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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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 email or the web: http://bugzilla.bioperl.org/ Email jason-at-bioperl.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

matrix_id
Title : matrix_id Usage : my $id = $matrix->matrix_id Function: Get the matrix ID Returns : string value Args :

matrix_name
Title : matrix_name Usage : my $name = $matrix->matrix_name(); Function: Get the matrix name Returns : string value Args :

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

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