2 # BioPerl module for Bio::Matrix::Mlagan
4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
6 # Cared for by Sendu Bala <bix@sendu.me.uk>
10 # You may distribute this module under the same terms as perl itself
12 # POD documentation - main docs before the code
16 Bio::Matrix::Mlagan - A generic matrix with mlagan fields
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);
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.)
31 It also limits the structure to a 6x6 matrix with row & column names 'A', 'C',
32 'G', 'T', '.' and 'N'.
38 User feedback is an integral part of the evolution of this and other
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42 bioperl-l@bioperl.org - General discussion
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47 Please direct usage questions or support issues to the mailing list:
49 I<bioperl-l@bioperl.org>
51 rather than to the module maintainer directly. Many experienced and
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53 address it. Please include a thorough description of the problem
54 with code and data examples if at all possible.
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
62 https://redmine.open-bio.org/projects/bioperl/
64 =head1 AUTHOR - Sendu Bala
70 The rest of the documentation details each of the object methods.
71 Internal methods are usually preceded with a _
75 package Bio
::Matrix
::Mlagan
;
78 use base
qw(Bio::Matrix::Generic);
84 Usage : my $obj = Bio::Matrix::Generic->new();
85 Function: Builds a new Bio::Matrix::Generic object
86 Returns : an instance of Bio::Matrix::Generic
87 Args : -values => arrayref of arrayrefs of data initialization
88 -matrix_id => id of the matrix
89 -matrix_name => name of the matrix
90 -matrix_init_value => default value to initialize empty cells
91 -gap_open => gap open penalty (int)
92 -gap_continue => gap continue penalty (int)
94 NB: -rownames and -colnames should not be given here, since they are
95 always being set to 'A', 'C', 'G', 'T', '.' and 'N'.
100 my($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);
105 $self->_set_from_args(\
@args, -methods
=> [qw(gap_open gap_continue)]);
113 Usage : $obj->gap_open(-400);
114 Function: Get/set the gap open amount.
116 Args : none to get, OR int to set
122 if (@_) { $self->{gap_open
} = shift }
123 return $self->{gap_open
} || return;
129 Usage : $obj->gap_continue(-25);
130 Function: Get/set the gap continue amount.
132 Args : none to get, OR int to set
138 if (@_) { $self->{gap_continue
} = shift }
139 return $self->{gap_continue
} || return;
146 Function: This generic method is not suitable for mlagan, where the number of
154 shift->warn("Mlagan matricies are fixed at 6x6");
161 Function: This generic method is not suitable for mlagan, where the number of
169 shift->warn("Mlagan matricies are fixed at 6x6");
176 Function: This generic method is not suitable for mlagan, where the number of
184 shift->warn("Mlagan matricies are fixed at 6x6");
189 Title : remove_column
191 Function: This generic method is not suitable for mlagan, where the number of
199 shift->warn("Mlagan matricies are fixed at 6x6");