Bio::Matrix::MatrixI(3pm)				User Contributed Perl Documentation				 Bio::Matrix::MatrixI(3pm)

NAME

       Bio::Matrix::MatrixI - An interface for describing a Matrix

SYNOPSIS

	 # Get a Matrix object

DESCRIPTION

       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.

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
       email or the web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason-at-bioperl.org

APPENDIX

       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

   reverse
	Title	: reverse
	Usage	: my $matrix = $matrix->reverse
	Function: Get the reverse of a matrix
	Returns :
	Args	:

   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

perl v5.14.2							    2012-03-02						 Bio::Matrix::MatrixI(3pm)