Bio::Matrix::MatrixI(3User Contributed Perl DocumentatiBio::Matrix::MatrixI(3)NAMEBio::Matrix::MatrixI - An interface for describing a Matrix
SYNOPSIS
# Get a Matrix object
DESCRIPTION
This is an interface describing how one should be able to interact with
a matrix. One can have a lot of information I suppose and this outline
won't really work for PWM or PSSMs. We will have to derive a
particular interface for those.
FEEDBACK
Mailing Lists
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
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 Bugs
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 email
or the web:
http://bugzilla.open-bio.org/
AUTHOR - Jason Stajich
Email jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
matrix_id
Title : matrix_id
Usage : my $id = $matrix->matrix_id
Function: Get the matrix ID
Returns : string value
Args :
matrix_name
Title : matrix_name
Usage : my $name = $matrix->matrix_name();
Function: Get the matrix name
Returns : string value
Args :
get_entry
Title : get_entry
Usage : my $entry = $matrix->get_entry($rowname,$columname)
Function: Get the entry for a given row,column pair
Returns : scalar
Args : $row name
$column name
get_column
Title : get_column
Usage : my @row = $matrix->get_column('ALPHA');
Function: Get a particular column
Returns : Array (in array context) or arrayref (in scalar context)
of values
Args : name of the column
get_row
Title : get_row
Usage : my @row = $matrix->get_row('ALPHA');
Function: Get a particular row
Returns : Array (in array context) or arrayref (in scalar context)
of values
Args : name of the row
get_diagonal
Title : get_diagonal
Usage : my @diagonal = $matrix->get_diagonal;
Function: Get the diagonal of the matrix
Returns : Array (in array context) or arrayref (in scalar context)
Args : none
column_num_for_name
Title : column_num_for_name
Usage : my $num = $matrix->column_num_for_name($name)
Function: Gets the column number for a particular column name
Returns : integer
Args : string
row_num_for_name
Title : row_num_for_name
Usage : my $num = $matrix->row_num_for_name($name)
Function: Gets the row number for a particular row name
Returns : integer
Args : string
num_rows
Title : num_rows
Usage : my $rowcount = $matrix->num_rows;
Function: Get the number of rows
Returns : integer
Args : none
num_columns
Title : num_columns
Usage : my $colcount = $matrix->num_columns
Function: Get the number of columns
Returns : integer
Args : none
reverse
Title : reverse
Usage : my $matrix = $matrix->reverse
Function: Get the reverse of a matrix
Returns :
Args :
row_names
Title : row_names
Usage : my @rows = $matrix->row_names
Function: The names of all the rows
Returns : array in array context, arrayref in scalar context
Args : none
column_names
Title : column_names
Usage : my @columns = $matrix->column_names
Function: The names of all the columns
Returns : array in array context, arrayref in scalar context
Args : none
perl v5.14.1 2011-07-22 Bio::Matrix::MatrixI(3)
