- AUTHOR - Sendu Bala
Bio::Matrix::IO::mlagan - A parser for the mlagan substitution matrix
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;
Use to read in and write out substitution matrix files suitable for use by mlagan.
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.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 :
Title : next_matrix Usage : my $matrix = $obj->next_matrix(); Function: parses a matrix file Returns : L<Bio::Matrix::Mlagan> Args : none
Title : write_matrix Usage : $obj->write_matrix($matrix) Function: Write out a matrix in mlagan format Returns : n/a Args : L<Bio::Matrix::Generic>