| Bio::Matrix::Generic(3pm) | User Contributed Perl Documentation | Bio::Matrix::Generic(3pm) |
Bio::Matrix::Generic - A generic matrix implementation
# 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);
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.
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
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.
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
Email jason-at-bioperl-dot-org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
Title : matrix_name Usage : my $name = $matrix->matrix_name(); Function: Get/Set the matrix name Returns : scalar value Args : [optional] new matrix name value
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Title : column_header Usage : my $name = $matrix->column_header(0) Function: Gets the column header for a particular column number Returns : string Args : integer
Title : row_header Usage : my $name = $matrix->row_header(0) Function: Gets the row header for a particular row number Returns : string Args : integer
Title : num_rows Usage : my $rowcount = $matrix->num_rows; Function: Get the number of rows Returns : integer Args : none
Title : num_columns Usage : my $colcount = $matrix->num_columns Function: Get the number of columns Returns : integer Args : none
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
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 for a Generic Matrix
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
| 2021-08-15 | perl v5.32.1 |