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

NAME

       Bio::Matrix::Mlagan - A generic matrix with mlagan fields

SYNOPSIS

	 # See L<Bio::Matrix::Generic> for most methods.
	 # These are relevant for mlagan IO:
	 $matrix->gap_open(-400);
	 $matrix->gap_continue(-25);

DESCRIPTION

       This is based on Bio::Matrix::Generic, differing by storing gap_open and gap_continue data members to allow mlagan IO (see
       Bio::Matrix::IO::mlagan).  (Those values are 'outside' the matrix.)

       It also limits the structure to a 6x6 matrix with row & column names 'A', 'C', 'G', 'T', '.' and 'N'.

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

AUTHOR - Sendu Bala
       Email bix@sendu.me.uk

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
		  -matrix_id	     => id of the matrix
		  -matrix_name	     => name of the matrix
		  -matrix_init_value => default value to initialize empty cells
		  -gap_open	     => gap open penalty (int)
		  -gap_continue      => gap continue penalty (int)

		  NB: -rownames and -colnames should not be given here, since they are
		  always being set to 'A', 'C', 'G', 'T', '.' and 'N'.

   gap_open
	Title	: gap_open
	Usage	: $obj->gap_open(-400);
	Function: Get/set the gap open amount.
	Returns : int
	Args	: none to get, OR int to set

   gap_continue
	Title	: gap_continue
	Usage	: $obj->gap_continue(-25);
	Function: Get/set the gap continue amount.
	Returns : int
	Args	: none to get, OR int to set

   add_row
	Title	: add_row
	Usage	: Do not use
	Function: This generic method is not suitable for mlagan, where the number of
		  rows is fixed.
	Returns : Warning
	Args	: none

   remove_row
	Title	: remove_row
	Usage	: Do not use
	Function: This generic method is not suitable for mlagan, where the number of
		  rows is fixed.
	Returns : Warning
	Args	: none

   add_column
	Title	: add_column
	Usage	: Do not use
	Function: This generic method is not suitable for mlagan, where the number of
		  columns is fixed.
	Returns : Warning
	Args	: none

   remove_column
	Title	: remove_column
	Usage	: Do not use
	Function: This generic method is not suitable for mlagan, where the number of
		  columns is fixed.
	Returns : Warning
	Args	: none

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