Bio::Matrix::IO::mlagan.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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>