| Bio::Matrix::Mlagan(3pm) | User Contributed Perl Documentation | Bio::Matrix::Mlagan(3pm) |
Bio::Matrix::Mlagan - A generic matrix with mlagan fields
# See L<Bio::Matrix::Generic> for most methods. # These are relevant for mlagan IO: $matrix->gap_open(-400); $matrix->gap_continue(-25);
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'.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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'.
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
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
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
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
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
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
| 2020-10-28 | perl v5.30.3 |