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:

https://github.com/bioperl/bioperl-live/issues

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>