lib/Bio/Matrix/Mlagan.pm

   1 #
   2 # BioPerl module for Bio::Matrix::Mlagan
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Sendu Bala <bix@sendu.me.uk>
   7 #
   8 # Copyright Sendu Bala
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Matrix::Mlagan - A generic matrix with mlagan fields
  17
  18 =head1 SYNOPSIS
  19
  20   # See L<Bio::Matrix::Generic> for most methods.
  21   # These are relevant for mlagan IO:
  22   $matrix->gap_open(-400);
  23   $matrix->gap_continue(-25);
  24
  25 =head1 DESCRIPTION
  26
  27 This is based on Bio::Matrix::Generic, differing by storing gap_open and
  28 gap_continue data members to allow mlagan IO (see Bio::Matrix::IO::mlagan).
  29 (Those values are 'outside' the matrix.)
  30
  31 It also limits the structure to a 6x6 matrix with row & column names 'A', 'C',
  32 'G', 'T', '.' and 'N'.
  33
  34 =head1 FEEDBACK
  35
  36 =head2 Mailing Lists
  37
  38 User feedback is an integral part of the evolution of this and other
  39 Bioperl modules. Send your comments and suggestions preferably to
  40 the Bioperl mailing list.  Your participation is much appreciated.
  41
  42   bioperl-l@bioperl.org                  - General discussion
  43   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  44
  45 =head2 Support
  46
  47 Please direct usage questions or support issues to the mailing list:
  48
  49 I<bioperl-l@bioperl.org>
  50
  51 rather than to the module maintainer directly. Many experienced and
  52 reponsive experts will be able look at the problem and quickly
  53 address it. Please include a thorough description of the problem
  54 with code and data examples if at all possible.
  55
  56 =head2 Reporting Bugs
  57
  58 Report bugs to the Bioperl bug tracking system to help us keep track
  59 of the bugs and their resolution. Bug reports can be submitted via the
  60 web:
  61
  62   https://github.com/bioperl/bioperl-live/issues
  63
  64 =head1 AUTHOR - Sendu Bala
  65
  66 Email bix@sendu.me.uk
  67
  68 =head1 APPENDIX
  69
  70 The rest of the documentation details each of the object methods.
  71 Internal methods are usually preceded with a _
  72
  73 =cut
  74
  75 package Bio::Matrix::Mlagan;
  76 use strict;
  77
  78 use base qw(Bio::Matrix::Generic);
  79
  80
  81 =head2 new
  82
  83  Title   : new
  84  Usage   : my $obj = Bio::Matrix::Generic->new();
  85  Function: Builds a new Bio::Matrix::Generic object
  86  Returns : an instance of Bio::Matrix::Generic
  87  Args    : -values            => arrayref of arrayrefs of data initialization
  88            -matrix_id         => id of the matrix
  89            -matrix_name       => name of the matrix
  90            -matrix_init_value => default value to initialize empty cells
  91            -gap_open          => gap open penalty (int)
  92            -gap_continue      => gap continue penalty (int)
  93
  94            NB: -rownames and -colnames should not be given here, since they are
  95            always being set to 'A', 'C', 'G', 'T', '.' and 'N'.
  96
  97 =cut
  98
  99 sub new {
 100     my($class, @args) = @_;
 101     my %args = (@args, -rownames => [qw(A C G T . N)],
 102                        -colnames => [qw(A C G T . N)]);
 103     my $self = $class->SUPER::new(%args);
 104
 105     $self->_set_from_args(\@args, -methods => [qw(gap_open gap_continue)]);
 106
 107     return $self;
 108 }
 109
 110 =head2 gap_open
 111
 112  Title   : gap_open
 113  Usage   : $obj->gap_open(-400);
 114  Function: Get/set the gap open amount.
 115  Returns : int
 116  Args    : none to get, OR int to set
 117
 118 =cut
 119
 120 sub gap_open {
 121     my $self = shift;
 122     if (@_) { $self->{gap_open} = shift }
 123     return $self->{gap_open} || return;
 124 }
 125
 126 =head2 gap_continue
 127
 128  Title   : gap_continue
 129  Usage   : $obj->gap_continue(-25);
 130  Function: Get/set the gap continue amount.
 131  Returns : int
 132  Args    : none to get, OR int to set
 133
 134 =cut
 135
 136 sub gap_continue {
 137     my $self = shift;
 138     if (@_) { $self->{gap_continue} = shift }
 139     return $self->{gap_continue} || return;
 140 }
 141
 142 =head2 add_row
 143
 144  Title   : add_row
 145  Usage   : Do not use
 146  Function: This generic method is not suitable for mlagan, where the number of
 147            rows is fixed.
 148  Returns : Warning
 149  Args    : none
 150
 151 =cut
 152
 153 sub add_row {
 154     shift->warn("Mlagan matricies are fixed at 6x6");
 155 }
 156
 157 =head2 remove_row
 158
 159  Title   : remove_row
 160  Usage   : Do not use
 161  Function: This generic method is not suitable for mlagan, where the number of
 162            rows is fixed.
 163  Returns : Warning
 164  Args    : none
 165
 166 =cut
 167
 168 sub remove_row {
 169     shift->warn("Mlagan matricies are fixed at 6x6");
 170 }
 171
 172 =head2 add_column
 173
 174  Title   : add_column
 175  Usage   : Do not use
 176  Function: This generic method is not suitable for mlagan, where the number of
 177            columns is fixed.
 178  Returns : Warning
 179  Args    : none
 180
 181 =cut
 182
 183 sub add_column {
 184     shift->warn("Mlagan matricies are fixed at 6x6");
 185 }
 186
 187 =head2 remove_column
 188
 189  Title   : remove_column
 190  Usage   : Do not use
 191  Function: This generic method is not suitable for mlagan, where the number of
 192            columns is fixed.
 193  Returns : Warning
 194  Args    : none
 195
 196 =cut
 197
 198 sub remove_column {
 199     shift->warn("Mlagan matricies are fixed at 6x6");
 200 }
 201
 202 1;