -colnames should not be given here, since they are
          always being set to 'A', 'C', 'G', 'T', '.' and 'N'.

here's the args broken down for you, bestie:

• -values — an arrayref of arrayrefs of data initialization 👀
• -matrix_id — the id of the matrix
• -matrix_name — the name of the matrix
• -matrix_init_value — the default value used to initialize empty cells
• -gap_open — gap open penalty (an int)
• -gap_continue — gap continue penalty (an int)

🚨 NB: do not pass -rownames and -colnames here. they're always being set to 'A', 'C', 'G', 'T', '.' and 'N', so there's literally nothing for you to decide. don't fight it. 💅

💫 gap_open

Title   : gap_open
Usage   : $obj->gap_open(-400);
Function: Get/set the gap open amount.
Returns : int
Args    : none to get, OR int to set

get/set the gap open amount. returns an int. pass nothing to get it, pass an int to set it. that's it, that's the whole method 🫶

💫 gap_continue

Title   : gap_continue
Usage   : $obj->gap_continue(-25);
Function: Get/set the gap continue amount.
Returns : int
Args    : none to get, OR int to set

same energy as above but for the gap continue amount. returns an int. no args = get, int = set. iconic behavior, honestly ✨

💫 add_row

Title   : add_row
Usage   : Do not use
Function: This generic method is not suitable for mlagan, where the number of
          rows is fixed.
Returns : Warning
Args    : none

💀 do not use. this generic method is not suitable for mlagan, because the number of rows is fixed. if you call it you're getting a warning, not a new row. nope.

💫 remove_row

Title   : remove_row
Usage   : Do not use
Function: This generic method is not suitable for mlagan, where the number of
          rows is fixed.
Returns : Warning
Args    : none

💀 do not use. same situation — the number of rows is fixed, so this generic method doesn't fit here. all you get back is a warning.

💫 add_column

Title   : add_column
Usage   : Do not use
Function: This generic method is not suitable for mlagan, where the number of
          columns is fixed.
Returns : Warning
Args    : none

💀 do not use. columns are fixed in mlagan, so this generic method is a no. warning incoming.

💫 remove_column

Title   : remove_column
Usage   : Do not use
Function: This generic method is not suitable for mlagan, where the number of
          columns is fixed.
Returns : Warning
Args    : none

💀 do not use. the number of columns is fixed, so this generic method does not belong here. it returns a warning and that's the tea.

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and that's the whole page bestie, you ate it up 🍓 that was perl v5.32.1, dated 2021-08-15, from the Bio::M...:Mlagan(3pm) manual. go forth and matrix, mwah 💋💖