Bio::Matrix::IO::mlagan man page on Pidora

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Bio::Matrix::IO::mlagaUser Contributed Perl DocumentBio::Matrix::IO::mlagan(3)

NAME
       Bio::Matrix::IO::mlagan - A parser for the mlagan substitution matrix

SYNOPSIS
	 use Bio::Matrix::IO;
	 my $parser = Bio::Matrix::IO->new(-format => 'mlagan',
					  -file	  => 'nucmatrix.txt');
	 my $matrix = $parser->next_matrix;
	 my $gap_open = $parser->gap_open;
	 my $gap_continue = $parser->gap_continue;

DESCRIPTION
       Use to read in and write out substitution matrix files suitable for use
       by mlagan.

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:

	 http://bugzilla.open-bio.org/

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::IO::mlagan->new();
	Function: Builds a new Bio::Matrix::IO::mlagan object
	Returns : an instance of Bio::Matrix::IO::mlagan
	Args	:

   next_matrix
	Title	: next_matrix
	Usage	: my $matrix = $obj->next_matrix();
	Function: parses a matrix file
	Returns : L<Bio::Matrix::Mlagan>
	Args	: none

   write_matrix
	Title	: write_matrix
	Usage	: $obj->write_matrix($matrix)
	Function: Write out a matrix in mlagan format
	Returns : n/a
	Args	: L<Bio::Matrix::Generic>

perl v5.14.1			  2011-07-22	    Bio::Matrix::IO::mlagan(3)
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