Bio::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:

  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>