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
  77 use strict;
  78
  79 use base qw(Bio::Matrix::Generic);
  80
  81
  82 =head2 new
  83
  84  Title   : new
  85  Usage   : my $obj = Bio::Matrix::Generic->new();
  86  Function: Builds a new Bio::Matrix::Generic object
  87  Returns : an instance of Bio::Matrix::Generic
  88  Args    : -values            => arrayref of arrayrefs of data initialization
  89            -matrix_id         => id of the matrix
  90            -matrix_name       => name of the matrix
  91            -matrix_init_value => default value to initialize empty cells
  92            -gap_open          => gap open penalty (int)
  93            -gap_continue      => gap continue penalty (int)
  94
  95            NB: -rownames and -colnames should not be given here, since they are
  96            always being set to 'A', 'C', 'G', 'T', '.' and 'N'.
  97
  98 =cut
  99
 100 sub new {
 101     my($class, @args) = @_;
 102     my %args = (@args, -rownames => [qw(A C G T . N)],
 103                        -colnames => [qw(A C G T . N)]);
 104     my $self = $class->SUPER::new(%args);
 105
 106     $self->_set_from_args(\@args, -methods => [qw(gap_open gap_continue)]);
 107
 108     return $self;
 109 }
 110
 111 =head2 gap_open
 112
 113  Title   : gap_open
 114  Usage   : $obj->gap_open(-400);
 115  Function: Get/set the gap open amount.
 116  Returns : int
 117  Args    : none to get, OR int to set
 118
 119 =cut
 120
 121 sub gap_open {
 122     my $self = shift;
 123     if (@_) { $self->{gap_open} = shift }
 124     return $self->{gap_open} || return;
 125 }
 126
 127 =head2 gap_continue
 128
 129  Title   : gap_continue
 130  Usage   : $obj->gap_continue(-25);
 131  Function: Get/set the gap continue amount.
 132  Returns : int
 133  Args    : none to get, OR int to set
 134
 135 =cut
 136
 137 sub gap_continue {
 138     my $self = shift;
 139     if (@_) { $self->{gap_continue} = shift }
 140     return $self->{gap_continue} || return;
 141 }
 142
 143 =head2 add_row
 144
 145  Title   : add_row
 146  Usage   : Do not use
 147  Function: This generic method is not suitable for mlagan, where the number of
 148            rows is fixed.
 149  Returns : Warning
 150  Args    : none
 151
 152 =cut
 153
 154 sub add_row {
 155     shift->warn("Mlagan matricies are fixed at 6x6");
 156 }
 157
 158 =head2 remove_row
 159
 160  Title   : remove_row
 161  Usage   : Do not use
 162  Function: This generic method is not suitable for mlagan, where the number of
 163            rows is fixed.
 164  Returns : Warning
 165  Args    : none
 166
 167 =cut
 168
 169 sub remove_row {
 170     shift->warn("Mlagan matricies are fixed at 6x6");
 171 }
 172
 173 =head2 add_column
 174
 175  Title   : add_column
 176  Usage   : Do not use
 177  Function: This generic method is not suitable for mlagan, where the number of
 178            columns is fixed.
 179  Returns : Warning
 180  Args    : none
 181
 182 =cut
 183
 184 sub add_column {
 185     shift->warn("Mlagan matricies are fixed at 6x6");
 186 }
 187
 188 =head2 remove_column
 189
 190  Title   : remove_column
 191  Usage   : Do not use
 192  Function: This generic method is not suitable for mlagan, where the number of
 193            columns is fixed.
 194  Returns : Warning
 195  Args    : none
 196
 197 =cut
 198
 199 sub remove_column {
 200     shift->warn("Mlagan matricies are fixed at 6x6");
 201 }
 202
 203 1;