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Man Pages


Manual Reference Pages  -  BIO::MATRIX::MLAGAN (3)

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NAME

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

CONTENTS

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



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perl v5.20.3 BIO::MATRIX::MLAGAN (3) 2016-04-05

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