Provided by: libbio-perl-perl_1.7.8-1_all 
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