Bio::Matrix::MatrixI - An interface for describing a Matrix
# Get a Matrix object
This is an interface describing how one should be able to interact with a
matrix. One can have a lot of information I suppose and this outline won't
really work for PWM or PSSMs. We will have to derive a particular interface
for those.
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The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Title : matrix_id
Usage : my $id = $matrix->matrix_id
Function: Get the matrix ID
Returns : string value
Args :
Title : matrix_name
Usage : my $name = $matrix->matrix_name();
Function: Get the matrix name
Returns : string value
Args :
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
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 : 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 : 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
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 = $matrix->row_num_for_name($name)
Function: Gets the row number for a particular row name
Returns : integer
Args : string
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 : reverse
Usage : my $matrix = $matrix->reverse
Function: Get the reverse of a matrix
Returns :
Args :
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