Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::Matrix::Mlagan.3pm

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:

   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::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