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BioPerl-1.007002
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Matrix::MatrixI

NAME

Bio::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:

https://github.com/bioperl/bioperl-live/issues

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