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

💖 Bio::Matrix::MatrixI(3pm) 💖

okay bestie, welcome to Bio::Matrix::MatrixI, a page from the User Contributed Perl Documentation for the Bioperl project. yes it's an interface, yes it's iconic, let's get into it 🫶

---

✨ NAME ✨

Bio::Matrix::MatrixI — an interface for describing a Matrix. that's it, that's the whole vibe 💅

---

🌈 SYNOPSIS 🌈

# Get a Matrix object

short, sweet, and honestly kind of mysterious of it 😌

---

🦋 DESCRIPTION 🦋

so like, this is an interface describing how you should be able to interact with a matrix. you can have a LOT of information in one, I suppose, and this outline lowkey won't really work for PWM or PSSMs. the plan is we'll have to derive a particular interface for those. so this is the general one, the blueprint, the main character, and the fancy ones come later ✨

---

🎀 FEEDBACK 🎀

Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, it's giving community, it's giving we need you. send your comments and suggestions preferably to the Bioperl mailing list, and just know your participation is much appreciated 💖

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, bestie. that way many experienced and reponsive experts will be able look at the problem and quickly address it 👑 and please include a thorough description of the problem with code and data examples if at all possible. 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 — yes, the receipts are being kept 📝 bug reports can be submitted via email or the web:

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

---

💜 AUTHOR - Jason Stajich 💜

Email jason-at-bioperl.org — yes the "at" is doing that on purpose, that's not a typo, that's anti-spam chic 🎀

---

📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk 👀)

⭐ matrix_id

• Title: matrix_id
• Usage: my $id = $matrix->matrix_id
• Function: get the matrix ID
• Returns: string value
• Args: (none listed)

⭐ matrix_name

• Title: matrix_name
• Usage: my $name = $matrix->matrix_name();
• Function: get the matrix name
• Returns: string value
• Args: (none listed)

⭐ get_entry

• Title: get_entry
• Usage: my $entry = $matrix->get_entry($rowname,$columname)
• Function: get the entry for a given row,column pair
• Returns: scalar
• Args: $row name, $column name

⭐ get_column

• Title: get_column
• Usage: my @row = $matrix->get_column('ALPHA');
• Function: get a particular column
• Returns: Array (in array context) or arrayref (in scalar context) of values
• Args: name of the column

⭐ get_row

• Title: get_row
• Usage: my @row = $matrix->get_row('ALPHA');
• Function: get a particular row
• Returns: Array (in array context) or arrayref (in scalar context) of values
• Args: name of the row

⭐ get_diagonal

• Title: get_diagonal
• Usage: my @diagonal = $matrix->get_diagonal;
• Function: get the diagonal of the matrix
• Returns: Array (in array context) or arrayref (in scalar context)
• Args: none

⭐ column_num_for_name

• Title: column_num_for_name
• Usage: my $num = $matrix->column_num_for_name($name)
• Function: gets the column number for a particular column name
• Returns: integer
• Args: string

⭐ row_num_for_name

• Title: row_num_for_name
• Usage: my $num = $matrix->row_num_for_name($name)
• Function: gets the row number for a particular row name
• Returns: integer
• Args: string

⭐ num_rows

• Title: num_rows
• Usage: my $rowcount = $matrix->num_rows;
• Function: get the number of rows
• Returns: integer
• Args: none

⭐ num_columns

• Title: num_columns
• Usage: my $colcount = $matrix->num_columns
• Function: get the number of columns
• Returns: integer
• Args: none

⭐ reverse

• Title: reverse
• Usage: my $matrix = $matrix->reverse
• Function: get the reverse of a matrix
• Returns: (blank in the original, bestie — it's giving mystery)
• Args: (blank in the original too)

⭐ row_names

• Title: row_names
• Usage: my @rows = $matrix->row_names
• Function: the names of all the rows
• Returns: array in array context, arrayref in scalar context
• Args: none

⭐ column_names

• Title: column_names
• Usage: my @columns = $matrix->column_names
• Function: the names of all the columns
• Returns: array in array context, arrayref in scalar context
• Args: none

---

and that's the whole page, no notes. interface understood, matrix described, slay 💅

okay byeee 🦋 this was Bio::M...atrixI(3pm), documented with perl v5.32.1 and dated 2021-08-15 — a whole vintage moment, we love her 🎀✨