/ 
BioPerl-1.6.921
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Matrix::Mlagan

NAME

Bio::Matrix::Mlagan - A generic matrix with mlagan fields

SYNOPSIS

# See L<Bio::Matrix::Generic> for most methods.
# These are relevant for mlagan IO:
$matrix->gap_open(-400);
$matrix->gap_continue(-25);

DESCRIPTION

This is based on Bio::Matrix::Generic, differing by storing gap_open and gap_continue data members to allow mlagan IO (see Bio::Matrix::IO::mlagan). (Those values are 'outside' the matrix.)

It also limits the structure to a 6x6 matrix with row & column names 'A', 'C', 'G', 'T', '.' and 'N'.

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://redmine.open-bio.org/projects/bioperl/

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::Generic->new();
Function: Builds a new Bio::Matrix::Generic object 
Returns : an instance of Bio::Matrix::Generic
Args    : -values            => arrayref of arrayrefs of data initialization
          -matrix_id         => id of the matrix
          -matrix_name       => name of the matrix
          -matrix_init_value => default value to initialize empty cells
          -gap_open          => gap open penalty (int)
          -gap_continue      => gap continue penalty (int)

          NB: -rownames and -colnames should not be given here, since they are
          always being set to 'A', 'C', 'G', 'T', '.' and 'N'.

gap_open

Title   : gap_open
Usage   : $obj->gap_open(-400);
Function: Get/set the gap open amount.
Returns : int
Args    : none to get, OR int to set

gap_continue

Title   : gap_continue
Usage   : $obj->gap_continue(-25);
Function: Get/set the gap continue amount.
Returns : int
Args    : none to get, OR int to set

add_row

Title   : add_row
Usage   : Do not use
Function: This generic method is not suitable for mlagan, where the number of
          rows is fixed.
Returns : Warning
Args    : none

remove_row

Title   : remove_row
Usage   : Do not use
Function: This generic method is not suitable for mlagan, where the number of
          rows is fixed.
Returns : Warning
Args    : none

add_column

Title   : add_column
Usage   : Do not use
Function: This generic method is not suitable for mlagan, where the number of
          columns is fixed.
Returns : Warning
Args    : none

remove_column

Title   : remove_column
Usage   : Do not use
Function: This generic method is not suitable for mlagan, where the number of
          columns is fixed.
Returns : Warning
Args    : none