Bio::Matrix Mlagan
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Summary
Bio::Matrix::Mlagan - A generic matrix with mlagan fields
Package variables
No package variables defined.
Inherit
Bio::Matrix::Generic
Synopsis
  # See 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'.
Methods
newDescriptionCode
gap_openDescriptionCode
gap_continueDescriptionCode
add_rowDescriptionCode
remove_rowDescriptionCode
add_columnDescriptionCode
remove_columnDescriptionCode
Methods description
newcode    nextTop
 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_opencodeprevnextTop
 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_continuecodeprevnextTop
 Title   : gap_continue
Usage : $obj->gap_continue(-25);
Function: Get/set the gap continue amount.
Returns : int
Args : none to get, OR int to set
add_rowcodeprevnextTop
 Title   : add_row
Usage : Do not use
Function: This generic method is not suitable for mlagan, where the number of
rows is fixed.
Returns : Warning
Args : none
remove_rowcodeprevnextTop
 Title   : remove_row
Usage : Do not use
Function: This generic method is not suitable for mlagan, where the number of
rows is fixed.
Returns : Warning
Args : none
add_columncodeprevnextTop
 Title   : add_column
Usage : Do not use
Function: This generic method is not suitable for mlagan, where the number of
columns is fixed.
Returns : Warning
Args : none
remove_columncodeprevnextTop
 Title   : remove_column
Usage : Do not use
Function: This generic method is not suitable for mlagan, where the number of
columns is fixed.
Returns : Warning
Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my($class, @args) = @_;
    my %args = (@args, -rownames => [qw(A C G T . N)],
                       -colnames => [qw(A C G T . N)]);
    my $self = $class->SUPER::new(%args);
    
    $self->_set_from_args(\@args, -methods => [qw(gap_open gap_continue)]);
    
    return $self;
}
gap_opendescriptionprevnextTop
sub gap_open {
    my $self = shift;
    if (@_) { $self->{gap_open} = shift }
    return $self->{gap_open} || return;
}
gap_continuedescriptionprevnextTop
sub gap_continue {
    my $self = shift;
    if (@_) { $self->{gap_continue} = shift }
    return $self->{gap_continue} || return;
}
add_rowdescriptionprevnextTop
sub add_row {
    shift->warn("Mlagan matricies are fixed at 6x6");
}
remove_rowdescriptionprevnextTop
sub remove_row {
    shift->warn("Mlagan matricies are fixed at 6x6");
}
add_columndescriptionprevnextTop
sub add_column {
    shift->warn("Mlagan matricies are fixed at 6x6");
}
remove_columndescriptionprevnextTop
sub remove_column {
    shift->warn("Mlagan matricies are fixed at 6x6");
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu BalaTop
Email bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _