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://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::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