The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
BioPerl-1.7.8
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Matrix::Generic

NAME

Bio::Matrix::Generic - A generic matrix implementation

SYNOPSIS

# A matrix has columns and rows 
my $matrix = Bio::Matrix::Generic->new;
$matrix->add_column(1,$column1);
$matrix->add_column(2,$column2);

my $element = $matrix->entry_by_num(1,2);
$matrix->entry_by_num(1,2,$newval);

my $entry = $matrix->entry('human', 'mouse');

$matrix->entry('human','mouse', $newval);

DESCRIPTION

This is a general purpose matrix object for dealing with row+column data which is typical when enumerating all the pairwise combinations and desiring to get slices of the data.

Data can be accessed by column and row names or indexes. Matrix indexes start at 0.

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

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.

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/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

APPENDIX

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

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 
          -rownames   => arrayref of row names
          -colnames   => arrayref of col names
          -matrix_id  => id of the matrix
          -matrix_name=> name of the matrix
          -matrix_init_value => default value to initialize empty cells

matrix_id

Title   : matrix_id
Usage   : my $id = $matrix->matrix_id
Function: Get/Set the matrix ID
Returns : scalar value
Args    : [optional] new id value to store

matrix_name

Title   : matrix_name
Usage   : my $name = $matrix->matrix_name();
Function: Get/Set the matrix name
Returns : scalar value
Args    : [optional] new matrix name value

entry

Title   : entry
Usage   : my $entry = $matrix->entry($row,$col,$value)
Function: Get the value for a specific cell as specified
          by the row and column names
Returns : scalar value or undef if row or col does not
          exist
Args    : $rowname - name of the row
          $colname - column name
          $value   - [optional] New value for the entry

get_entry

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

entry_by_num

Title   : entry_by_num
Usage   : my $entry = $matrix->entry_by_num($rownum,$colnum)
Function: Get an entry by row and column numbers instead of by name
          (rows and columns start at 0)
Returns : scalar value or undef if row or column name does not
          exist
Args    : $row - row number
          $col - column number
          [optional] $newvalue to store at this cell

column

Title   : column
Usage   : my @col = $matrix->column('ALPHA');
          OR
          $matrix->column('ALPHA', \@col);
Function: Get/Set a particular column
Returns : Array (in array context) or arrayref (in scalar context)
          of values.  
          For setting will warn if the new column is of a different
          length from the rest of the columns.
Args    : name of the column
          [optional] new column to store here

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

column_by_num

Title   : column_by_num
Usage   : my @col = $matrix->column_by_num(1);
          OR
          $matrix->column_by_num(1,\@newcol);
Function: Get/Set a column by its number instead of name
          (cols/rows start at 0)
Returns : Array (in array context) or arrayref (in scalar context)
          of values
Args    : name of the column
          [optional] new value to store for a particular column

row

Title   : row
Usage   : my @row = $matrix->row($rowname);
            OR
          $matrix->row($rowname,\@rowvalues);
Function: Get/Set the row of the matrix
Returns : Array (in array context) or arrayref (in scalar context)
Args    : rowname
          [optional] new value of row to store

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

row_by_num

Title   : row_by_num
Usage   : my @row = $matrix->row_by_num($rownum);
            OR
          $matrix->row($rownum,\@rowvalues);
Function: Get/Set the row of the matrix
Returns : Array (in array context) or arrayref (in scalar context)
Args    : rowname
          [optional] new value of row to store

diagonal

Title   : diagonal
Usage   : my @diagonal = $matrix->get_diagonal()
Function: Get the diagonal of a matrix
Returns : Array (in array context) or arrayref (in scalar context)
          of values which lie along the diagonal
Args    : none

add_row

Title   : add_row
Usage   : $matrix->add_row($index,\@newrow);
Function: Adds a row at particular location in the matrix.
          If $index < the rowcount will shift all the rows down
          by the number of new rows.
          To add a single empty row, simply call
          $matrix->add_row($index,undef);
Returns : the updated number of total rows in the matrix
Args    : index to store
          name of the row (header)
          newrow to add, if this is undef will add a single
                    row with all values set to undef

remove_row

Title   : remove_row
Usage   : $matrix->remove_row($colnum)
Function: remove a row from the matrix shifting all the rows
          up by one
Returns : Updated number of rows in the matrix
Args    : row index

add_column

Title   : add_column
Usage   : $matrix->add_column($index,$colname,\@newcol);
Function: Adds a column at particular location in the matrix.
          If $index < the colcount will shift all the columns right
          by the number of new columns.
          To add a single empty column, simply call
          $matrix->add_column($index,undef);
Returns : the updated number of total columns in the matrix
Args    : index to store
          name of the column (header)
          newcolumn to add, if this is undef will add a single
                column with all values set to undef

remove_column

Title   : remove_column
Usage   : $matrix->remove_column($colnum)
Function: remove a column from the matrix shifting all the columns
          to the left by one
Returns : Updated number of columns in the matrix
Args    : column index

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
Function: Gets the row number for a particular row name
Returns : integer
Args    : string

column_header

Title   : column_header
Usage   : my $name = $matrix->column_header(0)
Function: Gets the column header for a particular column number
Returns : string
Args    : integer

row_header

Title   : row_header
Usage   : my $name = $matrix->row_header(0)
Function: Gets the row header for a particular row number
Returns : string
Args    : integer

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

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

private methods

Private methods for a Generic Matrix

_values

Title   : _values
Usage   : $matrix->_values();
Function: get/set for array ref of the matrix containing
          distance values 
Returns : an array reference 
Args    : an array reference